EPA/600/R-06/163 

December 2006 

 

ANNOTATED BIBLIOGRAPHY 

OF HISTORICAL CONDITIONS IN 

STREAMS AND RIVERS OF 

THE WESTERN UNITED STATES 

OFFICE OF RESEARCH AND DEVELOPMENT 

WASHINGTON D.C.
EPA/600/R-06/163 

December 2006 

ANNOTATED BIBLIOGRAPHY 

OF HISTORICAL CONDITIONS IN STREAMS AND RIVERS 

OF THE WESTERN UNITED STATES 

Compiled by 

Lynne S. McAllister 

Sandra A. Bryce 

Shannon S. Chapman 

Peter D. Lattin 

Dynamac Corporation 

National Health and Environmental Effects Research Laboratory 

Western Ecology Division 

200 SW 35th Street 

Corvallis, OR, 97333 

Contract EP-D-06-013 

Work Assignment Contracting Officer Representative 

Paul Ringold 

U.S. Environmental Protection Agency 

National Health and Environmental Effects Research Laboratory 

Western Ecology Division 

Corvallis, OR 97333 

ENVIRONMENTAL MONITORING AND ASSESSMENT PROGRAM 

NATIONAL HEALTH AND ENVIRONMENTAL EFFECTS LABORATORY 

OFFICE OF RESEARCH AND DEVELOPOMENT 

U.S. ENVIRONMENTAL PROTECTION AGENCY 
Abstract 

Resource managers are often challenged by the lack of adequate benchmarks, or 

reference conditions, for assessing the biological condition of streams. Increasing human 

alteration of landscapes reduces the availability of minimally-disturbed stream sites that can be 

used to represent a reference condition in regional assessments. Historical data offer an 

alternative point of reference for gauging the relative deviation of current conditions from an 

established minimally-disturbed condition and can thereby contribute to better-informed 

management decisions within the context of present-day land uses and range of attainable 

conditions. This collection of over 150 annotated references represents a significant portion of 

the literature that reports historical conditions and changes due to human impacts that have 

occurred since European settlement relevant to fish, aquatic insects, amphibians, and physical 

habitat. Its intent is to provide sources of information for those involved in historical 

reconstructions of stream conditions. Key references providing the most comprehensive 

syntheses at basin or regional scales in the western United States were selected for the 

bibliography. Bibliographic subsections are tailored toward EPA’s Environmental Monitoring 

and Assessment Program (EMAP), although the information should be useful in a wide range of 

environmental assessments and restorations that address basin- or regional-scale stream 

conditions. 

Notice 

The information in this document has been funded wholly or in part by the U.S. 

Environmental Protection Agency under Contracts 68-D-01-005 and EP-D-06-013 to 

Dynamac Corporation. It has been subject to review by the National Health and 

Environmental Effects Research Laboratory and approved for publication. Approval 

does not signify that the contents reflect the views of the Agency, nor does mention 

of trade names or commercial products constitute endorsement or recommendation 

for use. 

Preferred Citation: 

McAllister, L.S., S.A. Bryce, S.S. Chapman, and P.D. Lattin. 2007. Annotated Bibliography of 

Historical Conditions in Streams and Rivers of the Western United States. EPA/600/R-06/163. 

U.S. Environmental Protection Agency, Office of Research and Development, National Health 

and Environmental Effects Research Laboratory, Washington, D.C. 

ii
PREFACE 

This collection of annotated references represents a significant portion of the literature 

that reports historical conditions and changes due to human impacts that have occurred since 

European settlement relevant to fish, aquatic insects, amphibians, and physical habitat 

(including riparian vegetation). The geographic scope of the literature includes 12 western 

states comprising the assessment area for the Environmental Monitoring and Assessment 

Program’s Western Pilot Study (EMAP-West), encompassing EPA Regions 8-10. 

This project grew out of the need for benchmarks, summaries, and ancillary information 

about minimally disturbed conditions that could enhance EMAP-West assessments of current 

stream condition. However, the information should apply to a variety of environmental 

assessments and restorations that are conducted at a basin or regional scale. It is particularly 

relevant in regions that have undergone extensive land-use alterations and where existing leastdisturbed reference sites may set unrealistically low reference benchmarks, resulting in 

inadequate protection of the resource. Historical data can provide a model of regional 

ecosystem bio-integrity that can be used to assess the relative deviation of present day stream 

condition from a pre-settlement, or minimally disturbed, condition. The data are not intended for 

re-creating historical conditions and landscapes but, rather, they offer a point of reference for 

making better-informed management decisions within the context of present-day land uses and 

range of attainable conditions. 

Content and Format 

The bibliography includes primary literature sources (e.g., results of historical fish 

surveys conducted in the 19th century), as well as more current literature syntheses that report 

changes from the historical condition (e.g., estimated declines in fish populations) and the 

causes of the changes. References report conditions and changes over broad regions or river 

basins. Publications reporting results of small-scale or site-specific studies (e.g., stream 

segments in a single drainage) are not included. Instead of including every reference identified 

for a specific topic (e.g., salmon losses in the Columbia River basin), we attempted to select key 

publications that provided the broadest and most thorough syntheses of historical data or 

changes from the historical condition. Cited publications include historical documents, journal 

articles, books and book chapters, reports, web sites, and gray literature. Gray literature was 

considered valuable since it comprises numerous syntheses of changes in historical ranges and 

populations, which was precisely the topic of interest for this project. As in any use of gray 

literature, therefore, it should be applied accordingly. 

When possible, bibliographic entries report a minimally disturbed condition, defined as 

pre-settlement or early settlement (i.e., 19th century). Since much of the earliest documentation 

of stream conditions was not made until the 20th century, later publications are also included in 

the bibliography. This is particularly true for the macroinvertebrate literature, much of which did 

not appear until the mid-1900s. In addition, literature that contrasts a perceived minimally 

disturbed condition with a changed condition is also included. For example, dam construction in 

the Colorado River basin beginning in the 1930s drastically changed native fish habitat and 

populations, which were considered relatively unchanged prior to that time. To a limited extent, 

literature that contrasts before/after conditions in a more recent time period are also included, 

for example, large-scale studies of fish assemblages and stream habitat in logged vs. unlogged 

watersheds within relatively undisturbed forests. 

References focus on stream habitats, although a broader landscape perspective is often 

found in the literature for the Plains aggregated ecoregion because of the intermittent nature of 

most streams and a closer association between stream and non-stream habitats in that region. 

Also, early (pre-settlement) stream surveys in the Plains ecoregion are rare or non-existent, so 

iii
historical stream conditions may have to be inferred from characteristics of the broader 

landscape. 

The annotated portion of each reference contains five summary fields: abstract (when 

available), geographic location (see below for descriptors), value of the reference, results 

relevant to EMAP, and keywords. The ‘value of the reference’ field describes the general topic 

of the publication and why it is considered useful for EMAP applications. It also may include the 

type of publication (e.g., historical survey results vs. current synthesis), the format in which 

information is presented, the degree of data synthesis already done, and the prominence of the 

work in the literature. The ‘results relevant to EMAP’ field briefly summarizes the major points 

or findings of the publication relevant to EMAP topics of interest. Its purpose is to help the user 

determine whether the publication is worth acquiring and reading in further detail. The 

‘geographic location’ field includes state, river basin, EPA ecoregion level III, EPA administrative 

region, and EPA aggregate ecoregion (mountains, xeric, plains). The ‘keywords’ field specifies 

the affected attribute (physical habitat, fish, macroinvertebrates, etc.) and the human impacts 

that caused the change to historical condition. 

 References are listed alphabetically. Within each citation, a number of search variables 

are included in the geographic location and keyword fields to allow a user to more easily find 

references for specific geographic areas, human disturbances, and impacted biota using the 

“Find” function in the edit menu. The following lists show, in italics, potential search variables in 

each category. 

 

• Geographic Location 

State: Arizona, California, Colorado, Idaho, Montana, Nevada, North Dakota, Oregon, 

South Dakota, Utah, Washington, Wyoming

EPA administrative region: region ‘x’ (e.g., region 8) 

EPA level III ecoregion: Eco‘xx’ (e.g., eco20) 

EMAP aggregate ecoregion: mountains, plains, xeric 

River basin: ‘xxxxxx’ basin (major basins such as the Columbia River basin, Colorado 

River basin, or river tributaries within major basins, e.g., Snake River basin, Gila River 

basin) 

• Keywords 

Human disturbances—activities that have brought about changes in streams or biota: 

grazing 

 agriculture 

 mining 

 roads 

 dams 

 fishing (commercial or sport) 

nonnative species 

 recreation 

 urban 

 water diversion 

 channelization 

iv
 groundwater pumping 

 general (referring to any human impact; non-specific) 

Impacted Attribute: 

fish 

 macroinvertebrates 

 amphibians 

 riparian vegetation 

 phab (physical habitat) 

Application 

Information in the publications cited in this bibliography can be applied in a variety of 

basin- or regional-scale assessments and restorations. Two examples of using the bibliography 

in the context of EMAP stream assessments are illustrated here. 

Riparian Vegetation in the Missouri River Basin 

Historical documentation indicates that, with the exception of badlands, riparian habitats 

in the Northwestern Great Plains (Ecoregion 43; Missouri River basin) were composed largely of 

forest and shrub habitats prior to settlement (Warren 1856, Evermann and Cox 1896, Johnson 

1992, Rumble et al. 1998). Descriptions in these references note extensive forests dominated 

by cottonwood and willow; “extensive native woodlands”; canyons filled with deciduous trees 

including cottonwood, willow, ash, oak, and wild plum; heavily-forested floodplains; “abundance 

of wood”; “swarms of beaver”; “excellent timber of ash, oak, elm, and box-elder”. At leastdisturbed reference sites in Ecoregion 43 today, however, EMAP physical habitat 

measurements show that riparian canopy averages only 4% of the riparian cover. Total riparian 

woody cover (the sum of woody cover in each of three vegetation layers, with highest potential 

value of 300% due to overlapping layers) averages just 41%, less than half of today’s total 

riparian cover including herbaceous species. This comparison suggests that canopy cover at 

least-disturbed sites is much less than what would be expected based on historical 

documentation, and that woody vegetation as a proportion of the total is likely underrepresented. 

Fish Assemblage Biotic Integrity in the South Platte River basin. 

Another useful application of historical information is in the development of multimetric 

indices of biotic integrity (IBIs), which translate biological indicator abundance data into a 

numeric score to evaluate stream condition. In a highly altered region, historical information can 

be used to set expectations for the number of species that would have been found in minimally 

disturbed ecosystems of the region (Hughes et al. 1998). For example, EMAP field crews 

sampled 23 native species of fish at 19 sites on the upper South Platte River in the foothills of 

the Rocky Mountains of Colorado. In a paper that reviewed historical collections on the South 

Platte River, Probst and Carlson (1986) determined that three fish species had been extirpated 

from the South Platte basin and several others were now rare. Seven of these historically 

recorded species were not collected during the EMAP-West survey. If we were to construct an 

IBI for the South Platte basin, we might increase the total number of species from 23 to 30 to 

more closely represent a state of biointegrity. Since total number of species is the denominator 

in species proportionate metrics (for example, % tolerant species or % native vagile species), all 

such metrics would be scored somewhat lower than metrics based on present day field data 

alone, and the lower IBI score would more accurately reflect the departure of sites in developed 

regions from a minimally disturbed condition. 

v
ANNOTATED BIBLIOGRAPHY 

Author: Abruzzi, W., others 

Year: 2002 

Title: Riparian Area Loss and Degradation 

Reference Type: Electronic Source 

Access Year: 2005 

Access Date: July 25 

Value of reference: Web site addresses reduction in riparian areas, the causes, and 

associations between losses and fish distribution. It proposes a link between native fish 

presence and intact riparian areas. The focus of numerous other publications is on the 

devastating effects of river regulation and introduced species on the Colorado River native 

fishery; this overview proposes that the presence of healthy riparian areas seems related to the 

survival of some of the only remaining populations of native fish. 

Results relevant to EMAP: Overall, a 90% loss of pre-settlement riparian ecosystems has 

occurred in Arizona and New Mexico, beginning in the early 19th century with the near 

extirpation of the beaver. 

As a result of various human-related impacts, water tables are lowered, surface sediments are 

desiccated, channels are less complex and more static, erosion increases, suitable habitat for 

establishment of riparian vegetation such as cottonwood and willow is limited, and plant 

community structure changes. 

The few remaining fish stocks native to smaller riparian systems on the Plateau survive only in 

those areas with intact riparian habitats, often in remote upper-elevation watersheds.

Geographic location: Colorado Plateau, xeric, Arizona, New Mexico, eco20, eco21, eco22, 

eco23, EPA Region 9 

Keywords: phab, fish, riparian vegetation, beaver, dams, agriculture, channelization, grazing, 

logging, nonnative species, roads, urban 

URL: http://www.cpluhna.nau.edu/Biota/riparian_degradation.htm 

1
Author: Adams, S. B.; Frissell C.A.; Rieman, B.E. 

Year: 2001 

Title: Geography of invasions in mountain streams: consequences of headwater lake fish 

introductions 

Reference Type: Journal Article 

Journal: Ecosystems 

Volume: 2001 

Pages: 296-307 

Value of reference: This paper reviews the potential consequences of fish introductions into 

headwater streams and lakes in the western United States, and the nature of the impacts upon 

downstream aquatic ecosystems. A review of the literature is provided describing the 

consequences of nonnative fish species invasions in higher elevation mountainous regions. 

The authors suggest that knowledge of the differential effectiveness of barriers can be used in 

conjunction with stocking history to interpret where stocking activities may have had impacts 

upon native ichthyofauna, macroinvertebrates, and amphibians. This information can be of 

value for interpreting the quality of vertebrate faunal metrics, particularly for stream reference 

sites.

Results relevant to EMAP: Headwater streams historically provided refuges for native fish, 

amphibians and aquatic macroinvertebrates. Approximately 95% of all high-mountain lakes in 

the western United States lie above Pleistocene-age barriers to fish dispersal (Bahls 1992). 

Where native fish species existed, stream dispersal barriers have prevented influences of 

downstream communities which have been impacted by intentional and unintentional fish 

introductions. Downstream dispersal of fish is more effective than upstream dispersal, 

consequently upstream or isolated drainages represent refugia for both native fish and non-fish 

fauna such as amphibians and invertebrates. 

Intentional and accidental introduction of fish species such as brook trout (Salvalinus fontinalis) 

have occurred at upper elevations throughout the west since the late 1800s. Such introductions 

have impacted native fauna through a wide range of mechanisms, and have often led to 

displacement. Brook trout (S. fontinalis), for example, have been implicated in the displacement 

of both native bull trout (Salvalinus confluentus) and cutthroat trout (Oncorhynchus clarki).

Geographic location: Region 8, Region 9, Idaho, Montana, Rocky Mountains, MOUNTAINS, 

MT-NROCK, SF Salmon River, eco15, eco16, Northern Rockies, Idaho Batholith 

Keywords: fish; invasion; dispersal; landscape; demography; conservation; nonnative species; 

salmonids; lake; stream; Columbia River basin; Idaho, Montana 

Abstract: The introduction of fish into high-elevation lakes can provide a geographic 

and demographic boost to their invasion of stream networks, thereby further endangering the 

native stream fauna. Increasingly remaining populations of native salmonids are concentrated in 

fragmented headwater refugia that are protected by physical or biological barriers from 

introduced fishes that originate in the pervasive source populations established at lower 

elevations. Although fish introduced near mainstem rivers frequently encounter obstacles to 

upstream dispersal, such as steep slopes or falls, we found brook trout (Salvelinus fontinalis) 

dispersed downstream through channel slopes of 80% and 18-m-high falls. Thus, headwater 

lake stocking provides source populations that may be capable of invading most downstream 

habitats, including headwater refugia of native fishes. The extent of additional area invasible 

2
from lakes, beyond that invasible from downstream, depends on the geography of the stream 

network, particularly the density and distribution of headwater lakes and their location relative to 

barriers inhibiting upstream dispersal. In the thermal and trophic environments downstream of 

lakes, fish commonly grow faster and thus mature earlier and have higher fecundity-at-age than 

their counterparts in other high-elevation streams. The resulting higher rates of population 

growth facilitate invasion. Larger body sizes also potentially aid the fish in overcoming barriers 

to invasion. Trout introductions to high-elevation headwater lakes thus pose disproportionately 

large risks to native fishes -- even when the place of introduction may appear to be spatially 

disassociated from populations of the native species. Mapping the potential invasible area can 

help to establish priorities in stocking and eradication efforts. 

Notes: Bahls, P. 1992. The status of fish populations and management of high mountain lakes 

in the western United States. Northwest Science 66:183-93 

3
Author: Arizona Game and Fish Department 

Year: 1994 

Title: Gila Chub (Gila intermedia), unpublished abstract 

Reference Type: Electronic Source 

Producer: Heritage Data Management System, Arizona Game and Fish Department 

Access Year: 2005 

Access Date: October 6 

Last Update Date: December 4, 2002 

Value of reference: This is a short synopsis of this species, which includes a short description 

of its historical and current distribution. It is useful for defining the historical range of the species 

and estimating the proportion of it that is no longer occupied.

Results relevant to EMAP: Historically the Gila chub was found in headwater streams of the 

Gila River in Arizona, New Mexico and likely in Sonora, Mexico. It is currently considered 

extirpated from New Mexico and from 3 waterways in AZ: Cave Creek, Fish Creek, and Monkey 

Spring. This report lists a number of creeks in Arizona where it is still found. The Gila chub 

was commonly found in association with Gila topminnow, desert and Sonora sucker and longfin 

and speckled dace. 

Populations have slowly been disappearing but are expected to fluctuate with habitat changes 

due to climatic events. Threats to this species include aquifer pumping, stream diversion, 

reduced flows, habitat alteration, competition by nonnative crayfishes and competition and 

predation by nonnative fishes

Geographic location: Arizona, EPA Region 9, eco22, eco23, xeric, Gila River basin 

Keywords: fish, water diversion, groundwater pumping, impoundment, nonnative species, 

habitat degradation 

URL: http://www.gf.state.az.us/w_c/edits/documents/Gilainte.fo_001.pdf

4
Author: Beechie, T.; Beamer, E.; Wasserman, L. 

Year: 1994 

Title: Estimating coho salmon rearing habitat and smolt production losses in a large river basin, 

and implications for habitat restoration 

Reference Type: Journal Article 

Journal: North American Journal of Fisheries Management 

Volume: 14 

Pages: 797-811 

Value of reference: An extremely valuable reference that uses the historical record to estimate 

the loss of summer and winter coho salmon rearing habitats and the associated loss of coho 

smolt production for the entire Skagit River basin. In addition, the amount of lost habitat was 

apportioned to particular land use impacts, an analysis that is not often seen.

Results relevant to EMAP: See abstract for loss of coho smolt production. 

Early hydromodifications on the Skagit River, such as diking, dredging, and damming, caused 

comparatively larger losses of physical habitat areas than more recent modifications, which are 

more incremental impacts from multiple activities such as timber harvest, flood protection, and 

residential and urban development. 

Prior to settlement the river wandered freely over its floodplain creating new side channels, 

oxbows, sloughs, and wetlands. In the lower river valley over 25% of the floodplain and delta 

area consisted of beaver ponds, sloughs, and wetlands.(The authors were not able to estimate 

lost beaver pond area.) Diking and reclaiming the land for agriculture began in the early 1860's. 

The lower elevation uplands were logged in the early 20th Century; reports as early as 1921 

reported habitat degradation and loss due to logging and hydroelectric dams. 

The largest estimated losses in habitat area and smolt production have occurred in the sidechannel and distributary sloughs. Over 115 km - nearly 700,000 m2

 - of Skagit River side 

channel and distributary sloughs have been eliminated in the past century.

Geographic location: mountains, eco2, eco77, Skagit River basin, Puget Sound, EPA Region 

10 

Keywords: salmonids, rivers, fish habitat, fish losses, coho salmon, agriculture, urban, 

channelization, dredging, logging, phab 

Abstract: To develop a habitat restoration strategy for the 8270 km2

 Skagit River basin, we 

estimated changes in smolt production of coho salmon (Oncorhynchus kisutch) since European 

settlement began in the basin, based on changes in summer and winter rearing habitat areas. 

We assessed changes in coho salmon smolt production by habitat type and by cause of habitat 

alteration. We estimated that the coho salmon smolt production capacity of summer habitats in 

the Skagit River basin has been reduced from 1.28 million smolts to 0.98 million smolts (--24%) 

and that the production capacity of winter habitats has been reduced from 1.77 million to 1.17 

million smolts (--34%). The largest proportion of summer non-main-stem habitat losses has 

occurred in side-channel sloughs (41%), followed by losses in small tributaries (31%) and 

distributary sloughs (29%). The largest loss of winter habitats has occurred in side-channel 

sloughs (52%), followed by losses in distributary sloughs (37%) and small tributaries (11%). By 

type of impact, hydromodification (diking, ditching, dredging) associated with agricultural and 

urban lands accounts for 73% of summer habitat losses and 91% of winter habitat losses. [33] 

5
Blocking culverts on [37 km of] small tributaries account for 13% of the decrease in summer 

habitat and 6% of the decrease in winter habitat. Forestry activities account for 9% of summer 

habitat losses and 3% of winter habitat losses. Limitations of the analysis and implications for 

developing a habitat restoration strategy are discussed. 

6
Author: Behnke, R.J. 

Year: 1992 

Title: Native Trout of Western North America 

Reference Type: Book 

City: Bethesda, MD 

Publisher: American Fisheries Society, Monograph 6 

Number of Pages: 275 

Value of reference: Book presents baseline information about historical presence by basin of 

native trout (given for most species in the Distribution subsection). Information can be further 

used to assist in reconstructing historical trout occurrence and distribution in basins throughout 

the West. 

This reference is frequently cited and used. For example, the Interior Columbia Basin 

Ecosystem Management Project (ICBEMP) used it to help define the historical ranges of fish 

species in the Interior Columbia Basin (see Lee et al. 1997, in this bibliography). Availability of 

historical information is inconsistent among species, and it takes some piecing together of text 

to isolate portions that are relevant to pre-settlement distributions. Nevertheless, this work 

seems to be a significant synopsis of trout species in the West.

Results relevant to EMAP: This book gives species-by-species distributions, original native 

ranges (in some cases, but presented with different details) and status of western trout species. 

Summaries also include trout occurrence in lakes. Text is somewhat laborious for EMAP 

purposes, but presents good information about historical presence by basin and whether native 

or exotic (i.e., many trout species have been introduced into streams where they did not occur 

historically). This information would be valuable if there was an interest or need to know the 

historic occurrences of trout species in river basins of the West in order to determine whether 

trout of a particular basin have been introduced or are native or to assist in reconstructing presettlement fish communities. Bulk of book is text, but also includes a few maps and illustrations.

Geographic location: westwide distributions of multiple species of trout 

Keywords: fish, trout, historical distribution, status, xeric, mountain, westwide 

7
Author: Bilby, R. E.; Ward, J. W. 

Year: 1991 

Title: Characteristics and function of large woody debris in streams draining old-growth, clearcut, and second-growth forests in southwestern Washington 

Reference Type: Journal Article 

Journal: Canadian Journal of Fisheries and Aquatic Sciences 

Volume: 48 

Pages: 2499-2508 

Value of reference: This article compares woody debris at present day minimally disturbed 

sites with that at logged sites. By examining the characteristics of large woody debris in streams 

bordered by forests of different age classes, the authors document the ways in which large 

woody debris volume changes following timber removal from the riparian area. They also record 

the influence of large woody debris on stream channel morphology. A companion article to 

Bisson et al. 1987 which relates old growth large woody debris distribution to salmon biomass.

Results relevant to EMAP: Plunge pools formed by large woody debris were significantly more 

common at old-growth sites than at second-growth sites for all stream-size classes and at clearcut sites in streams < 7 m wide. The frequency of large woody debris associated pools 

decreased with increasing stream size for all three stand age classes, but was significantly 

greater at old growth sites than at the other two stand age classes. Average pool surface area 

was significantly greater in streams > 10 m wide at old growth sites.

Geographic location: Pacific Northwest, Willapa Hills, southwest Washington, western 

Cascades, eco1, eco4, EPA Region 10, mountains 

Keywords: phab, large woody debris, sediments, logging, fish, pools, salmonids 

Abstract: Amount of large woody debris (LWD) surveyed in 70 stream reaches flowing through 

old-growth, clear-cut, and second-growth forests decreased with increasing stream size for all 

stand types but was greatest at old-growth sites. Average piece volume was larger at old-growth 

sites than at other stand types in streams > 10 m wide, but no differences were seen in smaller 

streams. Scour pools accounted for 90% of the wood-associated pools at second-growth and 

clear-cut sites but only 50% at old-growth sites, which contained more pools than other stand 

types, particularly for larger streams. Pool size was similar for all stand types in smaller streams, 

but averaged 10 m2

 in streams > 10 m wide at old-growth sites and 4 m2 for other stand types. 

Sediment and fine organic matter retained by woody debris decreased with increasing stream 

size for all stand types, but old-growth sites contained greater amounts of both materials than 

other stand types. The frequency of pool formation, the type of pool formed, and sediment 

accumulation were influenced by the amount of fine debris associated with LWD. Changes in 

LWD amount, characteristics, and function occurred very rapidly following removal of 

streamside vegetation. 

Notes: This reference is a companion article to Bisson et al. 1987 which relates old growth large 

woody debris distribution to salmon biomass. 

8
Author: Birken, A.S.; Cooper, D.J. 

Year: 2006 

Title: Processes of Tamarix invasion and floodplain development along the lower Green River, 

Utah 

Reference Type: Journal Article 

Journal: Ecological Applications 

Volume: 16 

Issue: 3 

Pages: 1103-1120 

Value of reference: The study attempted to determine the cause and role of the invasion of 

Tamarix with the intent of 1) providing insights into when, how, and why recent fluvial 

adjustments may have occurred and 2) assessing the influence of exotic plant invasions in 

altering geomorphic and ecological processes, which have implications for river restoration 

efforts. It is notable for its finding that Tamarix invasion did not start because of river regulation. 

The paper gives background on how Tamarix has changed southwestern riparian areas and 

altered hydrogeomorphological processes. It is also an example of how historical information 

can be used to address current resource management issues.

Results relevant to EMAP: Throughout the Southwest, floodplain vegetation was historically 

dominated by Fremont cottonwood (Populus deltoides), but Populus has declined during the 

20th century, while Tamarix has invaded and now dominates most floodplain ecosystems, 

displacing native vegetation and reducing diversity. The invasion of Tamarix has altered the 

hydraulic characteristics of floodplain surfaces, causing many rivers in the southwest to accrete 

and narrow. The invasion coincided with reduced flows and sediment transport in the mid-20th 

century caused by climate fluctuation, so it is difficult to determine whether Tamarix drove the 

fluvial adjustments or whether it benefited from climate-or dam-induced reductions in peak flows 

and sediment transport. 

An increase in Tamarix establishment is more likely when peak flow is substantially lower in the 

year following recruitment. Tamarix began invading long before river regulation. Other factors, 

such as multiple years of low flows and changing precipitation patterns in the 1930s, allowed it 

to invade a previously unoccupied niche with little competition from native vegetation. By 1951, 

Tamarix had already occupied nearly all the floodplain area it presently occupies. It decreased 

flow velocities and stabilized floodplain landforms long before construction of Flaming Gorge 

Dam; the species established and proliferated in unregulated river conditions. The return of 

larger floods in the 1950s did not result in the erosion of landforms that Tamarix then occupied 

because of its dense growth and anchoring ability. 

Geographic location: Utah, Green River basin, EPA region 8, eco20, xeric 

Keywords: phab, riparian vegetation, climate fluctuation, invasion, channel narrowing, exotic 

plants, floodplain development, river regulation, Populus deltoides, Tamarix ramosissima.

Abstract: Significant ecological, hydrologic, and geomorphic changes have occurred during the 

20th century along many large floodplain rivers in the American Southwest. Native Populus 

forests have declined, while the exotic Eurasian shrub, Tamarix, has proliferated and now 

dominates most floodplain ecosystems. Photographs from late 19th and early 20th centuries 

illustrate wide river channels with largely bare in-channel landforms and shrubby higher channel 

margin floodplains. However, by the mid-20th century, floodplains supporting dense Tamarix

9
stands had expanded, and river channels had narrowed. Along the lower Green River in eastern 

Utah, the causal mechanism of channel and floodplain changes remains ambiguous due to the 

confounding effects of climatically driven reductions in flood magnitude, river regulation by 

Flaming Gorge Dam, and Tamarix invasion. This study addressed whether Tamarix

establishment and spread followed climate- or dam-induced reductions in annual peak flows or 

whether Tamarix was potentially a driver of floodplain changes. We aged 235 Tamarix and 57 

Populus individuals, determined the hydrologic and geomorphic processes that controlled 

recruitment, identified the spatial relationships of germination sites within floodplain stratigraphic 

transects, and mapped woody riparian vegetation cohorts along three segments of the lower 

Green River. The oldest Tamarix established along several sampling reaches in 1938, and 1.50-

2.25 m of alluvium has accreted above their germination surfaces. Nearly 90% of the Tamarix

and Populus samples established during flood years that exceeded the 2.5-year recurrence 

interval. Recruitment was most common when large floods were followed by years with smaller 

peak flows. The majority of Tamarix establishment and Green River channel narrowing occurred 

long before river regulation by Flaming Gorge Dam. Tamarix initially colonized bare instream 

sand deposits (e.g., islands and bars), and most channel and floodplain changes followed the 

establishment of Tamarix. Our results suggest that Tamarix recruitment was triggered by large 

annual floods that were followed by years with lower peak flows, not by periods of low flow 

alone. Tamarix appears to have actively invaded floodplains, while Populus colonization has 

been limited. Thus, Tamarix invasion may have greatly influenced floodplain development and 

riparian vegetation composition along the lower Green River since the early 20th century. 

10
Author: Bisson, P. A.; Bilby, R. E.; Bryant, M. D.; Dolloff, C. A.; Grette, G. B.; House, R. A.; 

Murphy, M. L.; Koski, K. V.; Sedell, J. R. 

Year: 1987 

Title: Large woody debris in forested streams in the Pacific Northwest: Past, present, and future 

Reference Type: Book Section 

Editor: Salo, E. O.; Cundy, T. W. 

Book Title: Streamside Management: Forestry and Fishery Interactions 

City: Seattle, Washington 

Publisher: University of Washington 

Pages: 143-190 

Value of reference: The reference includes a very complete examination of the functions of 

large woody debris, its frequency in old growth forests, the history of its decline as a result of 

logging practices over the last 150 years, and how its presence or absence affects salmon 

densities. Companion article to Bilby and Ward 1991 that discusses how large woody debris 

shapes stream channel morphology.

Results relevant to EMAP: "The combination of debris removal for fish passage in headwater 

areas of watersheds, historical splash damming, and removal of snags and logjams from large 

rivers has led to situations where whole drainage systems no longer possess the debris load 

present in pristine, undisturbed river basins." 

Graph, p. 156 shows increasing densities of coho salmon with increasing volumes of large 

organic debris. 

Table, p. 160 showing biomass of large woody debris (kg/m2

) in streams flowing through 

regional examples of unmanaged old-growth forests in the Pacific Northwest

Geographic location: Pacific Northwest, Washington, Oregon, Alaska, British Columbia, eco1, 

eco4, mountains, EPA Region 10 

Keywords: phab, large woody debris, sediments, temperature, dissolved oxygen, logging, fish, 

pools, salmonids 

Abstract: This paper reviews the form, function, and management of woody debris in streams, 

and reaches three major conclusions: (1) Large woody debris enhances the quality of fish 

habitat in all sizes of streams. (2) Removal of most trees in the riparian zone during logging, 

combined with thorough stream cleaning and short-rotation timber harvest, has altered the 

sources, delivery mechanisms, and redistribution of debris in drainage systems, leading to 

changes in fish population abundance and species composition. (3) There is an urgent need for 

controlled field experiments and long-term studies that focus on the protection of existing large 

woody debris in stream channels and the recruitment of new debris from the surrounding forest. 

Woody debris has long been considered a potential source of logjams that could block river 

navigation, water-based log transport, and the upstream passage of salmon and trout on their 

way to spawning grounds, but is now understood to play an important role in the creation and 

maintenance of fish habitat throughout entire rivers. Although wood itself eventually enters the 

food web of the stream ecosystem as it gradually decays, the major importance of debris lies in 

its structural characteristics and the way these features influence channel hydraulics. Physical 

processes associated with debris in streams include the formation of pools and other important 

rearing areas, control of sediment and organic matter storage, and modification of water quality. 

11
Biological properties of debris-created structures can include blockages to fish migration, 

provision of cover from predators and from high stream flow, and maintenance of organic matter 

processing sites within the benthic community. The locations and principal roles of woody debris 

change throughout the river system. In steep headwater streams where logs span the channel, 

debris creates a stepped longitudinal profile that governs the storage and release of sediment 

and detritus, a function that facilitates the biological processing of organic inputs from the 

surrounding forest. When the stream channel becomes too wide for spanning by large logs, 

debris is deposited along the channel margins, where it often forms the most productive fish 

habitat in main stem rivers. In all but the smallest streams there is some degree of clumping, 

although the size and spacing of debris clumps generally increase in a downstream direction. 

Debris related fish habitat can be found anywhere in small forested streams. In large rivers it is 

primarily associated with debris accumulations along the margins and secondary channel 

systems of the floodplain, although it also occurs behind and under very large pieces (intact 

boles and root wads) along main stem gravel bars. 

Changes in tree species composition, abundance, and input rates to streams resulting from 

forest management practices have differed according to location in the watershed, and many 

physical and biological processes have been altered by these changes in the river system's 

debris load. Several questions have not been fully explored, particularly with regard to the longterm consequences of streamside management for debris recruitment. Yet the majority of 

studies of streams in second-growth forests have demonstrated that the input of large, 

potentially stable debris from second growth stands in which nearly all large merchantable trees 

had been harvested was significantly reduced relative to debris inputs from old growth stands. 

Other studies have shown that loss of large debris has led to a shift in stream habitat 

composition that favored underyearling steelhead (Salmo gairdneri) and cutthroat trout (S. 

clarki) at the expense of the older trout age classes as well as both underyearling and yearling 

coho salmon (Oncorhynchus kisutch). Loss of debris has also reduced overwinter survival of all 

species. In order to develop procedures that will protect existing instream debris, as well as 

provide a continues supply of the proper quantity and quality of large woody debris for the 

future, it will be necessary to test scientifically a variety of management options over a wide 

range of stream sizes. Many management procedures have been proposed, including 

techniques for removing slash from stream channels after logging, determining the configuration 

of buffer strips, selective harvesting within the streamside management zone, and deliberately 

adding debris to streams for habitat enhancement. Evaluation of these proposals will require a 

great deal of time and effort, as well as the cooperation of many resource management 

organizations. However, long term research is essential in view of the complexity of debris 

management issues. 

Notes: This reference is a companion article to Bilby and Ward 1991 that discusses how large 

woody debris shapes stream channel morphology. 

12
Author: Blinn, D.W.; Cole, G.A. 

Year: 1991 

Title: Algal and invertebrate biota in the Colorado River: Comparison of pre-and post-dam 

conditions 

Reference Type: Book Section 

Editor: Committee on Glen Canyon Environmental Studies 

Book Title: Colorado River Ecology and Dam Management. 

City: Washington, D.C. 

Publisher: National Academy Press 

Pages: 102-122 

Value of reference: This is one of very few summary documents about algal and invertebrate 

biota in a basin and is thus worth noting even though the historical information it contains is from 

the mid-1900s (pre-dam) and the focus is on the mainstem lower Colorado River. It presents a 

broad overview of changes in the biota of the Colorado River between Glen Canyon Dam and 

Lake Mead, including some documentation for backwater and tributary conditions, as a result of 

the closure of Glen Canyon Dam in 1963. It also gives several examples of invertebrate 

introductions in the Colorado River basin. The authors present material in a general summary 

format (i.e., no data are presented) that synthesizes an extensive body of literature and includes 

a useful bibliography. 

Results relevant to EMAP: The average suspended sediment load in the lower Colorado River 

before impoundment was 3.5 times higher than after the construction of Glen Canyon Dam. 

Substrata available for attachment were more numerous. Flowers (1959) reported 53 taxa of 

riverine algae including 28 chlorophytes and 20 diatom taxa in tributaries of the canyon. The 

authors note the lack of pre-impoundment data for macroinvertebrates in the main stem but cite 

several studies pertaining to species in tributaries or springs, dating back to 1911 (see Notes 

section). The difficulty in reconstructing historical invertebrate communities is due to both the 

lack of historical data and the changes in native communities as a result of numerous 

introductions of invertebrates from other parts of the continent. 

Cell densities for diatom species in the Colorado River after impoundment were over 1600-fold 

lower than prior to the impoundment of the river. (Williams 1964). 

The authors mention numerous invertebrate introductions, beginning in the late 1800s. 

The species diversity of macroinvertebrates in the Colorado River is much lower than in the 

tributaries, despite numerous introductions. General community change in algal and 

macroinvertebrate communities as a result of dams is also discussed.

Geographic location: Arizona, Colorado River basin, eco22, xeric, EPA region 9 

Keywords: macroinvertebrates, algae, phab, dams, invertebrate introductions, nonnative 

species 

Abstract: Few reports exist on the physicochemical conditions of the pre-impounded Colorado 

River that relate to the growth and development of algal and aquatic invertebrate communities. 

Post-impoundment studies indicate that Cladophora glomerata is the dominant attached 

filamentous green algal species. Two hundred-thirty-five diatom taxa from the Colorado River 

and tributaries and from springs in the Glen and Grand Canyon systems have been reported. 

Ephemeropterans, snails, leeches, species from at least 10 insect families, and crayfish were 

13
intentionally introduced into the Colorado River after the Glen Canyon dam was closed. 

Zooplankters show a richness of faunas in backwaters along the borders of the river channel 

and at the mouths of tributaries. The macroinvertebrates occurring in the Colorado River consist 

of only a few species. The amphipod Gammarus lacustris constitutes an important food for most 

of the fishes of the Colorado River. Exotic and unusual species such as Craspedacusta 

sowerbyi, Branchiura sowerbyi, and the parasite Lernaea cyprinacea have also been reported in 

the Colorado River. Damming of the river has caused stranding of some plant and animal 

communities during periods of low flow. Some species have shown adaptations to fluctuating 

flow regimens caused by dams. Regulated flow can increase the standing crops of both 

attached algae and aquatic macrophytes, as well as aquatic mosses. Creation of reservoirs may 

cause enrichment of some nutrients that affect algal growth. The most common effect of 

impounded rivers on the macroinvertebrate community is reduced species diversity 

accompanied by high density and biomass. Modifications in thermal conditions also contribute 

to the compositional changes in macroinvertebrates below reservoirs. Research priorities 

recommended are: seasonal studies of Cladophora glomerata, studies on optimal flow rates for 

Cladophora glomerata population growth, food web studies in tail waters of Glen Canyon Dam, 

phenological studies of invertebrates in the Colorado River ecosystem, and model development 

to study the effects of physicochemical parameters on plant and animal communities in 

regulated rivers. (See also W93-02624) (Geiger-PTT) 

Notes: See Musser, 1959 (in this bibliography) for a list of macroinvertebrate species found in 

Glen Canyon in 1958 (before dam closure). 

Flowers, S. 1959. Algae collected in Glen Canyon. Pages 203-205 IN C.E. Dibble (ed.), 

Ecological Studies of the Flora and Fauna in Glen Canyon, Appendix D. University of Utah 

Anthropology Papers, Salt lake City. 226 p.

14
Author: Bogan, M.A.; Allen, C.D.; Muldavin, E.H.; Platania, S.P.; Stuart, J.N.; Farley, G.H.; 

Mehlop, P.; Belnap, J. 

Year: 1998 

Title: Southwest 

Reference Type: Electronic Source 

Producer: United States Geological Survey, Biological Resources Division 

Access Year: 2005 

Access Date: June 15 

Value of reference: Synthesis article addresses changes in fish occurrence and distribution in 

a very large river basin (Colorado) as a whole and also mentions changes in specific tributaries. 

General historical ranges and declines or extinctions are given for four significant native fish 

species: Colorado squawfish, bonytail, razorback sucker, and humpback chub. Web site brings 

together a number of important references, including some from gray literature. 

Results relevant to EMAP: The percentage of the native fish fauna in the Colorado River basin 

that are threatened is 85% in AZ, 72% in CA, 30% in NM, and 42% in UT. 

The Colorado squawfish is now reduced to about 1/3 its original range, with natural populations 

extinct in the lower basin; Humpback chubs, once found in most large-river habitats of the CO 

River, now exists in only five canyon reaches in the upper basin; Bonytails, once one of the 

most abundant fishes in the basin, is now considered functionally extinct; Razorback suckers 

were once so numerous that they were commercially fished in southern AZ in the early 1900s, 

but now inhabit only 1208 river km in the upper basin. 

These conditions have been brought about by dams, impoundments, loss of physical habitat, 

habitat degradation, chemical pollution, overfishing, altered water flow regime, groundwater 

pumping, and introduction of at least 72 nonnative species. 

Geographic location: southwest, xeric, mountains, Colorado, Utah, New Mexico, Arizona, 

Colorado River basin, eco 20, eco22, eco23, eco81, eco14, xeric, EPA Region 8, EPA Region 9 

Keywords: fish, dams, nonnative species, fishing, habitat degradation, pollution, groundwater 

pumping 

URL: http://biology.usgs.gov/s+t/SNT/index.htm 

15
Author: Bradford, D.F.; Graber, D.M.; Tabatabai, F. 

Year: 1994 

Title: Population declines of the native frog, Rana muscosa, in Sequoia and Kings Canyon 

National Parks, California 

Reference Type: Journal Article 

Journal: The Southwestern Naturalist 

Volume: 39 

Issue: 4 

Pages: 323-327 

Value of reference: This article reports the dramatic decline of the mountain yellow-legged frog 

since 1955 from relatively undisturbed areas of the Sierra Nevada. Few accurate historical 

records are available prior to 1955; the "historical" period was thus defined as 1955-1979. 

Areas both within and outside Kings Canyon and Sequoia National Parks were compared on the 

basis of historical and current (1988-91) presence of the species. Historical geographic range is 

shown in Figure 1 (Zweifel 1955).

Results relevant to EMAP: In the current survey, Rana muscosa remained at 11 of 21 

historical sites within the parks but at only 3 out of 24 historical sites outside the parks. The 

authors conclude that the species has disappeared from about half of its historical localities in 

the two parks during the past three decades, and has been extirpated in some drainages. The 

magnitude of decline seems greater outside the parks. The causes for the declines are not 

clear. Several possible factors contributing the decline are discussed; the authors appear to 

favor the hypothesis that the cause is due to habitat fragmentation and isolation of populations 

by nonnative fishes (Bradford et al. 1993). The degree of isolation differs by about tenfold 

compared to the period prior to fish introduction.

Geographic location: Sierra Nevada, Kings Canyon National Park, Sequoia National Park, 

San Joaquin River, Kings River, Kaweah River, Kern River, EPA region 9, eco5, California, 

mountains 

Keywords: amphibians, declining populations, isolation, habitat fragmentation, headwater 

streams, high elevation 

Abstract: Rana muscosa (mountain yellow-legged frog) is one of a number of amphibians 

around the world that reportedly have declined in numbers in recent years in seemingly wellprotected environments. In Sequoia and Kings Canyon National Parks, California, two study 

areas comprising the headwaters of seven creek systems were surveyed for R. muscosa and 

Pseudacris regilla (Pacific chorus frog) in 1978-79 and again in 1989. R. muscosa was found at 

27 sites greater than 200 m apart in 1978-79, but at only one site in 1989, and the population at 

this site disappeared by 1991. In contrast, P. regilla was found at 15 to 17 sites both times. A 

comparison of 21 historical (1955-1979) and recent (1989-90) records scattered throughout the 

parks showed that R. muscosa remained at only 11 of these sites in 1989-90. A similar 

comparison of 24 historical and recent records elsewhere in the Sierra Nevada showed that R. 

muscosa remained at only three sites. We conclude that R. muscosa has disappeared from 

about half of the historical localities in Sequoia and Kings Canyon National Parks during the 

past three decades, and has been extirpated in some drainages. The magnitude of decline 

appears to be even more pronounced outside the parks. The causes for these declines are not 

clear. 

Notes: Zweifel, R.G. 1955. Ecology, distribution, and systematics of frogs of the Rana boylei

16
group. University of California Publ. Zool. 54:207-292. 

Bradford, D.F. et al. 1993. Isolation of remaining populations of the native frog, Rana muscosa, 

by introduced fishes in Sequoia and Kings Canyon National Parks, California. Conservation 

Biology 7:882-888. 

17
Author: Bradford, D.F.; Jaeger, J.R.; Jennings, R.D. 

Year: 2004 

Title: Population status and distribution of a decimated amphibian, the relict leopard frog (Rana 

onca) 

Reference Type: Journal Article 

Journal: The Southwestern Naturalist 

Volume: 49 

Issue: 2 

Pages: 218-228 

Value of reference: Previous publications describing this species' historical range (Jaeger et al. 

2001; Jennings 1988, Jennings and Hayes 1994) are questioned because of taxonomic 

uncertainties regarding various leopard frog populations within the region. This article 

synthesizes past (pre-1970) and recent information and reports the latest understanding of 

distribution, size, structure, and dynamics of extant and recently extinct R. onca populations. 

The authors also specifically define a minimum historical distribution of R. onca in light of recent 

taxonomic clarification and describe observations of habitat changes that seem to be causally 

associated with recent population extinctions.

Results relevant to EMAP: The historical range was identified by examining museum 

specimens, using morphological characters to distinguish between R. onca and R. pipiens. 

Since not all areas of the basins were sampled in the past, the study establishes a minimum

historical distribution. 

R. onca occurred in springs, streams, and wetlands within the Virgin River drainage 

downstream from the vicinity of Hurricane and Gunlock, Utah; along the Muddy River, Nevada; 

and along the Colorado River from its confluence with the Virgin River downstream to Black 

Canyon below Lake Mead in Nevada and Arizona. All historical localities are within a few km of 

these rivers, and many localities are at the river (Figure 1). The five populations currently 

remaining are small and isolated and concentrated in two areas: near the Overton Arm of Lake 

Mead and in Black Canyon along the Colorado River below Lake Mead, Nevada. All remaining 

populations inhabit spring systems with unaltered hydrology.

Possible causes of disappearance from the majority of its historical range include habitat 

alteration due to agriculture, impoundments, water diversions, and introduction of nonnative 

species such as bullfrogs, various fishes, and red swamp crayfish.

Geographic location: Arizona, Nevada, Colorado River basin, Virgin River basin, Black 

Canyon, Lake Mead, EPA Region 9, eco14, eco22, eco20, xeric 

Keywords: amphibians, agriculture, nonnative species, water diversion 

Abstract: The relict leopard frog (Rana onca) was once thought to be extinct, but has recently 

been shown to comprise a valid taxon with extant populations. We delineate the minimum 

historical range of the species based on records from 24 localities, report the extinction of 2 of 7 

populations extant in the 1990s, and estimate total population size. The 5 remaining populations 

occurred in 2 areas: near the Overton Arm of Lake Mead and in Black Canyon along the 

Colorado River below Lake Mead, Nevada. These 2 areas are only 3.6 and 5.1 km long, 

respectively. The 5 extant populations inhabited spring systems with largely unaltered hydrology 

and no introduced American bullfrogs (Rana catesbeiana) or game fishes. In a mark-recapture 

study conducted in the 

Overton Arm area, the estimated number of adult frogs averaged 36 over 555 m of stream 

18
habitat, and estimated annual survivorship of adults averaged 0.27. A single mark-recapture 

estimate for the size of the largest population within Black Canyon, at a site approximately 450 

m in length, was 637 adult frogs. An estimate for the total number of frogs at all sites, based on 

mark-recapture data, visual encounter surveys, and extent of habitat, was approximately 1,100 

adults (range 693–1,833). The 2 recent population extinctions occurred concomitantly with 

encroachment of emergent 

vegetation into pools. We speculate that this occurred as a result of natural processes in one 

case, and anthropogenic processes in the other. 

Notes: Jaeger, J.R. et al. 2001. Rediscovering Rana onca: evidence for phylogenetically distinct 

leopard frogs from the border region of Nevada, Utah, and Arizona. Copeia 2001:339-354. 

Jennings, M.R. 1988. Rana onca Cope, relict leopard frog. Catalogue of American Amphibians 

and Reptiles 417:1-2. 

Jennings and Hayes. 1994. Decline of native ranid frogs in the Desert Southwest. Pages 183-

211 IN Brown, P.R. and J.W. Wright, eds. Herpetology of the North American deserts. 

Southwestern Herpetologists Society, Special Publication Number 5. 

19
Author: Bradford, D. F.; Tabatabai, F.; Graber, D.M. 

Year: 1993 

Title: Isolation of remaining populations of the native frog, Rana muscosa, by introduced fishes 

in Sequoia and Kings Canyon National Parks 

Reference Type: Journal Article 

Journal: Conservation Biology 

Volume: 7 

Issue: 4 

Pages: 882-888 

Value of reference: This paper documents the decline of yellow-legged frogs (Rana muscosa) 

from a minimally-disturbed area within the Sierra Nevada during the past century. The decline is 

attributed to intentional fish introductions stocking of lakes and streams. This reference provides 

an example of how fish introductions can influence vertebrate assemblages, vertebrate metrics, 

and derived diversity indices. 

Results relevant to EMAP: The authors propose that the introduction of fish into previously 

fishless streams and lakes has resulted in increased isolation of populations of yellow-legged 

frogs (Rana muscosa). This isolation, they suggest, has made subpopulations more vulnerable 

to extinction through natural causes associated with fluctuations in the physical environment, 

and subsequent re-colonization through streams more difficult. 

Much of the water within Sequoia and Kings Canyon National Parks were historically fishless 

due to the steep gradients of connecting streams, with the exception of certain streams and 

possibly lakes containing golden trout (Oncorhynchus aguabonita), and some rainbow trout (O. 

mykiss). During the past century four species of trout and char, including golden trout, rainbow 

trout, brook trout (Salvalinus fontinalis) and brown trout (Salmo trutta) have been systematically 

introduced above fish barriers throughout the region. 

To assess the level of "connectivity" between sample sites, the number of potential dispersal 

links between present and former fishless stream networks were evaluated. Contemporary 

yellow-legged frog-bearing sites are much more isolated (approximately 10-fold) from one 

another than prior to beginning of fish introductions early in the twentieth century. This loss of 

connectivity is suggested as one cause of the decline of the species, attributed to natural 

extinction due to stochastic processes, in combination with decreased probability of recolonization.

Geographic location: California, Sierra Nevada, mountains, eco5, EPA Region 10 

Keywords: amphibians; nonnative species; predation; habitat fragmentation 

Abstract: Rana muscosa (mountain yellow-legged frog) was eliminated by introduced fishes 

early in this century in many of the lakes and streams in Sequoia and Kings Canyon National 

Parks, California. In waters not inhabited by fish, however, R. muscosa has disappeared from 

many sites within the past 30 years, and it appears to have gone extinct in some drainage 

systems. Fragmentation of populations may have caused or contributed to these recent 

extinctions, because R. muscosa populations are significantly more isolated from one another 

by fish at present than in pre-stocking conditions. A total of 312 lake-sites in 95 drainage basins 

were surveyed for amphibians and fish in 1989-90. For the 109 sites containing R. muscosa, we 

delineated networks of sites connected to one another via fishless streams, and we compared 

these present fishless networks ("present networks") to those expected for the same sites 

20
assuming that fish had not been introduced to the parks ("former networks"). Most present 

networks consist of only one site (mean 1.4), whereas the former networks average 5.2 sites. 

This difference represents approximately a 10-fold difference in connectivity of populations, 

which is defined as the mean number of potential links (fishless streams) per network. 

Connectivity averages only 0.43 in present networks, in contrast to 4.15 in former ones. 

21
Author: Brothers, T. S. 

Year: 1984 

Title: Historical vegetation change in the Owens River riparian woodland 

Reference Type: Book Section 

Editor: Warner, R. E.; Hendrix, K. M. 

Book Title: California riparian systems: Ecology, conservation, and productive management 

City: Berkeley, California 

Publisher: University of California Press 

Pages: 75-84 

Value of reference: The article attempts to reconstruct the pre-settlement riparian vegetation of 

the Owens River valley and compare it to present day riparian vegetation. Though there is very 

little information available from early explorers' journals, available references to original 

vegetation are compared with the subsequent land use and water management history to make 

inferences about changes in riparian vegetation since settlement.

Results relevant to EMAP: The author pieces together evidence of riparian vegetation from the 

Walker, Fremont, von Schmidt, and Brewer expeditions that passed through the Owens Valley 

between 1834 and 1864. Fremont mentions willow and cottonwood, but the others mention only 

a few small cottonwoods and no other timber. The author lists species recorded in the present 

day sample and discusses which species may have increased since pre-settlement times 

(narrowleaf willow and rabbitbrush tend to increase with grazing pressure). 

The diversion of Owens River water to Los Angeles may have affected regeneration of willows 

and cottonwoods that are dependent on periodic flooding to reproduce. Below the diversion 

aqueduct on the Owens River, the riverbed is dry and vegetated with the alien saltcedar, 

Russian olive, and herbaceous weeds. 

Geographic location: California, EPA Region 9, Owens River, xeric, eco13, central basin and 

range 

Keywords: phab, riparian vegetation, water diversion 

Abstract: This study evaluates human-caused vegetation change in the riparian woodland of 

Owens River (Inyo Co., California). the greatest change has occurred below the intake of the 

Los Angeles aqueduct, where drying of the channel has eliminated most native riparian cover 

and allowed invasion by saltcedar (Tamarix ramosissima) and Russian olive (Elaeagnus 

angustifolia). Fire, water management, and other factors may have reduced tree cover above 

the aqueduct intake and encouraged proliferation of weedy native shrubs. The present scarcity 

of tree seedlings suggests that one or more of these factors continues to inhibit tree 

regeneration. 

22
Author: Brown, L.A.; Moyle, P. B. 

Year: 2005 

Title: Native fishes of the Sacramento-San Joaquin drainage, California: A history of decline 

Reference Type: Book Section 

Editor: Rinne, J. N.; Hughes, R. M.; Calamusso, B. 

Book Title: Historical changes in large river fish assemblages of the Americas 

City: Bethesda, Maryland 

Publisher: American Fisheries Society Symposium 45 

Pages: 75-98 

Value of reference: This paper is a companion to other papers on the Sacramento-San 

Joaquin rivers in this collection (Skinner 1962 (salmon catch data), Katibah 1984 (riparian 

forest), Scott and Marquiss 1984 (sediment)) that covers the decline of a broad variety of fishes, 

both commercial and non-commercial, and how they have been affected by a range of human 

disturbances.

Results relevant to EMAP: The fish assemblages of the Sacramento and San Joaquin rivers 

and tributary streams are separated into elevational regions for the discussion of their historical 

distribution and present day status: mountains over 1000 m, fishless; mountains 450-1000 m, 

rainbow trout assemblage (5 species); foothills 30-450 m, pikeminnow/hardhead/sucker 

assemblage (up to 11 species); valley <30 m, deep bodied fish assemblage (10 species). 

The valley fish assemblage, that once occupied low elevation rivers, oxbows, and sloughs, only 

exists as remnant populations. The thicktail chub is globally extinct; the bull trout and coho 

salmon have been extirpated; the Sacramento perch was once common, but now exists mostly 

as transplanted populations in reservoirs; the splittail is commonly found in Native American 

middens in the Tulare basin where it is now scarce. 

The huge increases in sediments after mining in the mid-1800's may have facilitated the 

invasion by alien striped bass and American shad that are more likely to thrive in systems with 

high loads of fine sediment. The rise of agriculture and the loss of wetland habitats led to the 

extinction and decline of the valley fishes. Flow regime is a key factor in the reproductive 

success of native and alien fishes. The streams and rivers of the Sacramento system have a 

relatively higher representation of native species than the San Joaquin likely because there is 

less flow alteration on the Sacramento and no canal systems in agricultural areas. In the San 

Joaquin drainage the native species are restricted to the areas just below the reservoirs. Those 

above the reservoirs are threatened by alien species moving upstream from the lakes.

Geographic location: EPA Region 9, Sacramento River, San Joaquin River, Central Valley, 

eco6, eco7, xeric 

Keywords: fish, nonnative species, mining, sediment, agriculture, altered water flow regime, 

dams 

Abstract: In this paper, we review information regarding the status of the native fishes of the 

combined Sacramento River and San Joaquin River drainages (hereinafter the "SacramentoSan Joaquin drainage") and the factors associated with their declines. The Sacramento-San 

Joaquin drainage is the center of fish evolution in California, giving rise to 17 endemic species 

of a total native fish fauna of 28 species. Rapid changes in land use and water use beginning 

with the Gold Rush in the 1850's and continuing to the present have resulted in the extinction, 

extirpation, and reduction in range and abundance of the native fishes. Multiple factors are 

23
associated with the declines of native fishes, including habitat alteration and loss, water storage 

and diversion, flow alteration, water quality, and invasions of alien species. Although native 

fishes can be quite tolerant of stressful physical conditions, in some rivers of the drainage the 

physical habitat has been altered to the extent that it is now more suited for alien species. This 

interaction of environmental changes and invasions of alien species makes it difficult to predict 

the benefits of restoration efforts to native fishes. Possible effects of climate change on 

California's aquatic habitats add additional complexity to restoration of native fishes. Unless 

protection and restoration of native fishes is explicitly considered in future water management 

decisions, declines are likely to continue. 

24
Author: Brown, L. R.; Moyle, P. B.; Yoshiyama, R. M. 

Year: 1994 

Title: Historical decline and current status of coho salmon in California 

Reference Type: Journal Article 

Journal: North American Journal of Fisheries Management 

Volume: 14 

Issue: 2 

Pages: 237-261 

Value of reference: The article gives an overview of the vulnerable status of coho salmon in 

California. Historical information on coho salmon is limited; here it is given in terms of historical 

and current presence/absence records in individual streams. 

Results relevant to EMAP: Unfortunately, much of the "historic" information in this article is 

from the 1930's, 50's, and 70's as abundance figures from gill net or sport fish catches. 

Examples: Klamath River, lower river 1919 - 11,162 in gill net fishery; 1955 - 1145 in sport 

catch. Klamath River; 301 km from mouth - Coho termed abundant in 1923. By 1956, none 

counted. Table of historic and recent abundance data for adult coho salmon in some California 

Rivers, p. 244. 

There are 582 California streams known to have supported coho salmon at some time. 

Information on the recent presence or absence of coho salmon was available for only 248 of 

those streams. Of these 248 streams, 54% still contained coho salmon and 46% did not. By 

1956, it was estimated that over 1600 km of streams in California had been lost as important 

fish habitat. 

Juvenile coho salmon require deep, cold pool habitats for high survival. Their wide distribution 

over many small coastal streams and their relatively short life span (3 years) make California 

coho salmon more vulnerable to severe declines during drought years. Inadequate protection of 

watersheds from the effects of logging, grazing, and urbanization has resulted in increased 

water temperatures, the loss of pools through sedimentation, and the removal of large woody 

debris needed for cover and pool formation.

Geographic location: xeric, California, Central Valley, Klamath River, Smith River, Redwood 

Creek, Eel River, eco6, eco7, EPA Region 9 

Keywords: fish, coho salmon, dams, logging, genetic integrity, roads, grazing, urbanization 

Abstract: The southernmost populations of coho salmon (Oncorhynchus kisutch) occur in 

California where native coho stocks have declined or disappeared from all streams in which 

they were historically recorded. Coho salmon previously occurred in as many as 582 streams, 

from the Smith River near the Oregon border to the San Lorenzo River on the central coast. 

Information on the recent presence or absence of coho salmon was available for only 248 (43%) 

of those streams. Of these 248 streams, 54% still contained coho salmon and 46% did not. The 

farther south a stream is located, the more likely it is to have lost its coho salmon population. 

We estimate that the total number of adult coho salmon entering California streams in 1987-

1991 averaged around 31,000 fish per year, with hatchery populations making up 57% of this 

total. Thus, about 13,000 non-hatchery coho salmon have been spawning in California streams 

each year since 1987, an estimate that includes naturalized stocks containing about 9,000 fish 

of recent hatchery ancestry. There are now probably less than 5,000 native coho salmon (with 

no known hatchery ancestry) spawning in California each year, many of them in populations of 

25
less than 100 individuals. Coho populations today are probably less than 6% of what they were 

in the 1940's, and there has been at least a 70% decline since the 1960's. There is every 

reason to believe that California coho populations, including hatchery stocks, will continue to 

decline. The reasons for the decline of coho salmon in California include: stream alterations 

brought about by poor land use practices (especially those related to logging and urbanization) 

and by the effects of periodic floods and drought, the breakdown of genetic integrity of native 

stocks, introduced diseases, over-harvest, and climatic change. We believe that coho salmon in 

California qualify for listing as a threatened species under state law, and certain populations 

may qualify for listing as threatened or endangered under federal law. 

26
Author: Burroughs, Raymond Darwin 

Year: 1961 

Title: The natural history of the Lewis and Clark Expedition 

Reference Type: Book 

City: East Lansing, Michigan 

Publisher: Michigan State University Press 

Number of Pages: 340 

Value of reference: This book summarizes the journals from the Lewis and Clark Expedition 

and groups the information into chapters by species observed. The chapters include: 

Introduction, bears and raccoons, weasel family, wild dogs and cats, rodents and rabbits, deerelk and antelope, bison, mountain goats and bighorn sheep, diving and wading birds, ducks - 

geese and swans, birds of prey, marsh and shore birds, gulls and terns, pigeons - parroquets - 

goatsuckers and hummingbirds, woodpeckers, passerine birds, fishes, reptiles and amphibians. 

Results relevant to EMAP: The information listed in the journals helps reconstruct habitats and 

landscape elements at the time of observation. The presence of certain mammals, birds, fish, 

and plant species can paint a picture of what the riparian and landscape habitat was like when 

first encountered by early explorers. A summary of the many fish, mammals, and other natural 

history data collected on the expedition is included in the chapters of this book. 

The chapters require some sifting through to extract small pieces of anecdotal information or to 

reconstruct stream related attributes, however; the information is quite valuable and may be the 

only source of pre-settlement conditions of the plains. This is a good broad reference and 

inventory that includes specific information about pre-settlement conditions along the route of 

the expedition.

Geographic location: Great Plains, plains, mountains, Lewis & Clark expedition route, 

Kansas, Missouri, Nebraska, Iowa, North Dakota, South Dakota, Montana, Idaho, Oregon, 

Missouri River Basin, EPA region 7, EPA region 8, eco47, eco42, eco43, eco46, 

Keywords: Lewis & Clark expedition, pre-settlement, mammals, phab, fish, natural history 

27
Author: Bury, R. B.; Corn, P. S. 

Year: 1988 

Title: Responses of aquatic and streamside amphibians to timber harvest: A review 

Reference Type: Book Section 

Editor: Raedeke, K. J. 

Book Title: Streamside management: Riparian wildlife and forestry interactions 

City: Seattle, Washington 

Publisher: College of Forest Resources, University of Washington 

Volume: 59 

Pages: 165-181 

Value of reference: This study compared density estimates of four salamander species in 

uncut vs. cut riparian reaches on 43 streams in the Coast Range of Oregon. It is one of a limited 

number of papers examining the effects of logging on amphibians. Mature and old growth 

reference reaches are used in the absence of historical information on amphibians and their 

habitats.

Results relevant to EMAP: "There were marked differences in the occurrence, density, and 

biomass of amphibians between control streams and streams in logged sites. All four species 

(tailed frogs, Pacific giant salamanders, Olympic salamanders, and Dunn's salamanders) 

occurred significantly more often in the control streams than in the streams in logged stands" 

(bar graph, Figure 2, p. 172). The species differed in their sensitivity to temperatures and their 

ability to withstand some level of logging activity. 

Control streams had a higher percentage of cobbles and boulders in the substrate, while logged 

streams had significantly more sediment. Sediments can be attributed to logging in this case 

because there were no road crossings upstream from the sample reach in any of the streams in 

logged stands.

Geographic location: mountains, Pacific Northwest, Oregon, Coast Range, eco1, EPA Region 

10 

Keywords: amphibians, tailed frog, Olympic salamander, Pacific giant salamander, Dunn's 

salamander, logging, temperature, sediments, phab 

Abstract: Stream dwelling amphibians, which can be the dominant vertebrates of small streams 

and forests of the Pacific Northwest, are prototypic riparian organisms. Larvae of several 

species are totally aquatic, while adults use the terrestrial streamside (riparian) habitat to 

varying degrees. Impacts of timber harvest vary among species, physical habitats, and regions 

of the Pacific Northwest. Populations of giant salamanders (Dicamptodon) increase following 

clear cutting in the Oregon Cascades, while in the Oregon Coast Range, the long term effects of 

logging were negative and severe for all species. Timber harvest is less disruptive in high 

gradient streams and in streams where there is uncut timber remaining upstream. Buffer strips 

adjacent to headwater and small streams can provide shad and reduce ecological requirements 

of amphibians in headwaters, assess the effects of logging on amphibians in different regions 

and under varying climatic regimes, and determine what sizes of buffer strips or uncut patches 

are most effective and cost-efficient for protecting stream amphibians. 

28
Author: Carlson, C.A.; Muth, R.T. 

Year: 1989 

Title: The Colorado River: Lifeline of the American Southwest 

Reference Type: Journal Article 

Journal: Canadian Special Publication of Fisheries and Aquatic Sciences 

Volume: 106 

Pages: 220-239 

Value of reference: Important synthesis paper that summarizes many of the historical and 

current published and gray literature on status of CO river and its biota. This key reference 

presents an excellent summary of conditions prior to 1935 (date of Hoover Dam closure), 

including historic distributions of 54 species of fish in different sections of the basin (see Table 

2), specific historic locations where fish were found (also in Table 2), and historic riparian 

community composition. Historical conditions are contrasted with current conditions, and 

causes for the changes are presented.

Results relevant to EMAP: River regulation has lowered mainstream water temperatures 10-

15 degrees C, resulting in cooler summer and warmer winter water temperatures below dams 

(Stanford and Ward 1986a); lower summer temperatures have adversely affected native fishes. 

By 1957, salinity (about 250 mg/L) at Lee Ferry had doubled (reports of 600, 825, and 750 mg/L 

have been reported in various locations); paper also describes historical aquatic conditions for 

oxygen levels, algae, nutrient levels, and zoobenthos. 

Seventeen of the 54 native fish are either threatened, endangered, or extinct, and most have 

experienced drastic abundance and range reductions due to impacts including dams and 

impoundments, poisoning with rotenone, introduction of exotic species, and stocking of various 

invertebrates carried out in the mid 1900s. 

At least 2023 ha of cottonwood communities existed along 322 km of potentially suitable habitat 

on the lower river in the 1600s; due to water management, grazing, competition with tamarisk, 

and phreatophyte removal, only about 1130 ha of these communities remain, and less than 202 

ha can be considered pure cottonwood communities.

Geographic location: Colorado River Basin, Wyoming, Utah, Colorado, Arizona, New Mexico, 

Nevada, California, xeric, eco13, eco81, eco23, eco79, eco22, eco20, eco21, eco19, eco18, 

EPA Region 8, EPA Region 9. 

Keywords: dams, water diversion, nonnative species, grazing, water temperature, sediments, 

fish, macroinvertebrates, riparian vegetation 

Abstract: In less than a century, the wild Colorado River has been drastically and irreversibly 

transformed into a tamed, man-made system of regulated segments. The pristine Colorado, 

characterized by widely fluctuating flows and physico-chemical extremes, supported unique 

assemblages of indigenous flora and fauna. Closure of Hoover Dam in 1935 marked the end of 

the free-flowing river. The system has since become one of the most altered and intensively 

controlled in the United States; many mainstem and tributary dams, water diversions, and 

channelized river sections now exist in the basin. Despite having one of the most arid 

drainages in the world, the river supplies more water for consumptive use than any river in the 

United States. Its biota is dominated by non-native organisms, and about one third of its native 

fishes are threatened, endangered, or extinct. This paper treats the Colorado River holistically 

as an ecosystem and summarizes current knowledge on its ecology and management. Little 

29
has been published on productivity and fisheries of the mainstream river. 

30
Author: Chapman, D.W. 

Year: 1986 

Title: Salmon and steelhead abundance in the Columbia River in the nineteenth century 

Reference Type: Journal Article 

Journal: Transactions of the American Fisheries Society 

Volume: 115 

Pages: 662-670 

Value of reference: This reference synthesizes harvest data, early fish literature, and optimum 

exploitation rates to reconstruct peak-period run estimates for salmon (4 species) and steelhead 

in the Columbia River basin in the late 1800s. The estimation procedure is based on 5 

consecutive years of greatest total harvest and therefore overestimates the average year but 

better approximates what the basin was capable of supporting, i.e., potential historical 

production. 

Results relevant to EMAP: Peak-period runs for the entire Columbia River system estimated 

from optimum harvest rates were 2,623,000 sockeye, 4,338,000 chinook (Table 3 breaks down 

into summer, fall, and spring runs), 618,000 coho, 554,000 steelhead, and 748,000 chum--

8,881,000 adults altogether. These are based on optimum exploitation rates (rate at maximum 

sustained yield) from the literature of 0.77 for coho, 0.73 for sockeye, 0.68 for spring and 

summer chinook, 0.88 for fall chinook, 0.69 for steelhead, and 0.48 for chum. On the basis of 

the more probable harvest rates that produced overfishing (0.80-0.88), total run size was about 

7,505,000 adults, a single best estimate of total predevelopment runs. This estimate falls within 

the low range of previous run estimates (cited in this publication), which were partly speculative 

and varied drastically. 

Overfishing and environmental degradation caused numbers to rapidly decrease after catches 

peaked in the late 1800s. Mining, grazing, irrigation, dams, water diversions, and logging 

contributed habitat degradation. 

Losses can be estimated by subtracting current run sizes from predevelopment estimates of 

7.5-8.8 X 106

. This publication is dated, but it gives the 1977-1981 run data, with corrections for 

ocean harvest, as 2.5 X 106

. 

Geographic location: Columbia River basin, Oregon, Washington, Idaho, eco10, eco4, eco1, 

eco11, eco12, eco 15, eco16. eco3, eco9, EPA Region 10, xeric, mountains 

Keywords: fish, salmon, mining, grazing, irrigation, dams, water diversions, logging 

Abstract: I estimated peak runs of Pacific salmon Oncorhynchus sp. and steelhead Salmo 

gairdneri in the Columbia River during the 40 years centered on 1900 on the basis of peakperiod commercial catches and probable optimum exploitation rates. Peak-period catches were 

estimated from mean catch weights during the five consecutive years of greatest total harvest, 

and from mean weights of fish reported in the early literature. These catches were 1,700,000 

summer chinook salmon Oncorhynchus tshawytscha(1881-1885), 382,000 steelhead (1892-

1896), 1,100,000 fall chinook salmon (1915-1919), 400,000 spring chinook salmon 

(approximately), 476,000 coho salmon O. kisutch (1894-1898), 1,915,000 sockeye salmon O. 

nerka (1883-1887), and 359,000 chum salmon O. keta (1915-1991). Optimum harvest rates for 

maximum sustained yield from non-hatchery stocks were obtained from literature: 0.77 for coho, 

0.73 for sockeye, 0.68 for spring and summer chinook, 0.88 for fall chinook, 0.69 for steelhead, 

and 0.48 for chum. Peak-period runs estimated from optimum harvest rates were 2,623,000 

31
sockeye, 4,338,000 chinook, 618,000 coho, 554,000 steelhead, and 748,000 chum--8,881,000 

adults altogether. On the basis of the more probable harvest rates that produced over-fishing (-

.80-0.88), total run size was about 7,505,000 adults, a single best estimate of total predevelopment runs. I discuss aboriginal catch in relation to the theory that decimation of Indian 

populations after 1800 permitted salmon and steelhead stocks to expand. Using the shape of 

stock-recruitment functions and appropriate commercial harvest rates, I support the alternative 

hypothesis that salmon stocks actually decreased in the early 1800s with decreased Indian 

harvest, then increased after 1850 as commercial fisheries developed, and finally decreased in 

response to overfishing. Environmental degradation exacerbated the latter decrease. 

32
Author: Close, D. A.; Fitzpatrick, M.; Li, H.; Parker, B.; Hatch, D.; James, G. 

Year: 1995 

Title: Status report of the Pacific Lamprey (Lampetra tridentata) in the Columbia River Basin 

Reference Type: Report 

City: Portland, Oregon 

Institution: U. S. Department of Energy, Bonneville Power Administration, Division of Fish and 

Wildlife 

Pages: 40 

Report Number: BPA Report DOE/BP-39067-1 

Value of reference: This document provides a good synthesis of what is known of Pacific 

lamprey population changes in the Columbia River and Snake River Basins during the last 

century and suggests causes leading to dramatic declines in recent years. 

Results relevant to EMAP: Historically, Pacific lamprey were fairly common in the Columbia 

and Snake River drainages and occurred wherever salmon occurred. During the early part of 

the twentieth century, adult lamprey were used as food during artificial propagation of young 

salmon. Twenty seven tons were reported harvested for this purpose in 1913. A commercial 

market developed for this species, and 816 tons (approximately 10-20% of the total run) were 

reported harvested in the Willamette River drainage alone between 1943 and 1949. Dramatic 

declines in recent years are attributed to (1) problems for both adult and juvenile passage 

through dams; (2) loss of spawning and rearing habitat; (3) declines in marine prey species 

resulting from commercial fishing; and (4) chemical poisoning of streams to remove non-game 

species. 

Geographic location: EPA Region 10, mountains, xeric, Oregon, Washington, Columbia River 

basin, Snake River basin, Idaho, eco1, eco3, eco4, eco10, eco11, eco12, eco15, eco16, eco17 

Keywords: fish, Pacific lamprey (Lampetra tridentata), fishing, dams 

URL: http://www.efw.pba.gov/cgi-bin/efw/FW/publications.cgi 

33
Author: Collins, B.D.; Montgomery, D.R.; Hass, A.D. 

Year: 2002 

Title: Historical changes in the distribution and functions of large wood in Puget Lowland rivers 

Reference Type: Journal Article 

Journal: Canadian Journal of Fish and Aquatic Sciences 

Volume: 59 

Pages: 66-76 

Value of reference: The useful part of this reference, with respect to pre-settlement conditions, 

is the reconstruction of wood abundance, size, and log jamming using archival sources. The 

reference also demonstrates the use of historical information to evaluate the suitability of 

reference sites, and the integrated use of both historical information and current least-disturbed 

sites to re-create pre-settlement conditions. The link between wood and fish habitat value is 

mentioned on page 75, where two studies are referenced as support for large wood and wood 

jams in fish habitat sustainability.

Results relevant to EMAP: Early accounts document transport by rivers of vast amounts of 

wood, for example a Skagit river jam was described as 9 m deep, consisting of 5-8 tiers of logs, 

ranging from 3-8 feet in diameter and existed for at least a century, as its surface supported live 

trees 0.6-1.2 m in diameter (Interstate Publishing Company 1906); individual jams of this size 

could have stored several hundred thousand pieces of wood. 

Current numbers of snags are estimated at 0.2-0.4 pieces per km, which is 2 orders of 

magnitude less than possible snag recruitment rates suggested by data from 1881-1909. 

Annual maximum diameters between 1889 and 1909 were 3.6 to 5.3 m, based on snagboat 

records. 

A comparison of pool data from the Snohomish and Stillaguamish rivers with data from the 

Nisqually suggests that the transition from a freely migrating or avulsing river with mature 

floodplain forest to a leveed river with little riparian recruitment has reduced the number of pools 

by two to three times. Field studies in the Skagit River indicate that wood (particularly wood 

jams) significantly increases the fish habitat value of riverbanks. 

Geographic location: Puget Lowland, Washington, eco1, eco2, eco77, mountains, Nisqually 

River, Skykomish River, Snoqualmie River, EPA Region 10 

Keywords: phab, fish, large wood, wood jams, pools 

Abstract: We examined changes in wood abundance and functions in Puget Lowland rivers 

from the last ~150 years of land use by comparing field data from an 11-km-long protected 

reach of the Nisqually River with field data from the Snohomish and Stillaguamish rivers and 

with archival data from several Puget Lowland rivers. Current wood abundance is one to two 

orders of magnitude less than before European settlement in the Snohomish and Stillaguamish 

basins. Most importantly, wood jams are now rare because of a lack of very large wood that 

can function as key pieces and low rates of wood recruitment. These changes in wood 

abundance and size appear to have fundamentally changed the morphology, dynamics, and 

habitat abundance and characteristics of lowland rivers across scales from channel unit to 

valley bottom. Based on our field studies, rivers had substantially more and deeper pools 

historically. Archival data and field studies indicate that wood jams were integral to creating and 

maintaining a dynamic, anastomosing river pattern with numerous floodplain channels and 

abundant edge habitat and routed floodwaters and sediment onto floodplains. Establishing the 

34
condition of the riverine landscape before European settlement sets a reference against which 

to evaluate contemporary conditions and develop restoration objectives. 

35
Author: Collins, B.D.; Sheikh, A.J. 

Year: 2002 

Title: Mapping historical conditions in the Snoqualmie River valley (RM 0 - RM 40) 

Reference Type: Report

City: Seattle, WA 

Institution: King County Department of Natural Resources and Department of Earth and Space 

Sciences, University of Washington 

Pages: 30 

Value of reference: This study used a combination of maps and field notes from the General 

Land Office (GLO) cadastral survey 1871-1873 and aerial photographs from 1936. These data 

were then put in a GIS database and used to establish a baseline of "historic condition" by 

mapping the channel, wetland, forest, and oxbow ponds in the Snoqualmie River valley prior to 

Euro-American settlement, or about 1870. To evaluate subsequent change, conditions were 

also mapped from 1936 and 2000 aerial photos. 

The availability of pre-settlement accounts and inventories of an area varies by region, so the 

implementation of a combination of resources to establish a baseline may be the only way to try 

to determine what the conditions were like before Euro-American settlement. This report is a 

good example of this type of method and is a useful tool to identify changes in stream habitat 

since settlement.

Results relevant to EMAP: This study provides a good baseline of historic condition and 

documents the changes to the system since settlement. 

Much of the forest present prior to Euro-American settlement had been cleared, and much of 

the wetland cleared and drained by 1936. Riparian vegetation remained along river channels 

and oxbows in some areas in 1936 

 

Since ~1870, only a few additional oxbows have been created, because the river migration rate 

is generally low; most oxbows that now exist were created prior to the earliest mapping in 

~1870. Valley wetlands, on the other hand, are substantially diminished in area, in 2000 being 

less than one-fifth (19%) the pre-settlement wetland area. Forest cover in 2000 is about onesixth (16%) its mapped pre-settlement extent. The small rate of change to the river itself 

contrasts with the extensive historical changes to wetlands and forests, which have been greatly 

diminished. 

Geographic location: Washington, Snoqualmie River Valley, EPA region 10, eco77, mountains 

Keywords: phab, riparian wetlands, forest cover, oxbow, river valley, historical change, presettlement, Euro-American settlement 

URL: http://dnr.metrokc.gov/wlr/waterres/streams/snoqhist.htm 

36
Author: Confluence Consulting Inc. 

Year: 2004 

Title: Powder River biological survey and implications for coalbed methane development 

Reference Type: Report

City: Bozeman, MT 

Institution: Confluence Consulting, Inc 

Pages: 179 

Value of reference: Land use practices in the Great Plains dramatically affect stream health 

and watershed habitat. This report outlines the changes to the greater watershed looking at presettlement and current conditions. The study includes: physiochemical water quality 

measurements; count summaries and listings for, macroinvertebrates, periphyton, fish, reptiles, 

amphibians, and birds; and overall habitat health summaries. 

In addition, "this study provides a limited opportunity to evaluate the effects of coalbed methane 

(CBM) development already occurring in the Powder River basin in Wyoming. Site selection 

provided comparisons of biological, physical, and chemical condition above and below CBM 

development along the Powder River. These results allow inference on the effects of current 

CBM development on the biological, physical, and chemical integrity of waters in the Powder 

River basin."

Results relevant to EMAP: This report contains extensive sampling and survey information on 

the Powder River Basin. The detailed species listings and water quality information highlight the 

habitat diversity still present within this system. This system has remained relatively 

undisturbed and data from the early 1960's could be used to estimate pre-settlement conditions. 

The Powder River also has importance in terms of Wyoming’s natural heritage. In an evaluation 

of Wyoming’s fish fauna since the 1960s, Patton et al (1998) identified several declining native 

species, including flathead chub, plains minnow, river carpsucker, and channel catfish. The 

Powder River drainage " due to its relatively pristine conditions, remains one of the few places in 

Wyoming where these species are abundant." 

One of the few Great Plains prairie rivers lacking a main stem dam, the Powder River 

represents one of the last ecosystems of its kind (Hubert 1993). Moreover, it represents our last 

chance to conserve a community of fish and invertebrates that was once widespread. This 

community probably occurred throughout the northern Great Plains but dams and other water 

developments have changed the ecology of these rivers. As a result, this community is now 

relegated to the Powder River and short segments of the Yellowstone and Milk rivers in 

Montana. 

This report is a good source that illustrates a relatively undisturbed watershed (very close to 

historic condition) along with the changes and impacts the system is currently facing.

Geographic location: Wyoming, Montana, Powder River Basin, Powder River, Clear Creek, 

Piney Creek, eco43, EPA region 8 

Keywords: Coalbed methane, stream flow, Great Plains streams, disturbance, salinity, soil 

waterlogging, EIS, phab, native species, biological survey 

URL: 

http://www.powderriverbasin.org/cbm/confluence_study/CCI%20Powder%20River%20Biological

37
%20Survey%2010%20March%202004.pdf 

38
Author: Cross, Frank B.; Moss, Randle E. 

Year: 1987 

Title: Historic changes in fish communities and aquatic habitats in Plains stream of Kansas 

Reference Type: Book Section 

Editor: Matthews, W.J.; Heins, D.C. 

Book Title: Community and evolutionary ecology of North American stream fishes. 

City: Norman, Oklahoma 

Publisher: University of Oklahoma Press 

Pages: 155-165 

Value of reference: Article reviews early accounts and collections (mid to late 1800's) to try to 

establish pre-settlement conditions of plains streams in Kansas. Using this information as a 

baseline the article summarizes the changes in habitat and fish assemblages over time and 

current conditions. This reference also documents the drastic changes in water use and flows 

due to land uses, such as irrigation, cropland agriculture, and impoundments. A good overview 

of the changes and disturbances in plains riverine habitats since settlement. 

Although study area is outside of current EMAP region, the plains streams in Kansas are similar 

to ones found in the plains ecoregions within the EMAP area (e.g., eastern Colorado) and 

inferences may be drawn from this study. It is an important, frequently-cited article addressing 

historical fish communities in the Plains and is included here because of its prominence in the 

literature.

Results relevant to EMAP: Modified flow regimes have greatly altered the composition of the 

riverine community in the past decades. Species most highly adapted, morphologically and 

behaviorally, to plains rivers have been decimated, whereas fishes less specifically adapted to 

fluctuating, turbid rivers have increased. 

Changes documented in this article are predominately related to changes in water use and 

flows; most of the habitat changes are within the last two to three decades. 

Chapter is a good overview of change to historical stream conditions due to water use impacts. 

Includes an extensive bibliography.

Geographic location: Kansas, plains, Arkansas river, Smokey hill river, Solomon river, 

Kansas river, Missouri River, eco25, High Plains, eco27, Central Irregular Plains, eco 47, 

Western Corn Belt Plains, EPA region 7 

Keywords: phab, fish, nonnative species, turbidity, fish communities, modified flow, historic 

condition, plains rivers, impoundments, agriculture, irrigation 

Abstract: Most fishes native to Plains streams have wide distributions in eastern North 

America. Species richness declines from east to west as aridity increases; taxonomic diversity 

also decreases, with a few minnow and fewer killifishes becoming increasingly dominant 

westward. Subordinate to that trend, the fauna contains distinguishable communities 

characteristic of (1) large streams with erratically variable flow, sandy substrate, and high levels 

of turbidity and dissolved solids, (2) prairie ponds, marshes, and small streams that are clear 

and relatively stable, sustained by high water tables, and (3) residual pools of highly intermittent 

streams. 

 

The first community is most distinctive, including several endemic species with sensory and 

39
reproductive adaptations to extreme turbidity and widely fluctuating discharge. The second 

community includes relic populations of species whose occurrence in the Great Plains is 

traceable to glacial climates. The third community consists of four or five exceedingly 

widespread, nearly ubiquitous species. Historically the small-stream community in Kansas was 

extirpated or reduced in complexity soon after settlement of the western plains in the last 

quarter of the nineteenth century. Dominant species of the turbid-river community persisted 

longer, but many declined precipitously in 1950-80 coincident with receding water tables in the 

west and regulated flows in the east (following impoundment of nearly all rivers in the region). 

The endemic riverine fauna was largely replaced by sight-feeding planktivores and piscivores 

adapted to lentic habitats and clear, moderate flow. Several plains species that were common 

30 year ago are now seriously threatened. 

40
Author: Cross, Frank B.; Moss, Randle E.; Collins, Joseph T. 

Year: 1985 

Title: Assessment of dewatering impacts on stream fisheries in the Arkansas and Cimarron 

Rivers 

Reference Type: Report 

City: Lawrence, KS 

Institution: Kansas Fish and Game Commission and Museum of Natural History, University of 

Kansas 

Pages: 161 

Value of reference: Report summarizes status of fishes in Arkansas River basin in Kansas. 

The summary utilizes reports from 1853 to 1983 to establish baseline information on fish 

communities and stream flow and discharge for the basin. The report includes hydrologic data 

and fish habitat information (historic and present). It is a good summary of what historic 

conditions may have been like (based on the historic accounts available) and how the region 

has changed post-settlement. 

 

The results of this project are arranged under the following headings: 1) Hydrologic records; 2) 

Fish faunas and habitat notes at sites (or stream reaches) for which an historic record is 

available; 3) Accounts of species of primary concern; 4) Accounts of other species captured in 

1979-83; 5) Summary: and 6) Appendix - field notes on collections made in 1983. 

Although study area is outside of current EMAP region; the plains streams in Kansas are similar 

to ones found in the plains ecoregions within the EMAP area and inferences may be drawn from 

this study. This study highlights similar conditions and issues found in other plains streams 

farther west. 

Results relevant to EMAP: The objectives of the study were to locate populations of several 

species characteristic of the western Plains segment of the Arkansas River basin; to assess the 

extent to which these fishes are threatened, by comparison of current and historical 

distributional records; and to examine the relationship between changes in stream flows and 

changes in the status of each species. 

The first impact of changes on native fishes was extirpation or reduction in range of species 

characteristic of small spring-fed streams and marshes. For example, the blacknose shiner and 

the Topeka shiner have been extirpated, probably early in this century, before 1950. The 

blacknose shiner was listed as abundant (1891), but has not been found anywhere in Kansas 

since 1900. The second major impact on the native fish fauna of the region was the decline or 

disappearance of several species characteristic of shallow, sandy river channels. Fishes 

affected adversely are the Flathead chub, Speckled chub, Arkansas river shiner, Emerald 

shiner, River shiner, Plains minnow, and Plains killifish. The lower numbers and distributional 

change is indicative of altered flow conditions. 

Altered flows in the larger rivers have not affected all native fishes in the same way. For 

example Red shiners have increased, probably as a result of reduced fluctuation and turbidity, 

increased lentic habitat, and reduced competition from native species that have declined. 

The riverine species that have declined most precipitously are those whose native ranges were 

confined to prairie streams. Species that have sustained or increased their abundance all range 

eastward into trans-Mississippi, forested watersheds. The composite effects of habitat 

alteration in streams of this region have "caught in a crunch" those species best adapted to 

41
highly unstable Plains rivers. The climatic and edaphic conditions which caused highly variable 

flows, unstable streambeds, high turbidity and salinity, and rapidly fluctuating stream 

temperatures were negated by "dewatering" of the western part of the basin. "Plains river" 

habitats are no longer attenuated down stream, due to loss of the western drainage, coupled 

with extensive impoundment of the eastern streams.

Geographic location: Kansas, Arkansas River basin, Cimarron River, eco25, High Plains, 

eco27, Central Irregular Plains, plains, EPA region 7 

Keywords: fish, native species, fish communities, historic condition, plains rivers, dewatering, 

discharge records, impoundments 

42
Author: Dodds, Walter K.; Gido, Keith; Whiles, Matt R.; Fritz, Ken M.; Matthews, William J. 

Year: 2004 

Title: Life on the Edge: The ecology of Great Plains prairie streams 

Reference Type: Journal Article 

Journal: BioScience 

Volume: 54 

Issue: 3 

Pages: 205-215 

Value of reference: This article presents a good overview of the ecology of plains streams. 

Humans have modified most prairie rivers and streams with dams, channelization, pollution, 

water abstraction, vast increases of impermeable surfaces in urbanized areas, and other 

watershed modifications. These alterations have had a substantial negative impact on a diverse 

fish fauna; loss of abundance, smaller or fragmented habitat range, and extirpation. They 

disrupt the connectivity of river systems, alter flooding regimes, increase or decrease sediment 

loads, decrease connection with riparian flood zones, and alter the food webs of the Great 

Plains rivers. 

Understanding the ecosystem function of small streams in the Great Plains region is essential, 

because those streams represent a key interface between terrestrial habitats and downstream 

areas, and substantial in-stream nutrient processing may control downstream water quality. 

Physical and biological factors that influence the ecosystem function of native prairie streams, 

including even small headwater reaches, must be studied to help assess current water quality 

issues on both local and continental scales. 

This reference has some limited historical information; primarily it is a good overview of the 

ecology and unique characteristics found in plains streams. It also highlights many of the 

disturbance issues that have occurred since settlement of the region in the mid to late 1800's. 

Results relevant to EMAP: Great Plains stream fishes are highly adapted to harsh conditions 

and can migrate to areas of permanent water, reproduce quickly, or withstand poor water quality 

in isolated pools. Nevertheless, water withdrawals in a number of semiarid regions including the 

Great Plains, have exacerbated stream drying and eliminated many spring refugia, while 

impoundments have restricted the movement of fishes and further fragmented population. 

These alterations to plains streams have had profound effects on the otherwise tolerant fish 

communities. Streams in prairies are even more endangered, because many of the remaining 

fragments of prairie are not large enough to encompass a significant, functional watershed. 

The most heavily affected guild of fishes consists of the large-river minnows. These fish have 

historically defined Great Plains river vertebrate communities. This article summarizes the 

ecology of the Great Plains streams and documents the changes in habitat extent, abundance, 

and assemblages in some fish communities due to land use practices. 

Geographic location: South Dakota, Wyoming, Nebraska, Platte River, Loup River, Little 

Missouri River, White River, Upper Missouri River, Big Sheyenne River, eco43, eco44, eco42, 

eco47, eco46, plains, EPA region 7, EPA region 8 

Keywords: disturbance, drying, flood, prairie, Great plains, streams, phab, fish, fragmentation 

Abstract: Great Plains streams are highly endangered and can serve as model systems for 

studying disturbance ecology and related issues of resistance and resilience in temperate 

43
freshwaters. These streams exist in a precarious balance between flood and drying. In general, 

microbial activity recovers in days to weeks after drying or flooding, and invertebrate and fish 

species are quick to follow. In lower forested reaches, floods may be more intense but drying 

less common. Upstream reaches of prairie streams are characterized by frequent drying, little 

canopy cover, and limited leaf input. Life history and adaptations alter the ways in which stream 

organisms respond to these linear patterns. Human modification has altered these patterns, 

leading to large-scale loss of native grassland streams. The future for Great Plains streams is 

bleak, given the land-use changes and water-use patterns in the region and the large areas 

required to preserve intact, ecologically functional watersheds. 

URL: http://www.bioone.org/bioone/?request=get-abstract&issn=0006-

3568&volume=054&issue=3&page=0205 

44
Author: Dose, J.J.; Roper, B.B. 

Year: 1995 

Title: Long-term changes in low-flow channel widths within the South Umpqua Watershed, 

Oregon 

Reference Type: Journal Article 

Journal: Water Resources Bulletin 

Volume: 30 

Issue: 4 

Pages: 993-1000 

Value of reference: Logging and associated road-building activities have been a major form of 

disturbance in the Western Forested Mountains, reducing large wood availability in stream 

channels. This paper documents evidence that this loss of wood from streams has resulted in 

consistent changes in physical habitat (large woody debris, low flow wetted width) between 

1937 and ~1990. The authors suggest that the condition of anadromous salmonid stocks is 

linked, at least in part, to the logging disturbance histories of the basins upon which the fish 

depend. 

A major value of this reference is that it records changes in physical habitat conditions at the 

same locations more than 50 years following logging, a primary form of anthropogenic 

disturbance in the Coast and Cascade Ranges of the Pacific Northwest.

Results relevant to EMAP: Most of the catchments in which timber harvest and road 

construction had occurred in the upper South Umpqua River experienced widening of low-flow 

wetted stream widths, perhaps attributable to a reduction in large woody debris in active 

channels. Streams that had not been historically logged generally had more wood within the 

active stream channel than those in which logging had occurred. Stream width was similarly 

associated with both percent harvest (r2

 = 0.44), and road density (r2 = 0.45). 

Three of four anadromous salmonid stocks in the South Umpqua River basin are considered atrisk for extinction, including chinook salmon (Oncorhynchus tschawytscha), coho salmon 

(Oncorhynchus kisutch), and searun cutthroat trout (Oncorhynchus clarki). The population of 

winter-run steelhead remained healthy at the time of the publication. 

These declines are attributed, in part, to impacts associated with timber harvest. The at-risk 

populations are found primarily in catchments impacted by silvicultural activities, while he 

healthier steelhead population utilizes upstream portions of the basin protected from road 

building and timber harvest. 

Geographic location: Region 10, South Umpqua River Basin, Oregon, Western Forested 

Mountains, mountains, eco1, eco4, eco78, Coast Range, Cascades, Klamath Mountains 

Keywords: phab; aquatic ecosystems; forest hydrology; habitat alteration; channel width; 

watershed management; logging; roads; salmonids; chinook salmon (Oncorhynchus 

tschawytscha); coho salmon (Oncorhynchus kisutch); steelhead trout (Oncorhynchus mykiss); 

searun cutthroat trout (Oncorhynchus clarki); large woody debris 

Abstract: Recent stream survey data (1989-1993) from 31 stream segments within the South 

Umpqua Watershed Oregon were compared to 1937 stream survey data collected from these 

same stream segments. Concurrent low-flow wetted stream widths of 22 of the 31 surveyed 

segments were significantly narrower. In only 1 of 8 tributaries to the South Umpqua River 

45
which originated from the lands designated as timber emphasis were significantly wider than in 

1937. The observed change in stream width was linearly related to timber harvest (r2

 = 0.44), 

road density (r2 = 0.45), and the amount of large organic debris remaining in the active stream 

channel (r2

 = 0.43). These findings suggest that timber harvest and road construction may have 

resulted in changes in channel characteristics. These channel changes may also be a factor in 

the observed decline of three of the four populations of anadromous salmonids within the basin. 

Notes: For the historic site sample descriptions, see: Roth, A.R. 1937. A survey of the waters of 

the South Umpqua Ranger District, Umpqua National Forest. U.S.D.A. Forest Service, Portland, 

Oregon. (Also available from the Umpqua National Forest, Roseburg, Oregon, 97470.) 

46
Author: Drost, C. A.; Fellers, G.M. 

Year: 1996 

Title: Collapse of a regional frog fauna in the Yosemite area of the California Sierra Nevada, 

USA 

Reference Type: Journal Article 

Journal: Conservation Biology 

Volume: 10 

Issue: 2 

Pages: 414-425 

Value of reference: The primary value of this study is that it represents a careful resurvey of 

the margins of streams, in addition to lakes and ponds, and documentation of change of seven 

species of amphibians at sites in the Sierra Nevada that were originally surveyed in 1915. The 

original survey was conducted prior to the majority of fish introductions or other types of 

anthropogenic disturbances. This study is of particular value because of the level of historical 

detail, and the range of taxa examined, and the implications related to changes in aquatic 

vertebrate indices through time. 

Results relevant to EMAP: Severe declines in most species of sampled amphibians were 

observed between the 1915 and 1992 surveys. The broad scale decline of an entire frog fauna 

over a diverse region is unprecedented. Intensive stocking of fish into the area began following 

the 1915 survey. Large lake populations of amphibians had historically provided opportunities 

for amphibian recolonization of small, isolated habitats which are most susceptible to the effects 

of natural drought cycles. 

The authors hypothesize that large lakes function as reservoirs for amphibian populations, while 

perennial streams function as corridors metapopulation dispersal. They suggest that major 

reductions of amphibian populations in large lakes following fish introduction may have reduced 

the probability of recolonization of other habitat types, including perennial streams as well as 

more isolated habitats following natural localized extinctions. 

The authors provide evidence that the introduction of nonnative fish alone, however, is 

insufficient to explain the general trends in amphibian declines. Toads, for example, have also 

declined, yet tend to breed in ephemeral waters lacking fish, and produce toxins that fish tend to 

avoid. Other, unidentified causes of the observed declines remain to be identified. The results 

have implications regarding interpretation of vertebrate metrics from reference sites in this 

ecoregion.

Geographic location: EPA Region 9, California, Sierra Nevada, eco5, mountains 

Keywords: amphibians; frogs; toads; introduced fish; nonnative species; amphibian decline; 

mountain yellow-legged frog; Rana muscosa; foothill yellow-legged frog; Rana boylii; redlegged frog; Rana aurora; Yosemite toad; Bufo canorus; western toad; Bufo boreas; Great 

Basin spadefoot; Scaphiopus intermontanus; Pacific treefrog; Hyla regilla

Abstract: There has been much concern about widespread declines among amphibians, but 

efforts to mine the extent and magnitude of these declines have been hampered by the scarcity 

of comparative inventory data. We surveyed a transect of the Sierra Nevada mountains in 

western North America that was carefully studied in the early 1900s. Our comparisons show 

that at least five of the seven frog and toad species in the area have suffered serious declines. 

One species has disappeared from the area entirely and a second species, formerly the most 

47
abundant amphibian in the area, has dwindled to a few small remnant populations. These 

declines have occurred in a relatively undisturbed, protected area and show some of the same 

patterns noted in other reports of amphibian declines. Introduced predatory fish, possibly 

interacting with drought-induced loss of refuge habitats, have contributed to the decline of some 

species. However, the overall cause of these dramatic losses remains unknown. 

48
Author: Duff, D. A. 

Year: 1988 

Title: Bonneville cutthroat trout: Current status and management 

Reference Type: Book Section

Editor: Gresswell, R. E. 

Book Title: Status and management of interior stocks of cutthroat trout. 

City: Bethesda, Maryland 

Publisher: American Fisheries Society 

Volume: Symposium 4 

Pages: 121-127 

Value of reference: The book chapter outlines the historical distribution of the Bonneville 

cutthroat trout, its presumed extinction, and the rediscovery of 39 pure strains in headwater 

streams of the Bonneville Basin.

Results relevant to EMAP: The article discusses the historic importance of the Bonneville 

cutthroat trout to Native American and early settlers' diets and an early commercial fishery. The 

fish was once widespread in all available habitats surrounding the Bonneville Basin. The paper 

includes a list of pure populations by state and state plans for managing the species, as well as 

a map of present day occurrences in the 4 state area. 

Fish numbers have been affected by dewatering of streams through irrigation, competition with 

nonnative species, and fishing pressure. Trout numbers began their decline after construction of 

early irrigation projects when large numbers of fish became trapped in irrigation ditches.

Geographic location: eco13, Utah, Wyoming, Nevada, Idaho, EPA Region 8, xeric, Bonneville 

Basin 

Keywords: fish, cutthroat trout, distribution, nonnative species, water diversion, habitat 

degradation 

Abstract: Only one trout subspecies, the Bonneville cutthroat trout, Salmo clarki utah, is 

endemic to the Bonneville Basin, the largest endorheic basin in the Great Basin of western 

North America. The subspecies was historically abundant throughout all suitable habitat of a 

vast area of Utah, Wyoming, Nevada, and Idaho until about 8,000 years ago, when the 

desiccation of ancient Lake Bonneville occurred. During this century, the subspecies suffered a 

catastrophic decline from introductions of nonnative trouts and habitat alteration. Today, only 41 

populations, primarily limited to small headwater streams, are known to be genetically pure. 

Habitat conditions existing in waters containing the Bonneville cutthroat trout are marginal, and 

the streams are generally small with depleted flows. Yet, in many of these streams, Bonneville 

cutthroat trout still survive. Introductions of nonnative trout have been largely unsuccessful in 

these marginal streams, but they have led to the demise of the native cutthroat trout. The 

Bonneville cutthroat trout has promising possibilities for enhancing wild trout fishery 

management programs within the Great Basin states. As a result of the subspecies' limited 

distribution and present threats to its survival, protection of the few remaining populations is 

being considered. This paper summarizes the current status and management direction for this 

subspecies. 

Notes: Hickman, T. J. 1978. Systematic study of the native trout of the Bonneville Basin. MS 

Thesis. Colorado State University, Fort Collins, Colorado, is a paper cited in Duff (1988) that 

discusses the taxonomy of the Bonneville cutthroat trout, the search for pure populations, and 

the reasons for the species' decline in more detail. 

49
Author: Eberle, Mark E.; Hargett, Eric G.; Wenke, Thomas L.; Mankdrak, Nicholas E. 

Year: 2002 

Title: Changes in fish assemblages, Solomon River basin, Kansas: habitat alterations, 

extirpations, and introductions 

Reference Type: Journal Article 

Journal: Transactions of the Kansas Academy of Science 

Volume: 105 

Issue: 3-4 

Pages: 178-192 

Value of reference: This paper summarizes changes in fish communities from likely early fish 

assemblages to current assemblages. The study area is outside of the EMAP-West study area, 

but is very similar to surrounding plains ecoregions with respect to landscape characteristics, 

land uses, human impacts, and numerous fish species. Therefore, some aspects from this 

paper can be applied to plains regions in EMAP-West, particularly those in Colorado. 

Results relevant to EMAP: The authors reviewed historic literature related to fish accounts to 

establish likely native fish assemblages. Using this baseline the study attempts to establish what 

changes in fish assemblages have occurred in the Solomon River basin. Within the whole 

basin, 32% of the native species of fishes have been extirpated, and 51% of the present 

assemblage was comprised of nonnative species. Extant native species in the basin are more 

tolerant of a wide range of conditions. 

Segments of the historical headwater sections of the rivers and tributary streams had clear, cool 

water maintained by springs and groundwater seepage. Conversion of grassland to cropland 

increased turbidity in small streams, and most of the fish species extirpations occurred in these 

streams. 

Stream widths in the two tributary forks were 18-30 m in the 1860s, but were reduced to 2-20 m 

by the 1990s, and substrates contained more fine sediments in the 1990s. Lower stream flows 

have resulted from decreases in surface runoff and base flow. 

Changes in fish populations are due to extirpations, range contractions, introductions, and range 

expansions associated with alteration in physicochemical attributes of the streams as a 

consequence of agricultural developments and the construction of impoundments. 

Geographic location: Kansas, Solomon River basin, eco27, plains, Central Irregular Plains, 

EPA region 7 

Keywords: fish, habitat alterations, turbidity, stream discharge, extirpations, introduction, 

nonnative species, impoundment, agriculture, eco27 

Abstract: We sampled fishes four times each year at 12 sites on the Solomon, North Fork 

Solomon, and South Fork Solomon rivers in north-central Kansas during 1996 and 1997. Kirwin 

and Webster reservoirs are located on the North Fork Solomon River and South Fork Solomon 

River, respectively, and Waconda Reservoir inundates the confluence of these two rivers at the 

head of the Solomon River. Multivariate analyses identified two fish assemblages that were 

related to stream discharge. One fish assemblage was associated with stream segments that 

had lower discharges, such as those located upstream from Kirwin and Webster reservoirs. 

This assemblage was characterized by equal numbers of extirpations of native species and 

introductions of nonnative species. The other fish assemblage was associated with the 

50
reservoirs and stream segments that had higher discharges. This assemblage was 

characterized by a large number of species that were introduced or had immigrated into these 

areas. For the basin as a whole, 32% of the native species of fishes have been extirpated, and 

51% of the present assemblage was comprised of nonnative species. Most of the extirpations 

and introductions are associated with habitat changes caused by agricultural development and 

the construction of impoundments. The relatively large component of the fish assemblage 

comprised of nonnative species reflects the trend toward homogenization of fish assemblages 

throughout the United States. 

51
Author: Eby, L. A.; Fagan, W. F.; Minckley, W. L. 

Year: 2003 

Title: Variability and dynamics of a desert stream community 

Reference Type: Journal Article

Journal: Ecological Applications 

Volume: 13 

Issue: 6 

Pages: 1566-1579 

Value of reference: Minimally disturbed reference streams in desert regions are rare. Aravaipa 

Creek, a tributary to the San Pedro River in Arizona, retains its historic complement of native 

fish species, and it is often studied to develop expectations for other desert streams.

Results relevant to EMAP: Seven native fish species inhabit Aravaipa Creek, including 2 

federally listed species and five candidate species. The mid- and upper reaches retained the full 

complement of fish species over the last 30 years, though there was variation in the proportional 

abundances of the dominant fish species (longfin dace, Gila spikedace, and desert sucker). The 

lower reaches of Aravaipa Creek did show a decline in species richness, likely due to the 

invasion of eight exotic species. Two species, spikedace and loach minnow, have disappeared 

from the lower reaches of Aravaipa Creek; both are susceptible to replacement by the nonnative 

red shiner 

The authors conclude that one of the major factors central to maintaining a full complement of 

native fish species in desert streams is flow variability. Flash floods and high spring runoff favor 

native fish that are adapted to such conditions and discourage the establishment and 

domination of exotic (nonnative) species.

Geographic location: Aravaipa Creek, Sonoran Desert, Region 9, Arizona, San Pedro River, 

eco23, eco81, xeric 

Keywords: Aravaipa Creek, community composition, conservation, desert stream, exotics, fish, 

flow variability, measures of community change, Sonoran Desert, hydrologic variability, flash 

floods, runoff, nonnative species 

Abstract: Communities can be highly variable over a few years, but remain fairly constant over 

the long term. Evaluating measures and examining the variability associated with long term 

change is useful because it increases our understanding of and our ability to predict responses 

to disturbances. We used long term fish community data from Aravaipa Creek, Arizona, USA, a 

Sonoran Desert stream, to determine whether there had been long term changes in the 

community composition, what measures best describe these shifts, and what environmental 

factors are correlated with the changes. Aravaipa Creek is an intrinsically variable system and 

one of the few remaining desert streams to support its complete historical assemblage of native 

fishes. Multivariate analyses illustrated important changes in composition of the native fish 

community that were not described by traditional measures of persistence and stability. In the 

early 1980's, changes in community composition were correlated with alterations in base flow, 

while more recent changes are likely associated with the presence of exotic species. Changes 

in stream morphology, hydrology, and climate have decreased flow variability, thereby 

increasing the likelihood of exotic establishment, and may have increased the downstream 

connection between Aravaipa Creek and the San Pedro River thus increasing the likelihood of 

repeated invasions by nonnative species. These results support previous research in 

intrinsically variable desert systems, which conclude that retention of high flow variability is 

52
important to conservation of the native fish community. In addition, although connectivity in 

aquatic lotic systems is important, isolation from large river systems teeming with exotics may 

be important in preserving these remnant native fish assemblages. 

URL: www.esajournals.org/esaonline/?request=get-toc&issn=1051-

0761&volume=013&issue=06 

53
Author: Echelle, A.A.; Luttrell, G.R.; Larson, R.D.; Zale, A.V.; Fisher, W.L.; Leslie, D.M., Jr. 

Year: 1995 

Title: The Great Plains: decline of native prairie fishes 

Reference Type: Report

City: Washington, DC. 

Institution: U.S. Department of the Interior, National Biological Service 

Pages: 530 

Value of reference: This reports specifically on declines of the Arkansas River shiner and the 

Arkansas River speckled chub, both of which once occurred in the upper Arkansas River in 

Colorado, as well as other states that are outside the EMAP-West region. The text reports both 

as historically inhabiting Colorado, although the historical range maps (Figures 1 and 2) do not 

show historical collections in Colorado. The authors may have used anecdotal information to 

define historical ranges even if the species were not formally sampled historically in some 

portions of the basin; however, they do not cite these ancillary sources, if used. The reference 

is one of very few that represent a modern synthesis of historical fish distributions in the Plains.

Results relevant to EMAP: The Arkansas River shiner was historically widespread in the 

Arkansas River basin. It has been extirpated from about 75% of the river reaches in its range, 

as assessed before 1985, and is now considered extirpated in Colorado. It experienced great 

decline between 1983 and 1985. 

The speckled chub occurred throughout the Arkansas River basin, including Colorado. By the 

early 1990s, the chub had declined notably, and it is believed to be extirpated from Colorado 

and reduced by about 75% of its total historic range. 

Low stream flow during the breeding season, a period historically associated with peak flows, 

has affected successful reproduction and recruitment. Intensive agriculture has resulted in 

demand for irrigation water and creation of numerous reservoirs, resulting in degraded habitat 

Impoundments fragment the landscape, limiting access to suitable habitat and isolating 

populations.

Geographic location: Colorado, Arkansas River basin, eco26, eco25, plains, EPA region 8 

Keywords: fish, habitat fragmentation, altered water flow regime, agriculture, dams 

URL: http://biology.usgs.gov/s+t/pdf/Plains.pdf 

54
Author: Erman, N.A. 

Year: 1996 

Title: Sierra Nevada Ecosystem Project: Final Report to Congress, vol. II, Assessments and 

scientific basis for management options. Status of Aquatic Invertebrates. 

Reference Type: Report 

City: Davis, CA 

Institution: University of California, Centers for Water and Wildland Resources 

Pages: 987-1008 

Report Number: Report No. 39 

Value of reference: An important paper based upon a systematic review of standard library 

databases, including taxonomic studies, impact studies, geographic surveys of specific 

taxonomic groups, and behavioral studies, unpublished, non-refereed reports, and experts on 

specific taxonomic groups. Museum collection information was not examined. 

This resource thoroughly reviews the types of anthropogenic disturbances (mining, logging, 

damming, diversions, roads, grazing) and associated stressors which have impacted Sierra 

Nevada streams during the last 200 - 300 years. The author discusses changes in physical 

habitat, macroinvertebrates, and elaborates on problems associated with reconstructing historic 

macroinvertebrate distributions in the face of limited reference collections and revisions of 

taxonomic relationships. This document can be of use for guiding best professional judgment 

regarding probable changes in macroinvertebrate assemblages and derived metrics following 

anthropogenic disturbances characteristic to the region. 

Results relevant to EMAP: Prior to the immigration of Europeans and Asians 200-300 years 

ago, the Sierra Nevada systems contained macroinvertebrate taxa characteristic of continuously 

flowing waters. Major changes in the region have occurred in flow regimes as a result of dams 

(see Fig. 35.1), sediment budgets, substrate characteristics, stream temperature, and channel 

morphology. Over the last 200 years, many rock-bottomed perennial streams have been filled 

with sediment due to hydraulic gold mining activities to the point where surface flow no longer 

exists (Mount 1995). Dispersal barriers have been destroyed, major changes have occurred to 

riparian vegetation, streams have been intentionally poisoned with rotenone and actinomycine, 

and unintentionally contaminated with heavy metals, herbicides, and pesticides. Nonnative 

organisms have been both intentionally and unintentionally introduced. 

As a result of these changes, the author uses deductive reasoning to conclude that there has 

probably been a reduction in macroinvertebrate richness, macroinvertebrate species diversity, 

and relative abundance of certain species in streams. In reservoirs, portions of streams that 

once contained fauna characteristic of free-flowing water, such as Plecoptera for example, are 

now dominated by taxa characteristic of habitats where sediments accumulate, such as 

burrowing Chironomidae larvae, other midges, and oligochaetes. 

Habitat destruction such as alteration of natural hydrology and accumulation of excess 

sediment is of special concern due to the high degree of endemism in the region. Twenty five 

percent of known Plecoptera species, 19% of Trichoptera, 9% of Blephariceridae midges, 25% 

of Deuterophlebeiidae midges, 20% of molluscs, and 10% of fairy and brine shrimp (Anostraca) 

are endemic. The author stresses, however, that a systematic survey of aquatic 

macroinvertebrates has yet to be conducted in the Sierra Nevada. While some groups have 

been reasonably well surveyed, such as Plecoptera and Trichoptera, others require more 

attention, such as Diptera and Ephemeroptera. 

55
Geographic location: EPA Region 9, California, Sierra Nevada, mountains, Eco5 

Keywords: macroinvertebrates; fish; pre-European; change; Sierra Nevada; California; dams; 

water diversion; roads; mining; grazing; sediments; intentional invertebrate introductions; 

opossum shrimp; Mysis relicta, signal crayfish; Pacificasticus leniusculus; rotenone; antimycin 

Abstract: The aquatic invertebrate fauna of the Sierra Nevada is diverse and extensive, with 

many endemic species throughout the range. Aquatic systems differ widely in the Sierra 

because of such natural factors as elevation, climate patterns, geology, substrate type, water 

source, water volume, slope, exposure, and riparian vegetation. These differences are reflected 

in the aquatic invertebrate fauna. Small, isolated aquatic habitats such as springs, seeps, 

peatlands, and small permanent and temporary streams have a high probability of containing 

rare or endemic invertebrates. Aquatic invertebrates are a major source of food for birds, 

mammals, amphibians, reptiles, fish, and other invertebrates in both aquatic and terrestrial 

habitats. Changes in a food source of such importance as aquatic invertebrates can have 

repercussions in many parts of the food web. The life cycles of aquatic invertebrates are 

intricately connected to land as well as water, and the majority of aquatic invertebrates spend 

part of their life cycle in terrestrial habitats. Aquatic invertebrates are affected by human-caused 

activities on land as well as activities in the water. Land and water uses and impacts are 

reflected in species assemblages in streams and lakes. Changes in aquatic invertebrate 

assemblages have been used for many decades to monitor impacts on land and in water. 

However, the level of detail of most monitoring is not sufficient to track species losses in aquatic 

invertebrates. Aquatic invertebrates have not been inventoried or well-studied at the species 

level in most of the Sierra. Aquatic invertebrates are rarely considered or evaluated in 

environmental impact assessments in the Sierra. Major changes have occurred in aquatic and 

terrestrial habitats in the Sierra of the last 200 years: we must logically assume that 

corresponding changes have occurred in aquatic invertebrate assemblages. 

Notes: Mount, J.F. 1995. California rivers and streams: The conflict between fluvial process and 

land use. Berkeley and Los Angeles: University of California Press. 

URL: http://ceres.ca.gov/snep/pubs 

56
Author: Evermann, B.W. 

Year: 1891 

Title: A Reconnaissance of the Streams and Lakes of Western Montana and Northwestern 

Wyoming 

Reference Type: Journal Article 

Journal: Bulletin of the United States Fish Commission 

Volume: 11 

Pages: 3-60 

Value of reference: This is a primary data source that reports the physical and natural-history 

features of the streams and lakes of the region, including size, depth, current, stream 

obstructions, source of water, water temperature, water clarity, composition of bottom and 

banks, human impacts, fish species, abundance, size, condition, and distribution, and 

invertebrates (crustaceans, insects, mollusks) that could be fish prey. The authors had a 

particular focus on geographical distribution of fishes and attempted to trace the limits in the 

range of species. All waters examined are given, which include locations on the Clarke Fork 

and Snake River of the Columbia basin and the Yellowstone River, Madison, River, Gallatin 

River, Jefferson River, and Prickly Pear Creek of the Missouri River basin. 

The first part of the report is a series of description of the streams visited, including physical 

habitat, and lists of fish, invertebrates, and frogs present. The second part is an annotated list 

of each fish species, including all the locations where it was found and the number of each that 

were collected. This section also contains species descriptions and taxonomic notes. The third 

part is an annotated list of reptiles and batrachians collected. 

This information is valuable for constructing the historical distribution of indigenous fish species 

in the region and to assign the presence of invertebrates and amphibians to particular streams. 

It may also be useful for comparing historical physical habitat attributes with current conditions.

Results relevant to EMAP: The total collection of indigenous fish obtained on this expedition 

was only 16. The author was confident that it represented the fish fauna of the region fairly well. 

The species included genera in the following families: Catostomidae, Cyprinidae, Salmonidae, 

Cottidae, and Gadidae. Four introduced Salmonids were also noted. Reports of amphibians 

and reptiles were incidental, i.e., no time was devoted to searching for them. Nevertheless, 

over 2 pages of the report are devoted to reporting results of findings of (primarily) amphibians 

in the genus Rana. 

The report should be consulted for details of fish species occurrences and physical habitat 

descriptions of the streams visited.

Geographic location: Montana, Wyoming, Columbia River basin, Missouri River basin, Clarke 

Fork River, Snake River, Yellowstone River, Madison River, Gallatin River, Jefferson River, 

Prickly Pear Creek, EPA region 8, mountains, eco17 

Keywords: fish, amphibians, phab, macroinvertebrates, historical data, historical distribution, 

primary source 

57
Author: Evermann, B.W. 

Year: 1896 

Title: A report upon salmon investigations in the headwaters of the Columbia River, in the state 

of Idaho, in 1895 together with notes upon the fishes observed in that state in 1894 and 1895 

Reference Type: Report 

City: Washington, D.C. 

Institution: Government Printing Office 

Value of reference: This report covers 2 areas in central Idaho: 1) the headwaters of the 

Salmon River and 2) several inlets and outlet streams in the Redfish Lakes region on the west 

side of the Salmon River Valley at the east base of the Sawtooth Mountains. The first part of 

the report describes physical habitat (riparian vegetation, width, depth, sediment type, woody 

debris, water temperature) and presence of salmon and other fish species, as well as extent of 

spawning habitat in the inlet and outlets streams and in Salmon River headwater tributaries. 

The second part is a detailed report on each species of fish observed, including information 

about relative abundance and distribution and specific tributary streams where each species 

was seen or collected. Known distribution and abundance of each species in other portions of 

the Snake or Columbia basins is also mentioned for some of the species. The focus of the 

report is salmon, particularly the sockeye; therefore these species receive more treatment in the 

text. The report is an important synopsis of historical fish distribution in an area that is not often 

reported in the historical literature (see other citation in Notes section below). It also documents 

the distribution of chinook and sockeye salmon and gives other detailed descriptions, such as 

length and weight of individuals collected.

Results relevant to EMAP: The report covers 21 species of fish from the central region of 

Idaho, including lamprey, sturgeon, suckers, chubs, shiners, dace, whitefish, salmon, steelhead, 

bull trout, and sculpins. Details about distribution, relative abundance, and stream physical 

habitat descriptions occur throughout; the report should therefore be consulted for specific 

information. 

Geographic location: Idaho, eco16, EPA region 10, mountains, Salmon River basin 

Keywords: fish, phab, historical data, primary source, baseline information 

Notes: A related document focusing on salmon in the same region: 

Evermann, B.W. 1896. A preliminary report upon salmon investigations in Idaho in 1894. 

Bulletin of the U.S/ Fish Commission 1896:253-284. 

58
Author: Evermann, B.W.; Cox, U.O. 

Year: 1896 

Title: Report upon the Fishes of the Missouri River Basin 

Reference Type: Report

City: Washington, D.C. 

Institution: U.S. Commission of Fish and Fisheries 

Value of reference: This primary source is an excellent synthesis of the fishes known to the 

Missouri River basin in the late 1800s. The report is presented in four sections, beginning with 

results of fish examinations done in various streams the authors visited in South Dakota, 

Nebraska, and Wyoming in 1892-1893. Results include physical habitat descriptions of streams 

visited and a notations of fish in each location. Following that report is an annotated 

bibliography (in chronological order) of the ichthyology of the entire Missouri River basin, 

including all known faunal lists at the time. Complete citations of these works is given for further 

consultation, if desired. Each entry lists the locations examined, a list of the fish species found 

and their locations. Next is an annotated list of the fishes based on sources listed in the 

bibliography, including all the locations in the basin where each species had been documented 

prior to 1896. This section can be cross-referenced, by source, with the annotated bibliography 

in the preceding section. Finally, the table on pages 426-428 summarizes the occurrence of 

143 fish species by state in the Missouri River basin. In addition to these 143 species, a list of 

74 nominal species is given on pages 424-425; of these, 52 had been recognized at the time of 

this report. 

This is an important historical synthesis and would be useful for reconstructing historical ranges 

and fish communities before major fish introductions and interbasin transfers had occurred. It 

may also be useful for comparing historical and current physical habitat attributes of streams 

and river tributaries. 

Results relevant to EMAP: Lists of fish species, by sub-basin and state, and physical habitat 

descriptions (for sites visited in South Dakota, Nebraska, and Wyoming in the late 1800s) can 

be found in detail in this report. The results synthesize what had been published on species 

occurrences in the basin, beginning with the explorations of Lewis and Clark in 1803-06. The 

report should be consulted for details. 

The total number of species and subspecies of fishes known from the Missouri Basin in 1896 

was 143. These were distributed among 24 families and 68 genera (see table, pages 426-428), 

and among 9 states. The majority of species occurred in non-EMAP states in the lower basin 

and in the eastern portion of the basin; only 55 species were known from North Dakota, 

Montana, Wyoming, and Colorado, and 10 of those were endemic. The authors present a 

section on the unique community of 15 species found in the isolated Black Hills region. They 

also acknowledge introduced species--notably carp, rainbow trout VonBehr trout (brown trout), 

and Eastern brook trout. They note that there may be others that have been introduced by state 

fish agencies, but do not provide any further detail about nonnative species (possibly there were 

not many to report). 

Geographic location: Missouri River basin, Montana, North Dakota, South Dakota, Wyoming, 

Colorado, eco17, eco18, eco26, eco21, eco42, eco43, eco46, eco25, plains, mountains, xeric, 

EPA region 8 

Keywords: fish, phab, historical data, Missouri River basin, historical occurrence, primary 

source 

59
Notes: This report is Appendix 5 from the Report of the U.S. Commissioner of Fish and 

Fisheries for 1894, pages 325-429. It was extracted and published as a stand-alone report. 

60
Author: Evermann, B.W.; Rutter, C. 

Year: 1894 

Title: The Fishes of the Colorado Basin 

Reference Type: Journal Article 

Journal: Bulletin of the United States Fish Commission 

Volume: 9 

Pages: 473-486 

Value of reference: This is a frequently-cited, early, primary data source that presents a 

comprehensive synthesis of the earliest documentations of fishes in the Colorado River basin, 

based on publications dating from 1848 to1891. An annotated bibliography (18 citations) of the 

ichthyology of the Colorado Basin is included to provide the background material the authors 

use to construct, in chronological order, the different places in the Colorado Basin where each 

species was recorded during the period of 1849-91. Since fish documentation was not based 

on surveys or a systematic census, the data indicate only presence (not absence); the historical 

accounts also differ in their geographic scopes. The paper lists, by species, locations where 

present, as reported in the literature (all of which is referenced in the annotated bibliography). 

Most of the historical collections on which this work was based were made in river tributaries of 

the Colorado River. 

Results relevant to EMAP: Thirty-two native fish species, representing 5 families and 18 

genera, were recognized for the Colorado Basin by 1891 (list by family and genus, with number 

of species in each genus is given in this publication). The Cyprinidae, by far, contained the 

greatest number of species, comprising almost 60% of the species, followed by Catostomidae 

with 25% of the species. Approximately 78% of the species of fishes known in 1891 from the 

CO Basin were endemic. 

The approximate locations where each species was documented on each tributary are given in 

tabular format for each species separately. These lists are cross-referenced with the citations in 

the annotated bibliography. The text contains scattered notes about relative abundance (e.g., 

common, abundant...) for some of the species. 

Geographic location: Colorado River basin, EPA Region 8, EPA Region 9, xeric, mountains, 

eco21, eco22, eco23, eco20, eco18, eco81, Colorado, Wyoming, Utah, Arizona, New Mexico 

Keywords: fish, historical data, geographic distribution 

61
Author: Fausch, Kurt D.; Bestgen, Kevin R. 

Year: 1997 

Title: Ecology of fishes indigenous to the Central and Southwestern Great Plains 

Reference Type: Book Section

Editor: Knopf, Fritz L.; Samson, Fred B. 

Book Title: Ecology and Conservation of Great Plains Vertebrates. 

City: New York, NY 

Publisher: Springer 

Pages: 131-166 

Series Title: Ecological Studies 125 

Value of reference: Journals from early scientific expeditions, such as John C. Fremont's two 

trips up the Platte River system in 1842 and 1843 are assumed to be accurate representations 

of undisturbed Plains ecosystems. However this information is sparse and does not include 

detailed accounts of fish assemblages of the time. Little is known about the indigenous fishes of 

the Great Plains, especially considering the extensive modification of aquatic environments that 

began about 1860. Distributions of some species were likely altered by transfers among waters, 

whereas others were probably locally extirpated before any specimens were collected. 

This chapter attempts to draw together information about the distribution and ecology of fishes 

indigenous to the central and southern Great Plains, a region encompassed largely by 

upstream reaches of the Platte, Kansas, Arkansas, Canadian, and Pecos rivers; includes presettlement and post-settlement information. 

Chapter includes descriptions of the physical characteristics of Plains streams and what is 

known of the original fish fauna and its characteristics, reproductive ecology of Plains fishes, 

and factors influencing variability of populations and assemblages. Summary is a synthesis of 

ecological mechanisms with broad implications for conservation of plains fishes of the region. 

Results relevant to EMAP: Describes the ecology of the region; based on historic data and 

current information about the biota, streams, and physical characteristics of the streams and 

landscape. 

Chapter highlights what is known about the distribution of fish fauna and factors influencing 

variability of populations and assemblages. 

This provides a synthesis of the changes in fish distribution, assemblages, and habitat that have 

occurred since settlement due to factors like; impoundments, water diversions; introductions, 

etc.

Geographic location: Colorado, Platte River, Kansas River, Arkansas River, Canadian River, 

Pecos River, eco 25, High Plains, eco27 Central Irregular Plains, plains, EPA region 8 

Keywords: 

Great plains, plains, phab, fish, native species, pre-settlement, water diversion, impoundments, 

Abstract: The Great Plains of western North America are a harsh environment for fishes. Due 

to the increasing aridity and general lack of permanent water one finds traveling westward 

across the Plains, even trained biologists rarely consider fishes or their habitats when 

transversing the region. The same was true of early explorers. For example, none of the four 

scientific expeditions that ascended the Platte River in the first half of the 1800s described 

62
Plains fishes, whereas flora and other fauna were collected and described extensively (e.g. 

Fremont expedition , 1843-1843; Jackson and Spence 1970). Indeed, no collections of fish from 

the Plains region of the South Platte River Basin in Colorado were preserved until 1873 (Cope 

and Yarrow 1875). 

It is therefore not surprising that relatively little is known about the indigenous fishes of the Great 

Plains, especially considering the extensive modification of aquatic environments that began 

about 1860 (Eschener et al. 1983). Distributions of some species were likely altered by transfers 

among waters, whereas others were probably locally extirpated before any specimens were 

curated (cf. Jordon 1891). Moreover, little is known about the basic life history of many fishes 

that range widely throughout the Plains, and even less is understood about the ecology of other 

biota in Plains streams and riparian zones (Matthews 1988, Zale et al. 1989, Brown and 

Mathews 1995). This information is urgently needed, due to the continued acceleration of 

human degradation and loss of species populations from these aquatic ecosystems (Cross and 

Moss 1987). 

Our goal in this chapter is to draw together information about the distribution and ecology of 

fishes indigenous to the central and southern Great Plains, a physiographic region 

encompassed largely by upstream reaches of the Platte, Kansas, Arkansas, Canadian, and 

Pecos rivers (Cross et al. 1986) (Fig 6.1). We emphasize the Platte and Arkansas rivers in 

eastern Colorado and the Pecos River in New Mexico, because we have firsthand knowledge 

and experience in these basins. However, we incorporate literature from other Plains rivers and 

from similar rivers in the adjacent Central Lowlands to the east, where appropriate. 

Because one can interpret little about the ecology of organisms without understanding the 

physical template to which they are adapted (cf. Southwood 1988), we begin by describing the 

physical characteristics of Plains streams. We then discuss what is known of the original fish 

fauna and its characteristics, reproductive ecology of Plains fishes, and factors influencing 

variability of populations and assemblages. We end by attempting a synthesis of ecological 

mechanisms with broad implications for conservation of plains fishes of the region and by 

summarizing needs for further research. 

63
Author: Fisher, R. N.; Shaffer, H. B. 

Year: 1996 

Title: The decline of amphibians in California's Great Central Valley 

Reference Type: Journal Article

Journal: Conservation Biology 

Volume: 10 

Issue: 5 

Pages: 1387-1397 

Value of reference: This is one of a very few historical trend analyses of amphibians in the 

western United States.

Results relevant to EMAP: Historical distribution data were compiled for six native species of 

amphibians based on museum specimens (see Notes below) for the Sacramento Valley, San 

Joaquin Valley, and the Coast Range near San Francisco. These data were compared with field 

data collected between 1986 and 1994 at 315 ponds distributed across the same geographic 

area to document species declines. Six amphibian species were historically widespread in this 

habitat and a single aquatic breeding site would generally contain between two and five species. 

Results record a statistically significant decline in the number of species currently found in most 

counties compared with that found historically. Declines varied from 1 out of 28 counties lost for 

Pacific treefrog (P. regilla) to 24 out of 28 counties lost for California red-legged frog (R. aurora). 

Graphs and distribution maps are given for 5 species (four natives plus introduced bullfrog) 

showing historical records compared to recent detections. Table 1 shows that there is a 

significant inverse relationship between introduced exotics and native amphibians. For three 

species, historical localities were significantly lower in elevation than are current viable 

populations. Most of low elevation sites sampled were unoccupied by native species, compared 

with their historical pattern of distribution, implying they have been lost from these areas. 

Causes of decline are attributed to exotic and introduced species predation and competition, 

pond alteration or loss.

Geographic location: xeric, Central Valley, California, coast range, San Joaquin valley, 

Sacramento valley, eco6, eco7, EPA Region 9 

Keywords: amphibians, historical data, museum records, California newt, California tiger 

salamander, Pacific treefrog, western spadefoot toad, western toad, California red-legged frog, 

bullfrog, nonnative species, habitat degradation, habitat loss 

Abstract: Declines in amphibian populations are rarely reported on the community or 

ecosystem level. We combined broad-scale field sampling with historical analysis of museum 

records to quantify amphibian declines in California's Great Central Valley. Overall, amphibians 

showed an unambiguous pattern of decline, although the intensity of decline varied both 

geographically and taxonomically. The greatest geographical decline was detected in the 

counties of the Sacramento and San Joaquin valleys. Two species, Rana aurora and Bufo 

boreas, were identified as the most affected by decline, whereas Pseudacris regilla was the 

least affected. The Coast Range counties had little or no detectable decline. We provide new 

evidence implicating introduced predators as a primary threat. Introduced predators occur at 

lower elevations than native species, and our data indicate that for some native species there 

has been significant restriction to higher elevation sites from a formerly broader distribution. Our 

historical approach provides a strategy for identifying declining amphibian communities that 

64
complements more detailed, long-term monitoring programs and provides an assessment of the 

pattern of change that is a necessary prerequisite for the development of field experiments that 

test hypothesized mechanisms of change. 

Notes: See Schaffer et al. 1998 in this bibliography for general discussion of the use of 

museum specimens for reconstructing historical aquatic communities. 

65
Author: Frissell, C.A. 

Year: 1993 

Title: Topology of extinction and endangerment of native fishes in the Pacific Northwest and 

California (U.S.A.) 

Reference Type: Journal Article 

Journal: Conservation Biology 

Volume: 7 

Issue: 2 

Pages: 342-354 

Value of reference: Existing information is synthesized into a synoptic map of WA, OR, ID, and 

CA with isopleths showing patches representing numbers of native fish species extinct, 

endangered, or threatened. Also included is Table 1, listing basins in CA, OR, and WA, the 

number of native fish taxa in each, and the proportions that are extinct, endangered, threatened, 

or of special concern. The mapping procedure can identify regions and ecosystems at high risk, 

which can be targeted for more intensive monitoring. 

Results relevant to EMAP: The native ichthyofauna that has become extinct, endangered, or 

threatened (EET) is highest in CA (mean 48%), lower but still high in OR (mean 33%) and 

lowest in WA (mean 13.5%); the proportion of native fauna that is EET declines as native 

species richness in the basin increases. 

The spatial patterns of EET are influenced more by the many basin-specific population groups 

of seven widely distributed species of anadromous salmonids than by the more than 60 locally 

endemic species and subspecies of suckers, minnow, pupfishes, and other fishes. 

The simultaneous decline of numerous taxa in basins with and without dams or diversions 

suggests that cumulative damage to aquatic habitats caused by logging, grazing, urbanization, 

and other land uses plays a major role in ichthyofaunal impoverishment.

Geographic location: mountains, xeric, eco1, eco3, eco7, eco6, eco78, west coast, California, 

Oregon, Washington, EPA Region 9, EPA Region 10 

Keywords: fish, status, extinction, mapping, dams, logging, grazing, urban 

Abstract: Recent studies have provided a broad data base on extinction and endangerment of 

species, subspecies, and distinct populations of inland fishes in western North America. 

Development of a synoptic, regional-scale image of extinction and risk of extinction is 

complicated by the small size and linear distribution of fluvial aquatic habitats and by 

interspecific variation in areal extent of populations. I developed a regional map of extinctionrisk isopleths based on the number of extinct and persistently declining species in drainage 

basins of the Pacific Northwest and CA. This topological synthesis is useful for delineating and 

monitoring areas of historic and ongoing loss of aquatic biodiversity, and for relating losses to 

patterns of land use and habitat modification, climate, hydrology, and geomorphology. From an 

ecological perspective, endangerment of numerous indigenous populations of seven widely 

distributed species of anadromous salmonids in this region is as important as the more local, 

diffuse effects of declines in more than 60 endemic, non-anadromous species and subspecies. 

The simultaneous decline of numerous taxa in basins not afflicted with dams or diversions 

suggests that cumulative damage to aquatic habitats caused by logging, grazing, urbanization, 

and other land uses plays a major role in ichthyofaunal impoverishment. 

66
Author: Fulton, L.A. 

Year: 1968 

Title: Spawning areas and abundance of chinook salmon (Oncorhynchus tshawytscha) in the 

Columbia River Basin--past and present 

Reference Type: Report

City: Washington, D.C. 

Institution: U.S. Department of Interior. Fish and Wildlife Service, Bureau of Commercial 

Fisheries 

Report Number: Special Scientific Report--Fisheries No. 571 

Value of reference: This article shows status and trends based on run estimates for a middle 

period of time (1930s to 1960s), as well as the commercial catch trend for the Columbia River, 

1865-1962 (see Figure 1) as an indicator of chinook salmon population changes through time. 

Since much degradation had already occurred by the 30s, the 1930s numbers of salmonids are 

probably lower than pre-settlement, but estimates still represents a period when chinook salmon 

were much more numerous and widely distributed than today. The losses of spawning areas 

since the 30s indicate changes in distribution, reduction in range, habitat destruction, physical 

barriers, and impacts on reproduction. Locations of spawning areas and their status (past and 

present) are given in a tabular format for multiple tributaries of the Columbia River basin. 

Results relevant to EMAP: Commercial catch trends for Columbia River 1865-1962 were 

fluctuating but stable from the late 1800s through 1920, but then fell to about 1/3 the previous 

numbers. This decline was attributed to advancing civilization in the PNW--irrigation, logging, 

mining, dam construction, and other activities reduced the size and capacity of spawning areas; 

for most species, many spawning areas had been completely lost by 1968. 

Spring and summer runs of chinook in the Columbia River 1939-55 (excludes catches by sport 

fishery in the ocean and lower Columbia River, landings by the offshore troll fishery, and 

escapement to tributary streams entering the Col River below Bonneville Dam with the 

exception of the Willamette River run) had an increasing trend. Runs of fall chinook in the 

Columbia R. and escapement to areas above Bonneville Dam (excludes same as above), 1938-

66, showed a fairly steep declining trend.

Geographic location: Columbia River basin, mountains, xeric, eco1, eco3, eco4, eco2, eco10, 

eco11, eco15, eco16, eco12, eco17, eco9, Washington, Oregon, Idaho, EPA Region 10 

Keywords: fish, Chinook salmon, water diversion, logging, mining, dams 

Abstract: Chinook salmon, the most abundant species of salmon in the Columbia Basin, 

formerly spawned in nearly all tributaries of the Columbia River and in many areas of the main 

river. Over the past 60 years, the construction of dams has inundated, impeded, or blocked 

access to spawning areas. Despite these heavy losses, large areas of spawning grounds in the 

middle and lower portions of the drainage are still available to chinook salmon. Stream 

improvements by State and Federal fishery agencies have rehabilitated some areas and have 

brought others into production for the first time. Important spawning areas are listed and 

charted in this report according to their past use (before 1965) and present use (1966). 

Estimates of recent spawning populations in major tributaries and in segments of the main stem 

are also given. Former and present levels of abundance are listed according to three major 

runs--spring, summer, and fall. 

Notes: This reference is a companion to Fulton 1970, which provides synopses for steelhead 

67
trout, coho, chum, and sockeye salmon 

68
Author: Fulton, L.A. 

Year: 1970 

Title: Spawning areas and abundance of steelhead trout and coho, sockeye, and chum salmon 

in the Columbia River Basin--past and present 

Reference Type: Report

City: Washington, D.C. 

Institution: U.S. Department of Commerce, National Oceanic and Atmospheric Administration, 

National Marine Fisheries Service 

Report Number: Special Scientific Report--Fisheries No. 618 

Value of reference: Conditions in the mid to late 1800s are scattered throughout this 

document, much in the form of commercial catch or production records, which are used as 

surrogates of relative population sizes. Also shown are status and trends for 1930s to 1960s, 

using run counts. Spawning areas and their status (past/present) are given per creek or river in 

a tabular format. 

Results relevant to EMAP: The Columbia river run and commercial catch estimates have 

fluctuated greatly with time, but the general trends have been substantial declines for all four 

species since the turn of the century. Coho had a slight rebound in the early 60s; chum were 

practically extinct at the end of the 1960s. Tabular detail in the paper shows how the changes in 

spawning ranges contributed to the declines in each tributary in the Columbia River drainage, by 

species, for 1938-66 (fish runs) and 1890/1900 --1966 (commercial catch). 

Declining catches and loss of spawning areas are attributed to logging, highway construction, 

agricultural cultivation, placer mining, and dumping of wastes. Report lists parts of 

subwatersheds where these fish species once spawned and where they no longer occurred in 

1969. 

Geographic location: Columbia River basin, mountains, xeric, Oregon, Washington, EPA 

Region 10, eco10, eco4, eco11, eco 15, eco16. eco3, eco9 

Keywords: fish, salmonids, logging, roads, agriculture, mining, pollution, dams, water diversion 

Abstract: Past spawning areas (those removed from use before 1969) and present ones (those 

in use in 1969) are described for steelhead, trout, Salmo gairdneri; coho salmon, Oncorhynchus 

kisutch; sockeye salmon, O. nerka; and chum salmon, O. keta. The different species 

characteristically spawn in the following areas: 1) steelhead trout--in streams of all sizes (widely 

dispersed throughout the watershed, 2) coho salmon--in small streams (mostly in the lower 

tributaries) and in a few areas in the middle watershed, 3) sockeye salmon--in lakes and 

tributaries of lakes (in the middle portion of the watershed), and 4) chum salmon--in lower 

portions of tributaries that enter the Columbia River below The Dalles dam. All four species 

have lost many spawning areas because of water-use developments and changes in the 

watershed resulting from logging, highway construction, agricultural cultivation, placer mining, 

and dumping of wastes. Serious depletion of the runs of all four species is evident from the 

available data (the commercial catches before 1938 and since 1938 augmented by information 

on escapement and sport catch). The future prospects are fair for steelhead trout, good for 

coho salmon, and poor for sockeye and chum salmon. 

Notes: This reference is a companion to Fulton 1968, which provides similar synopses for 

Chinook Salmon 

69
Author: Gerstung, E.R. 

Year: 1988 

Title: Status, life history, and management of the Lahontan cutthroat trout 

Reference Type: Journal Article

Journal: American Fisheries Society Symposium 

Volume: 4 

Pages: 93-106 

Value of reference: This is the most complete summary found of the decline of the Lahontan 

cutthroat trout (Oncorhynchus clarki henshawi) and its causes. It thoroughly describes the 

historic distribution and decline separately for 5 sub-basins: Truckee River, Carson River, 

Walker River, Humboldt River, and Smoke Creek/Black Rock sub-basins. Populations that 

have been established outside their native waters of the Lahontan Basin, as a result of stocking 

hatchery-reared fish, are also covered. 

Although possibly not of as much use to EMAP, this publication also summarizes the life history 

of Lahontan cutthroat trout, including migration, breeding, habitat preferences, feeding, and 

growth. In full, it is an excellent synopsis of the species and its historical and current status (as 

of 1988). 

Results relevant to EMAP: At the time of early settlement of the region, Lahontan cutthroat 

trout reportedly existed in waters throughout the basin, including most cooler perennial streams 

downstream from impassable falls, totaling at least 6,100 km of stream habitat (as well as in 11 

lakes). A map is included (Figure 1) that shows the probable historic and present distribution of 

the trout in the 5 sub-basins of the region. Also shown are the locations of introgressed 

populations. Following European settlement, the species was extirpated from much of the 

native range. Currently (1982) self-sustaining populations are found in a total of only 490 stream 

miles, which represents only 7% of the historic range in stream habitats. 

Historical distributions are described in detail for each of the sub-basins and contrasted with the 

subspecies' current distribution; reasons for decline are given for each as well. Table 1 gives 

the probable historic and present (1982) habitat extent (stream km) for each of the sub-basins. 

From this, one could calculate the percent of probable historic stream km occupied presently. 

There is dispute among authors over whether the Humboldt River sub-basin populations are the 

same subspecies as those in other sub-basins, but they are covered here as if they are the 

same. The Humboldt populations differ taxonomically and also seem better adapted for life in a 

fluvial system than in a lacustrine one. 

Reasons for severe decline of this subspecies include over-fishing, competition and 

interbreeding with nonnative trout, construction of dams, water diversions, and general habitat 

degradation. 

Geographic location: Nevada, California, Lahontan basin, eco80, eco13, eco5, EPA Region 9, 

xeric, mountains 

Keywords: fish, fishing, nonnative species, dams, water diversion, habitat degradation 

Abstract: The Lahontan cutthroat trout Salmo clarki henshawi is believed to have occupied at 

least 6,100 km of stream habitat and 135,000 ha of lake habitat in its historic range. Some lake 

populations such as those in Lake Tahoe, California-Nevada and in Pyramid and Walker lakes 

70
in Nevada were large enough to support thriving commercial fisheries. Pure self-sustaining 

stocks of Lahontan cutthroat are now limited to headwater streams within the Humboldt River 

drainage, to Summit and Independence lakes, and to several small tributaries of the Truckee, 

Carson, and Walker rivers. A small number of additional populations have been established 

outside the Lahontan Basin in both California and Nevada by transplants and hatchery 

production in each of these states. Self-sustaining Lahontan cutthroat trout populations are 

known to occur in 100 locations, representing about 7% of the historic stream habitat and 0.4% 

of the historic lake habitat. Competition from and hybridization with introduced nonnative trout, 

the construction of dams and diversions on important spawning streams, and water quality 

deterioration are largely responsible for the decline of Lahontan cutthroat trout. Restoration 

efforts in California and Nevada will involve, eliminating nonnative trout from selected streams, 

restocking with endemic stocks where possible, and improving and protecting habitat. 

Hatchery-reared stocks will continue to be utilized in various lake and reservoir recreational 

fishing programs, including those existing in Pyramid and Walker lakes. 

Notes: Dunham et al. (1997) (citation below) discuss the effects of habitat fragmentation and 

loss of connectivity throughout the range of this trout as being a major obstacle in its survival as 

a subspecies. 

Dunham, J.B., G.L. Vinyard, and B.E. Rieman. 1997. Habitat fragmentation and extinction risk 

of Lahontan cutthroat trout. North American Journal of Fisheries Management 17:1126-1133. 

71
Author: Gilbert, C.H.; Evermann, B.W. 

Year: 1894 

Title: A report upon investigations in the Columbia River basin, with descriptions of four new 

species of fishes 

Reference Type: Journal Article

Journal: Bulletin of the United States Fish Commission 

Volume: 1 

Pages: 169-207 

Value of reference: This is a detailed primary literature source reporting fish specimens 

collected as part of a survey begun in 1892 to locate a hatchery site in the Columbia basin. It 

contains a list of the river tributaries and streams examined and a report on each, including brief 

descriptions of physical habitat (substrate, riparian vegetation, water temperature, channel 

width, depth, nature of banks, pools, and current), general abundance of fish, and a short list of 

the dominant fish species. Following stream descriptions is a list of fish species, the locations 

where they were collected, and the numbers collected. Results are useful for determining 

historical presence and distribution. Report contains scattered anecdotal notes on what was 

known about distribution and abundance based on surveys or other work prior to 1892. 

The information about fish presence and relative abundance would be useful for reconstructing 

historical ranges and fish assemblages in river tributaries. Some reconstruction of taxonomy 

based on type specimens and location from the historical text would be necessary for 

interpreting results and making comparisons with present-day taxonomy. A variety of physical 

habitat information can also be extracted from this source for use in reconstructing historical 

physical conditions for specific streams in the Columbia basin. 

Results relevant to EMAP: A variety of baseline data can be extracted from this document, 

including fish species presence, relative abundance, and dominance in various tributary basins, 

as well as physical habitat features of streams. 

The specimens collected include lamprey, sturgeon, suckers, minnows, chub, squawfish, dace, 

salmon, steelhead, trout, and sculpin; mention also of carp, which at that time had been recently 

introduced. 

Geographic location: Columbia River basin, Oregon, Washington, Idaho, EPA Region 10, 

mountains, xeric, eco10, eco11, eco12, eco16, eco15, eco9, eco4, eco3, eco1 

Keywords: fish, phab, historical data, fish presence, fish abundance 

72
Author: Gilbert, C.H.; Scofield, N.B. 

Year: 1895 

Title: Notes on a collection of fishes from the Colorado basin in Arizona 

Reference Type: Journal Article

Journal: Proceedings of the U.S. National Museum 

Volume: 20 

Issue: 1131 

Pages: 487-499 

Value of reference: This account details the occurrence in the Colorado River basin of 19 fish 

species in the late 1800s. It also makes corrections to a previous collection and archival 

account by Evermann and Rutter (1894, this bibliography).

Results relevant to EMAP: The primary objective of the research expedition was to investigate 

the alleged occurrence of shad in the Lower Colorado. In the process, the authors made 

reports and descriptions of other fish they found and their locations in the lower basin. 

Therefore, this was not a complete or systematic survey of the river basin, but it can be used for 

developing a list of species and general locations where species were present in the late 19th 

century. 

The number of specimens (or relative number, e.g., "numerous specimens"), collection 

locations, and sometimes the relative abundance at the location are given at the beginning of 

each species account for each of 19 species. Locations are specified very generally, e.g., "in 

the Salt River at Tempe, AZ"; "Chino, AZ, in a tributary of the Rio Verde". The great majority of 

text is descriptions of fish and not of much use to EMAP. It is a good supplement to the 1894 

account of Colorado Fishes by Evermann and Rutter (in this bibliography) for describing 

historical fish community composition and species distributions.

Geographic location: Colorado River Basin, Arizona, eco81, eco23, eco22, eco14,eco20, EPA 

Region 9, xeric 

Keywords: fish, historical data 

Notes: This reference is a supplement to Evermann and Rutter (1894)--in this bibliography 

73
Author: Gilbert, E.W.; Litt, B. 

Year: 1966 

Title: The exploration of Western America 1800 - 1850 

Reference Type: Book

City: New York 

Publisher: Cooper Square Publishers, Inc. 

Number of Pages: 233 

Original Publication: 1933 

Reprint Edition: 1966 

Value of reference: These early explorations of the west are the first observations of the region 

by European-Americans. Observation of the landscape and plants and animals of the area help 

establish what pre-settlement conditions were like. This book contains documentation of 

several explorations ranging from 1800 to 1850 and provides good descriptions of the physical 

habitat, geology, flora and fauna of the region..

Results relevant to EMAP: The book contains chapters on the Physical geography, climate, 

natural drainage, natural vegetation, and animals of the region. In addition to overall 

descriptions of the landscape, many of the expeditions include information about the 

characteristics of the streams and rivers. This mainly consists of physical characteristics 

including: flow, sinuosity, riparian vegetation, and some fish information. This baseline is helpful 

in establishing pre-settlement condition of the streams before navigation and irrigation 

modifications had been made. 

The chapters require some sifting through to extract pieces of anecdotal information or to 

reconstruct stream related attributes, however; the information is quite valuable and may be the 

only source of pre-settlement conditions of the region. This is a good broad reference and 

inventory that includes specific information about pre-settlement conditions. 

Geographic location: Western United States, North Dakota, South Dakota, Nebraska, Kansas, 

Missouri, Colorado, Wyoming, Oregon, Washington, Utah, EPA Region 7, EPA Region 8, EPA 

Region 9, eco47, eco27, eco25, eco44, eco42, eco46, eco17, eco18, eco21, eco17, eco80, 

eco16, eco15, eco3, eco4, eco10, eco11 

Keywords: exploration, phab, resource inventories, pre-settlement condition, historic condition, 

historical geography, geology, expeditions 

74
Author: Gregory, S.C; Deacon, J.E. 

Year: 1994 

Title: Human induced changes to native fishes in the Virgin River drainage 

Reference Type: Book Section

Editor: Marston, R.A. 

Book Title: Effects of Human Induced Changes on Hydrologic Systems. 

City: Middleburg, VA 

Publisher: American Water Resources Association 

Pages: 435-444 

Series Title: Technical Publication Series No. 94-3 

Value of reference: Article addresses the native fish of the Virgin River, the impacts that have 

caused their declines beginning in the 1930s, and the reduction of these species from different 

parts of the drainage. It is a good and thorough synopsis, including graphics of the trends in 

native and nonnative species abundances, and describing the trends in species distribution in 

different sections of the drainage as a result of multiple impacts.

Results relevant to EMAP: Despite early settlement of the Virgin River, (1850s-90s), the six 

native fish species of the Virgin River remained relatively unaffected until large scale habitat 

changes occurred, beginning in 1935 with the Hoover Dam, which eliminated the native fish 

community in the lower 25 miles of the river. 

Tributary populations were depleted in the 1960s and 1970s due to reservoir construction and 

dewatering (diversions) and poisoning of fish, followed by introduction of trout and cattle 

grazing, while middle mainstream fishes were most affected during 1980s by municipal and 

agricultural water management that altered both variability and volume of flow and by the 

upstream invasion by the introduced red shiner. 

Today, the Virgin chub and woundfin are federally endangered, and the Virgin spinedace is a 

candidate for threatened status--all three are endemic to the Virgin River. Water diversions and 

dewatering is the greatest threat to native fish, followed by dams and other flow alterations; 

more recently, population pressures and municipal water development projects have put 

demands on the river.

Geographic location: xeric, eco20, eco22, eco14, Nevada, Utah, Arizona, Virgin River basin, 

EPA Region 8, EPA Region 9 

Keywords: fish, historical data, dams, nonnative species, grazing, water diversion, fish 

poisoning, endangered species, Federal Reserved Water Rights 

Abstract: The Virgin River originates in southwestern Utah and joins the Colorado River in 

southern Nevada where it flows into the Overton Arm of Lake Mead. Analysis of a considerable 

database on native fishes collected over the past 17 years, supplemented by historical records, 

reveals reductions in both distribution and abundance of the native fish community. Following 

construction of Hoover Dam, Lake Mead flooded the lower 25 miles of the Virgin River, 

eliminating the native fish community in the 1930s. Reservoir construction, development of trout 

fisheries, and cattle grazing, depleted native fish communities in tributary streams during the 

1960s and 1970s. The middle mainstream fish fauna was most severely affected during the 

1980s following upstream invasion by the introduced red shiner and construction of a 45,000 

acre-foot off-stream reservoir. The native fish community of the Virgin River Drainage maintains 

relatively natural abundance today only in Zion National Park and for a short distance 

75
downstream, and in a segment of the Santa Clara River above Gunlock Reservoir. Water 

development plans for the future threaten the fish community in those areas. Federal Reserved 

Water Rights, management of endangered species, sport fish management, irrigation rights, 

and pressure to provide water for urban growth place conflicting demands on the Virgin River 

and highlight ethical dilemmas of a human population faced with adjusting to a world with limits. 

76
Author: Gresh, T.; Lichatowich, J.; Schoonmaker, P. 

Year: 2000 

Title: An estimation of historic and current levels of salmon production in the Northeast Pacific 

ecosystem 

Reference Type: Journal Article

Journal: Fisheries 

Volume: 25 

Issue: 1 

Pages: 15-21 

Value of reference: This work reviews estimates of historic salmonid run sizes in western North 

America, based upon historic cannery records and previously published estimates of historical 

abundance dating back to 1866. It also provides an estimate of the amount of marine-derived 

nitrogen and phosphorous that were delivered to regional streams annually in the form of 

salmon carcasses, which, the authors argue, were important for the survival of juvenile 

salmonids in nutrient-poor streams. It provides a review of what is known about the influence of 

marine-derived carbon (MDC) upon algal growth, macroinvertebrate abundance, growth and 

survival of juvenile coho salmon (Oncorhynchus kisutch). This paper may be helpful in 

reconstructing 'reference conditions' in stream systems that were historically dependent upon 

marine-derived nutrients. 

Results relevant to EMAP: Marine-derived nitrogen, phosphorous, and carbon, which play an 

important role in algal growth, macroinvertebrate abundance, and juvenile salmonid growth and 

abundance in western streams, have dropped to 6 - 7% of historic (1880s) levels, associated 

with the decline of historic salmon (Oncorhynchus spp.) runs. Regionally, the Pacific salmon 

biomass return has dropped from an estimated 156 - 254 million kilograms to 12 - 13 million 

kilograms. Anthropogenic disturbances such as extirpation of beaver, logging, irrigation, 

grazing, pollution, dams, sport and commercial fishing have contributed to the decline of 

salmonids, and possibly a spiraling ecosystem failure in streams of Washington, Oregon, and 

California. 

Geographic location: Region 10, Region 9, Washington, Oregon, California, Sacramento 

River, Columbia River, Fraser River, Coastal Oregon Rivers, Klamath River, Coastal 

Washington Rivers, eco1, eco2, eco3, eco4, eco78, eco6, eco7, eco9, eco10, eco11, eco77, 

Coast Range, Puget Lowland, North Cascades, Willamette Valley, Cascades, Klamath 

Mountains, Southern and Central California Chaparral and Oak Woodland, Central California 

Valley, Eastern Cascades Slopes and Foothills, Columbia Plateau, Blue Mountains, mountains 

Keywords: fish, phab, salmon populations; coho; Oncorhynchus kisutch; fishing; logging; 

agriculture; grazing, pollution; dams; nutrient deficit; nitrogen; phosphorous 

Abstract: We used historical cannery records and current escapement and harvest records to 

estimate historical and current salmon escapement to western North American river systems, in 

order to determine the biomass and marine-derived nitrogen and phosphorous levels delivered 

by adult salmon, and deficits corresponding to the diminished returns of adult salmon over the 

past century. We have estimated the historic biomass of salmon returning to the Pacific 

Northwest (Washington, Oregon, Idaho, and California) to be 160-226 million kg. The numbers 

indicate that just 6-7% of the marine-derived nitrogen and phosphorous once delivered to the 

rivers of the Pacific Northwest is currently reaching those streams. This nutrient deficit may be 

one indication of ecosystem failure that has contributed to the downward spiral of salmonid 

abundance and diversity in general, further diminishing the possibility of salmon population 

77
recovery to self-sustaining levels. 

78
Author: Haden, G. A.; Shannon, J. P.; Wilson, K. P.; Blinn, D. W. 

Year: 2003 

Title: Benthic community structure of the Green and Colorado rivers through Canyonlands 

National Park, Utah, USA 

Reference Type: Journal Article

Journal: Southwestern Naturalist 

Volume: 48 

Issue: 1 

Pages: 23-35 

Value of reference: The authors suggest a model of the pre-settlement benthic flora and fauna 

of the Colorado River system by examining the invertebrate communities in the free flowing 

sections of the Green and Colorado Rivers in Canyonlands National Park. These river reaches 

are the farthest downstream of large impoundments and they retain similar hydrographs to predam condition.

Results relevant to EMAP: This study provides the first description of the abundance, standing 

mass, taxa, feeding guilds, and primary carbon sources for benthic macroinvertebrates at six 

remote sites on the Green and Colorado rivers and provides an example of how the pre-dam 

Colorado River system might have functioned. The authors hypothesized that the aquatic 

community adjusted to flooding and high suspended sediment and that macroinvertebrate 

standing mass was relatively stable even with seasonal community composition changes. 

They found that macroinvertebrate food resources were limited to allochthonous sources due to 

high suspended sediment concentrations; however, there was an invertebrate assemblage that 

processed this form of carbon and provided food for higher trophic levels. 

Hard substrates were limited, but the complexity of riverine habitats, such as side channels, 

backwaters, and wetlands, and the presence of wood might have augmented the standing mass 

and species richness of the invertebrate assemblage.

Geographic location: Region 8, Utah, Green River, Colorado River, eco20, xeric, Canyonlands 

National Park 

Keywords: macroinvertebrates, phab, dams, sediment, hydrologic variability, historic reference 

Abstract: We sampled the aquatic benthos at 6 remote sites on the Colorado and Green rivers 

through Canyonlands National Park, Utah, USA. This study provides the first published 

description of benthic standing mass, invertebrate community composition, and primary carbon 

source for this portion of the Colorado River system. High suspended sediment concentrations 

prohibited growth of primary producers. The primary carbon source for benthic invertebrates 

was terrestrial organic matter. The invertebrate community was composed of 49 taxa, mostly 

mayflies, caddisflies, and Diptera, which were dominated by filterer/collector species. A smaller 

portion of the community was made up of predatory stoneflies and odonates. Standing mass of 

invertebrates on cobble substrates within a given site was stable over the multiyear sample 

period (1993 through 1996) and was comparable with other southwestern streams (overall 

mean = 0.41 g/m2 ash-free dry mass). Invertebrate standing mass at each site was controlled by 

the availability of primary carbon. Primary carbon availability was controlled by supply to the site 

and retention within the site. Both aspects might be influenced by anthropogenic alteration of 

the river basin and discharge patterns upstream of the study site. 

79
Author: Hamilton, J.B.; Curtis, G.L.; Snedaker, S.M.; White, D.K. 

Year: 2005 

Title: Distribution of anadromous fishes in the upper Klamath River watershed prior to 

hydropower dams--a synthesis of the historical evidence 

Reference Type: Journal Article

Journal: Fisheries 

Volume: 30 

Issue: 4 

Pages: 10-20 

Value of reference: This publication uses a variety of historical information to reconstruct the 

distribution of anadromous fish above the Iron Gate Dam, which now restricts fish passage to 

the upper Klamath River basin. It is significant in its use of multiple sources as lines of evidence 

of fish species' historical presence at multiple sites throughout the upper basin. Detailed 

historical documentation about presence and distribution in the upper basin is provided for: 

Chinook salmon (spring and fall runs), steelhead, coho salmon, anadromous Pacific lamprey, 

sockeye salmon, green sturgeon, eulachon, cutthroat trout, chum salmon, and pink salmon

Results relevant to EMAP: Prior to dam construction on the Klamath system, anadromous fish 

migrated beyond the current site of Iron Gate dam (closed in 1962). This dam, at river km 307, 

is the current limit of upstream passage. 

Numerous sources of information (many dating to the 19th century) are presented regarding the 

occurrence of Chinook salmon, steelhead, coho salmon, and Pacific lamprey above the current 

location of Iron Gate Dam. A map (Figure 1) plots the cited incidents of each species in the 

upper basin, with cross-references to the literature documentation used as evidence (listed in 

Table 1). 

Chum salmon, pink salmon, eulachon, and cutthroat trout were limited historically to the lower 

Klamath River, well below current location of Iron Gate Dam.

Geographic location: Klamath River basin, Oregon, California, eco78, eco4, eco9, EPA 

Region 10, mountains 

Keywords: fish, dams, anadromous fish distribution, historical documentation, historical 

photographs, fish passage 

Abstract: Knowledge of the historical distribution of anadromous fish is important to guide 

management decisions regarding the Klamath River including ongoing restoration and regional 

recovery of coho salmon (Oncorhynchus kisutch). Using various sources, we determined the 

historical distribution of anadromous fish above Iron Gate Dam. 

Evidence for the largest, most utilized species, Chinook salmon (Oncorhynchus 

tshawytscha), was available from multiple sources and clearly showed that this species 

historically migrated upstream into tributaries of Upper Klamath Lake. Available information 

indicates that the distribution of steelhead (Oncorhynchus mykiss) extended to the Klamath 

Upper Basin as well. Coho salmon and anadromous lamprey (Lampetra tridentata) likely were 

distributed upstream at least to the vicinity of Spencer Creek. A 

population of anadromous sockeye salmon (Oncorhynchus nerka) may have occurred 

historically above Iron Gate Dam. Green sturgeon (Acipenser medirostris), chum salmon 

(Oncorhynchus keta), pink salmon (Oncorhynchus gorbuscha), coastal cutthroat trout 

(Oncorhynchus clarki clarki), and eulachon (Thaleichthys pacificus) were restricted to the 

80
Klamath River well below Iron Gate Dam. This synthesis of available sources regarding the 

historical extent of these species’ upstream distribution provides key 

information necessary to guide management and habitat restoration efforts. 

URL: http://www.fisheries.org/html/fisheries/F3004/F3004p10-20Hamilton.pdf 

81
Author: Hasse, Adelaide R. 

Year: 1899 (digital version: 2003) 

Title: Reports of Explorations Printed in the Documents of the United States Government: a 

Contribution Toward a Bibliography 

Reference Type: Electronic Source

Producer: U.S. Government Printing Office 

Access Year: 2005 

Access Date: August 25, 2005 

Last Update Date: Aug. 25, 2005 

Value of reference: A great source of surveys, reports, and exploration made during the mid to 

late 1800's by the US government. This listing is a comprehensive source of any type of 

resource inventory, observation, report, etc. made throughout the US and could be a valuable 

look at the "historic conditions" of these areas. 

This is a digitized edition of Reports of Explorations Printed in the Documents of the United 

States Government taken from a 1st edition (1899) copy held by the University of Minnesota 

libraries: 

Reports of Explorations Printed in the Documents of the United States Government: a 

Contribution Toward a Bibliography. Compiled by Adelaide R. Hasse. (Washington, D.C.: U.S. 

Government Printing Office, 1899. (GP 3.5:2 1899)). Transcription and encoding by Jennifer 

Claybourne Torkelson, 2000. XML Source Encoding. Navigation elements added by Amy West, 

Government Publications Library, 2003. 

Results relevant to EMAP: A good source to locate available pre-settlement literature and 

references. This web site includes listings of many early exploration accounts and 

observations, which may be the only sources for pre-settlement conditions in some areas of the 

Western United States. Stream conditions and species inventories may be limited; however, 

some baseline information can be gleaned from some of these references.

Geographic location: western United States 

Keywords: Explorations, phab, resource inventories, pre-settlement condition, historical data, 

historical condition, geography, geology, expeditions 

URL: http://govpubs.lib.umn.edu/digdoc/hasse.phtml 

82
Author: Hassemer, P. F.; Kiefer, S. W.; Petrosky, C. E. 

Year: 1997 

Title: Idaho's salmon: Can we count every one? 

Reference Type: Book Section

Editor: D. J. Stouder; P. A. Bisson; R. J. Naiman 

Book Title: Pacific Salmon and their Ecosystems: Status and Future Options. 

City: New York, NY 

Publisher: Chapman and Hall 

Pages: 113-125 

Value of reference: The article's main focus is present day salmonid status and monitoring, but 

there is a section on habitat loss over the last 100 years. 

Results relevant to EMAP: Dam construction has been the major factor resulting in loss of 

access to salmon spawning and rearing habitat in Idaho. About 62% of Idaho's historical 

spawning and rearing habitat for spring/summer chinook and steelhead remains available, but 

only 17% of the historical habitat remains available for Snake River fall chinook salmon due to 

the construction of the 3 dam Hell's Canyon complex in the 1960's. 

The 62% that is still accessible to spring and summer chinook and steelhead represents approx. 

6055 river km out of 9741 km estimated to exist in predevelopment times. Similarly, 172 km of 

suitable habitat is available to fall chinook out of and estimated 989 river km (17% of 

predevelopment km). 

Approximately 30% of Idaho's stream kilometers inhabited by salmon and steelhead are located 

within designated wilderness areas or waterways classified as wild and scenic rivers. 

Geographic location: Idaho, Salmon River, Snake River, Clearwater River, mountains, 

Columbia River, eco15, Northern Rockies, EPA Region 10 

Keywords: fish, habitat loss, phab, dams, chinook salmon, spawning habitat 

Abstract: Since the late 1950's, Idaho Dept. of Fish and Game (IDFG) biologists have collected 

standardized information about the status of salmon (Oncorhynchus spp.) in Idaho to assist 

fisheries management. Currently, IDFG uses indices of production such as redd and parr counts 

for streams, and adult salmon counts at dams and weirs, to assess the recent history of our 

salmon runs. We depict Idaho anadromous salmon trends using indices for sockeye, spring, 

summer, and fall chinook salmon, and steelhead. Counts of redds in index areas provide the 

best historical indicator of trends and status of spring and summer chinook salmon. Numbers of 

redds have declined sharply through the last 33 years. All of the naturally reproducing Snake 

River anadromous salmonid populations, excluding chinook salmon in the Clearwater River 

drainage and Snake River steelhead, have been listed as endangered pursuant to the federal 

Endangered Species Act. Hydroelectric development of the mainstem Snake and Columbia 

rivers is widely recognized as the major factor causing the decline of these populations. 

Aggregated trend information is useful, but alone does not provide information needed for future 

management. We must augment historical information with knowledge about brood-year 

performance of multiple populations. We are using our indexed production information for life 

cycle modeling to assess productivity, a key to assessing recovery actions. Increased 

monitoring and analyses of indicator populations will better describe salmon status and trends to 

meet management needs for the future. 

83
Author: Hatch, M. H. 

Year: 1949 

Title: A century of entomology in the Pacific Northwest 

Reference Type: Book

City: Seattle 

Publisher: University of Washington Press 

Number of Pages: 43 

Value of reference: This short reference provides the best historical overview of who collected 

what types of macroinvertebrates, where, and when in the Pacific Northwest. The author divides 

entomological activities into four periods, including (1) the period of itinerate collectors, (2) the 

period of resident collectors, (3) the period of established laboratories from 1890-1930, and the 

'present' (4) 1930 - 1949. The work contains a taxonomic index by order to guide readers to 

references to specific historic materials. 

This is baseline information, and, although sparse in coverage, it should help to define the 

limitations of historical reconstructions of aquatic macroinvertebrate assemblages in this region. 

It also lists important literature for macroinvertebrates in the region by order. [Note: Many of the 

collections mentioned in this reference have subsequently been assembled in the entomological 

museum collection housed at Oregon State University]

Results relevant to EMAP: Macroinvertebrates were first collected in the Pacific Northwest in 

the mid 1830's, but most collection activities were focused upon certain terrestrial orders 

(Coleoptera, Lepidoptera) or those of importance to humans at that time, such as horticultural 

pests, rather than aquatic macroinvertebrates. References to aquatic orders discussed in this 

reference include Coleoptera, Diptera, Hemiptera, Neuroptera, Odonata, and Plecoptera.

Geographic location: Oregon, Washington, Idaho, Region 10, Mountains, Xeric, Eco1, Eco2, 

Eco3, Eco4, Eco9, Eco78, Eco77, Eco10, Eco11, Eco12, Eco15, Eco16, Eco17, Eco80 

Keywords: Macroinvertebrates; historical data; taxonomy; Coleoptera; Diptera; Hemiptera; 

Neuroptera; Odonata; Plecoptera; Pacific Northwest 

84
Author: Hatch, M. H. 

Year: 1953 

Title: The beetles of the Pacific Northwest 

Reference Type: Book

City: Seattle, WA 

Publisher: University of Washington 

Volume: 16 

Number of Pages: 340 

Value of reference: There are few works which synthesize early information on aquatic 

macroinvertebrates other than taxonomic keys. Keys such as this one provide a brief overview 

of the history of the collection and study of specific groups within the western United States, 

bringing together links to hundreds to thousands of individual published taxonomic records. This 

key contains records of Coleoptera collected in the Pacific Northwest as early as 1834. It 

provides the starting point for identifying who collected aquatic Coleoptera, where, when, and 

who described the taxa, dating back to the 1850s. The key provides information on generalized 

occurrence information by state, and qualitative abundance. This may be useful for beginning to 

reconstruct expected macroinvertebrate faunal composition and diversity metrics.

Results relevant to EMAP: Coleoptera were among the first insect orders collected in the 

western United States. By the end of the 1870s, 500-600 species of Coleoptera were known 

from the Pacific Northwest, most of which were terrestrial. Descriptions of the families 

Amphizoidae and Dytiscidae, which inhabit stream margins date to the early 1850s (LeConte 

1852). 

Geographic location: EPA Region 9, EPA Region 10, mountains, xeric, Oregon, Washington, 

Idaho, California 

Keywords: macroinvertebrates; historical data; Coleoptera; Amphizoidae; Dytiscidae 

Notes: LeConte, John L. 1852. Descriptions of some new species of Coleoptera from California. 

Ann. Lyc. Nat. Hist. N. Y. V:125-216. 

85
Author: Henshall, J.A. 

Year: 1906 

Title: A list of the fishes of Montana with notes on the game fishes 

Reference Type: Report

City: Missoula, MT 

Institution: University of Montana 

Pages: 13 

Report Number: Bulletin of the University of Montana, No. 34-11 

Value of reference: This is a compilation from multiple sources of the 36 native fish known in 

Montana in 1906. It is arranged by family and species and gives the names of rivers and 

streams or general portion of the state where each species had been documented up to that 

time. Several species were identified from descriptions of Lewis and Clark; but most species 

were collected on U.S. government railroad surveys and, more recently, by the U.S. Bureau of 

Fisheries. The list is followed by the list of species that had been introduced in Montana at that 

time. The final section, notes on game fish, is not as relevant to EMAP as the initial list. The 

location information can be used to reconstruct historical ranges of species and species 

composition of major tributaries

Results relevant to EMAP: As of 1906, 36 species of fishes had been recorded as native in 

Montana, and numerous introductions had occurred. The locations for each species listed here 

might not be the complete list of where they actually occurred; however, this list can provide 

information on general historical distribution of the fish species (primarily in the Missouri River 

basin of Montana) and might be useful cross-referenced with Evermann and Cox 1896 (in this 

bibliography)

Geographic location: Missouri River basin, Montana, EPA region 8, eco17, eco42, eco43, 

mountains, plains 

Keywords: fish, historical data, geographic distribution, primary source, baseline information 

86
Author: Holden, P. B.; Deacon, J. E.; Golden, M. E. 

Year: 2005 

Title: Historical changes in fishes of the Virgin-Moapa River system: Continuing decline of a 

unique native fauna 

Reference Type: Book Section

Editor: J.N. Rinne; R.M. Hughes; Calamusso, B. 

Book Title: Historical Changes in Large River Fish Assemblages of the Americas. 

City: Bethesda, Maryland 

Publisher: American Fisheries Society 

Pages: 99-114 

Value of reference: The chapter gathers what is known about the historical distribution of 

native fishes in the Virgin-Moapa Rivers and their tributaries, and compares that with more 

recent trends from the 1970's to the present. The river valleys were populated with settlers in 

the 1850's but were little studied until the 1930's (Hubbs and Miller) and 1970's (Cross).

Results relevant to EMAP: The authors describe the native fish species and their typical 

habitats in both the mainstem and the tributary streams of the Virgin and Moapa Rivers. They 

present very limited evidence of fish collections from early surveys (1870's) and attribute the 

shrinking habitat left for native fish to irrigation diversions, drowning of the lower rivers by Lake 

Mead, and competition from warm water exotics and introduced trout. 

Of the 9 native fish species and subspecies in the Virgin-Moapa River system 5 are endemic, 

which is indicative of the unique habitats in these rivers. Map (p. 100) showing refugia for native 

fishes in 1970 compared with 2002. Table (p. 104) of native and nonnative species in the VirginMoapa Rivers, listing extirpated species (desert sucker, woundfin) and endangered species 

(Moapa dace, Virgin River chub).

Geographic location: EPA Region 9, EPA Region 8, Utah, Nevada, Arizona, Virgin River, 

Moapa River, eco19, eco13, eco14, xeric, mountains 

Keywords: fish, nonnative species, water diversions, agriculture, dams, urban 

Abstract: The Virgin-Moapa River system supports nine native fish species or subspecies, of 

which five are endemic. Woundfin (Plagopterus argentissimus) and Virgin River chub (Gila 

seminuda) are endemic to the main-stem Virgin River, whereas cooler and clearer tributaries 

are home to the Virgin spinedace (Lepidomeda mollispinis). Moapa dace (Moapa coriacea) and 

Moapa White River springfish (Crenichthys baileyi moapae) are found in thermal springs that 

form the Moapa River, and Moapa speckled dace (Rhinichthys osculus moapae) is generally 

found below the springs in cooler waters. The agricultural heritage of the Virgin-Moapa River 

system resulted in numerous diversions that increased as municipal demands rose in recent 

years. In the early 1900's, trout were introduced into some of the cooler tributary streams, 

adversely affecting Virgin spinedace and other native species. The creation of Lake Mead in 

1935 inundated the lower 80 km of the Virgin River and the lower 8 km of the Moapa River. 

Shortly thereafter, nonnative fishes invaded upstream from Lake Mead, and these species have 

continued to proliferate. Growing communities continue to compete for Virgin River water. 

These anthropogenic changes have reduced distribution and abundance of the native VirginMoapa River system fish fauna. The woundfin, Virgin River chub, and Moapa dace are listed as 

endangered, and the Virgin spinedace has been proposed for listing. In this paper we document 

how the abundance of these species has declined since the Endangered Species Act of 1973. 

Currently, there is no strong main stem refugium for the Virgin River native fishes, tributary 

87
refugia continue to be shortened, and the Moapa River native fishes continue to be jeopardized. 

Recovery efforts for the listed and other native fishes, especially in the Virgin River, have 

monitored the declines, but have not implemented recovery actions effective in reversing them. 

88
Author: Hoppe, G. N. 

Year: 1938 

Title: Plecoptera of Washington 

Reference Type: Journal Article

Journal: University of Washington Publications in Biology 

Volume: 4 

Issue: 2 

Pages: 139-174 

Value of reference: This valuable reference provides a well documented example of the 

paucity of knowledge of aquatic macroinvertebrates prior to the period of systematic surveys 

conducted between the 1920s - 30s, long after settlement of the region. Although this 

represents only one order, it reflects the level of familiarity with western macroinvertebrate fauna 

prior to the 1930s. The author also describes the general distribution, and the location of 

specific recorded samples dating back to 1895, although most of the early descriptions date 

from the early 1920s to 30s.

Results relevant to EMAP: The diversity of aquatic macroinvertebrates is poorly represented in 

early literature. Prior to 1930, for example, only 30 species of Plecoptera had been recorded 

and described from Washington State. Following a series of surveys between 1930 and 1937, 

an additional 41 species were collected and recorded, representing 137% increase in recorded 

Plecoptera diversity for that state. This clearly illustrates the challenges facing those interested 

in reconstructing changes in macroinvertebrate assemblage characteristics from pre-settlement 

or early settlement conditions and suggests that a later time frame, although confounded by 

human alteration that occurred after European settlement, may be a more realistic benchmark 

for historically reconstructing macroinvertebrate distribution.

Geographic location: Region10, Washington, mountains, xeric, eco1, eco2, eco3, eco4, eco9, 

eco10, eco15, eco77 

Keywords: macroinvertebrates; Plecoptera; Washington; change detection 

Notes: Hatch, M. H. 1949. A century of entomology in the Pacific Northwest. University of 

Washington Press. 43 pp. (in this bibliography) 

89
Author: Jewett, Jr., S. G. 

Year: 1959 

Title: The Stoneflies (Plecoptera) of the Pacific Northwest 

Reference Type: Book 

City: Corvallis, OR 

Publisher: Oregon State College Press 

Number of Pages: 95 

Value of reference: The primary value of this document is that it makes reference to the 

original description and relevant taxonomic references. The author provides basic geographic 

range information in addition to relative abundance and seasonal occurrence of adults, although 

it is difficult to determine both time frame and geographic localities for which this abundance 

information is relevant. Unfortunately, papers devoted to distributional records that lack 

taxonomic treatment were not included in the preparation of this resource. This may be useful 

for beginning to reconstruct expected macroinvertebrate faunal composition and diversity 

metrics.

Results relevant to EMAP: Of the approximately 400 species of Plecoptera identified in the 

United States, 146 were reported in Washington, Oregon, Idaho, and British Columbia by 1959. 

Geographic location: EPA Region 10, Washington, Oregon, Idaho, mountains, xeric, Eco1, 

Eco2, Eco3, Eco4, Eco78, Eco77, Eco9, Eco10, Eco11, Eco80, Eco15, Eco16, Eco12, Eco17 

Keywords: macroinvertebrates; stoneflies; Plecoptera; Oregon; Washington; Idaho; Pacific 

Northwest 

90
Author: Jewett, S.G., Jr. 

Year: 1960 

Title: The Stoneflies (Plecoptera) of California 

Reference Type: Journal Article

Journal: Bulletin of the California Insect Survey 

Volume: 6 

Issue: 6 

Pages: 125-177 

Value of reference: This very useful resource contains county-level records of 101 species of 

Plecoptera in California. It also provides an overview of the Plecoptera literature relevant to the 

state ca. 1960. Most of the citations date from the 1930s -1950s. The primary value of this 

document is that it synthesizes collection information on each species, including location, date, 

often elevation, and occasionally stream size. Some information on relative abundance by 

locality is also provided, although it is difficult to determine the time frame for which this 

information is relevant. This may be useful for beginning to reconstruct expected 

macroinvertebrate faunal composition and diversity metrics.

Results relevant to EMAP: Of the 6 families and 350 species of Plecoptera described in the 

United States, all 6 families and 101 species have been recorded in California. The California 

stonefly fauna is very similar to that throughout the western cordilleran region. More than 70 

percent of the species are also found in Oregon, and approximately 60 percent in Washington. 

None of the holarctic species of Plecoptera have been collected in California. The author reports 

that many species have limited range, and distinct regional differences in stonefly faunal 

assemblages are apparent. 

Geographic location: California, EPA Region 9, mountains, xeric, Eco1, Eco4, Eco5, Eco6, 

Eco7, Eco8, Eco9, Eco13, Eco14, Eco80, Eco81 

Keywords: macroinvertebrates; Plecoptera 

91
Author: Johnsgard, Paul A. 

Year: 2003 

Title: Lewis and Clark on the Great Plains: A Natural History 

Reference Type: Book

City: Lincoln, Nebraska 

Publisher: University of Nebraska Press 

Value of reference: This book chronicles the Lewis & Clark expedition and summarizes the 

extensive natural history information collected over the Great Plains. In addition the web page 

access to the book includes links to other journals and texts associated with the expedition.

Results relevant to EMAP: A summary of the many plants, mammals, fish, and other natural 

history data collected on the expedition. The book includes geographical information that uses 

present day locations to correlate where the original observations occurred. This is a very good 

broad reference that also includes very specific information about pre-settlement conditions in 

the Great Plains.

Geographic location: Kansas, Missouri, Nebraska, Iowa, North Dakota, South Dakota, 

Montana, Missouri River Basin, EPA region 7, EPA region 8, eco47, eco42, eco43, eco46, 

Keywords: Lewis & Clark expedition, pre-settlement, mammals, phab, birds, fish, natural 

history 

Abstract: Lewis and Clark on the Great Plains is an easy-to-use reference on the wildlife that 

Meriwether Lewis and William Clark encountered during their 1804-6 Corps of Discovery 

expedition. Over one hundred animals and plants that were first carefully described and in some 

cases discovered by Lewis and Clark are identified here. More than an expedition reference 

guide, Lewis and Clark on the Great Plains also examines the lasting importance of the 

expedition's discoveries, the significance of the Plains plants and animals to local Native 

Americans, and the current status of Plains wildlife. Lavishly illustrated with Paul A. Johnsgard's 

drawings of mammals, birds, fish, reptiles, and plants, the book also includes a guide to the 

Lewis and Clark sites of botanical and zoological interest and more than seventy sites where 

readers can follow in the footsteps of two of America's greatest pioneering naturalists. Visit the 

Journals of the Lewis and Clark Expedition Online Project, based on Gary E. Moulton's 

celebrated edition of the Lewis and Clark Journals. Initially offering almost two hundred pages 

from volume 4, the site will eventually feature the full text of the Journals--almost five thousand 

pages. Also view a gallery of images and hear acclaimed poet William Kloefkorn reading 

selected passages. With full-text searchability and ease of navigation, the Journals of the Lewis 

and Clark Expedition Online Project is a useful tool for students and scholars and an engaging 

website for the general public. Sponsored by the University of Nebraska Press, the Center for 

Great Plains Studies, and the University of Nebraska E-Text 

Center.lewisandclarkjournals.unl.edu 

URL: 

http://libtextcenter.unl.edu/examples/servlet/transform/tamino/Library/lewisandclarkjournals?&_x

mlsrc=http://libtextcenter.unl.edu/lewisandclark/files/xml/lc.johnsgard.01.xml&_xslsrc=http://libte

xtcenter.unl.edu/lewisandclark/LCstyles.xsl#ch1

92
Author: Johnson, W.C. 

Year: 1992 

Title: Dams and riparian forests: case study from the upper Missouri River 

Reference Type: Journal Article

Journal: Rivers

Volume: 3 

Issue: 4 

Pages: 229-242 

Value of reference: This article reports the effects of altered flow and meander rate on 

floodplain forest composition along the Missouri River in central North Dakota as a result of the 

closing of the Garrison Dam in 1953. Several historical time periods, dating back to the late 

1800s, were used to reconstruct changes due to construction of the dam. Over time, river 

dynamics have changed due to hydrological alteration, which has changed forest cover 

composition and succession. 

Erosion and deposition over time are estimated. General Land Office Survey notes and maps 

were used to determine the proportional composition of riparian forest successional categories 

at the time of settlement. Pre-settlement data for meander and forest successional rates are 

used to create a model to predict future forest compositional shifts. 

Results relevant to EMAP: Mean annual flows have changed slightly in the 25 post-dam years, 

as compared with the early 1900s, while peak flows have changed dramatically (see Figure 3). 

The seasonal timing of peak and minimum flows has been reversed. Flooding now occurs only 

on very low terraces. The mean annual flood has been reduced by about 70%, while the 

maximum annual flood has reduced 81%. Historically, the Missouri River was a rapidly 

meandering stream. Post-dam erosion rates were 25% of pre-dam rates, while deposition rates 

were only 1% of pre-dam rates. The result was a reduction in new alluvium for formation of bars 

for colonization by cottonwood and willow. 

On the upper Missouri River, pioneering young forests occupied only 6% of the total forest area 

in 1979, down from 47% prior to settlement. In contrast, transitional forests occupied 48% of 

the area in 1979, as compared with 21% pre-settlement (see Table 5). Over 90% of presettlement forests had cottonwood as a significant member of the forest overstory. By 1938, 

approximately 38% of the floodplain forest had been cleared. In 1979, forest vegetation 

comprised about 44% of the area. 

Model simulations showed that the pre-settlement dominance of the floodplain by cottonwood 

and willow cannot be maintained under current low meander rates. The prediction is a rapid 

increase in proportion of equilibrium forests as pioneer forests age and are not replaced. River 

regulation and agriculture are given as the primary impacts bringing about this change. 

Geographic location: North Dakota, EPA region 8, eco43, eco42, Missouri River basin, plains 

Keywords: phab, dams, agriculture, meander rates, deposition, erosion, riparian forest 

composition, forest succession 

Abstract: This research examined the effects of altered flow and meandering rate of the 

Missouri River in central North Dakota on the compositional dynamics of floodplain forests. This 

was accomplished by estimating the rates of river erosion and deposition during pre-dam and 

post-dam periods from historical maps and aerial photographs. Future changes in forest 

93
composition were simulated using a simple mathematical model based on measured rates of 

forest succession and river meandering for pre- and post-dam periods. Simulations indicated a 

future decline in the areal extent of pioneer forests (cottonwood, willow) due to river regulation. 

Later successional species (primarily green ash) will dominate the future forests. 

Experimentation is needed in order to regenerate pioneer forests to maintain current levels of 

species diversity on the floodplain. (DBO) 

Notes: A general overview and comparison of the effects of river regulation on meandering 

(e.g., Missouri River) vs. braided (e.g., Platte River) channels in areas of differing water usage is 

given by Johnson, 1998, who synthesizes results from this publication (Johnson 1992) and 

Johnson 1994 (also in this bibliography), as well as other publications. 

Johnson, W.C. 1998. Adjustment of riparian vegetation to river regulation in the Great Plains, 

USA. Wetlands 18(4):608-618. 

Another relevant and cited article: 

Bragg, T.B. and A.K. Tatschl. 1977. Changes in flood-plain vegetation and land use along the 

Missouri River from 1826 to 1972. Environmental Management 1(4):343-348. 

94
Author: Johnson, W.C. 

Year: 1994 

Title: Woodland expansion in the Platte River, Nebraska: patterns and causes 

Reference Type: Journal Article

Journal: Ecological Monographs 

Volume: 64 

Issue: 1 

Pages: 45-84 

Value of reference: This article uses historical sources (GLO notes, time-series photographs) 

to reconstruct pre-settlement vegetation along the Platte River and its tributaries, including 

areas in Colorado, Wyoming, and similar Ecoregion 25 in western Nebraska. The causes of 

riparian vegetation changes are discussed. The results are notable because, rather than loss of 

woodland, there has been an increase in woodland, despite regulation of the river. This is in 

marked contrast to historic changes on the Missouri River in South Dakota (see Rumble et al. 

1998 in this bibliography) and in many other places in the West where river regulation has led to 

a decline in cottonwood and willow recruitment.

Results relevant to EMAP: Prior to settlement, scattered trees occurred on river banks and on 

islands in central Nebraska, but farther upstream on the South Platte River in Colorado, 

woodland was scarce and few trees were present; thus, riparian woodland decreased in a 

westward direction. Cottonwood, American elm, and willow were the dominant trees; minor 

species were box elder, ash, and oak in central Nebraska and pine and cedar in western 

Nebraska. The river was described as a very shallow stream that could be crossed at any point 

in most seasons and filled with islands of all sizes covered with grass, bushes, and small trees. 

Woodland began to expand into the North Platte River about 1900, occurring earliest in 

upstream reaches. By the late 1930s, much of the pre-settlement active channel in the North 

and South Platte rivers had transformed to woodland, resulting in a reduction of channel area. 

This process occurred in a west to east direction from the Colorado and Wyoming tributaries 

into central Nebraska. Woodland expansion rates since the 1930s have been highly variable, 

and the river has become more homogenous from east to west with respect to the mix of 

channel and woodland cover. The system appears to have reached a new equilibrium between 

flow and forest successional stage. The author postulates that the balance between woodland 

extent and active channel area was quite dynamic historically, changing during climatic cycles 

and sensitive to small but persistent changes in flow. 

Irrigation and impoundments, beginning on a large scale in the early 1900s, may have set this 

process into motion. The effect of consistently-reduced flows, in combination with tree life 

histories, climatic factors, and hydrogeomorphology, provided conditions more amenable to 

establishment and recruitment of trees. The factors that restricted tree growth in the presettlement period were high June flows (which would have restricted seedling recruitment) and 

ice on sand bars (which would have reduced survivorship of tree seedlings). Water 

developments curtailed both of these factors, and woodland expansion was the result. The 

system is now reaching a new equilibrium, and the process of forest expansion is actually 

reversing itself to some extent; for example, some of the forests that have expanded into the 

upper tributaries have already declined substantially in recent years. 

Geographic location: Wyoming, Colorado, eco25, EPA region 8, Platte River basin, plains 

Keywords: phab, dams, agriculture, demography, geomorphology, hydrology, management, 

95
Populus, primary succession, remote sensing, riparian woodland, Salix, sandbar colonization 

Abstract: This research was conducted to identify the factors that have permitted Populus-Salix

woodland to expand into the formerly active channels of the Platte River and its two major 

tributaries, the South and North Platte rivers. The research included: pre-settlement vegetation 

reconstruction based on the General Land Office survey notes, a statistical comparison between 

historic rates of woodland expansion from aerial photographs and environmental variables, and 

a field study of seedling demography to isolate the factors controlling recruitment and survival in 

the modern river. Woodland expansion began in the South and North Platte rivers around 1900 

and spread downstream into the Platte River. By the late 1930s, vegetation had occupied most 

of the former channel area of the South and North Platte rivers and was expanding into Platte 

River channels. Rates of channel loss in the Platte River have been as great as 10%/yr during 

droughts. By 1986, channel-to-woodland proportions were relatively uniform throughout the 

Platte River system. Statistical models indicated that sandbar succession to woodland was 

regulated by three environmental factors: June flows, summer drought, and ice. June flow 

regulated seedling recruitment and initial survival because it coincided with the main PopulusSalix seed germination period. Historic reductions in flow at this time for irrigation and to fill 

reservoirs exposed much of the riverbed and elevated recruitment and seedling survivorship. 

Late-summer seedling survival was regulated by factors that affect seedling water balance, 

including river stage, seedling elevation in the riverbed, and rainfall. Winter conditions exerted 

the largest effect on seedling survivorship. Dominant factors were air temperature, stream flow, 

and seedling elevation in the riverbed. Lowest survivorship occurred during cold, icy winters with 

relatively high flow and when most seedlings were growing on low sandbars. The dominant 

historic trend, of losses in channel area and gains in woodland area, has ceased in recent 

years. No significant declines in channel area have occurred since 1969; in several reaches 

channel area has significantly increased since 1969. Comparatively small changes in channel 

and woodland proportions are expected in the future as long as water use and climate do not 

change markedly. The steady state has developed because flows have come into balance with 

active channel area, thereby reducing recruitment and increasing the mortality of tree seedlings. 

Because of the importance of wide, unvegetated channels to certain avifauna, it may be 

desirable to manage future flows to ensure no further reduction in channel widths, even if 

narrowing is only temporary. Dominance by Populus and Salix on new sandbars can be 

explained by life history characteristics. These include large and dependable seed crops that 

are effectively dispersed by wind and water to optimal germination sites; rapid germination; 

rapid root and height growth to withstand flooding, drought, and sedimentation; tolerance of low 

soil fertility; and the ability of Salix to reproduce vegetatively. Pioneer vegetation and 

geomorphic processes (principally sedimentation) facilitate succession on floodplains by 

modifying the highly variable riverbed environment suitable for early successional species into 

relatively stable surfaces favorable for recruitment of later successional species. Much of the 

extensive Populus-Salix woodlands that now occupy the Platte River will be replaced by later 

successional tree and shrub species with lower associated faunal diversity. Maintenance of the 

current biotic diversity may require artificial regeneration, as is taking place along other river 

systems in western North America. The response of the Platte River to altered flow differed from 

that of other rivers. This divergent response despite similar disturbances points out the complex 

interrelationships among plants and hydrogeomorphic processes operating on floodplains and 

the difficulties associated with understanding, generalizing, and predicting the effects of human 

modification of stream flow on natural ecosystems. 

Notes: A general overview and comparison of the effects of river regulation on meandering 

(e.g., Missouri River) vs. braided (e.g., Platte River) channels in areas of differing water usage is 

given by Johnson, 1998, who synthesizes results from this publication (Johnson 1994) and 

96
Johnson 1992 (also in this bibliography), as well as other publications. 

Johnson, W.C. 1998. Adjustment of riparian vegetation to river regulation in the Great Plains, 

USA. Wetlands 18(4):608-618. 

For further supporting documentation of physical changes in the Platte River system, see 

Knopf, F.L. 1986. Changing landscapes and the cosmopolitism of the eastern Colorado 

avifauna. Wildlife Society Bulletin 14:132-142. 

97
Author: Jordan, D.S. 

Year: 1878 

Title: Report on the collection of fishes made by Dr. Elliott Coues U.S.A. in Dakota and Montana 

during the seasons of 1873 and 1874. 

Reference Type: Journal Article

Journal: Bulletin of the U.S. Geologic and Geographic Survey of the Territories 

Volume: 5 

Pages: 777-799 

Value of reference: This report is an inventory of the fish species collected during 1873 and 

1874 in northern Montana and North Dakota and surrounding areas into Canada. Its focus is on 

taxonomy. It adds Dr. Coues findings to existing museum records. It includes descriptions, 

relative abundance of specimens collected, and (rarely) location observed. The report is broken 

down by family and then species.

Results relevant to EMAP: This is one of the few baseline inventories to be found for the 

northern plains. Any information found in this inventory is helpful in establishing the presettlement species and "historic range" for the fishes of the Great Plains.

Geographic location: Montana, North Dakota, EPA Region 8, eco43, eco42, Missouri River 

basin, Red River, Milk River, Mouse River, Saint Mary's River, Plains 

Keywords: fish, historical data, plains 

98
Author: Jordan, D.S. 

Year: 1889 

Title: A Reconnaissance of the Streams and Lakes of the Yellowstone National Park, Wyoming, 

in the Interest of the United States Fish Commission 

Reference Type: Journal Article

Journal: U.S. Fish Commission Bulletin 

Volume: 9 

Pages: 41-63 

Value of reference: This is a primary source that contains much detail about the fish species 

and physical habitat of streams at the headwaters of the Missouri and Columbia basins. Since 

this area had been little explored and not yet settled at the time of this report, this is good 

baseline information for constructing pre-settlement, high-elevation stream conditions and fish 

communities. Although its focus is in Yellowstone National Park, it covers streams that originate 

outside the park, spanning 2 major basins on either side of the continental divide. 

The report is aimed at identifying waters where trout could be introduced. Its focus is therefore 

on current trout distribution; nevertheless, it contains much baseline information about the 

streams and fish community at the headwaters of the Missouri and Columbia River basins, a 

region influenced by geothermal activity. 

Results relevant to EMAP: The author lists 10 fish species that were found and the locations 

where specimens were collected in and surrounding the Park, as well as those species that had 

been introduced prior to this exploration. Following that are notes, by species, of the fish found, 

including locations and relative abundance, with notes on physical barriers to some of the 

streams. There is also discussion of a common parasitic worm on the suckers and trout of the 

warmer waters. 

The last section is a description of all the creeks and rivers in the Park, categorized by 3 major 

drainages: Yellowstone basin, Missouri River drainage, and Columbia River drainage. This 

section includes notes on fish species and abundance, stream physical habitat, vegetation, 

invertebrate abundance, stream width and depth, water temperature, waterfalls as physical 

barriers to fish movement, water permanence, and known fish introductions. Some of the 

information is second-hand. This section is summarized with a list of the streams in the Park 

suitable for trout and those where trout were not found (primarily due to barriers). The article 

should be consulted for specific details.

Geographic location: Wyoming, eco17, EPA region 8, Columbia River basin, Missouri River 

basin, mountains 

Keywords: fish, macroinvertebrates, phab, historical data, geographic distribution, primary 

source, baseline information 

99
Author: Jordan, D.S. 

Year: 1891 

Title: Report of explorations in Colorado and Utah during the summer of 1889, with an account 

of the fishes found in each of the river basins examined 

Reference Type: Journal Article

Journal: U.S. Fish Commission Bulletin 

Volume: 89 

Pages: 1-40 

Value of reference: Reference is a useful primary historical reference of the presence and 

relative abundance of fish in main stem and tributaries of 6 major river basins encompassing 

areas of Colorado and Utah on both sides of the continental divide in 1889. It reports early 

stream conditions and is valuable as a reference, since it represents a condition that is relatively 

close to pre-settlement and largely before major extinctions or changes in fish communities 

(although some fish species were already experiencing mortalities due to early impacts). 

Results relevant to EMAP: Reference systematically describes the historical condition in 

basins of Colorado and Utah. River and tributaries were examined in the following basins: 

Platte River, Arkansas River, Rio Grande, Colorado River, Salt Lake Basin, Sevier Lake Basin. 

The physical character (e.g., water clarity, substrate, flow, width, depth, general fish community) 

of each stream is briefly described, and a summary is given, by species, of fish distribution in 

the various tributaries and relative abundance in the late 1800s. Abundance is described as 

scarce, not common, common, very common, abundant, very abundant, etc. 

Geographic location: eco19, eco20, eco21, eco26, eco25, eco26, Colorado, Utah, xeric, 

mountains, plains, Platte River basin, Arkansas River basin, Rio Grande River basin, Colorado 

River basin, Salt Lake Basin, Sevier Lake Basin, EPA Region 8, EPA Region 9 

Keywords: fish, phab, fish distribution, fish abundance, historical data, primary source, baseline 

data 

100
Author: Katibah, E. F. 

Year: 1984 

Title: A brief history of riparian forests in the Central Valley of California 

Reference Type: Book Section

Editor: Warner, R. E.; Hendrix, K. M. 

Book Title: California Riparian Systems: Ecology, Conservation, and Productive Management. 

City: Berkeley, California 

Publisher: University of California Press 

Pages: 23-29 

Value of reference: A comprehensive treatment of pre-settlement hydrology, riparian 

vegetation, and patterns of degradation of Central Valley riparian forests over the last 150 

years.

Results relevant to EMAP: The chapter gives a description and map of surface hydrology of 

the Central Valley circa 1850 (page 24) recording flow and flood regimes. There are also 

descriptions of the pattern of natural riparian forest growth on natural levees, the riparian 

species found there, and the history of decline of riparian forests. 

Estimates of extent of riparian forest circa 1848 from literature: 

Sacramento Valley - 324,000 ha (800,000 ac) 

San Joaquin Valley - 57,000 ha (140,600 ac) 

Tulare sub-basin (Kings, Kaweah, Tule, Kern rivers) - 20,000 ha (50,000 ac) 

Tributary streams, sloughs, marshes - 40,500 ha (100,000 ac) 

Author's revised estimate of the total 1848 riparian forest coverage in the Central Valley - 

373,000 ha (921,000 ac) 

Estimates of present day riparian forest from a mapping project begun in 1979 - 41,300 ha 

(102,000 ac) remaining in the Central Valley. 19,800 ha (49,000 ac) were in a disturbed or 

degraded condition. 21,500 ha (53,000 ac) were identified then as mature riparian forest, no 

condition specified.

Geographic location: California, xeric, San Joaquin River, Sacramento River, eco6, eco7, EPA 

Region 9 

Keywords: phab, riparian vegetation, historical, EPA Region 9, pre-settlement, agriculture, 

water diversion, channelization, dams 

Abstract: Riparian forests once occupied substantially greater areas in the Central Valley of 

California than they do today. This paper explores the hydrologic influences which allowed the 

original riparian forests to establish themselves, the extent and the reasons for the decline of the 

pre-settlement forests, as well as an estimate of the extent of today's remaining forests. 

101
Author: Knapp, R.A. 

Year: 1996 

Title: Non-native trout in natural lakes of the Sierra Nevada: an analysis of their distribution and 

impacts on native aquatic biota. 

Reference Type: Report

City: Davis, CA 

Institution: University of California, Centers for Water and Wildland Resources 

Value of reference: Although the focus of this article is on fish introductions in lakes, the effects 

of these introductions on biota in associated streams is also addressed. Native trout, 

amphibians, and invertebrates occurring in watersheds of formerly fishless lakes have been 

impacted by trout introductions in this region when introduced fish move into stream habitats 

and compete with native biota that are not adapted to compete. 

This reference presents a map of the region above 1800 m that was formerly fishless.

Results relevant to EMAP: Historically, trout were absent above approximately 1800 m in the 

Sierra Nevada. Trout introductions to streams and lakes began in the mid-1800s and all 

watersheds currently contain as many as 5 nonnative trout species. Although stocking has 

been terminated in the National Parks of the region, data from Yosemite NP suggest that trout 

are likely to occur in at least 60% of all streams. The effects of introductions on naturally 

fishless ecosystems can have severe impacts on native trout in perimeter streams, amphibians, 

and macroinvertebrates; this paper provides some support for this, although limited quantitative 

examples. Native trout are impacted by introductions due to hybridization/introgression and 

resource competition. 

Historically, the mountain yellow-legged frog was widespread throughout the Sierra Nevada at 

elevations above 1500 m, and found in all major watersheds, whereas it is now present in fewer 

than 15% of the sites where it was found in 1915. The decline is attributed to predation by 

nonnative trout. 

Geographic location: California, eco7, EPA region 9, mountains, Sierra Nevada, nonnative 

species, predation, competition, fishless streams 

Keywords: fish, nonnative species, alpine habitats, biodiversity, cold water fisheries, lakes, 

streams, recreation, watersheds, wilderness, food chains, amphibians, aquatic invertebrates, 

introduced species, plankton, Sierra bioregion, conservation biology, endangered species, 

federal lands, geographic information systems, land management, park management, 

restoration. 

Abstract: The objective of this study was to describe the current distribution of introduced trout 

in the Sierra Nevada relative to the historic fish distribution, and to review the impacts of 

introduced trout on native aquatic biota. Historically, trout were absent above approximately 

1800 m in the Sierra Nevada. In the mid-1800's, however, widespread trout introductions were 

begun to move fish into formerly fishless lakes and streams to enhance recreational fishing. 

Trout stocking is now conducted by the California Department of Fish and Game, and the 

current program is intended to supplement and maintain existing populations of non-native trout. 

As a result of past and current trout stocking, the proportion of trout-containing lakes in the 

Sierra Nevada has increased from less than 1% of all lakes larger than 1 ha (N=4000+) to 

approximately 63% of all such lakes. National forests have a much higher proportion of lakes 

containing non-native trout than national parks, with trout in at least 85% of the lakes larger than 

102
1 ha. Only 7% are known to be fishless. In Sequoia, Kings Canyon, and Yosemite National 

Parks, the proportion of lakes with fish has increased from less than 1% to approximately 35-

50% of such lakes. The greater number of fishless lakes in the national parks than national 

forests is due in part to the termination of fish stocking in park lakes in the 1970's. Recent 

surveys in Sequoia, Kings Canyon, and Yosemite National Parks show that trout have 

disappeared from 29-44% of previously stocked lakes. Although data on the distribution of nonnative trout in Sierran streams is generally lacking, data from Yosemite National Park suggests 

that trout are likely to occur in at least 60% of all streams. Given the current ubiquity of trout in 

the formerly fishless portion of the Sierra Nevada, their impacts on native aquatic biota are likely 

widespread. 

Introduced trout are affecting the distribution of a wide range of native aquatic species in the 

Sierra Nevada, including native fishes, amphibians, zooplankton, and benthic 

macroinvertebrates. The introduction of non-native trout has caused widespread declines of 

native trout species such as golden trout as a result of hybridization, competition, and predation. 

The decline of at least one amphibian species, the mountain yellow-legged frog, has been 

attributed largely to predation by introduced trout. Predation by introduced trout has also caused 

dramatic changes in zooplankton and benthic invertebrate species composition in lakes, shifting 

the dominant species in these communities from large-bodied to small-bodied forms. 

The majority of lakes stocked by the California Department of Fish and Game lie within 

designated wilderness areas, areas managed for their natural values. Given that trout stocking 

serves to maintain an artificial fishery that has substantial impacts on native aquatic biota, and 

that continuation of this fishery is strongly supported by portions of the public, the ongoing 

stocking of trout poses inherent management conflicts. Resolution of these conflicts will require 

additional research on the ecological and sociological consequences of alternatives to the 

current trout stocking program that provide a better balance between the needs of aquatic 

ecosystems and those of recreational interests. 

103
Author: Knapp, R. A.; Matthews, K.R. 

Year: 2000 

Title: Non-native fish introductions and the decline of the mountain yellow-legged frog from 

within protected areas 

Reference Type: Journal Article

Journal: Conservation Biology 

Volume: 14 

Issue: 2 

Pages: 428-438 

Value of reference: Although the focus of this paper is on the impact of introduced trout on 

yellow-legged frogs, the greater value of this study may be that it represents a very large spacefor-time investigation of the impact that introduced fish species can have upon native biota. This 

study investigates patterns of amphibian distribution across multiple spatial scales to better 

investigate alternate explanations for observed amphibian declines. This reference provides 

strong support for the interpretation that fish introductions have influenced aquatic vertebrate 

assemblages, and derived indices.

Results relevant to EMAP: After factoring out the influence of habitat conditions, there was a 

negative correlation between trout and yellow-legged frogs at the landscape scale; at the 

watershed-scale, the presence of introduced trout accounted for approximately 60% of the 

variance in the distribution of yellow-legged frogs; and at the scale of the individual water body 

(n = 1728), the effect of trout on frog presence or absence was very significant (p < 0.0001). 

Although the species has disappeared from sites lacking trout, there is some evidence to 

indicate that these areas may represent marginal habitat containing non-equilibrium 

metapopulations. The authors surmise that the decline of the yellow-legged frog in the Sierra 

Nevada began shortly after fish introductions in the 1850s.

Geographic location: California; Sierra Nevada; mountains; eco5; EPA Region 9 

Keywords: amphibians; introduced fish; nonnative species; predation; yellow-legged frog; Rana 

muscosa

Abstract: One of the most puzzling aspects of the worldwide decline of amphibians is their 

disappearance from within protected areas. Because these areas are ostensibly undisturbed, 

habitat alterations are generally perceived as unlikely causes. The introduction of non-native 

fishes into protected areas, however, is a common practice throughout the world and may exert 

an influence on amphibian distributions. We quantified the role of introduced fishes (several 

species of trout) in the decline of the mountain yellow-legged frog (Rana muscosa) in 

California's Sierra Nevada through surveys of >1700 sites in two adjacent and historically 

fishless protected areas that differed primarily in the distribution of introduced fish. Negative 

effects of fishes on the distribution of frogs were evident at three spatial scales. At the 

landscape scale, comparisons between the two protected areas indicated that fish distribution 

was strongly negatively correlated with the distribution of frogs. At the watershed scale, the 

percentage of total water-body surface area occupied by fishes was a highly significant predictor 

of the percentage of total water-body surface area occupied by frogs. At the scale of individual 

water-bodies, frogs were three times more likely to be found and six times more abundant in 

fishless than in fish-containing water-bodies, after habitat effects were accounted for. The strong 

effect of introduced fishes on mountain yellow-legged frogs appears to result from the unique 

life history of this amphibian which frequently restricts larvae to deeper water bodies, the same 

habitats into which fishes have most frequently been introduced. Because fish populations in at 

104
least some Sierra Nevada lakes can be removed with minimal effort, our results suggest that the 

decline of the mountain yellow-legged frog might be relatively easy to reverse. 

105
Author: Lavier, D.C. 

Year: 1976 

Title: Distribution of salmon and steelhead in the Columbia River Basin, 1850-1976: a summary 

of data from maps prepared for the Columbia Fisheries Project, Pacific Northwest Regional 

Commission 

Reference Type: Report

City: Olympia, WA 

Institution: Washington Department of Game 

Value of reference: This is a series of tabular synopses of river miles available to and in use by 

steelhead, spring, summer, and fall chinook, coho, chum, and sockeye salmon in 8 different 

river sections of the Columbia, Snake, Yakima, and Willamette Rivers in 1850 vs. 1975. The 

tributaries included in each river section are listed with each table. 

Since this is a summary from maps, the original mapped areas of use by each species are 

presumably available from the Columbia River Fisheries Project, but the maps are not part of 

this particular summary. There is also no text, explanation of methods, or interpretation, 

although the tabular results are straightforward and can be very useful for quantitative 

comparisons of pre-settlement and 1970s conditions. For more detail and clarification, this 

tabular summary may need to be supplemented with background information or reporting from 

the Washington Department of Game or the Columbia River Fisheries Project.. 

Results relevant to EMAP: A wide range of information can be extracted from these tables 

including: river length (miles), miles accessible to fish, miles blocked to fish, and miles in use by 

several species of salmonids in 1850 and 1975. River miles accessible to fish can be compared 

to accessibility prior to major impacts (1850). For example, sockeye salmon used 320 miles of 

the Yakima drainage in 1850, but did not use any of the river miles in 1975. In comparison to 

1850, an additional 136 miles of the basin were blocked to fish in 1975. Between 1850 and 

1975, steelhead use decreased by 143 miles (22%), spring chinook use by 232 miles (40%), 

and coho use by 61 miles (19%) in the Yakima River basin. All river miles can easily be 

converted to proportions or percentages of a basin. The summary does not address causes of 

decline, but increases in blockage to fish since 1850 were likely associated with dams. 

Geographic location: Washington, Oregon, Idaho, EPA region 10, eco3, eco4, eco9, eco10, 

eco11, eco12, eco15, eco16 eco80, Columbia River basin, mountains, xeric 

Keywords: fish, blockage to fish, fish use, map summaries 

106
Author: Lee, D.; Sedell, J.; Rieman, B.; Thurow, R.; Williams, J.; others 

Year: 1997 

Title: A broad-scale assessment of aquatic species and habitats [Chapter 4] 

Reference Type: Report

City: Portland, OR 

Institution: USDA Forest Service, Pacific Northwest Research Station 

Report Number: General Technical Report PNW-GTR-405 

Value of reference: This long and detailed chapter represents a very large synthesis of current 

data, knowledge (including professional judgment), historical information, and predictive 

modeling. Current status is given in relation to historical range, reconstructed from 1) actual 

samples and 2) predicted occurrences based on landscape features (i.e., potential range), 

using classification tree analysis. The report synthesizes an immense literature and, along with 

professional judgment and predictive modeling, reconstructs and maps the historical ranges of 

46 fish species in the Columbia Basin and compares them with current ranges; habitat 

requirements and key factors influencing status are also discussed for each. A separate section 

presents historical changes in pool habitats.

Results relevant to EMAP: Approximately 50% of the native fish taxa in the assessment area 

has exhibited significant declines from historical levels. Presently, 45 of the 88 native fish taxa 

(51%) in the assessment area are identified as threatened, endangered, sensitive, or of special 

concern by state or Federal agencies or by the American Fisheries Society. Overall changes in 

composition, distribution, and status of fishes are dramatic and extensive; a wide range of 

human impacts on these populations are given in discussions of each species. 

Example status conclusion: "Bull trout are known or predicted to occur in 45% of watersheds in 

the historical range and to be absent in 55%. We found bull trout less widely distributed within 

the potential historical range than other non-anadromous salmonids...Watersheds believed or 

predicted to be strong spawning and initial rearing areas represented only 6% of the historical 

range..." 

In managed streams, roads and accompanying human activities including timber harvest, 

highway construction, grazing, agricultural practices, and loss of riparian vegetation have 

combined to create major decreases in pool habitats, which appear to have been the greatest in 

the low-gradient, biologically productive areas of river basins most disturbed by humans. 

Geographic location: eco 10, eco11, eco15, eco16, eco80, eco12, mountains, xeric, Oregon, 

Washington, Idaho, Interior Columbia Basin, EPA Region 10 

Keywords: fish, human impacts, historical range 

Notes: A 9-page Executive Summary of this chapter is in Volume I, Chapter 1 of this series. 

The portion of this reference discussing pool habitats is largely from McIntosh 1995. In addition, 

see McIntosh 1994 in this bibliography. 

McIntosh, B.A. 1995. Historical changes in stream habitats in the Columbia River Basin. 

Corvallis, OR: Oregon State University. Ph.D. dissertation. 

107
Author: Leidy, R.A.; Becker, G.; Harvey, B.N. 

Year: 2005 

Title: Historical status of coho salmon in streams of the urbanized San Francisco estuary, 

California 

Reference Type: Journal Article

Journal: California Fish and Game 

Volume: 94 

Issue: 4 

Pages: 1-36 

Value of reference: The article represents an in-depth investigation and synthesis of historical 

literature, museum specimens, agency files, and long-term data records to reconstruct the 

relative probability of the past presence of coho salmon in 65 watersheds around San Francisco 

estuary. Probability of presence was based on a combination of documented historical 

presence of the species and the likelihood of occurrence of essential habitat requirements 

historically. 

The information in this document is useful for reconstructing the historical range of the species 

and its presence in specific estuary watersheds of the region. 

Results relevant to EMAP: Coho salmon were last documented from an estuary stream in the 

early to mid-1980s. Coho salmon populations have experienced declines throughout California 

attributable primarily to human activities, including water diversions, creation of migration 

barriers, streambed alteration for flood control, impaired water quality, removal of riparian 

vegetation, disruption of natural hydrological processes, and reduced instream habitat 

complexity. 

At least 4 of 65 estuary watersheds (6%) historically supported coho salmon. A minimum of an 

additional 11 watersheds (17%) may also have supported coho salmon. These 15 watersheds 

and supporting evidence for the occurrence of coho salmon are summarized in Table 1. Habitat 

characteristics of the 15 watersheds are shown in Table 2. 

Although broadly distributed, the environmental characteristics of streams known historically to 

contain coho salmon shared several characteristics: cool summer water temperatures, suitable 

spawning and juvenile rearing habitat, distinct surface water connections to the estuarine and 

marine environments, as well as stream flows during the months of February through May 

suitable for smolt out-migration. 

Estuary coho salmon typically were members of three-to-six species assemblages of native 

fishes, including Pacific lamprey, steelhead, California roach, juvenile Sacramento sucker, 

threespine stickleback, riffle sculpin, prickly sculpin, and/or tidewater goby. 

Geographic location: California, eco6, EPA Region 9, local watersheds of the San Francisco 

Bay Estuary, xeric 

Keywords: fish, urban, water diversion, dams 

108
Author: Lichatowich, J. A. 

Year: 1997 

Title: Evaluating salmon management institutions: The importance of performance measures, 

temporal scales, and production cycles 

Reference Type: Book Section

Editor: D.J. Stouder; P. A. Bisson; Naiman, R. J. 

Book Title: Pacific Salmon and their Ecosystems. 

City: New York, New York 

Publisher: Chapman and Hall 

Pages: 69-87 

Value of reference: The article makes an argument for historical reconstruction to set 

meaningful goals for restoration of salmon runs and to evaluate the success of management 

strategies to date.

Results relevant to EMAP: Lichatowich uses salmon productivity graphs to show what 

happens when managers work on short temporal scales without considering the historic 

baseline. A short time frame, particularly during favorable climatic conditions, may make 

managers overly optimistic in their predictions of increased productivity when the real result is 

the preservation of the status quo or a continual adjustment of the baseline downward to 

extinction. An ecosystem's history determines the system's present state and helps establish 

the range of possibilities for future development trajectories. Developing baselines from 

historical reconstruction of salmon abundance and habitats is a critical step in salmon 

restoration. 

By considering only the currently available habitat, Oregon and Washington have compressed 

the habitat baseline. There is no historical component. Past habitat loss is not taken into 

account in either definition. The implication is that we are satisfied with the status quo, the 

current condition of salmon habitat. This has led to stocks being listed as healthy that have 

exhibited dramatic declines. For example, the Tillamook Bay chum salmon is listed as a healthy 

stock even though the annual run declined from an average of 92,000 fish in the late 1940's and 

early 50's to an average of 17,000 fish in recent years. 

If each generation is allowed to reset the temporal scale of the baselines used to evaluate 

management performance, the result will be no evaluation or accountability, a misinformed 

public, and a spiral of decline for which the outcome will be the inevitable extinction of Pacific 

salmon in much of their range.

Geographic location: mountains, xeric, Columbia River, coastal rivers, eco10, eco1, eco4, 

eco3, Oregon, Washington, EPA Region 10 

Keywords: historic fish abundance, historical reconstruction, baseline, chinook salmon, coho 

salmon, temporal scale, institutional learning, management expectations 

Abstract: Management of renewable resources from an ecosystem perspective will require 

institutional changes. Management institutions will have to enhance their ability to learn, use 

what they learn, and promote more effective evaluation of performance. Development of 

appropriate management baselines is an important prerequisite to institutional learning and 

evaluation. Three important components of management baselines are biological performance 

measures, temporal scale of institutional evaluation, and natural environmental fluctuations in 

the ecosystems that produce Pacific salmon. Performance measures should broaden the 

109
traditional focus on harvest and economics to include measures of the condition of important 

ecological processes. Temporal scale will have to include the entire history of management 

institutions. Compressing the temporal scale and shifting baselines forward will create inevitable 

extinction of the resource. Natural cycles in production require flexibility in management 

programs and the development of realistic expectations. 

110
Author: Liknes, G. A.; Graham, P. J. 

Year: 1988 

Title: Westslope cutthroat trout in Montana: Life history, status and management 

Reference Type: Book Section

Editor: Gresswell, R. E. 

Book Title: Status and management of interior stocks of cutthroat trout. 

City: Bethesda, Maryland 

Publisher: American Fisheries Society 

Pages: 53-60 

Value of reference: The authors compare the historic and present range of the westslope 

cutthroat trout, identify the locations of pure populations, and list the important factors 

responsible for the decline of the subspecies.

Results relevant to EMAP: The historic range of the westslope cutthroat trout in Montana both 

east and west of the Continental Divide is estimated at 25,547 stream kilometers. The present 

distribution is at 6993 stream km or 27.4% of the historic range (includes hybridized trout). 

Genetically pure populations are present in 72 streams (nine river drainages) representing 2.5% 

of their historic range. 

Westslope cutthroat trout are sensitive to riparian disturbance, and they are often replaced by 

the alien brook trout following disturbances such as logging, grazing, or mining. 

As with other cutthroat trout populations (Lahontan and Bonneville, see references Duff 

(1988)and Gerstung (1988)), the authors believe that the major factor in the trout's decline is 

hybridization with rainbow trout, golden trout, and Yellowstone cutthroat trout.

Geographic location: Region 8, Montana, mountains, Flathead River, eco17, eco41 

Keywords: fish, westslope cutthroat trout, historic distribution, habitat degradation, nonnative 

species 

Abstract: The historic range of westslope cutthroat trout Salmo clarki lewisi included western 

Montana, central and northern Idaho, a small portion of Wyoming, and portions of three 

Canadian provinces. The distribution and abundance of westslope cutthroat trout have 

drastically declined from its historic range during the last 100 years. Although previous studies 

in Montana identified strongholds of populations, the status of westslope cutthroat trout over its 

complete range is uncertain. Three life history forms are found within this range: 1) lacustrineadfluvial stocks, 2) fluvial-adfluvial populations, and 3) fluvial fish. Migratory adults travel long 

distances during periods of high stream flow and spawn when water temperatures are near 10 

degrees C. Most migratory adults quickly leave the spawning grounds following the spawning 

act. Sexual maturity is attained at age 3 or older. In some drainages, repeat spawning occurs 

predominantly in alternate years. Westslope cutthroat trout are opportunistic in their food habits, 

but are not highly piscivorous; they tend to specialize as invertebrate feeders. The decline of 

westslope cutthroat trout has been attributed to overexploitation, genetic introgression, 

competition from or replacement by nonnative species, and habitat degradation. Westslope 

cutthroat trout occupy only 27.4% of their original range in Montana, and genetically pure 

populations are present in only about 2.5% of their historic range. As a whole, westslope 

cutthroat trout populations in Idaho and British Columbia, Canada, have fared better than in 

Montana. Management programs designed to protect the westslope cutthroat trout have helped 

to maintain or increase existing populations, and even to create new populations. 

111
Author: Lytle, D. A. 

Year: 2003 

Title: Reconstructing long term flood regimes with rainfall data: Effects of flood timing on 

caddisfly populations 

Reference Type: Journal Article

Journal: The Southwestern Naturalist 

Volume: 48 

Issue: 1 

Pages: 36-42 

Value of reference: This article is one of several that demonstrate how natural flow regimes 

(e.g., flash floods, spring runoff) historically affected desert stream biota. The author integrates 

short term flood data with long term rainfall data to infer patterns of the influence of flooding on 

caddisfly populations. This approach is particularly useful for a biological indicator for which 

there is little or no historical data.

Results relevant to EMAP: There is a large interannual variation in caddisfly population sizes 

due to the stochastic nature of flash floods. 

"Mortality of aquatic insects from flash floods exceeds 90% for most taxa, and some species are 

locally extirpated by floods, so recolonization of flooded streams from adjacent, non-flooded 

drainages might also be important for maintaining species diversity." 

"The timing of individual floods relative to the long term average strongly affected caddisfly 

populations; early and timely floods had little affect on population size in the next year, but late 

floods significantly reduced population size in the next year."

Geographic location: Region 9, eco79, Arizona, Chiricahua Mountains, xeric 

Keywords: desert streams, hydrographic variability, flash floods, macroinvertebrates, phab, 

precipitation, flood frequency, caddisfly, recruitment, 

Abstract: Flash floods are a defining feature of desert streams, but flow records are not always 

available to characterize long term flood dynamics. In this study, rainfall data spanning 100 

years were used as a proxy to quantify long term flood regimes for southeastern Arizona (USA) 

streams. The frequency and seasonal timing of severe floods (>50% substrate movement) were 

highly variable at short temporal scales (days to several years), but clear patterns emerged in 

the long term (several years to a century). To explore the ecological effects of flood timing, 

populations of the caddisfly Phylloicus aeneus were monitored in 2 streams over 3 years. The 

timing of individual floods relative to the long term average strongly affected P. aeneus

populations: early and timely floods had little effect on population size in the next year, but late 

floods significantly reduced population size in the next year. Thus, flood timing might play a role 

in regulating populations of desert stream organisms. 

112
Author: MacCoy, D.; Blew, D. 

Year: 2005 

Title: Impacts of land-use changes and hydrologic modification on the lower Boise River, Idaho, 

USA 

Reference Type: Book Section

Editor: L.R. Brown; R.H. Gray; R.M. Hughes; M. Meador 

Book Title: Effects of Urbanization on Stream Ecosystems. 

City: Bethesda, MD 

Publisher: American Fisheries Society 

Volume: 47 

Pages: 133-156 

Value of reference: This research uses cadastral survey notes from the late 1800s to recreate 

the historical lower Boise River and assess changes in the structure and function. Historical 

hydrogeomorphology and riparian conditions were reconstructed: average bankfull width, 

channel forms, parafluvial surfaces, sloughs, and riparian vegetation. The changes in these 

features since the 1800s, as a result of human alteration, are described. 

Results relevant to EMAP: Today, the average bankfull width is about one-quarter to one-half 

the historical width, and parafluvial surfaces are stabilized by trees and shrubs. Historically, an 

extensive network of sloughs was present, with numerous surface connections between sloughs 

and the main channel. Between 1868 and 1939, many sloughs were filled or converted to 

agricultural drains or canals. Today, many river channels are incised. 

River bottom substrate was historically dominated by cobble and gravel, and the banks were 

subject to frequent inundation and scouring; cottonwood stands were extensive, in some places 

reaching 900 m in width. In contrast, current flows do not produce adequate shear stress to 

mobilize bed material, resulting in sandy bottoms and embeddedness over 50% in many places; 

alien species dominate in most sections of river. Table 2 compares physical features (average 

bank-full width, channel forms, parafluvial surfaces, sloughs, and vegetation) of the historic 

(1867-1868) versus current (1994-2002) in four reaches of the lower Boise River, 

Modifications due to urbanization and agriculture have stabilized the river and reduced 

parafluvial surfaces and bankfull widths. Three large dams in the upper basin have altered flow 

regime and sediment supply to the river. Increased abundance of tolerant and alien species 

has lowered the quality of natural aquatic assemblages. Alien hardwoods have replaced native 

cottonwood stands, and alien herbaceous species are present along most of the lower river. 

Geographic location: Idaho, Boise River basin, eco12, EPA region 10, xeric 

Keywords: phab, hydrogeomorphology, riparian vegetation, cadastral surveys, urban, 

agriculture, dams 

Abstract: In less than two centuries, the lower Boise River below Lucky Peak Dam in 

southwestern Idaho has been transformed from a meandering, braided, gravel-bed river that 

supported large runs of salmon to a channelized, regulated, urban river that also provides 

irrigation water to more than 1300 km2

 of land. The construction of three large dams in the 

upper basin dramatically altered the flow regime and sediment supply to the lower river. Flows 

are no longer sufficient to mobilize bed sediments and have allowed cottonwood trees and alien 

hardwoods to stabilize parafluvial surfaces, thereby narrowing sections of the river channel. 

Cadastral survey notes of 1867 and 1868 were used to recreate features associated with the 

113
lower Boise River Valley and identify characteristics of the river channel prior to dam 

construction and urbanization. Gravel and sand bars, historically present throughout the river, 

which are necessary to maintain biodiversity and productivity, are currently scarce. Sloughs 

were a dominant feature on the floodplain of the late 1800s, but today have been converted to 

irrigation canals, drains, or residential and commercial land uses. Flow alterations, water quality 

degradation, and habitat loss due to urbanization near the lower Boise River have resulted in 

macroinvertebrate and fish assemblages dominated by tolerant and alien species. 

114
Author: Martin, B. A.; Saiki, M.K. 

Year: 1998 

Title: Effects of ambient water quality on the endangered Lost River Sucker in Upper Klamath 

Lake, Oregon 

Reference Type: Journal Article

Journal: Transactions of the American Fisheries Society 

Volume: 128 

Pages: 953-961 

Value of reference: This paper reviews historic literature documenting the dramatic changes in 

fish abundance and community characteristics in the upper Klamath River Basin, resulting from 

the cumulative effects of overharvest, mining, grazing, agriculture, impoundments, and water 

diversions. It also identifies the primary causal factors associated with recent fish mortality in the 

basin. 

Results relevant to EMAP: The Lost River sucker (Deltistes luxatus) was the most important 

food fish in the Klamath Lake region for the Klamath and Modoc Indians prior to the turn of the 

twentieth century (Gilbert 1898), and heavily used by white settlers for food and livestock feed 

(Cope 1879). It has subsequently been pushed to the edge of extinction by human impacts 

associated with damming of rivers, draining of marshes, water diversions, competition with or 

predation by exotic species, loss and isolation of habitat, and impacts on water quality by 

logging, agriculture, and grazing. In this study, hypoxia, associated with a dissolved oxygen 

deficit, was identified as the primary factor currently influencing juvenile Lost River sucker 

mortality. 

Geographic location: Upper Klamath River Basin, Oregon, California, eco78, Klamath 

Mountains, Region 10, mountains 

Keywords: fish; water quality; Lost River sucker; Deltistes luxatus; Shortnose sucker; 

Chasmistes brevirostris; Klamath largescale sucker; Catostomus snyderi; mortality; dissolved 

oxygen; population decline; logging; grazing; agriculture; dams, water diversion, nonnative 

species 

Abstract: Populations of the Lost River sucker Deltistes luxatus have declined so precipitously 

in the Upper Klamath Basin of Oregon and California that this fish was recently listed for federal 

protection as an endangered species. Although Upper Klamath Lake is a major refuge for this 

species, fish in the lake occasionally experience mass mortalities during summer and early fall. 

This field study was implemented to determine if fish mortalities resulted from degraded water 

quality conditions associated with seasonal blooms of phytoplankton, especially 

Aphanizomenon flos-aqua. Our results indicated that fish mortality did not always increase as 

water temperature, pH, and un-ionized ammonia concentration increased in Upper Klamath 

Lake. Little or no mortality occurred when these water quality variables attained their maximum 

values. On the other hand, an inverse relation existed between fish mortality and dissolved 

oxygen concentration. High mortality (>90%) occurred whenever dissolved oxygen 

concentrations decreased to 1.05 mg/L, whereas mortality was low (<10%) when dissolved 

oxygen concentrations equaled or exceeded 1.58 mg/L. Stepwise logistic regression also 

indicated that the minimum concentration of dissolved oxygen measured was the single most 

important determinant of fish mortality. 

Notes: Gilbert, C. H. 1898. The fishes of the Klamath basin. U.S. Fish Commission Bulletin 

17:1-13. 

115
Cope, E. D. 1879. The fishes of Klamath Lake, Oregon. American Naturalist 13:784-785. 

116
Author: McAllister, K.R.; Leonard, W.P.; Hays, D.W.; Friesz, R.C. 

Year: 1999 

Title: Washington state status report for the northern leopard frog 

Reference Type: Report

City: Olympia, WA 

Institution: Washington Department of Fish and Wildlife 

Pages: 36 

Value of reference: Report contains known historical records and distribution of the species, 

dating back to 1881. Reduction in distribution is assessed and reason for decline are 

discussed.

Results relevant to EMAP: Museum specimens indicate that northern leopard frogs were 

found historically in 8 counties in eastern Washington (see Table 1). They were considered 

abundant in the Walla Walla basin in 1960. The Snake River and its associated flood plain 

wetlands may have provided an aquatic corridor to historically abundant leopard frog 

populations in Idaho and Montana. In addition to the Walla Walla River populations, the link may 

have been responsible for colonization along the Columbia River downstream to Fort Dalles, 

Oregon. The species seems to have occurred in few locations, but in large numbers.

Geographic location: Washington, EPA Region 10, mountains, xeric, Columbia River basin, 

eco10, eco77, eco15 

URL: http://wdfw.wa.gov/wlm/diversty/soc/status/leopfrog/nlepfrog.pdf 

117
Author: McDowell, P. F. 

Year of Conference: 2000 

Title: Human impacts and river channel adjustment, northeastern Oregon: Implications for 

restoration 

Reference Type: Conference Proceedings

Editor: P.J. Wigington; R.L. Beschta 

Conference Name: Riparian Ecology and Management in Multi-Land Use Watersheds 

Publisher: American Water Resources Association, Middleburg, VA 

Pages: 257-261 

Value of reference: Though the title implies that the article is about the future rather than the 

past, the paper contains an example of reconstructing past river channel configuration. 

McDowell reconstructs channel changes for a 30 km section of the Middle Fork John Day River 

in eastern Oregon using 1881 land survey records, and aerial photos from 1939 and 1989. 

Results relevant to EMAP: The paper outlines human impacts contributing to declining salmon 

numbers in the John Day basin over the last 125 years, but it also provides a quantitative 

measure of sinuosity taken from aerial photographs in 1939 (prior to major changes in the 

segment) and 1989. Sinuosity decreased on all seven study channel segments. Not 

unexpectedly, there has been more direct human modification of the channel and riparian zone 

in wide valley (unconstrained) segments than in narrow valley (constrained) segments. 

1881 survey notes show dense willow thickets, or riparian communities of willow, cottonwood, 

and alder, in many places along the Middle Fork that today have little or no woody riparian 

vegetation (and no large woody debris). 1881 notes show that anabranching reaches with two 

or three active channels were present in 3 study segments. 

The only major human caused change between 1881 and 1939 was a km of channel cut off by 

the construction of the railroad. Between 1939 and 1989 sinuosity was reduced in every 

segment with wide valley segments experiencing the largest reductions in sinuosity. Other 

segments have dredged artificial channels and bank stabilizing structures that harden the banks 

and eliminate the possibility of future lateral migration of the channel. The segments with the 

most structures today had unconfined sinuous channels in 1881 and 1939.

Geographic location: John Day River, eco11, Blue Mountains, mountains, Northern Rockies, 

EPA Region 10, Oregon 

Keywords: phab, fluvial geomorphology, human impacts, channel adjustment, riparian 

restoration, bank stabilization, sinuosity, historical, mining, channelization 

Abstract: Historical data were used to reconstruct channel change in the Middle Fork John Day 

River, a tributary of the Columbia River. Human impacts on the channel from the 1800s to 

present include: beaver trapping, early alluvial gold mining, dredge mining, livestock grazing, 

haying and irrigation, railroad building, road building, and placing of bank stabilization 

structures. 1881 land survey records, 1939 aerial photos, 1989 aerial photos, and a detailed 

1996 channel habitat inventory were used to identify the extent and location of channel change, 

and to compare direct human modification of the channel with channel self-adjustment by fluvial 

processes. Channel change and human impacts have been expressed differently in wide valley 

segments, which are inherently sinuous with abundant pools, compared to narrow valley 

segments, which are inherently less sinuous. The major effects of human activities include loss 

of sinuosity, loss of riparian woody vegetation, probably loss of large woody debris and pools, 

118
and reduced potential for adjustment because of bank stabilization structures. Wide valley 

segments have more potential for fish habitat, but also have been the most affected by human 

impacts. Implications for restoration are discussed. 

Notes: Also see Welcher, K.E. 1993. Channel restoration plan and geomorphology of the 

Middle Fork John Day Preserve. Report prepared for The Nature Conservancy, Portland, OR 

(unpublished). 88 p. + appendices. 

119
Author: McFarling, L. 

Year: 1955 

Title: Exploring the Northern Plains 

Reference Type: Book

City: Caldwell, Idaho 

Publisher: The Caxton Printers, Ltd. 

Number of Pages: 441 

Value of reference: The early explorations into the northern Great Plains contain descriptive 

information of the landscape, geology, vegetation, and general river conditions within the region. 

There is also mention of the wildlife present. These accounts help establish what was present 

prior to and during settlement of the region.

Results relevant to EMAP: Descriptions of the Platte River, James River, White River, 

Missouri River, Niobrara River, and Ponca Creek (among others within the Missouri River basin) 

include physical characteristics, geology, flora, and large fauna. These early expeditions 

contain valuable baseline information of what landscape and riverine conditions were like prior 

to settlement of the region. The information is presented as descriptive text, maps, and explorer 

narratives including explanatory footnotes. 

The chapters require some sifting through to extract small pieces of anecdotal information or to 

reconstruct stream related attributes, however; the information present is quite valuable and 

may be the only source of pre-settlement conditions of the plains and plains streams. This is a 

good broad reference and inventory that includes specific information about pre-settlement 

conditions in the plains.

Geographic location: Nebraska, Wyoming, South Dakota, Montana, North Dakota, Niobrara 

River, Ponca Creek, Missouri River, James River, White River, eco43, eco42, eco17, plains, 

EPA region 7, EPA region 8 

Keywords: explorations, phab, resource inventories, pre-settlement condition, historic 

condition, geography, geology, expeditions 

120
Author: McIntosh, Bruce A.; Sedell, James R.; Smith, Jeanette E.; Wissmar, Robert C.; Clarke, 

Sharon E.; Reeves, Gordon H.; Brown, Lisa A. 

Year: 1994 

Title: Management History of Eastside Ecosystems: Changes in Fish Habitat Over 50 Years, 

1935 to 1992. Volume III: Assessment 

Reference Type: Report

City: Portland, OR 

Institution: USDA Forest Service, Pacific Northwest Research Station 

Pages: 55 

Report Number: General Technical Report PNW-GTR-321 

Value of reference: The most useful data from this publication (and reliable, in terms of its 

relevance to a true pre-settlement condition) are the historical run estimates given for coho, 

chinook, and steelhead in the Upper Grand Ronde, Yakima River, Metthow River, and 

Wenatchee River basins. For comparison, the present day (late 1980s) runs are given, but not 

consistently. In addition to historical runs, this publication reports changes in pool habitats 

between the 1930s and 1990s (see Notes section below for suggested citations). In some 

areas, the 1930s condition was quite degraded already. 

Results relevant to EMAP: Grand Ronde Basin historically had large runs of spring chinook 

and summer steelhead (see Northwest Power Planning Council 1990), which have been 

reduced to a small fraction of their predevelopment numbers (spring chinook are listed as 

threatened) due to dams, habitat degradation (from numerous human impacts), and over 

exploitation of mixed-stock fisheries. 

Yakima River Basin historic salmon runs were estimated at 790,000 adults before the 1870s 

(break down by species and run is included--also see Northwest Power Planning Council 1989). 

By 1900, >90% of runs were thought to be depleted as a result of dams, irrigation canals, log 

drives, local overfishing; present runs are estimated at only 7018. 

Wenatchee Basin historical runs (1850s): chinook=41,300; coho=3900; sockeye=228,100; 

steelhead=7300. Numbers for 1967-87 were higher but distributed much differently: coho=0, 

Chinook=204,800; sockeye=93,700, steelhead=8200 (from Mullan et al. 1992). 

Methow Basin historical runs (1850s): chinook=24,200, coho=36,000, steelhead=3600. 1967-

1987: chinook=86,100, coho=0; steelhead=5000 (see Mullan et al. 1992). Coho were near 

extinction by 1941, while the other species increased by the 1980s; decline of coho was due to 

impassable dams, unscreened irrigation diversions, overharvest, and the indiscriminate use of 

coho eggs for early hatchery programs.

Geographic location: mountains, xeric, Washington, Oregon, eco11, eco10, eco77, Grande 

Ronde River basin, Yakima River basin, Wenatchee River basin, Methow River basin, EPA 

Region 10 

Keywords: fish, anadromous, fish habitat, historical changes, land-use practices, pools, streamflow, fish, mountains, arid, general human impacts 

Abstract: From 1934 to 1942, the Bureau of Fisheries surveyed over 8000 km of streams in the 

Columbia River basin to determine the condition of fish habitat. To evaluate changes in stream 

habitat over time, a portion of the historically surveyed streams in the Grande Ronde, Methow, 

Wenatchee, and Yakima River basins were 

121
resurveyed from 1990 to 1992. Streams were chosen where the primary impacts were natural 

disturbance (unmanaged), such as wilderness and roadless areas, and where human impacts 

(managed) were the major disturbances. In addition, historical changes in land-use, streamflow, and climate regimes were also analyzed. Many of these streams had been degraded from 

land-use activities (riparian timber harvest, splash dams, stream channelization, livestock 

grazing, and mining) prior to the historical survey. While the general trend throughout the 

Columbia River basin has been towards a loss in fish habitat on managed lands and stable or 

improving conditions on unmanaged lands, the data for these four river basins suggest there is 

a regional pattern to this change. Based on this information, along with data on the status of 

anadromous fish runs in these basins, fish habitat has shown some improvement from past 

abuses in eastern Washington, while continuing to decline in eastern Oregon. This appears to 

be the result of different land-use histories in the two regions. The river basins of eastern 

Washington apparently had a period of recovery after World War I from past land-use practices, 

as the impacts of development decreased. In contrast, river basins of eastern Oregon have 

been affected continuously by land-use practices over the entire development period (1850-

present). From this information, it is clear that land-use practices have degraded fish habitat 

throughout eastern Washington and Oregon. Strategies to protect, restore, and maintain 

anadromous and resident fish populations and their habitat, must be based on a watershed 

approach that protects the remaining habitat and restores historical habitats. 

Notes: Mullan, J.W. et al. 1992. Production and habitat of salmonids in mid-Columbia River 

tributary streams. Leavenworth, WA: U.S. Department of Interior, Fish and Wildlife Service. 

Monograph I. 489 pp. 

Northwest Power Planning Council. 1989. Yakima River sub-basin salmon and steelhead plan: 

draft report. Portland, OR, 212 p. 

Northwest Power Planning Council. 1990. Grande Ronde River sub-basin salmon and 

steelhead production plan: draft report. Portland, OR. 129 p. 

Additional information on changes in fish habitat (namely pools) since the 1930s in basins of the 

Columbia River basin can be found in: 

McIntosh, B.A., J.R. Sedell, R.F. Thurow, S.E. Clarke, and G.L. Chandler. 2000. Historical 

changes in pool habitats in the Columbia River Basin. Ecological Applications 10(5):1478-1496. 

McIntosh, B.A., J.R. Sedell, J.E. Smith, R.C. Wissmar, S.E. Clarke, G.H. Reeves, and L.A. 

Brown. 1994. Historical changes in fish habitat for select river basins of Eastern Oregon and 

Washington. Northwest Science 68 (Special Issue):36-53. 

122
Author: Meengs, C.C.; Lackey, R.T. 

Year: 2005 

Title: Estimating the size of historical Oregon salmon runs 

Reference Type: Journal Article 

Journal: Reviews in Fisheries Science 

Volume: 13 

Pages: 51-66 

Value of reference: This research estimates pre-settlement salmon (coho, chinook) runs for the 

west coast of Oregon using 2 methods: 1) converting estimated aboriginal population levels into 

numbers of salmon; and 2) extrapolating cannery pack into numbers of salmon. It is unique in 

that its focus is on the streams and rivers that drain to the Pacific Ocean on Oregon's West 

Coast, excluding the Columbia River basin. 

The authors calculate estimates of coho and chinook salmon populations for the Oregon coastal 

rivers in 1850, before major European influence or impacts had altered salmon habitat, and the 

data are thus notable as pre-settlement conditions. The authors compare these estimates with 

today's estimates to obtain estimates of population losses. Based on spawning habitat loss, 

potential populations are also estimated.

Past publications and methods of estimating salmon populations in a similar manner are 

reviewed and provide good additional data and references. Some of the past estimates are also 

used in the calculations of this publication (e.g., Craig and Hacker 1940, estimates of aboriginal 

consumption and proportion of a run that was harvested). 

Results relevant to EMAP: Total pre-settlement salmon runs along the Oregon coast were 

estimated to be 1.75-5.36 million fish. Salmon runs may have been larger in the 1850s than any 

other time in post-glacial history because of the rapid decline in the aboriginal population and 

the resulting decline in harvest just prior to major European impacts such as gold mining, 

farming, and logging. 

The pre-1850 estimates were1.5-2.5 million fish in the coho run and 290,000-517,000 in the 

chinook run. During "poor" ocean years, the current run size for coho is 3-6% of the historical 

run size, whereas in "good" ocean years it is 11-19% of the historical run size. Overall, on the 

Oregon coast, coho runs have been reduced by 80-95% since the 1850s. Current population 

estimates are far below potential salmon numbers, which were calculated based on available 

habitat remaining. The authors conclude that, since spawning habitat has declined, ocean 

conditions are the dominant factor affecting fluctuations in run size. 

Reasons given for decline include deteriorating ocean conditions, competition with nonnative 

fish, predation, pollution, and past or current fishing levels. Mining, logging, and agriculture 

beginning in the 1800s have also impacted salmon populations.

Geographic location: Oregon, Coastal Oregon rivers and streams, EPA Region 10, eco1, 

mountains 

Keywords: fish, mining, logging, agriculture, habitat degradation, nonnative species, urban, 

fishing 

Abstract: Increasing the abundance of salmon in Oregon’s rivers and streams is a high priority 

public policy objective. Salmon runs have been reduced from pre-development conditions 

123
(typically defined as prior to 1850), but it is unclear by how much. Considerable public and 

private resources have been devoted to restoring salmon runs, but it is uncertain what the 

current recovery potential is because much of the freshwater and estuarine habitat for salmon 

has been altered and there is no expectation that it will be returned to a pre-development 

condition. The goals of all salmon recovery efforts are based on assumptions about the size of 

the runs prior to significant habitat alteration, coupled with an estimate of the amount and quality 

of freshwater and estuarine habitat currently available. We estimated the historical aggregate 

salmon run size in rivers along the Oregon coast (excluding the Columbia River) using two 

methods: (1) 

Converting estimated aboriginal population levels into numbers of salmon; (2) Extrapolating 

cannery pack into numbers of salmon. Annual aboriginal harvest of all salmon species is 

estimated to have been approximately 10 million pounds per year (4,500,000 kg) or 1.75-5.36 

million salmon, a harvest level similar to that occurring during the height of commercial fishing 

on Oregon’s coastal rivers in the late 1800s and early 1900s. Extrapolating cannery pack data, 

the estimated size of the late 1800s aggregate runs of coho salmon (Oncorhynchus kisutch) 

was 1.5-2.5 million. The estimated size of aggregate runs of chinook salmon (Oncorhynchus 

tshawytscha) runs was 290,000-517,000. Compared to our estimates of mid-1800s coho 

salmon levels, early 2000 runs (during favorable ocean conditions), were 11-19% of the 

historical level. 

During poor ocean conditions (1990s), current coho salmon runs were 3-6% of the historical 

size. 

Notes: Craig, J.A. and R.L. Hacker. 1940. The history and development of the fisheries of the 

Columbia River. Bulletin of the Bureau of Fisheries 49:133-216. 

URL: http://www.epa.gov/wed/pages/staff/lackey/recntpub.htm 

124
Author: Miller, A.I.; Counihan, T.D.; Parsley, M.J.; Beckman, L.G. 

Year: 1995 

Title: Columbia River Basin White Sturgeon 

Reference Type: Electronic Source

Producer: U.S. Department of Interior, National Biological Service 

Access Year: 2005 

Access Date: May 18 

Value of reference: This web site addresses a particular species (white sturgeon) in a large 

basin (Columbia River) and graphically shows the population status in sections of that basin in 

rough comparison with historical population levels. This might not have a wide application 

within EMAP-West, since the sturgeon is a large river fish, and EMAP focuses on smaller 

streams.

Results relevant to EMAP: Historically, white sturgeon inhabited the Columbia River from the 

mouth upstream into Canada, the Snake River upstream to Shoshone Falls, and the Kootenai 

River upstream to Kootenai Falls; they also used the extreme lower reaches of other tributaries, 

but not extensively. 

A commercial fishery that began in the 1880s peaked in 1892 when 2.5 million kg (5.5 million lb) 

were harvested (Craig and Hacker 1940). By 1899 the population had been severely depleted 

due to overfishing; more recent causes for populations declines include dam-building (which 

affects spawning habitat), and continued over-harvest. 

The Figure included on this web site shows portions of the Columbia River Basin in the U.S. 

where white sturgeon are currently abundant (lower Columbia River only), abundant but below 

historical levels (portion of Columbia River above Bonneville Dam, upper Columbia near 

Canadian border, between Lower Granite Dam and Hells Canyon Dam, and portion of upper 

Snake River), sparse, endangered, extirpated, and unknown.

Geographic location: eco1, eco3, eco4, eco10, eco11, eco15, eco12, Columbia River Basin, 

xeric, mountains, Washington, Oregon, Idaho, EPA Region 10 

Keywords: fish, dams, fishing 

URL: http://biology.usgs.gov/s+t/noframe/e065.htm 

125
Author: Miller, R.R.; Williams, J.D.; Williams, J.E. 

Year: 1989 

Title: Extinctions of North American fishes during the past century 

Reference Type: Journal Article

Journal: Fisheries 

Volume: 14 

Issue: 6 

Pages: 22-38 

Value of reference: Information about extinct species can be used to reconstruct a more 

complete species list to describe historical fish diversity. This article profiles 40 species or 

subspecies of North American fish that have become extinct. The list includes 14 species or 

subspecies from states within the EMAP-West 12-state region, plus 3 species in that region that 

inhabited only lakes. 

The article discusses human impacts that are thought to have caused extinction, and 

summarizes these, by species, in Table 2. It also lists erroneously reported extinctions of fishes 

from North America and their current (1989) status, e.g., endangered, threatened...)(Appendix).

Results relevant to EMAP: The following 14 species, originally found in streams of the EMAPWest region, have gone extinct as of 1989: Oncorhynchus clarki ssp., Gila bicolor isolata, Gila 

crassicauda, Lepidomeda altivelis, Pogonichthys ciscoides, Rhinichthys deaconi, R. osculus 

reliquus, Chasmistes l. liorus, C. muriei, Cyprinodon nevadensis calidae, C. sp., Empetrichthys 

latos concavus, E. l. pahrump, E. merriami. Species were lost from Colorado, Wyoming, Utah, 

Nevada, Oregon, California, and Arizona 

Most of these were originally known from a very small locale or number of streams or springs 

and may have had very specific geographic ranges and/or habitat requirements. Some had 

been known for only a short time and were presumably in decline for many years prior to being 

described, and therefore the original geographic ranges will never be fully known for most of 

these species or subspecies 

Reasons for extinction include physical habitat alteration, introduction of species, chemical 

alteration or pollution, hybridization, and overharvest. 

Geographic location: westwide, Colorado, Wyoming, Utah, Nevada, Oregon, California, 

Arizona, EPA region 8, EPA region 9, EPA region 10, mountains, plains, xeric 

Keywords: fish, habitat degradation, nonnative species, pollution, fishing 

Abstract: Extinctions of 3 genera, 27 species, and 13 subspecies of fishes from North America 

are documented during the past 100 years. Extinctions are recorded from all areas except 

northern Canada and Alaska. Regions suffering the greatest loss are the Great Lakes, Great 

Basin, Rio Grande, Valley of Mexico, and Parras Valley in Mexico. More than one factor 

contributed to the decline and extinction of 82% of the fishes. Physical habitat alteration was the 

most frequently cited causal factor (73%). Detrimental effects of introduced species also were 

cited in 68% of the extinctions. Chemical habitat alteration (including pollution) and hybridization 

each were cited in 38% of the extinctions, and over-harvesting adversely affected 15% of the 

fishes. This unfortunate and unprecedented rate of loss of the fishery resource is expected to 

increase as more of the native fauna of North America becomes endangered or threatened. 

126
Author: Minckley, W.L.; Deacon, J.E. 

Year: 1968 

Title: Southwestern fishes and the enigma of "endangered species" 

Reference Type: Journal Article

Journal: Science 

Volume: 159 

Pages: 1424-1432 

Value of reference: This paper is about extinction primarily, but in this context it gives 

examples of declining species and fauna and the changes in distribution that have occurred in 

the Gila basin. Paper describes historical ranges for a number of native fish of the Gila basin, 

the changes in distribution that had occurred as of 1968, and the causes of the declines in 

native fish. The historical and current distributions of several selected species are depicted in 

maps and juxtaposed with range maps for exotic species. Conditions in the Gila drainage are 

presented as an example of what was postulated to be happening in the Colorado River basin 

overall (in 1968).

Results relevant to EMAP: As an example of the changes in a whole fish fauna, data for 

occurrence or probable occurrence are given for 34 species in the Salt River tributary of the Gila 

basin from 1900 to 1960 (natives and exotics listed separately), showing the decline of natives 

(all but 2) and the appearance and increase in 20 exotics beginning in 1920 (see Table 1). 

Two other examples: 1) the Gila spinedace once occurred throughout the upper Gila River basin 

but more recently it has drastically declined, apparently replaced by the introduced red shiner 

(see historical maps Figure 2); 2) the Gila topminnow lived in off-channel habitats from a highelevation in western New Mexico to the area near Dome AZ and throughout the Gila drainage; 

once considered very common, they were considered rare in 1968 (see historical distribution 

map Figure 3). 

Historical distributions of larger river (mainstem) species--squawfish, humpback suckers, and 

woundfish--are also described. 

Declines have been the result of habitat destruction--including water diversions, impoundments, 

erosion and downcutting, agriculture, and pollution--and competition with introduced fish 

species. These impacts are discussed in more detail by Molles 1980 with respect to their 

present and likely future influences in the upper Colorado River basin. 

Geographic location: Gila River basin, Arizona, eco81, eco79, eco23, xeric, EPA Region 9 

Keywords: fish, nonnative species, dams, water diversion, erosion, agriculture 

Notes: Molles, M. 1980. The impacts of habitat alterations and introduced species on the native 

fishes of the upper Colorado River basin. Pages 163-81 IN Spofford, W.O., Jr., A.L. Parten, 

A.V. Kneese (eds.), Energy development in the southwest. Research paper 18. Resources for 

the future, Washington, D.C. 

127
Author: Minckley, W.L.; Marsh, P.C.; Brooks, J.E.; Johnson, J.E.; Jensen, B.L. 

Year: 1991 

Title: Management toward recovery of the razorback sucker 

Reference Type: Book Section

Editor: W.L. Minckley; Deacon, J.E. 

Book Title: Battle Against Extinction: Native Fish Management in the American West 

City: Tucson, AZ 

Publisher: The University of Arizona Press 

Pages: 303-357 

Value of reference: The first portion of this chapter summarizes what is known about the 

historical distribution of the razorback sucker in the Colorado River basin and chronicles the 

species' decline. It is extensively researched, using both peer-reviewed and published literature 

as well as personal contacts. The historical summary is largely a literature review, which 

includes many historical survey references and an overview of historical abundance in various 

portions of the river basin (see subsection 'Abundance in Aboriginal and Early Historical Times', 

on page 307). Other relevant sections summarize survey records from the 1900s, which 

provide evidence of declining populations, and reasons for decline.

Results relevant to EMAP: Although it is estimated that the species began declining before 

1912, much of the concern regarding the species status is more recent, beginning in the 1930s 

after closure of the Hoover Dam. 

Possible reasons for declining populations include dewatering, dams, water diversions, lower 

water temperatures, competition with non-native fishes, predation, and hybridization 

Historical records of presence and abundance are cited throughout the text. Figure 17-2 shows 

a map of present and historic distribution of the sucker in the Colorado River basin. 

Geographic location: Colorado River basin, xeric, mountains, eco20, eco18, eco22, eco14, 

eco23, eco81, EPA Region 8, EPA Region 9, Colorado, Wyoming, Arizona, California, Utah, 

Keywords: historical distribution, fish, razorback sucker, dams, water diversion, nonnative 

species 

128
Author: Minckley, W.L.; Rinne, J.N. 

Year: 1985 

Title: Large Woody debris in hot-desert streams: an historical review 

Reference Type: Journal Article

Journal: Desert Plants 

Volume: 7 

Issue: 3 

Pages: 142-153 

Value of reference: This work provides a good historical review of desert riparian communities 

in the mid 1800s. Many selected quotations from early literature help to illustrate riparian 

conditions. The fate of large wood in desert systems and the changes in human impacts 

between the late 1800s and late 1900s are addressed. The influence of wood and organic 

particulates on macroinvertebrates is also treated to link the physical and biological aspects of 

desert streams.

Results relevant to EMAP: Historically, large wood contributed to heterogeneity of the desert 

stream ecosystem. Lithographs, photographs, and written historical documentation provide 

evidence of dense riparian gallery forests, marshlands, densely-vegetated floodplains, and 

accumulations of large, woody debris along Sonoran Desert streams, much of which originated 

in the upper basin. Conditions along smaller tributaries included large stands of riparian trees 

(including cottonwood, mesquite, willow), and thus presumably substantial amounts of downed 

timber. Based on historical accounts, the authors conclude that substantial amounts of 

vegetative debris, including fine particulates, were available to streams of the Sonoran Desert. 

Extensive literature citations are given for historical documentation. 

A large percentage of southwestern riparian communities, especially at low elevations, have 

now been replaced by introduced saltcedar (Tamarix chinensis). Riparian communities have 

been further destroyed by woodcutting, agricultural development, urbanization, and desiccation 

from stream incision, impoundment, channelization, and over-grazing. In central AZ, cleared 

and irrigated agriculture land increased from less than 200 hectares in 1862 to many thousands 

of hectares in 1982., while the population of Phoenix grew from 100 to over a million. Dams 

now trap most particulate materials.

Geographic location: xeric, Arizona, California, EPA Region 9, Sonoran Desert, lower 

Colorado River basin, eco14, eco81, eco23, eco22, eco20 

Keywords: phab, large wood, riparian vegetation, particulate organic matter, Sonoran Desert, 

historical documentation, agriculture, urban, grazing, impoundment 

Abstract: Large-particulate organic debris is denied to present-day desert streams because of 

interception by impoundments and as a results of decimation of formerly extensive riparian 

vegetation. Historical records indicate a substantial, but sporadic, input of coarse debris, which 

was reduced to finer particles through molar action in canyon-bound reaches of desert rivers. 

Historical changes, functions of large debris in the system, and probable future conditions are 

reviewed. 

129
Author: Minshall, G. W.; Jensen, S. E.; Platts, W. S. 

Year: 1989 

Title: The ecology of stream and riparian habitats of the Great Basin region: A community 

profile 

Reference Type: Report

Institution: U.S. Fish and Wildlife Service 

Pages: 142 

Report Number: Biological Report 85(7.24) 

Value of reference: The reference provides a good overview of the fish of the Great Basin with 

an emphasis on the post-Pleistocene distribution of cutthroat trout and a timeline of fish 

introductions. It also has a section on the history of livestock grazing in the Great Basin.

Results relevant to EMAP: Introduction of exotic fish into Bonneville basin waters began in the 

late 1880's. Table 22 p. 86, lists fish presently established in the Great Basin with native species 

noted. In the Carson River system, nonnative trout introduced in the 1880's displaced the native 

cutthroat trout within a few decades, except where the natives had been stocked above 

impassable falls. The west face of the Ruby Mountains and East Humboldt Range in Elko 

County show the most significant impact of past trout stocking practices. Native cutthroat trout 

have been replaced by other salmonids, principally the eastern brook trout. 

Lahontan cutthroat trout have been eliminated from 95% of their native habitat as a result of 

human activity. p. 92. In the Humboldt River drainage Lahontan cutthroat trout still live in the 

headwaters, but occur in only about 12% of their former range. Lahontan cutthroat trout of the 

Humboldt River drainage fared better than the trout in the Truckee-Walker drainages because 

they were better adapted to stream life with its flood/drought cycle. The trout in the Humboldt 

drainage also have not experienced as much displacement or hybridization with other stocked 

trout species.

Geographic location: xeric, Nevada, Utah, Bonneville Basin, Lahontan Basin, eco13, eco80, 

Truckee River, Humboldt River basin, Carson River, EPA Region 9, EPA Region 8 

Keywords: fish, cutthroat trout, nonnative species, riparian vegetation, grazing 

130
Author: Mongillo, P.E. 

Year: 1993 

Title: The distribution and status of bull trout/Dolly Varden in Washington state June 1992 

Reference Type: Report

City: Olympia, WA 

Institution: Washington Department of Wildlife Fisheries Management Division 

Report Number: Report No. 93-22 

Value of reference: A rough estimate of past distribution of bull trout/Dolly Varden is presented, 

based on personal knowledge of the individuals interviewed and on historic creel records. 

Extrapolation and assumptions were made, based on limited location information from historical 

sources; therefore historical absence might only mean that no historical documentation was 

found for certain drainages or streams. The report is more of a current status of 77 populations 

of the species, but changes since pre-settlement are also embedded; Figure 1 gives the current 

knowledge on present and past distribution of bull trout/Dolly Varden.

Results relevant to EMAP: Most of the Columbia River was previously utilized by bull 

trout/Dolly Varden, whereas only sections of the river associated with larger tributary 

populations commonly contain bull trout/Dolly Varden today (see Figure 1); the species was 

likely never abundant in the mainstem River and never seems to have been present in the 

Cowlitz River drainage of southwest WA or the Quileute system below Solduc Falls on the 

coast. 

 

The Okanogan, Lake Chelan, and Lower Yakima River populations have been lost, while other 

populations or groups of populations have become fragmented or isolated, for example in the 

streams in the Blue Mountains of southeast WA, the upper Yakima River in central WA, the 

Lewis River in southwest WA, and the Cedar River near Seattle. 

 

Easy public access, poaching and presence of nonnative fish species (brook trout, brown trout, 

rainbow trout) are adversely impacting approximately the same number of populations; 

interbreeding between small resident populations of bull and brook trout will likely lead to 

elimination of bull trout. A number of human impacts harming the species are discussed; forest 

management is affecting the greatest number of populations, and grazing the least. 

Geographic location: Washington, eco77, eco15, eco10, eco1, eco2, eco4, Pacific Northwest, 

EPA Region 10, mountains, xeric 

Keywords: fish, nonnative species, logging, roads, fishing 

Abstract: Bull trout (Salvelinus confluentus), and Dolly Varden (Salvelinus malma), are 

generally present in all parts of Washington State except the area east of the Columbia River 

and north of the Snake River in eastern Washington (Columbia Basin) and the extreme 

southwest portion of the state. Distribution losses from historical levels have been confined 

mainly to eastern Washington. In addition to a reduced distribution from historical levels, 

several populations in both eastern and western Washington have become fragmented because 

lower river reaches are no longer utilized. A total of three populations have become extinct. It 

is estimated that a minimum of 77 distinct bull trout/Dolly Varden populations remain in 

Washington. Nine are at high risk of extinction, six are at moderate risk, 13 are at low risk and 

six are believed to be at no immediate risk. The remaining 43 populations do not have sufficient 

data on them to assign a level of risk. Additionally, the habitat and non-habitat factors affecting 

each population are identified and summarized. 

131
Author: Moyle, P.B.; Nichols, R.D. 

Year: 1974 

Title: Decline of the native fish fauna of the Sierra Nevada foothills, central California 

Reference Type: Journal Article

Journal: American Midland Naturalist

Volume: 92 

Issue: 1 

Pages: 72-83 

Value of reference: Historical data from three historical surveys were synthesized and 

compared to the 1970 survey. The results, shown in Table 2, show how the fish assemblage 

changed over time in reference to the construction of Friant Dam (1942) and with respect to the 

proportions of native and introduced species. Distribution maps, showing pre-1900 and 1970 

locations are presented for the most abundant species. General changes in numbers and 

distribution are discussed briefly for each species. 

The study was confined to streams between 90 and 1100 m elevation with a mean elevation of 

401 m.

Results relevant to EMAP: The San Joaquin foothill fish fauna has change dramatically in 

many areas as native fishes are replaced by introduces species. Table 2 illustrates the changes 

that have occurred since 1989, as documented in 4 surveys, published in 1898, 1934, 1941, 

and 1970 (present study). The 1898 survey indicates that the areas originally had a fish fauna 

transitional between those of the Valley floor and the foothills. 

The San Joaquin River systems experienced modification due to dam construction and the 

introduction of numerous fish species. By 1970, the river below Friant Dam (closed in 1942) 

was dominated by introduced species. Healthy populations of native fishes occurred only in a 

restricted region of relatively undisturbed foothill streams. 

Geographic location: xeric, eco7, California, EPA region 9, San Joaquin River basin 

Keywords: fish, nonnative species, dams, habitat fragmentation 

Abstract: A survey was made of the fishes occurring in streams of the Sierra Nevada foothills 

above the San Joaquin Valley, California. Twenty-four species were collected, 12 native, 12 

introduced. The present distributions of these fishes were compared to their pre-1900 

distributions, as inferred from old records. Overall, the ranges of introduced species and 

rainbow trout have expanded while the ranges of native species, especially California roach, 

hardhead, Sacramento squawfish and Sacramento sucker, have contracted. Healthy 

populations of native fishes were found only in a rather narrow middle elevation band of 

comparatively undisturbed sections of foothill streams. The native fish populations in different 

foothill stream systems are now isolated from each other and are, thus, in danger of local 

extinction as foothill development proceeds. The study indicates that populations of native 

stream fishes, even if they do not contain endangered species, should be protected, to make 

sure that severe natural conditions, when combined with human alterations to the streams, do 

not destroy unique assemblages of fishes. 

132
Author: Moyle, P.B.; Williams, J.E. 

Year: 1990 

Title: Biodiversity loss in the temperate zone: decline of the native fish fauna of California 

Reference Type: Journal Article

Journal: Conservation Biology 

Volume: 4 

Issue: 3 

Pages: 275-284 

Value of reference: This article synthesizes information and reports on the status of 113 native 

fish taxa in California, in a manner similar to that of Nehlsen et al. 1991 (this bibliography). It 

does not present historical information specifically, but uses historical information and 

knowledge of declining populations, based on past status, and assigns a status ranking of 1-6 

for each of several ratings of natural and artificial factors influencing the species distribution. 

Causes of decline are also summarized briefly.

Results relevant to EMAP: Of 113 native fish taxa in California, 6% are extinct, 57% are in 

various stages of decline, and 36% appear to be stable. Much of the decline has been recent, 

rapid, and unexpected. Fish taxa at particular risk are most likely to be endemic, restricted in 

range, part of a small fish assemblage, or found in isolated springs, warm water stream, or big 

rivers. Entire regional faunas are threatened with extinction or with being confined to isolated 

fragments of habitat. 

Cause for decline is attributed mainly to water diversions and introduced species, acting in 

concert. Habitat alterations associated with agricultural practices, grazing, and channelization 

are other contributors.

Geographic location: California, eco1, eco78, eco4, eco9, eco5, eco7, eco6, eco8, eco14, 

eco81, EPA Region 9, Mountains, Xeric. Non-specific to river basin, although some summaries 

used ichthyological provinces. 

Keywords: fish, status, water diversion, nonnative species, agriculture, grazing, channelization 

133
Author: Moyle, P.B.; Yoshiyama, R.M.; Knapp, R.A. 

Year: 1996 

Title: Status of Fish and Fisheries 

Reference Type: Report 

City: Davis, CA 

Institution: University of California, Centers for Water and Wildland Resources 

Pages: 953-973 

Value of reference: This is a good synthesis of changes in native fish populations in the Sierra 

Nevada range. Historical (pre-European) distributions (largely affected by elevation) are 

discussed briefly for each of four major basins and summarized in general in Figure 1. Current 

status and short species accounts of 40 native fish species are presented. Factors contributing 

to declines and the importance of their impact on native fishes of the region are summarized in 

Table 4. A special section is included for Chinook salmon, although a more thorough treatment 

of this species can be found in Yoshiyama et al. 1998, in this bibliography. 

Fish introductions in this region are treated in detail, since they are a major factor in the decline 

of native species. The effect of trout introductions on native biota--native trout, amphibians, and 

invertebrates--is included, although few specific details are presented.

Results relevant to EMAP: Since 1850, anadromous fishes have been excluded from most 

west side rivers; most resident native fishes have declined and aquatic communities have 

become fragmented; 30 species of nonnative fishes have been introduced or have invaded 

most waters, including historically fishless, high-elevation areas; and fisheries now focus on 

nonnative fish, rather than natives. Chinook salmon have lost 62% of the stream length 

originally available to them for spawning in the Central Valley (Table 3). 

Historically, all four of the major basins in the region were fishless at high elevation. Chinook 

salmon, steelhead trout, and Pacific lamprey were abundant in the Sacramento-San Joaquin 

drainage. The Lahontan drainage supported 10 native fish species and all were widespread 

and abundant. Known historical elevation limits are given for a number of species. 

Of the 40 fishes native to the Sierra Nevada, 15% have been listed as threatened or 

endangered, 30% are listed as species of special concern by Moyle et al. 1996, 10% are in 

severe decline in this region, and 45% seem to be stable or expanding. Chinook salmon, 

steelhead, and 5 native trout have mostly disappeared from the region. The mountain yellowlegged frog is found at fewer than 15% of the high-elevation sites at which it was present in 

1915 (Drost and Fellers 1994). 

The biggest declines in native fish abundance occurred between 1850 and 1950 as a result of 

hydraulic mining, construction of dams and diversions, and introductions of nonnative fish. 

Other factors include road building/urbanization, channelization, grazing, logging, and pollution. 

Geographic location: California, eco5, eco6, eco7, Sierra Nevada, EPA region 9, mountains, 

xeric, Sacramento-San Joaquin basin, Owens basin, Lahontan basin, Eagle Lake basin 

Keywords: fish, status, distribution, nonnative species, dams, urban, water diversion, logging, 

grazing, channelization, pollution 

Notes: Moyle et al. 1996. Fish species of special concern in California. California Department 

of Fish and Game, Sacramento, CA. 

134
Drost and Fellers 1994. Decline of frog species in the Yosemite section of the Sierra Nevada. 

U.S. Department of the Interior Technical Report NPS/WRUC/NRTR-94-02. Government 

Printing Office, Washington, D.C. 

135
Author: Mueller, G.; Marsh, P. 

Year: 1995 

Title: Bonytail and Razorback Sucker in the Colorado River Basin 

Reference Type: Electronic Source

Producer: U.S. Department of Interior, National Biological Service 

Access Year: 2005 

Access Date: June 21 

Value of reference: This is a summary paper printed by the National Biological Service on a 

web site. It is a comprehensive summary of the decline of razorback suckers and bonytails in 

the CO River basin. It reports the extent of their historical ranges, the tributaries where they 

were once common to abundant, and the major causes of their declines.

Results relevant to EMAP: Both species were common historically; today, no measurable 

recruitment is evident for either species, and old individuals are reaching the end of their 

lifespan. 

Bonytails were historically common in mainstem CO, Green, Gunnison, Yampa, Gila, and Salt 

rivers before construction of large dams. They now exist only in Lake Mohave, which comprises 

<2% of their former range (see Figure 3). 

Razorback suckers were historically common to abundant in the CO mainstem and portions of 

the Green San Juan, Animas, Duchesne, Gila, Salt, and Verde rivers, but today are very rare 

and found in <25% of the former range (see Figure 3). 

Declines have been caused by physical and biological changes to habitat cause by large dams, 

reservoirs, and diversion canals, direct competition with introduced fish species, and predation 

on young fish by non-native fishes. Promotion of recreational fisheries, introduction of sport fish 

more adapted to colder water, and poisoning compromised the native fish. 

Geographic location: Colorado River Basin, eco18, eco19, eco20, eco21, eco13, eco22, 

eco23, eco81, eco14, Wyoming, Utah, Colorado, Arizona, Nevada, xeric, mountains, EPA 

Region 8, EPA Region 9 

Keywords: fish, endangered species, dams, channelization, water diversion, nonnative species 

Notes: A related, but less current publication documenting historical range and the 1970s 

distribution in the Colorado R. system is: 

McAda, C.W. and R.S. Wydoski. 1980. The Razorback Sucker, Xyrauchen texanus, in the 

Upper Colorado River Basin, 1974-76. U.S. Department of Interior, Fish and Wildlife Service, 

Technical Paper 99. Washington, D.C. 

URL: http://biology.usgs.gov/s+t/noframe/r166.htm 

136
Author: Mueller, G.; Marsh, P. 

Year: 2002 

Title: Lost, A Desert River and Its Native Fishes: A Historical Perspective of the Lower Colorado 

River 

Reference Type: Report

City: Fort Collins, CO 

Institution: Geological Survey Fort Collins Science Center 

Pages: 80 

Report Number: Information and Technology Report USGS/BRD/ITR--2002-0010 

Value of reference: This detailed report documents the history, exploration, settlement, and 

historical fish community of the lower Colorado River basin, as well as the story of water 

development of the basin and the changes in physical habitat and the native fish community that 

followed. Information includes descriptions of channel characteristics, sediment loads, 

backwater habitats, vegetation, river dynamics, and flooding patterns typical of the undisturbed 

river. Changes occurring during the settlement and development period are chronicled in detail. 

The changes in physical properties of the water, channel configuration, riparian habitat, and 

aquatic biota as a result of human impacts are discussed at length. This discussion includes 

the survival strategies and life histories of all native fish of the lower river. Table 5 gives the 

relative historical abundance and current federal/state status of these species. Numerous 

historical accounts and photographs are included. 

Results relevant to EMAP: Prior to 1880, only 9 freshwater species were found in the lower 

CO river, representing 4 families and two marine species in the lower river (in 1880, this would 

have been in Mexico and not relevant to EMAP). Most fish were found in off-channel habitats 

where there were fewer suspended sediments and effects of flooding were less severe. Fish 

kills were common due to a hostile and unpredictable river environment. Fish communities 

periodically disappeared from the broader floodplains and extended portions of tributaries. 

Populations that numbered in the millions could be reduced to only a few dozen fish in a single 

season. 

In contrast to other reports, the authors claim that the majority of natives were lost long before 

the Hoover Dam was built in 1935, but the larger water developments after 1935 likely 

guaranteed their demise. Irrigated agriculture led to stranding of fish in fields. Commercial 

fishing, loss of habitat, migration barriers (dam construction, diversions, dewatering), and 

introduction of carp, bullhead, and channel catfish occurred before 1935. 

Profiles of past abundance and distribution in the basin and estimates of what remains are 

described for each of the native species (beginning on page 62, summarized in Table 5). 

Geographic location: Arizona, California, Utah, Colorado, eco81, eco23, eco22, eco20, lower 

Colorado River basin, Region 8, Region 9, xeric 

Keywords: human impacts, historic documentation, lower basin, native fish, agriculture, fishing, 

dams, water diversion, channelization, nonnative species, historical photographs, fish, phab 

Abstract: The Colorado River had one of the most unique fish communities in the world. 

Seventy-five percent of those species were found nowhere else in the world. Settlement of the 

lower basin brought dramatic change to both the river and its native fish. Those changes began 

more than 120 years ago as settlers began stocking nonnative fishes. By 1930, nonnative fish 

had spread throughout the lower basin and replaced native communities. All resemblance of 

137
historic river conditions faded with the construction of Hoover Dam in 1935 and other large 

water development projects. Today, few remember what the Colorado River was really like. 

Seven of the nine mainstream fishes are now Federally-protected as endangered. Federal and 

state agencies are attempting to recover these fish. However, progress has been frustrated due 

to the severity of human impact. This report represents testimony, old descriptions, and 

photographs describing the changes that have taken place in hopes that it will provide 

managers, biologists, and the interested public a better appreciation of the environment that 

shaped these unique fish. 

URL: http://www.stormingmedia.us/23/2322/A232214.html 

138
Author: Mueller, G.A.; Marsh, P.C.; Minckley, W.L. 

Year of Conference: 2005 

Title: A legacy of change: the lower Colorado River, Arizona-California-Nevada, USA, and 

Sonora-Baja California Norte, Mexico 

Reference Type: Conference Proceedings

Editor: Rinne, J.N.; Hughes, R.M.; Calumusso, B. 

Conference Name: Historical Changes in Large River Fish Assemblages of the Americas 

Conference Location: Phoenix, AZ 

Publisher: American Fisheries Society 

Volume: 45 

Pages: 139-156 

Value of reference: This chapter is a concise synopsis of what has happened to the Colorado 

River and its native fish community. The section on 'Native Fish Assemblage' describes the 

historical fish community and provides citations of numerous original historical documents and 

reports. 

A section on 'Physical Description' includes a few riparian descriptions. 

Factors causing the decline of native fish are discussed.

Results relevant to EMAP: Historically, the lower CO river had only 9 native fish species, 

which are today extirpated, federally endangered, or being reintroduced through stocking. 

Eighty alien species have been introduced to the lower basin, and 20 of these have become 

common. Predation by nonnative species and physical habitat degradation were the primary 

causes of the decline of native fauna. 

Table 1 summarizes historical abundance and current status of the native fish species. 

Geographic location: Colorado River basin, Colorado, Utah, Wyoming, Arizona, EPA Region 

8, EPA Region 9, eco18, eco19, eco20, eco21, eco22, eco23, xeric, mountains 

Keywords: fish, nonnative species, habitat degradation, historical abundance, status 

139
Author: Murphy, Peter J.; Randle, Timothy J.; Fotherby, Lisa M.; Daraio, Joseph A. 

Year: 2004 

Title: The Platte River Channel: History and Restoration 

Reference Type: Electronic Source

Producer: U.S. Department of the Interior; Bureau of Reclamation Technical Service Center 

Access Year: 2005 

Access Date: July 26, 2005 

Value of reference: Good summary of the human impacts and physical changes that have 

occurred to the Platte River valley since settlement (mid -late 1800's). Changes in 

geomorphology, flow and sediment transfer of the river are the main focus of the study. Includes 

an extensive bibliography.

Results relevant to EMAP: The emphasis of this study is a historic review and analysis of the 

geomorphology of the central Platte River. This analysis is based primarily on existing historic 

field data, historic mapping, aerial photos, written narrative, historic photos, recorded 

information on Platte River Basin development, and some recent field data collection associated 

with this study. Historic and recent field data include measurements of river discharge, climate 

indicators, bed-material size gradations, average un-vegetated channel widths or active channel 

widths, and stage-discharge relationships. 

Initial anthropogenic influences on the central Platte River in the 1800s are primarily raised 

sediment inputs from land use beginning in the 1840s, and flow depletions in the last decades of 

the century. The beaver trapping industry eradicated almost all beaver in the area by the mid 

1800s. The impact of this harvest may have contributed small increases in sediment load in the 

Rocky Mountain tributaries, through the gradual elimination of sediment-trapping beaver dams. 

Extensive gold mining and timber harvesting in the South Platte tributaries and some activity in 

the North Platte tributaries, may have increased sediment loads to the central Platte River. 

Reaches of the present channel have an un-vegetated or active channel width that is 50 to 90 

percent narrower than the channel that existed in the 1860s and in the period 1898 to 1902. The 

central Platte River has generally experienced channel narrowing throughout its length with 

greater reductions in un-vegetated or active channel width in the upper reaches. 

Geographic location: plains, Platte River Valley, Nebraska, Wyoming, Colorado, eco25, 

eco27, eco43, EPA region 7, EPA region 8 

Keywords: Platte River, phab, channel width, channel stability, pre-settlement, 

geomorphology, beaver trapping, mining, logging, sediments 

URL: http://www.platteriver.org/library/index.htm 

140
Author: Murray, T.B. 

Year: 1964 

Title: Chinook and steelhead historic spawning grounds, Shoshone Falls to Salmon River, 

Snake River drainage 

Reference Type: Report

City: Boise, ID 

Institution: Idaho Power Company 

Value of reference: The author uses multiple sources and personal observation to piece 

together what the distribution and range of steelhead and chinook salmon in the unobstructed, 

pre-settlement middle Snake River (mouth of Salmon-Imnaha Rivers to Shoshone Falls) would 

have been. Estimates of the river miles available as spawning habitat for these species before 

major human impacts and dam building are given for each tributary, extending as far as the 

Jarbidge and Santa Rosa mountain ranges in northern Nevada. Other pre-settlement 

conditions are mentioned throughout, such as vegetation, historical conditions in each basin that 

would have favored spawning and rearing of fingerling salmonids, human impacts that changed 

migration potential in the Snake River drainage, and Native American fisheries. 

The document gives a broad view of the fish population potential of the Snake River in presettlement times. It summarizes pre-settlement spawning conditions in each tributary in the 

basin for spring chinook, steelhead, and fall chinook. Information is presented in a draft format 

of text only. The information is not referenced, and some statements are based on secondhand knowledge.

Results relevant to EMAP: Prior to obstructed migration, the middle Snake River was a prime 

producer of fingerling salmonids. Pre-settlement conditions favorable for spawning and rearing, 

including the space available (in river miles) are summarized for the following Snake River 

tributaries: Boise, Owyhee, Payette, Malheur, Weiser, Burnt, Powder, and Wildhorse Rivers 

and Pine Creek. 

On page 32 is a summary of the river miles historically available for spawning and rearing in 

each sub-basin, totaling 2060 river miles. By 1955, the availability and use of this production 

potential had been reduced by 90% due to over-fishing, habitat alterations and blockage to fish 

passage caused by dams, agriculture, logging, pollution, water diversions, and climate changes. 

In 1955, remnant runs were spotty, and river habitat occupied by steelhead or chinook salmon 

totaled barely 200 miles on portions of Weiser and Wildhorse Rivers and Pine and Eagle 

Creeks. 

Geographic location: Idaho, Nevada, Snake River basin, eco80, eco12, EPA region 10, xeric 

141
Author: Musser, G.G. 

Year: 1959 

Title: Ecological Studies of the Flora and Fauna in Glen Canyon, Appendix E: Annotated check 

list of aquatic insects of Glen Canyon 

Reference Type: Report

City: Salt Lake City, UT 

Institution: University of Utah 

Pages: 207-221 

Report Number: Anthropology Papers No. 40 

Value of reference: Since historical macroinvertebrate data are very limited, this article is 

sufficiently notable to include here, even though it was published in the mid 1900s. It is 

considered the best comparable data for aquatic insects that exists for the geographic region. 

Although the data are reported for an area now under water, their historical presence in the 

region is notable for reconstruction of insect distribution and community composition before dam 

construction. 

Results relevant to EMAP: In a 1958 survey of the Glen Canyon (before impoundment), 2315 

individual aquatic insects were collected, including more than 91 species in 73 genera, 41 

families, and eight orders. The bulk of the collection was from tributaries, while only 247 were 

taken from the river. 

This listing provides 1-8 lines of text description for each species collected regarding presence, 

relative abundance, other locations where present, habitat preferences, and other anecdotal 

information. 

Geographic location: Arizona, Colorado River basin, eco22, xeric, EPA region 9 

Keywords: macroinvertebrates, baseline data, species list 

142
Author: Muth, R. T.; Crist, L.. W.; LaGory, K. E.; Hayse, J. W.; Bestgen, K. R.; Ryan, T. P.; 

Lyons, J. P.; Valdez, R. A. 

Year: 2000 

Title: Flow and temperature recommendations for endangered fishes in the Green River 

downstream of Flaming Gorge Dam 

Reference Type: Report 

Publisher: Upper Colorado Endangered Fish Recovery Program 

Report Number: Rpt. No. FG-53 

Value of reference: This is a comprehensive reference (344 pp.) for the changed conditions on 

the Green River downstream of the Flaming Gorge dam, how they affect the native warmwater 

fish populations (particularly the 3 major endangered species, humpback chub, Colorado 

pikeminnow, and the razorback sucker), and suggested mitigations of the adverse effects to 

ensure the continued existence of these fish species.

Results relevant to EMAP: The historic abundance and habitat needs of each of the species of 

interest is covered in a separate chapter. For example, critical habitat designated for Colorado 

pikeminnow makes up only about 29% of the species’ original range and occurs exclusively in 

the upper Colorado River basin, and 600 to 650 adult Colorado pikeminnow occur today in the 

Colorado River upstream of the Green River confluence. 

Geographic location: Region 8, Utah, Green River, xeric, eco20 

Keywords: fish, dams, water diversion, habitat degradation, nonnative species, flow variability, 

sediment, temperature 

URL: http://www.ead.anl.gov/pub/doc/flaminggorgeflowrecs.pdf

143
Author: Nehlsen, W.; Williams, J.E.; Lichatowich, J.A. 

Year: 1991 

Title: Pacific salmon at the crossroads: stocks at risk from California, Oregon, Idaho, and 

Washington 

Reference Type: Journal Article

Journal: Fisheries 

Volume: 16 

Issue: 2 

Pages: 4-21 

Value of reference: This is a landmark report of the status of salmon and steelhead on the 

West Coast of the U.S. It is extremely comprehensive and often cited. It lists the population 

status of 7 species (comprising 214 stocks), and the reasons for declines in individual bays and 

tributaries throughout the region; it also mentions changes from historical conditions. 

Few actual historical data are given; historical references reported are from varying years, 

depending upon what is available, and the year is usually not specified. For many of these 

species, the declines that have occurred even since the mid-1900s is so substantial, being 

closely associated with hydropower development which intensified at that time, that the most 

significant changes from an "historical" benchmark are captured in the period of the late 1900s. 

The data reported are therefore significant and noteworthy. 

Results relevant to EMAP: Since 1850s, development activities such as hydropower, fishing, 

logging, mining, agriculture, and urban growth have caused extensive losses in salmon and 

steelhead populations and habitats. 

A few examples of the numerous summary statements provided in this document: the Klamath 

River population of spring and summer chinook has undergone a 95% reduction from historical 

population levels, due to dams, irrigation diversions, mining, timber harvest, and floods; many 

native coho stocks on the southern Oregon coast have declined from historical levels of about 

2000 spawners to fewer than 100 and are now dominated by hatchery programs; in the 

Columbia River basin, historically large chum stocks in the lower river have declined to about 

0.5% of their historic level; at least 106 major populations of salmon and steelhead on the West 

Coast have been extirpated, and over 200 stocks have become extinct in the Columbia River 

basin, including 95 streams where chinook have disappeared, 83 for steelhead, 17 for coho, 

and 12 for sockeye (Oregon Trout, Personal communication by Nehlsen et al.) (see Table 2); 

natural production in the Columbia River basin is now about 4-7% of pre-development levels, 

which likely represents a significant loss of genetic diversity. 

With the loss of so many populations prior to our knowledge of stock structure, the historic 

richness of the salmon and steelhead resource of the West Coast will never be known; it is clear 

that what has survived is a small proportion of what once existed.

Geographic location: mountains, xeric, eco1, eco3, eco10, eco11, eco15, eco16, eco17, 

eco12, eco6, eco78, eco7, eco9, Pacific Northwest, Oregon, Washington, Idaho, California, 

Columbia River basin, Coast Range, West Coast, EPA Region 9, EPA Region 10 

Keywords: fish, salmon, status, habitat loss, agriculture, logging, dams, urban, nonnative 

species, fishing 

Abstract: The American Fisheries Society herein provides a list of depleted Pacific salmon, 

144
steelhead, and sea-run cutthroat stocks from California, Oregon, Idaho, and Washington, to 

accompany the list of rare inland fishes reported by Williams et al. (1989). The list includes 214 

native naturally-spawning stocks: 101 at high risk of extinction, 58 at moderate risk of extinction, 

54 of special concern, and one classified as threatened under the Endangered Species Act of 

1973 and as endangered by the state of California. The decline in native salmon, steelhead, 

and sea-run cutthroat populations has resulted from habitat loss and damage, and inadequate 

passage and flows caused by hydropower, agriculture, logging, and other developments; 

overfishing, primarily of weaker stocks in mixed-stock fisheries; and negative interactions with 

other fishes, including nonnative hatchery salmon and steelhead. While some attempts at 

remedying these threats have been made, they have not been enough to prevent the broad 

decline of stocks along the West Coast. A new paradigm that advanced habitat restoration and 

ecosystem function rather than hatchery production is needed for many of these stocks to 

survive and prosper into the next century. 

Notes: Williams, J.E. and others. 1989. Fishes of North America endangered, threatened, or of 

special concern: 1989. Fisheries (Bethesda) 14(6):2-20. 

145
Author: Nesler, T.P.; VanBuren, R.; Stafford, J.A.; Jones, M. 

Year: 1997 

Title: Inventory and status of South Platte River native fishes in Colorado 

Reference Type: Report

City: Fort Collins, CO 

Institution: Colorado Division of Wildlife, Aquatic Wildlife Section 

Value of reference: This report focuses primarily on current surveys of fish, but it also 

addresses the available historical information, utilizing Propst and Carlson 1986 (in this 

bibliography) as a basis for reporting and is thus a good companion article to that paper 

(although not a significant source of historical information on its own). The added useful 

information provided by this source is the mapped locations of historical vs. current collections 

in the basin (Figures 3-11). Although notable, the historical distributions cannot realistically be 

compared to modern distribution data because of a much lower sampling effort in the past. The 

article provides the list of native species, extirpated species, and species that are now 

considered common and at low risk of imperilment. It also provides a brief literature summary of 

the historical river (page 80). 

Results relevant to EMAP: The river channel of the South Platte is only 15% of its historical 

dimensions due to agricultural use and water diversions. Historically it was wide, shallow, 

braided, and sparsely vegetated. After spring runoff, the river was intermittent, often running 

underground. Today, irrigation return flows have created a perennial stream and raised water 

table. 

The historical composition of fish fauna and changes through time as a result of human impacts 

have not been well-documented. This article reviews the historical literature, but the lack of 

detail in historical survey literature prevents a meaningful comparison for most species. 

The article's focus is on the 1992-94 survey results, but the species list, historical summary, and 

maps are useful and will complement the historical information presented by Propst and Carlson 

1986--in this bibliography.

Geographic location: Colorado, South Platte River basin, eco25, plains, EPA region 8 

Keywords: fish, phab, agriculture, dams, water diversion 

Notes: Propst and Carlson. 1986. The distribution and status of warm water fishes in the Platte 

River drainage, Colorado. Southwestern Naturalist 31:149-67. 

146
Author: Northwest Power Planning Council 

Year: 1986 

Title: Compilation of Information on Salmon and Steelhead Losses in the Columbia River Basin 

Reference Type: Report

City: Portland, OR 

Institution: Columbia River Basin Fish and Wildlife Program 

Value of reference: This is a valuable document of over 200 pages that uses several different 

methods for estimating historical run sizes and losses of salmon and steelhead since presettlement. It was developed with extensive public review and comment and is frequently cited 

for the Pacific Northwest region. Numerous tables of historical data. 

It presents comprehensive information on historical and current run sizes of salmon and 

steelhead in the Columbia River basin. Data on historic fish runs have been gathered from 

every available source ranging from actual recorded fish counts over time to the accounts of 

Indian tribal elders and historical records from early settlers. Sources include historical, 

anthropological, and archaeological data. Descriptions of current runs are based on adult fish 

counts, redd (spawning nest) counts, and harvest records.

Results relevant to EMAP: Salmon and steelhead runs in the Columbia River basin ranged 

from about 10 to 16 million fish prior to a number of development activities by white settlers in 

the 1800s, whereas the current run size averages about 2.5 million fish, representing a loss of 

at least 75%. 

 

At one time, salmon and steelhead inhabited the entire Columbia River basin up to the Arrow 

Lakes in Canada and below Shoshone Falls on the Snake River. Since the mid-nineteenth 

century, the estimated salmon and steelhead habitat in the entire basin has declined from about 

13,000 miles of stream to only 9,000 miles, a 31% loss. 

The greatest losses of fish runs and habitat have occurred in the upper Columbia and upper 

Snake river areas, where much of the habitat has been permanently damaged by the federallyoperated Chief Joseph and Grand Coulee dams in the mid-Columbia River area and 

development in the Snake River Basin. 

The document examines the impact on fish runs of a variety of development activities including 

hydropower, fishing, irrigation, logging, mining, grazing, and agriculture. The major impacts 

caused by hydropower are blockage of fish habitat, alteration of fish habitat, and obstacles to 

juvenile fish passing downstream and to adult fish returning upstream to spawn.

Geographic location: Columbia River Basin, Oregon, Washington, Idaho, EPA Region 10, 

eco11, eco10, eco16, eco4, eco1, eco3, eco9, mountains, xeric 

Keywords: fish, salmon, steelhead, hydropower, dams, fishing, agriculture, logging, mining, 

grazing 

147
Author: Olden, J.D.; Poff, N.L.; Bestgen, K.R. 

Year: 2006 

Title: Life-history strategies predict fish invasions and extirpations in the Colorado River Basin 

Reference Type: Journal Article

Journal: Ecological Monographs 

Volume: 76 

Pages: 25-40 

Value of reference: Much of this paper is theoretical and provides a basis for assessing risk to 

native species from both biotic and abiotic drivers. It thereby illustrates the use of historical data 

to predict future risk of extinction. Of more direct use to EMAP is its summary of percent 

changes in native and nonnative fish species in the lower Colorado River basin before and after 

1980. This information constitutes Appendix D, which is on-line in the Ecological Archives 

M076-002-A4 (http://esapubs.org/archive/mono/M076/002/appendix-D.htm). 

The authors use historical data from the SONFISHES data base (developed by W.L. Minckley 

and others), which contains over 38,000 occurrence records for freshwater fishes from over 150 

years of research. Records include incidence, identity, and collection information for the 

complete holdings of major regional museum collections, numerous smaller holdings, and 

records from peer-reviewed and gray literature, and they are geo-referenced to within 1 km of 

their collection site in a GIS. This historical data base would likely be of value for other EMAP 

applications and data analyses (e.g., use of a different threshold year to define "historical"; or 

excluding records from Mexico) and is available on-line at 

http://desertfishes.org//na/gis/index.html. 

In this application, the historical period was defined as 1843-1980, and the modern period was 

1981 to 1999. The 1980 threshold corresponds with a major shift in sampling goals (see Fagan 

et al. 2005)

Results relevant to EMAP: Table D1 of the on-line Appendix D lists 23 native fish species and 

47 nonnative species of the lower Colorado River basin (including both U.S. and Mexican 

reaches between Glen Canyon Dam and the Gulf of California) and the distributional changes 

for each between the pre- and post-1980 threshold. Percent declines are given for native 

species, while the spread (km/yr) is given for each nonnative species. Declines range from 

100% to -14% (negative declines being an increase); nonnative species spread ranges from 0.0 

to 54.6 km/yr. 

Geographic location: Colorado River basin, Colorado, Utah, Arizona, EPA Region 8, EPA 

Region 9, xeric, mountains, eco21, eco20, eco22, eco23, eco81, eco14 

Keywords: fish, SONFISHES data base, nonnative species, prediction, extinction risk, historical 

occurrence data, species distribution, ranges, endangered fishes, functional niche, dams, river 

regulation 

Notes: For a related application, see Fagan et al. 2005 in this bibliography (different 2005 

publication than the one listed below). 

Two additional examples of the use of the SONFISHES data base to predict current risk of 

extinction and need for management and listing at different spatial scales can be found in: 

Fagan, W.L., C. Aumann, C.M. Kennedy, and P.J. Unmack. 2005. Rarity, fragmentation, and 

148
the scale dependence of extinction risk in desert fishes. Ecology 86(1):34-41. 

Olden, J.K., and N.L. Poff. 2005. Long-term trends of native and non-native fish faunas in the 

American Southwest. Animal Biodiversity and Conservation 28(1):75-89. 

149
Author: Osmundson, D. B.; Burnham, K. P. 

Year: 1998 

Title: Status and trends of the endangered Colorado squawfish in the upper Colorado River 

Reference Type: Journal Article

Journal: Transactions of the American Fisheries Society 

Volume: 127 

Issue: 6 

Pages: 957-970 

Value of reference: The article examines the factors that contribute to the episodic recruitment 

of young pikeminnow in the upper Colorado river. Though the link to historic abundance of 

pikeminnow is not presented in a quantitative fashion, the paper does relate what would have 

been historic hydrography and phab quality to successful pikeminnow reproduction.

Results relevant to EMAP: Colorado pikeminnow were once very abundant in the upper 

Colorado River basin including the Green, Yampa, White, and Uncompahgre tributaries. Today 

pikeminnow numbers are much reduced. Adult survival rates are fairly high (up to .87), 

indicating that adult survival is not a major constraint on population increase, but successful 

pikeminnow reproduction is rare. 

The results of this study show that high recruitment years follow extra high spring flows; 

historically, before dams and irrigation diversions, high spring flows were a common, almost 

yearly, phenomenon. High flows assist pikeminnow reproduction by flushing fine sediments from 

cobble bars and reducing the numbers of nonnative minnows.

Geographic location: Region 8, upper Colorado River basin, Colorado River, Green River, 

Yampa River, Utah, Colorado, eco20, xeric 

Keywords: Colorado squawfish, Colorado pikeminnow, upper Colorado River, endangered 

species, extirpation, recruitment, runoff, phab, fish, nonnative fish, hydrologic variability, 

sediment 

Abstract: Status of the Colorado River population of the endangered Colorado squawfish 

Ptychocheilus lucius (recently renamed the Colorado pikeminnow) was investigated by 1) 

estimating adult numbers, 2) evaluating frequency of reproduction and recruitment, 3) identifying 

trends via changes in size structure over time, and 4) examining historical accounts for clues to 

former abundance. Adults and subadults were systematically captured from 278 km of river 

during 1991-1994. Larvae and age 0 fish were systematically sampled in two reaches during 

1986-1994. Estimated number of adults in the upper 98 km averaged 253 individuals; estimated 

annual adult survival rate was 0.86. In the lower 181 km, estimates of subadults and adults 

combined averaged 344 individuals. A sizable pulse of subadults 300-400 mm long found in the 

lower reach in 1991 were from three year classes, 1985-1987. By 1992, these were distributed 

throughout the river. Although catch rates of larger adults did not increase significantly in the 

upper reach during 1991-1994, catch rates of fish less than 550 mm long increased fivefold. 

Size frequency analysis of lower reach fish indicated the 1985-1987 cohorts were the largest 

produced since before 1977, and no similarly strong year classes were produced subsequently. 

Estimated years of origin of these recruiting fish coincided with years of higher than average 

catch rates of larvae and age 0 fish in the upper reach and catch rates in subsequent years 

were comparatively low. Very few individuals less than 450 mm long were found in the upper 

reach during the past 15 years, suggesting that recruitment there is from colonization from the 

lower reach. In contrast, significant numbers of fish less than 400 mm in total length occurred in 

150
the upper reach during the mid-1970's. Abundance appears much lower than suggested in 

historical accounts. Low adult numbers and sporadic pulses of recruitment may make this 

population vulnerable to extirpation. Though adult survival rate is probably fairly constant, 

recruitment is highly variable and may represent the most important demographic factor to 

population persistence. 

151
Author: Patton, Timothy M.; Rahel, Frank J.; Hubert, Wayne A. 

Year: 1997 

Title: Using Historical Data to Assess Changes in Wyoming's Fish Fauna 

Reference Type: Journal Article

Journal: Conservation Biology 

Volume: 12 

Issue: 5 

Pages: 1120-1128 

Value of reference: The article details methodology for comparing historic (1960) fish survey 

data with recent (1990) fish survey data; even data with different sampling protocols. 

Comparisons of recent and historic data for the purpose of assessing species trends are 

frequently problematic due to differences in sampling designs, methodologies, and efficiencies. 

Nevertheless, historic data can be a valuable source of information for trend assessments. 

The article defines historic as "fish survey data from 1960". This would not be considered "presettlement"; however, few data exist on fish populations in this region that date back beyond the 

early part of the 20th century. A comparison of these different data sets is a place to start and a 

helpful benchmark to monitor change. 

Results relevant to EMAP: Findings include a general decline in species at the smaller spatial 

scale (reach, stream, etc), with less evidence of decline overall at the drainage scale. "Although 

this suggested that a drainage scale examination may be too coarse to detect changes in 

distribution, changes at this scale may be the most important: species extirpated at such a large 

scale represent the most serious declines and loss of evolutionary potential, and species 

expanding into new drainages likely represent artificial introductions." 

Among the declining native species, two habitat guilds are apparent. Species in the first guild 

(flathead chubs, plains minnows, silvery minnows, river carpsuckers, and channel catfish) are 

adapted to turbid rivers with silt and sand substrates historically common on the Great Plains. 

Reservoirs and diversion dams have stabilized flows and reduced silt loads and likely have led 

to declines among species in this guild. Species in the second guild (common shiners, finescale 

dace, horneyhead chubs, lake chubs, and mountain suckers) tend to occupy small to mediumsized streams with cool, clear water, and many require gravel substrates for spawning. Land 

management and irrigation practices have increased turbidity and siltation in many of these 

streams. 

Geographic location: Wyoming, Missouri River Drainage, eco17, eco18, eco25, eco43, plains, 

mountains, xeric, EPA region 8 

Keywords: historic fish survey, phab, fish, land management, irrigation practices, turbidity, 

reservoirs, diversion dams, plains, mountains, declining species 

Abstract: If conservation efforts are to be implemented before a species becomes imperiled, 

population declines must be identified before that species becomes extremely rare. Historic 

survey data are more useful than recent data for detecting such declines. We compared 1960's 

and 1990's fish survey data from 10 drainages in Wyoming (USA) in an effort to identify 

declining species, but these comparisons were problematic because of differences in sampling 

designs, methodologies, and efficiencies. We restricted our comparisons to locations common 

to both surveys and to presence and absence data; we adjusted our data to account for the 

more efficient sampling protocol of the 1990's survey; and we examined data at four nested 

152
spatial scales: site, stream, sub-drainage, and drainage. based on data not adjusted for gear 

bias, 12 our to 31 (39%) native species were collected in fewer locations during the 1990's 

survey even though we used more efficient sampling gear. Based on data adjusted for gear 

bias, the same 12 plus 4 additional native species (52%) showed declines. Fewer species 

appeared to have changing distributions at the drainage scale than at the smaller scales, but 

extirpations at the drainage scale represent the most serious declines. Despite the problems of 

comparing historic and recent surveys, we were able to make minimum estimates of species 

declines. Adjustment of data to account for gear bias allowed us to identify declines beyond a 

minimum estimate. 

153
Author: Pearson, W.D.; Kramer, R.H.; Franklin, D.R. 

Year: 1968 

Title: Macroinvertebrates in the Green River below Flaming Gorge Dam, 1964-65 and 1967 

Reference Type: Journal Article 

Journal: Proceedings of the Utah Academy of Science, Arts, and Letters 

Volume: 45 

Pages: 148-167 

Value of reference: This article reports conditions primarily in the mid-1900s, but since early 

macroinvertebrate data are generally scarce, it represents some of the only baseline data 

available for the basin. The Flaming Gorge Dam was closed in 1962. The authors summarize 

pre-1962 macroinvertebrate presence data from 5 sources (Table 3). These data are then 

compared to data collected after closure of the dam. 

The article serves 2 functions: 1) it provides baseline macroinvertebrate data from the early 

1960s for the Green River above Ouray, Utah; and 2) it allows a comparison of pre- and postimpoundment invertebrate communities for assessing the effects of the dam and changes in 

water physical attributes on the invertebrate community. Most invertebrate data are reported by 

genus or family. Table 3 reports presence data by taxon for pre- and post-impoundment 

periods. Table 4 gives abundance data (mean number per square meter) on rubble-gravel 

substrates at the first collection site downstream from the dam, 1965 and 1967 (postimpoundment). 

Results relevant to EMAP: Seasonal variations in flow were reduced after closure of the dam; 

summer, fall, and winter flows increased, and spring flow decreased (data in Table 1). Winter 

temperatures increased, while summer temperatures decreased, compared to preimpoundment years. Mean monthly pre-impoundment temperatures ranged from 0.5 to 21.0 

degrees C at Greendale, while mean monthly post-impoundment temperatures ranged from 2.0 

to 12.5 degrees C. At greater distances downstream from the dam, the river physical condition 

seemed to transition back to its pre-impoundment state. 

Nine invertebrate forms reported from the area prior to the dam were not collected in the postimpoundment study, while 10 groups not previously reported in the area were collected after 

impoundment. The latter group were not considered recent invaders, but were assumed to 

have been missed in previous sampling efforts. The community at the sampling location directly 

below the dam had a much lower species richness compared to pre-dam conditions. Species 

composition was not noticeably altered below the confluence of the Yampa River. Invertebrate 

communities between the dam and the confluence of Vermillion Creek were altered, likely as a 

response to lower summer water temperatures, which caused the near disappearance of one 

species of Baetis from the first 9.5 km below the dam. 

Mean number of individuals on rubble-gravel substrates ranged from 11 (several species) to 

40,124 (Baetis sp.) per m2

. Other abundance data are given in Table 4.

Geographic location: Utah, Colorado Green River basin, EPA region 8, eco20, xeric 

Keywords: macroinvertebrates, phab, dams, historical data, baseline data 

Notes: For additional information about invertebrates above Flaming Gorge, see Binns, N.A. 

1965. Effects of rotenone treatment on the fauna of the Green River, WY. Unpublished 

Master's Thesis, Oregon State University, Corvallis, OR. 258 p. 

154
Author: Peters, E. J.; Schainost, S. 

Year: 2005 

Title: Historical changes in fish distribution and abundance in the Platte River in Nebraska 

Reference Type: Book Section

Editor: Rinne, J. N.; Hughes, R. M.; Calamusso, B. 

Book Title: Historical changes in large river fish assemblages of the Americas. 

City: Bethesda, Maryland 

Publisher: American Fisheries Society 

Pages: 239-245 

Value of reference: The historical changes stated in the title are inferred rather than clearly 

stated due to a general lack of historical information and a presentation that only indirectly 

addresses the historical changes in fish assemblages. Though the mainstem of the Platte is 

mainly in Nebraska, there is some discussion in the article of the forks of the Platte, North and 

South. The chapter was included even though the mainstem of the Platte is outside the EMAP 

sampling region because there are few sources available about the fish assemblages of the 

plains.

Results relevant to EMAP: Little is known of the fishes from the Platte River basin prior to the 

time when diversions and damming had already altered flows. The earliest published fish 

collections are those of Meek (1895) and Evermann and Cox (1896). Collection records in 

Nebraska prior to 1945 documented 47 species from the Platte River of which one, the common 

carp, was an introduced species. Today Platte River fish species number 100, most of them 

introduced. In Table 1, p. 243, the authors show changes in ranks of percent frequency of 

occurrence for fish species reported in collections from the Platte River before 1945 (pre- large 

scale fish introductions) and after 1985. 

Two groups of fish species are declining for opposite reasons. Headwater or tributary species 

that favor clear warm water and clean gravel substrate (10 species listed), such as brook 

stickleback, central stoneroller, and johnny darter, are declining due to a shortage of habitat, 

and are listed as species of concern in the plains states. The other declining group contains 

species typical of large, turbid rivers, such as shovelnose sturgeon, flathead chub, and sauger. 

Goldeye and sauger, for example, have been extirpated from the North and South Platte and 

occur in small numbers in the lower Platte in Nebraska. The lower Platte River retains the wide, 

shifting sand bar habitats and high turbidity characteristic of the pre-settlement river. 

North Platte River - Reservoirs and diversion canals were completed in the mid-1940's. The 

river has been reduced from multiple channels to a single channel and sections are dewatered. 

South Platte River - River flow in Colorado is augmented from interbasin transfers of Colorado 

River water. However, virtually all flow is diverted in Colorado and returned to the river as 

sewage treatment water return flows downstream of the metropolitan areas along the front 

range.

Geographic location: EPA Region 7, EPA Region 8, Nebraska, Colorado, Wyoming, Platte 

River, North Platte River, South Platte River, eco25, eco21, high plains, southern Rockies 

Keywords: fish, dams, water diversion, agriculture, pollution, nonnative species 

Abstract: From its headwaters in the Rocky Mountains, the Platte River drains 230,362 km2

 in 

Colorado, Wyoming, and Nebraska. The Platte River is formed by the confluence of the North 

Platte and South Platte near the city of North Platte, Nebraska, and receives additional flow 

155
from the Loup and Elkhorn rivers that drain the Sand Hills region of Nebraska. Water diversions 

for mining and irrigation began in the 1840's in Colorado and Wyoming, and irrigation diversions 

in Nebraska began in the 1850's. Construction of dams for control of river flows commenced on 

the North Platte River in Wyoming in 1904. Additional dams and diversions in the North Platte, 

South Platte, and Platte rivers have extensively modified natural flow patterns and caused 

interruption of flows. Pollution from mining, industrial, municipal, and agricultural sources, and 

introductions of 24 nonnative species have also taken their toll. Fishes of the basin were little 

studied before changes in land use, pollution, and introduction of exotic species began. The 

current fish fauna totals approximately 100 species from 20 families. Native species richness 

declines westward, but some species find refugia in western headwaters streams. Declines in 

26 native species have led to their being listed as species of concern by one or more basin 

states. 

156
Author: Pilsbry, H.A.; Ferriss, J.H. 

Year: 1911 

Title: Mullusca of the southwestern states, V: the Grand Canyon and northern Arizona 

Reference Type: Journal Article

Journal: Proceedings of the Academy of Natural Sciences of Philadelphia 

Volume: 63 

Pages: 174-199 

Value of reference: The article provides baseline information on the snails of the Grand 

Canyon and the northern Arizona plateau, an area that had previously not been explored for 

snails. It lists the species collected, organized by family, listing all collection stations and the 

exact collection spot. Much of the document is taxonomic description of the species, but the 

presence and distribution in the region would be the most valuable information for EMAP. 

Collections were done by searching through sediment layers to find species that would likely be 

seeking refuge from the arid climate. Since snails are not active most of the year, they might be 

easier to miss in an EMAP sampling visit. Therefore this information is valuable as the most 

complete listing of species found historically in the area. 

Results relevant to EMAP: The annotated list of species found in the area begins on page 178 

and is organized by species and locality where collected. This baseline information can be used 

for reconstruction of species richness or presence for this area. It is difficult to discern from 

descriptions whether all collections sites are on a stream, but most seem to be associated with 

a spring or seep, if not a tributary stream; many locations were high in the canyon.

Geographic location: Arizona, Colorado River basin, EPA region 9, eco22, xeric 

Keywords: macroinvertebrates, snails, baseline data, historical data 

157
Author: Platts, W. S.; Gebhardt, K. A.; Jackson, W. L. 

Year of Conference: 1985 

Title: The effects of large storm events on basin-range riparian stream habitats 

Reference Type: Conference Proceedings

Editor: Johnson, R. R.; Zieball, C. D.; Patton, D. R.; Ffolliott, P. F.; Hamre, R. H. 

Conference Name: Riparian ecosystems and their management: Reconciling conflicting uses 

Conference Location: Tucson, Arizona 

Publisher: U.S. Forest Service General Technical Report RM-120 

Pages: 30-34 

Value of reference: The value of this reference is to document that woody debris was an 

important component of stream channel structure even in aspen-dominated Northern Great 

Basin riparian ecosystems. 

Results relevant to EMAP: In the Jarbidge Mountains of northeastern Nevada, where there is 

a concentration of EMAP sites, riparian zones historically were shaded by large aspen. 

Decomposing aspen logs in streams provide evidence of this. However, due to heavy grazing 

pressure (cattle eating young tree sprouts), the last generation of aspen has not been replaced. 

The disappearance of wood in the channel allows floods to scour the alluvium and cause 

accelerated erosion and incision of the stream channel. 

Cutthroat trout were able to survive the floods in these streams. The authors conclude that 

drought conditions may have more effect on cutthroat numbers than high water events. Where 

streamside vegetation was abundant, flood impacts to fish populations were minimal.

Geographic location: Nevada, mountains, xeric, eco80, Great Basin, basin and range, 

Jarbidge Mountains, EPA Region 9 

Keywords: fish, cutthroat trout, grazing, sediments, erosion, woody debris, riparian vegetation, 

phab 

158
Author: Propst, D.L. 

Year: 1999 

Title: Threatened and endangered fishes of New Mexico. 

Reference Type: Report

City: Santa Fe, NM 

Institution: New Mexico Department of Game and Fish 

Report Number: Tech. Rpt. No. 1 

Value of reference: Although New Mexico is not in the EMAP-West region, several major 

drainages flow out of the state into Arizona and Colorado, and the corresponding fish species 

occur in those neighboring states. The report focuses on the distribution of fish in New Mexico, 

but makes numerous statements about species' total historical ranges and relative abundance 

in portions of the basins outside of New Mexico. In the second part of the report, 23 species are 

profiled separately (although not all species were historically distributed in AZ or CO). For each 

profile, sections on listing status, distribution and current population status include known 

historical and current distribution throughout the species' ranges in all states and basins where 

they occurred, as well as factors contributing to their decline. This report would be valuable for 

reconstructing historic ranges and comparing them with the current, reduced ranges. 

The report includes an extensive bibliography, representing syntheses of numerous publications 

for each species' profile. "Historical" does not necessarily equate to pre-settlement, but it 

encompasses all of the known records of a species in its former distribution.

Results relevant to EMAP: Typical results are illustrated here, using Gila chub (the first 

species profile in the report) as an example: 

The Gila chub is a species of special concern in Arizona. Historically, it occurred in suitable and 

rather specialized habitat throughout much of the Gila River drainage in southwestern New 

Mexico and central and southeastern Arizona. Its preference historically was for cienéga 

habitats. In Arizona, Gila chub persist in small headwater streams (many are springs or 

cienégas) tributary to the San Pedro, Santa Clara, San Francisco, Gila, Verde, and Agua Fria 

rivers. Although Gila chub still occur in a moderate number of localities within its historic range 

in Arizona, its numbers are low at many locations, and populations are considered unstable. 

A variety of factors probably contributed to the decline of Gila chub, but loss of cienéga habitats 

by dewatering and channelization were probably the most detrimental. Introduction of nonnative 

piscivores also contributed to elimination of the chub from portions of its historic range.

Geographic location: Arizona, Colorado, eco23, eco26, eco20, eco21, eco22, EPA region 9, 

EPA region 8, Arkansas River basin, Colorado River basin, Gila River basin, xeric, mountains, 

plains 

Keywords: fish, altered water flow regime, channelization, nonnative species, historical ranges 

159
Author: Propst, D.L.; Carlson, C.A. 

Year: 1986 

Title: The distribution and status of warmwater fishes in the Platte River drainage, Colorado 

Reference Type: Journal Article

Journal: The Southwestern Naturalist 

Volume: 31 

Issue: 2 

Pages: 149-167 

Value of reference: Fish data of the late 1970s are compared with historical data to assess 

changes in community composition in the South Platte drainage. There have been few 

publications over time reporting on the warmwater ichthyofauna of the South Platte River and 

none for the North Platte, and most previous studies have been geographically restricted. 

Therefore, this article is of value for gathering and reporting compositional changes in the 

historical community. Historical data included all past reports of a species, dating as far back as 

1891. 

Annotated species accounts from present-day sampling are given in various levels of detail, 

including citations for studies in which a species was previously sampled, where the species is 

currently found or not found, presence/absence or relative abundance compared to historical 

reports, whether the species is exotic, and reasons for decline. 

The species assemblage is grouped into 4 categories: rare, common, uncommon, and 

nonnative. Each category is discussed, and reasons for decline or low numbers are given. 

Species in each category are addressed singly or as a group, and generalizations are made 

regarding their status as compared to historical abundance. 

Results relevant to EMAP: The native species composition of the Platte River in Colorado has 

never been diverse. Thirty-one fish species were historically present in the South Platte The 

lake chub, hornyhead chub, and blacknose shiner have been extirpated. Another three species 

were not collected in the present study, and it is not apparent whether they are still present. 

Current distribution and abundance is a factor of historical distribution and status, and habitat 

alterations due to human impacts. Extensive alterations in the basin are due to water 

diversions, dams, impoundments, ground water pumping, channelization, and pollution. 

Table 2 lists all fish species grouped by abundance category, excluding three reported 

historically but not collected and three known to be extirpated, and including nine non-native 

species. Rare species (8 of 31 historical species) have been restricted historically and more 

recently have experienced habitat reduction as a result of human impacts. Uncommon species 

(6 of 31 historical species) were considerably more widespread and common historically than 

they are presently; common species (11 of 31 historical species) have maintained their 

populations largely because of wide environmental tolerances, but they have been affected by 

habitat degradation or pollution in stressed reaches. 

Geographic location: Colorado, South Platte River basin, eco25, EPA region 8, plains 

Keywords: fish, water diversion, dams, ground water pumping, channelization, pollution, 

warmwater fishes 

160
Abstract: In a 2.5 year (1978-1980) study of the lotic warmwater fish communities of the Platte 

River Basin, Colorado, 25 native and 9 non-native species were collected. Three natives 

(Nocomis biguttatus, Couesius plumbeus, and Notropis heterolepis) have been extirpated. 

Salmo clarki stomins was not collected, nor were the provisional natives, Stizostedion vitreum

and Carpoides cyprinus. Eleven native species were rare in the basin. The rarity of each was 

strongly correlated with their limited historic distributions, rather special habitat requirements, 

and intolerance of environmental stresses. Six native species were historically more common 

and widespread, but habitat deterioration associated with European settlement has caused their 

decline. The remaining native species (8) were common and widely distributed. The common 

carp (Cyprinus carpio) was the only common non-native fish. Lack of suitable habitat is 

believed responsible for the rarity of other non-native species. 

Notes: See also Nesler et al. 1997 (in this bibliography) as a companion article which provides 

maps of plotted collection locations from "historical" surveys in the South Platte drainage. 

Nesler, T.P., R. VanBuren, J.A. Stafford, and M. Jones. 1997. Inventory and status of South 

Platte River native fishes in Colorado. Colorado Division of Wildlife, Aquatic Wildlife Section, 

Fort Collins, CO. 

161
Author: Rahel, F.J.; Thel, L.A. 

Year: 2004 

Title: Flathead Chub (Platygobio gracilis): a technical conservation assessment 

Reference Type: Electronic Source

Producer: USDA Forest Service, Rocky Mountain Region. 

Access Year: 2006 

Access Date: June 14 

Value of reference: This is primarily a management document, but it contains information on 

what is known of the historical distribution of the flathead chub. It also reports on current listing 

and population status, habitat requirements, and threats to the species. Although a significant 

portion of the chub's range is in Montana, this report does not address it because it is outside of 

the Forest Service region 2 management jurisdiction. 

Results relevant to EMAP: In Colorado, flathead chubs historically occurred in the Arkansas 

River up to Salida, but specimens have not been collected recently upstream of a large 

diversion on the Arkansas River near Florence, Colorado. It is considered a species of special 

concern in Colorado and as threatened in Kansas where it historically occurred in the large 

rivers draining from Colorado. With only one exception, it has not been sampled in Kansas 

since 1994. In South Dakota, flathead chubs were common and characterized as the dominant 

minnow species in the western tributary rivers and larger streams of the Missouri River. To the 

north and east of the Missouri River, flathead chubs occurred only in the lower portions of larger 

tributaries. Currently flathead chubs continue to be considered common in the rivers and larger 

streams of western South Dakota. Recent surveys found flathead chubs to be common in the 

Moreau River, the Cheyenne River, and the Belle Fourche River. In Wyoming, flathead chubs 

were historically present in the North Platte and Little Missouri rivers but are now known to 

occur only in very low numbers in the North Platte River and are likely much reduced in 

numbers in the Little Missouri River. Currently, they are widely distributed in the rivers of the 

northeast part of the state, including the Big Horn, Tongue, Powder, Little Powder, Belle 

Fourche, and Cheyenne river systems. 

Loss of turbid conditions, adequate in-channel flow, and habitat connectivity associated with 

water impoundment are major threats to this species. The species remains widespread 

throughout much of its historical range, but it is unknown if remaining populations are stable or if 

the species is continuing to decline. Competition with nonnative species also has a negative 

effect on populations of the flathead chub. 

Geographic location: South Dakota, Wyoming, Colorado, Missouri River basin, Arkansas 

River basin, EPA Region 8, eco43, eco42, eco25, eco26, plains, Missouri River basin, Arkansas 

River basin, Platte River basin 

Keywords: fish, altered water flow regime, dams, nonnative species 

URL: http://www.fs.fed.us/r2/projects/scp/assessments/flatheadchub.pdf

162
Author: Rees, D.E.; Carr, R.J.; Miller, W.J. 

Year: 2005 

Title: Plains minnow (Hybognathus placitus): a technical conservation assessment 

Reference Type: Electronic Source

Producer: USDA Forest Service, Rocky Mountain Region 

Access Year: 2006 

Access Date: June 12 

Value of reference: This report expands on Cross and Moss 1987 (also in this bibliography) 

with respect to a single species in the plains. The authors cite Cross and Moss frequently, but 

their summary covers the broader region outside of Kansas, including states in EPA Region 8. 

They note the absence of distributional data for plains minnow prior to settlement, and state that 

it impossible to know the entire historical distribution of the species. However, trends since the 

mid-20th century and human impacts in the region are discussed. The status and decline of 

plains minnow is summarized for the major basins draining the east side of the Rocky 

Mountains. 

Results relevant to EMAP: The plains minnow was historically distributed in suitable habitat 

throughout the Arkansas River, Platte River, Kansas River, and Missouri River basins, including 

the following states in the EMAP-West region: North and South Dakota, Montana, Wyoming, 

and Colorado (they have been introduced into Utah). It maintains stable populations locally, but 

its range has been restricted in South Dakota and Montana, while both its range and abundance 

are in decline in Montana, Wyoming, North Dakota, and Colorado. 

It was once the most common fish of the Arkansas River system, but its abundance and 

distribution have decreased substantially, and it now constitutes less than 1% of the overall fish 

population in that basin; it has possibly been extirpated from some drainages in Colorado. 

Changes in the Missouri River have led to a less severe decline of the species there, and 

tributary populations in eastern Wyoming are currently stable. The potential for further declines 

in distribution and abundance is high across the species' range. 

An altered flow regime, groundwater pumping, and impoundments have reduced water quality 

and altered the natural flood regime necessary to induce spawning. A loss of shifting channels 

and gravel bars has resulted from water diversions, impoundments, land uses that alter flow 

regimes, and groundwater mining, leading to degraded habitat and loss of natural disturbances 

to which the plains minnow is adapted. The larger impact of these pressures has been the 

fragmentation of metapopulations. Competition with and predation by nonnative fish species is 

an important potential impact, but it is not fully understood at present.

Geographic location: North Dakota, South Dakota, Montana, Wyoming, Colorado, EPA 

Region 8, eco43, eco25, eco26, eco42, plains, Missouri River basin, Arkansas River basin, 

Platte River basin 

Keywords: fish, nonnative species, habitat degradation, habitat fragmentation, altered water 

flow regime, groundwater pumping, water diversion 

URL: http://www.fs.fed.us/r2/projects/scp/assessments/plainsminnow.pdf 

163
Author: Rinne, J. N. 

Year of Conference: 2004 

Title: Forest and fishes: Effects of flows and foreigners on southwestern native fishes 

Reference Type: Conference Proceedings

Editor: Scrimgeour, G. J.; Eisler, G.; McCulloch, B.; Silins, U.; Monita, M. 

Conference Name: Forest Land-Fish Conference II: Ecosystem stewardship through 

collaboration 

Conference Location: Edmonton, Alberta 

Pages: 119-124 

Value of reference: The author reviews the historic and present day occurrence of the fishes of 

Arizona as well as the chronology of alterations to the natural hydrology of the state. 

Results relevant to EMAP: 75% of the riverine habitats in Arizona have been either lost or 

altered between 1911 and 1970. Diversions on the Gila River constructed in 1928 dried the Gila 

River to its confluence with the Salt River. Other major tributaries to the Gila, such as the San 

Pedro, San Simon and Santa Cruz Rivers have been dried due to groundwater pumping. 

Six species of fish are now on the endangered or threatened list in Arizona. The Gila topminnow 

was very common during early settlement times. Now it persists in fewer than a dozen isolated 

springs in southern Arizona. The razorback sucker was once so abundant that it was pitchforked 

from canals and used as fertilizer. The Colorado pikeminnow (formerly squawfish) and bonytail 

chub persist today only as a result of restoration programs. 

The paper includes tables that illustrate how flood flows favor native fishes and drought periods 

(e.g., 1994-2003) result in increases in nonnative species.

Geographic location: eco81, eco79, eco22, eco23, eco14, Arizona, Region 9, xeric, 

mountains, Gila River, San Pedro River, Salt River 

Keywords: fish, Colorado pikeminnow (squawfish), dams, habitat degradation, nonnative 

species, hydrologic variability, water diversions 

Abstract: Habitat alteration in physical (stream channel characteristics), chemical (nutrients, 

temperature), or biological (introduced species) form can have dramatic effects on native 

southwestern USA fishes. Southwestern flow regimes, their alterations, and introduction of alien 

species have had a dramatic, negative impact on native southwestern fishes. The cumulative 

and interactive impacts may result in various responses by native fish assemblages. Managers 

should not expect the same result when one or more factors are in operation that may affect an 

aquatic ecosystem in the southwestern USA. Ultimately, consideration of temporal-spatial 

influences, natural factors, interactions of factors, and sound monitoring or research activities 

will determine which factors most influence southwestern fish assemblages in respective 

situations. 

Notes: A related paper that includes a description of the historic hydrologic variability (i.e., rivers 

turbid during spring runoff, clear during base flow, and intermittent in lower reaches during 

drought), and a map of the hydrology of Arizona showing 20th Century changes: 

Rinne, J. N., and J. A. Stefferud. 1999. Single versus multiple species management: Native 

fishes in Arizona. Forest Ecology and Management 114:357-365. 

164
Author: Rinne, J. N.; Simms, J. R.; Blasius, H. 

Year: 2005 

Title: Changes in hydrology and fish fauna in the Gila River, Arizona-New Mexico epitaph for a 

native fish fauna? 

Reference Type: Book Section

Editor: Rinne, J. N.; Hughes, R. M.; Calamusso, B. 

Book Title: Historical changes in large river fish assemblages of the Americas. 

City: Bethesda, Maryland 

Publisher: American Fisheries Society 

Pages: 127-137 

Value of reference: This book chapter summarizes earlier articles and gathers results from the 

gray literature about the Gila River and its tributaries concerning historic hydrology and native 

fish species and their present day status.

Results relevant to EMAP: Historically, the Gila River between Florence and Phoenix, Arizona 

was about a kilometer wide, scattered with beaver ponds, shaded by cottonwood gallery forest, 

and "teeming with fishes." The Gila was described as a large, essentially permanent stream of 

clear to sea green water with a well-defined channel flanked by numerous cottonwoods and a 

dense growth of willows and cane. In 1848 Emory described the river as "wide and rich" and 

alive with geese and ducks. By 1920 this same area was described by Ross (1923) as "desolate 

wastes of sand and silt." 

Twenty fish species were native to the Gila River basin (listed in Table 1 on p. 130). Four of 

these species (Monkey Spring chub, Santa Cruz pupfish, Colorado pikeminnow, razorback 

sucker) have been extirpated, 8 species are endangered (includes pikeminnow and razorback 

sucker), two species are threatened, and two species are state listed species of concern. The 

pikeminnow and razorback sucker once ran in spawning schools up the Gila and Salt rivers. 

Razorback suckers were once removed from canals in the Phoenix valley with pitchforks 

because they were so numerous they blocked the water flow. The last pikeminnow was taken in 

the Gila basin in 1950. The razorback sucker has been reintroduced, but is not self sustaining. 

Gila trout persist naturally in a few headwater streams in New Mexico. Nonnative fish (40 

species) dominate the Gila River today, particularly in the lower reaches where there are no 

native fish present.

Geographic location: Arizona, Gila River, EPA Region 9, eco23, eco79, eco81, xeric 

Keywords: dams, water diversion, nonnative species, historical, hydrology, fish, xeric 

Abstract: The Gila River originates in southwestern New Mexico and courses its way for over 

700 km to the west before emptying into the main-stem Colorado River near Yuma, Arizona. 

Historically, this river was a major watercourse across the Sonora Desert of Arizona. At present, 

main-stem dams and numerous diversions have markedly altered the historic hydrology of the 

river. Seventeen native species once occupied the main stem of this large southwest desert 

river. More than twice that number (40) of nonnative fish species have been introduced into the 

waters of the Gila over the past century. Currently, less than half of the native fauna is present 

in the main stem and then primarily in the upper three reaches of the river. The majority of the 

species (70%) are federally listed as threatened, endangered, or sensitive. The combination of 

hydrological alteration and accompanying introductions of nonnative, principally sport fishes has 

basically extirpated the native fauna in all but the uppermost reaches of the Gila River main 

stem. 

165
Author: Robison, R.S. 

Year: 1957 

Title: The Yakima River--historical and present Indian fishery 

Reference Type: Report

City: Seattle, WA 

Institution: Washington Department of Fisheries 

Pages: 13 

Value of reference: Report provides rough estimates of pre-settlement salmonid abundance 

and catches by Native Americans in the Yakima River basin. The earliest estimates are for the 

period prior to 1848, which is significant because the Yakima Valley was developed very early 

for agriculture, and this represents probably the best estimate of a true pre-settlement salmon 

population. These estimates provide baseline data for numbers of salmonids that the basin was 

capable of supporting before major impacts destroyed or prevented access to spawning habitat.

Results relevant to EMAP: The dominant native fish species of the Yakima River were chinook 

salmon, sockeye salmon, coho salmon, steelhead trout, cutthroat trout, dolly varden trout, 

whitefish, squawfish and suckers. Salmon ran up to Keechellus Lake in the headwaters of the 

Yakima River in the Cascade Mountains. Based on the estimated number of pre-settlement 

Indian families and average consumption per family, the author estimates that the total Yakima 

River catch was 160,000 salmon annually prior to settlement. He further states that the actual 

run to the river and its tributaries could easily have been 3 times the catch or 480-500 thousand 

salmon. 

From 1847 to 1875, harvest by Native Americans apparently dropped from 160,000 to 20,000 

salmon annually. From 1875-1906, runs were still declining, but greater fishing effort kept the 

catches at 20,000 annually. The catch dropped to a low of 1000 by 1930 

Streambed assessments in the 1950s led to the conclusion that available habitat in the basin 

could support at least 500,000 spawning salmon each year. The construction of irrigation 

diversion dams, beginning in 1850, created migration barriers, and diversion ditches led salmon 

into orchards where they died. Other early impacts were log drives, mining, and over-fishing. 

(Note: The report does not address impacts occurring downstream in the Columbia River, 

which could have impacted runs if their timing coincided.)

Geographic location: Yakima River basin, Washington, EPA region 10, mountains, xeric, 

eco10 

Keywords: fish, water diversion, dams, mining, logging, fishing 

166
Author: Roemhild, G. 

Year: 1982 

Title: The Trichoptera of Montana and ecological notes 

Reference Type: Journal Article

Journal: Northwest Science 

Volume: 56 

Issue: 1 

Pages: 8-13 

Value of reference: The diversity of aquatic macroinvertebrates is poorly represented in early 

literature. Although this synthesis report of Trichoptera distribution in Montana was made more 

than a century after settlement, it can be used to gauge the level of knowledge of the diversity of 

this order prior to 1980. Following five years of surveys, the author collected 78 species 

reported from Montana for the first time (54% increase in recorded diversity). The author also 

identifies portions of the region where more work was needed to adequately describe the 

Trichoptera fauna, including the southwestern, southeastern, and northeastern portions of the 

state. While this is a recent work, it helps to characterize some of the challenges of using 

anecdotal historical macroinvertebrate data for reconstructing reference conditions. References 

such as this help to highlight the limits of what can be gleaned regarding macroinvertebrate 

diversity and geographic distributions from historic literature prior to systematic collection 

activities. 

Results relevant to EMAP: Between 1970 and 1980, the number of recorded species of 

Trichoptera from Montana increased from 100 (Newell 1970) to 222 (122% increase in recorded 

species diversity), resulting from a series of systematic surveys. This reference provides useful 

baseline data for Trichoptera distribution in Montana up to that date, since the notes concerning 

ecological preferences and distribution are drawn from a number of previous publications. The 

author collected 204 of 222 species (92%) known to exist in Montana during the late 1970s and 

1980, including 78 species that had not previously been reported. During the same general 

timeframe, others collected specimens of many of the remaining 18 species known to exist in 

the state, but not collected by the author. Geographic distribution, altitudinal distribution, habitat 

affinity, water temperature preference, and relative abundance information are provided that 

may be helpful for reconstructing potential historical distributions for each species. 

Geographic location: Region8, Region10, Plains, Mountains, Montana, North Dakota, Idaho, 

Oregon, Eco15, Eco16, Eco17, Eco18, Eco41, Eco42, Eco43 

Keywords: macroinvertebrates; Trichoptera; historical data 

Abstract: The known Montana Trichoptera is comprised of 14 families, 69 genera, and 222 

species. Seventy-eight species are reported from Montana for the first time. One hundred sixtyseven species (77 % of the total) are known to occur on both sides of the continental divide, 22 

species (10 %) occur on the east side only, and 29 species (13 %) occur only west of the divide. 

Notes: Newell, R. L. 1970. Checklist of some aquatic insects from Montana. Proc. Mont. Acad. 

Sci. 30:45-56. 

167
Author: Rucks, M.J. 

Year: 1984 

Title: Composition and trend of riparian vegetation on five perennial streams in southeastern 

Arizona 

Reference Type: Book Section 

Editor: Warner, R.E.; Hendrix, K.M. 

Book Title: California Riparian Systems: Ecology, Conservation, and Productive Management. 

City: Berkeley, California 

Publisher: University of California Press 

Pages: 97-107 

Value of reference: Though the sample size is small, the more highly disturbed streams are 

compared to a reference stream where grazing had been excluded since 1973. There is no 

historical data used in the study, and there is an assumption that the broadleaf community was 

once more prevalent along Arizona streams. It is also unclear whether the streams/rivers are 

similar in size and discharge. They were selected because they all occur on BLM lands. The 

value of this article is in the observation that riparian vegetation on Arizona streams that is 

subject to prolonged disturbance evolves away from a broadleaf community toward a so-called 

riparian scrub community. 

Results relevant to EMAP: The reference stream where grazing had been excluded was the 

only one of the five streams to have a good representation of broadleaf tree seedlings (Fremont 

cottonwood, Arizona sycamore, Arizona walnut, velvet ash) in the 1-3 inch size class. Other 

sample sites may have had mature broadleaf species represented, but the seedling size class in 

each case was absent or heavily browsed by cattle. 

The author recorded the % of broadleaf trees in the seedling size class and the % of seedlings 

browsed by cattle. For example, at Bonita Creek, 1.5% of willows were in the seedling sizeclass, and 67% of these were browsed. 

The author concludes by saying that three of the five streams show a trend toward replacement 

of the broadleaf riparian community by riparian scrub (such as saltcedar, burro brush, and 

mesquite).

Geographic location: Arizona, xeric, EPA Region 9, eco79, eco23, Aravaipa Creek, Gila River, 

San Francisco River 

Keywords: riparian vegetation, phab, grazing 

Abstract: Composition and trend of 78 km (49 mi) of riparian vegetation on five watercourses 

was determined. Aravaipa Creek has been excluded from cattle since 1973 and was the only 

study area with a dominant broadleaf riparian community and a trend towards maintaining this 

community. 

168
Author: Rumble, M.M.; Sieg, C.H.; Uresk, D.W.; Javersak, J. 

Year: 1998 

Title: Native woodlands and birds of South Dakota: past and present 

Reference Type: Report

City: Fort Collins, CO 

Institution: U.S. Department of Agriculture, Forest Service, Rocky Mountain Research Station 

Pages: 11 

Report Number: Research Paper No. 8 

Value of reference: The authors use historical and present bird community and General Land 

Office Surveys, historical photos, and early journal excerpts to reconstruct the general character 

of pre-settlement riparian areas along the Missouri River and its tributaries in South Dakota. 

The intent was to test the hypothesis that woodlands were expanding and the bird community 

was changing as a result, a process which had been hypothesized for the Platte River in 

eastern Colorado (Knopf 1986). This paper does not attempt to determine change in the 

amount of woodlands between pre-settlement and the present; it simply reported an historical 

condition based on several pieces of evidence. It includes a section describing woodlands 

along the Missouri River and larger tributary streams in pre-settlement times.

Results relevant to EMAP: Extensive native woodlands occurred in the valleys of the Missouri 

River and its tributaries in central and western South Dakota in the 1870s and 1880s. Canyons 

were filled with deciduous trees, including cottonwood, green ash, willow, oak, and wild plum. In 

many places the under story was very thick. Many large pieces of driftwood were left by 

torrents and floods that scoured the floodplain and exposed roots. Early 20th century 

photographs of mature trees indicate that trees were established well before settlement.

Geographic location: South Dakota, Missouri River basin, eco43, EPA region 8, plains 

Keywords: phab, historical data, GLO notes, historical photographs 

Notes: Knopf, F.L. 1986. Changing landscapes and the cosmopolitism of the eastern Colorado 

avifauna. Wildlife Society Bulletin 14:132-142. 

169
Author: Samson, Fred B.; Knopf, Fritz L.; Ostlie, Wayne R. 

Year: 1998 

Title: Status and Trends of the Nation's Biological Resources: Regional Trends of Biological 

Resources--Grasslands 

Reference Type: Electronic Source 

Producer: Northern Prairie Wildlife Research Center Online 

Access Year: 2005 

Access Date: July 2005 

Last Update Date: January 21, 2000 

Value of reference: This chapter highlights the status and trends of the main bodies of North 

American grasslands; the tall-grass prairie, the mixed-grass prairie, and the short-grass prairie. 

It features the animals and plants dependent on native grassland and attempt to provide insight 

into the relationship between remaining native grassland and biological resources by reviewing 

available, current information and by describing threats. 

Great Plains stream ecology is closely connected to the land use practices now common to the 

region. This source outlines the changes in grassland habitats and how in turn these changes 

affect streams. Impoundments and irrigation practices have altered the sediment content and 

stream flow. This in turn has contributed to changes in fish populations. Decades of intensive 

agricultural development and modified flow regimes are held responsible for declines in the 

fishes endemic to the small streams and turbid rivers of the Great Plains (Cross and Moss 

1987--in this bibliography).

Results relevant to EMAP: A good overview of prairie ecosystems in North America. This is a 

comprehensive source that documents changes to the prairie ecosystem since settlement and 

the development of agriculture. The article describes the flora, fauna, soil characteristics, and 

overall ecology of the various regions (short grass to tall grass prairies) of the Great Plains. 

Chapters include; prairie past and present (prairie grasses, land resources and management, 

prairie insects and animals), prairie integrity and legacies, resource and research needs, and 

literature cited. 

This reference is a good all-around source that catalogs the ecosystem structure, the biotic 

community, and the changes that have occurred since agricultural development. This source 

also contains an extensive bibliography.

Geographic location: Great Plains, plains, EPA region 6, EPA region 7, EPA region 8, Kansas, 

Nebraska, Oklahoma, Texas, New Mexico, Colorado, North Dakota, South Dakota, Wyoming, 

Montana, eco25, High Plains, eco26, Southwestern Tablelands. eco27, Central Great Plains, 

eco44, Nebraska Sand Hills, eco43, Northwestern Great Plains 

Keywords: phab, fish, native species, turbidity, fish communities, altered water flow regime, 

grasslands, prairie insects, prairie animals, historic condition, plains rivers, impoundments, 

agriculture 

URL: http://www.npwrc.usgs.gov/resource/2000/grlands/grlands.htm

170
Author: Say, T. 

Year: 1825 

Title: Descriptions of new hemipterous insects collected in the expedition to the Rocky 

Mountains, performed by order of Mr. Calhoun, Secretary of War, under command of major 

Long 

Reference Type: Journal Article

Journal: Journal of the Academy of Natural Sciences Philadelphia 

Volume: 4 

Issue: 2 

Pages: 307-345 

Value of reference: This reference provides an example of the qualitative characteristics of the 

earliest macroinvertebrate collection literature in western North America. Although Say was a 

zoologist, and the descriptions of collected Hemiptera specimens are provided in detail, 

important collection information is lacking. Dates and specific collection locations are usually 

not provided, although they may be recorded on museum specimens. Distribution information is 

very generalized, such as "inhabits North America", "inhabits Missouri", "inhabits Arkansas near 

Rocky Mountains". 

Results relevant to EMAP: The earliest macroinvertebrate collection data in western North 

America provides some anecdotal information regarding species encountered during 

expeditions. The collection was made in a very non-systematic fashion; information on collection 

date was not recorded (although this information may be available in the museum records) , and 

location information is very coarse. In this case, only a few of the specimens collected are 

aquatic. The relevance of this reference to EMAP is that it establishes coarse baseline data and 

elucidates the limitations of what can and cannot be reconstructed of aquatic macroinvertebrate 

communities prior to European settlement.

Geographic location: EPA Region7, EPA Region8, Mountains, Plains, Rocky Mountains 

Keywords: macroinvertebrates; Hemiptera; baseline conditions 

171
Author: Schalk, R.F. 

Year: 1986 

Title: Estimating salmon and steelhead usage in the Columbia basin before 1850: the 

anthropological perspective. 

Reference Type: Journal Article

Journal: Northwest Environmental Journal 

Volume: 2 

Issue: 2 

Pages: 1-30 

Value of reference: Evidence of salmonid declines were reported as early as 1882; thus many 

"historical" population data do not reflect an approximate pre-settlement condition. In this 

article, salmon runs are estimated for a very early time period, producing probably the best 

supported approximations of pre-settlement salmon runs for the Columbia basin (also see 

Meengs and Lackey 2005--in this bibliography--who used similar approaches for calculating 

historical coastal runs). Estimates are based on native American fish catches, consumption, 

population data, and catch efficiency. The catch estimate adjusts earlier estimates by Hewes 

(1973) and Craig and Hacker (1940)--both cited below--by accounting for variation in 

consumption rates among tribes, inclusion of a migration calorie loss factor, and an inedible 

waste loss factor. Catches are converted into total run size by dividing by an catch efficiency 

rate. 

This reference illustrates the use of anthropological data for determining the former importance 

of salmon and steelhead to the Indian tribes of the Columbia basin, estimating the magnitude of 

the aboriginal salmon and steelhead catch in the early 19th century, and translating to total fish. 

It provides a baseline historical datum for gauging the magnitude of total losses and for broad 

application in managing and sustaining current populations.

Results relevant to EMAP: The annual salmonid catch by Indians in the early 19th century was 

estimated to be 41,754,800 pounds, which is almost twice as large as previous estimates, but 

which is considered a minimal catch, capable of sustaining human populations, even in years of 

low salmon production. 

This translates into a total run size range estimate of 9 to 12.6 million fish per year, which 

compares well with the low end of the estimate by the Northwest Power Planning Council 

(NWPPC 1986, in this bibliography), yet is consistent with the conclusion that it is a minimum 

estimate, not including fish catches for uses other than human consumption, e.g., dog food, fuel. 

Geographic location: Oregon, Washington, Idaho, EPA region 10, eco3, eco4, eco11, eco10, 

eco9, 3co15, eco12, eco16, mountains, xeric, Columbia River basin 

Keywords: fish, salmon, steelhead, pre-settlement population estimate, anthropological data, 

native American fish catch 

Notes: Craig, J.A. and R.L. Hacker. 1940. The history and development of the fisheries of the 

Columbia River. Bulletin of the Bureau of Fisheries 49:133-216. 

Hewes, G.W. 1973. Indian fisheries productivity in pre-contact times in the Pacific salmon area. 

Northwest Anthropological Research Notes 7(2):133-155. 

172
Author: Scheurer, Julie A.; Bestgen, Kevin R.; Fausch, Kurt D. 

Year: 2003 

Title: Resolving Taxonomy and Historic Distribution for Conservation of Rare Great Plains 

Fishes: Hybognathus (Teleostei: Cyprinidae) in Eastern Colorado Basins 

Reference Type: Journal Article

Journal: Copeia 

Volume: 3 

Issue: 1 

Pages: 1-12 

Value of reference: This article highlights the difficulty in establishing historic fish distribution 

and numbers. “Few early collections exist and most of these were made after habitats were 

already altered, some native species were extirpated and nonnative species ere introduced." 

For example, fish collections are known from only 12 locations before 1900 in the Great Plains 

portion of eastern Colorado (Fausch and Bestgen, 1997), yet diversion of water for irrigation 

was well developed by the 1860's. As a result, the historic distributions of fishes described only 

in early reports are not fully known. A second main problem is that identification of some taxa is 

difficult, resulting in inaccurate field surveys. 

The goal of the research was to develop a technique to distinguish H. hankinsoni from H. 

placitus in western Great Plains watersheds where they are sympatric. The model is then used 

to accurately identify all available museum specimens of Hybognathis, this allowed for 

clarification of historic distributions of H. hankinsoni and H. placitus. 

This study helps document the importance of museum collections and the correct species 

identification for the determination historic conditions and establish changes in distribution and 

habitat over time. 

Results relevant to EMAP: The different morphologies of H. hankinsoni and H. placitus are 

consistent with adaptations for their preferred habitats. H. hankinsoni prefers small, clear 

streams with low velocity. In contrast, H. placitus prefer medium to large plains streams with 

more turbid environments. 

Correct identification of these two species helped establish what the historic stream 

environment was like in the area of collection. In addition, better identification of museum 

specimens provides a more accurate conclusion about historic distributions and range of 

species within the stream system. Based on the finding of this study, the current distribution for 

these two species is believed to be contracting from the western edge of their former range. 

Article also contains an extensive bibliography. 

Geographic location: Colorado, eco25, Great Plains, plains, EPA region 8, Platte River, 

Republican River, Smoky Hill River 

Keywords: native fish, historical distribution, fish, early collections, taxonomy 

Abstract: Similar morphology and confused historical taxonomy of Hybognathus hankinsoni

(brassy minnow) and Hybognathus placitus (plains minnow) have made determination of their 

historic distributions and conservation status unclear in eastern Colorado basins. We developed 

logistic regression models from morphometric measurements to predict species identity of 

Hybognathus collections from Colorado and adjacent counties (n = 1154 specimens in 134 lots). 

A model based on orbit diameter, standard length, and eye position correctly predicted 98% of 

173
the specimens examined and 100% of the museum lots. Hybognathus hankinsoni have larger 

eyes centered on a horizontal line through the tip of the snout, whereas H. placitus have smaller 

eyes centered above the tip of the snout. The two species were historically sympatric in the 

Platte, Republican, and Smoky Hill River basins, whereas H. placitus was allopatric in the 

Arkansas River basin. The taxonomic characters defined here will allow accurate identification 

of future collections to determine the status of these native fishes. 

URL: http://www.bioone.org/bioone/?request=get-abstract&issn=0045-

8511&volume=003&issue=1&page=0001 

174
Author: Scott, L. B.; Marquiss, S. K. 

Year: 1984 

Title: An historical overview of the Sacramento River 

Reference Type: Book Section

Editor: Warner, R. E.; Hendrix, K. M. 

Book Title: California Riparian Systems: Energy, Conservation, and Productive Management. 

City: Berkeley, California 

Publisher: University of California Press 

Pages: 51-67 

Value of reference: This article contains a useful description of the early (1850's) effects of 

hydraulic mining. 

This paper summarizes an analysis of two aspects of the history of the Sacramento River: the 

fluvial process; and man's development of the floodplain over the last 130 years. The analysis 

was made to trace the origins of problems - seepage, loss of riparian vegetation, and limited 

public access - occurring in the riparian zone, and to establish a perspective from which to study 

these problems. Significant historical aspects of these problems must be considered in a 

comprehensive study of the river.

Results relevant to EMAP: Thirty five years of hydraulic mining created an estimated 

equivalent of 100 years of sediment delivered from the Sacramento Basin into San Francisco 

Bay--three times the average delivery under natural conditions. It is estimated that the 

elevations of the Sacramento, Feather, Yuba, Bear, and American Rivers rose as much as 6 m 

(20 ft). The higher streambeds led to a series of floods in the 1860's and 70's and finally an act 

of the legislature banning hydraulic mining. The floods literally buried farms under many feet of 

mud and debris. 

Graph on p. 55 of changes in bed elevation of the Sacramento and Yuba rivers from 1850 to 

1950.

Geographic location: California, Central Valley, Sacramento River, eco7, eco6, EPA Region 9, 

xeric, mountains 

Keywords: riparian vegetation, phab, xeric, mountains, sediment, water diversions, dams, 

mining, agriculture 

175
Author: Sedell, J. R.; Froggatt, J.L. 

Year: 1984 

Title: Importance of streamside forests to large rivers: The isolation of the Willamette River, 

Oregon, U.S.A., from its floodplain by snagging and streamside forest removal 

Reference Type: Journal Article

Journal: Verh. Internat. Verein. Limnol. 

Volume: 22 

Pages: 1828-1834 

Value of reference: The authors provide a well documented example of changes in 

morphological characteristics, general physical habitat, and riparian conditions within the 10th 

largest river in the continental U.S., dramatically altered by agricultural activities and snagging 

over the last 150 years. The links to locations of original source material for reconstructing river 

channel characteristics and riparian forests at the time of settlement (1850's) may be of use for 

tracking down historical material for other watersheds and regions. 

Human disturbance types and associated changes in stream and riparian conditions are clearly 

documented, with quantitative estimates made that can be compared against current conditions. 

Although the authors discuss the implications of the habitat changes in terms of possible 

generalized changes in aquatic macroinvertebrate and fish community characteristics, the 

primary value of the paper lies in its detailed documentation of changes in physical habitat and 

riparian conditions.

Results relevant to EMAP: Channel complexity and riparian gallery forest composition 

changed dramatically since settlement began in earnest in the 1850's (see Fig. 2). Between 

1870 and 1950, more than 65,000 snags and streamside trees were removed from 114 km of 

river to aid navigation. Channel simplification began when channels and sloughs were closed off 

with wing dams by 1872. 

By 1983, surface water volume, coarse and fine organic inputs had decreased to 25 percent of 

their historic levels in the upper portion of the watershed. Gallery forests, which had extended 

1.5 - 3.5 km on either side of the river, were reduced to narrow, discontinuous ribbon, 

immediately adjacent to the main channels and primary tributaries. 

Conversion to agriculture was the primary factor responsible for loss of riparian woodlands. 

Secondary and tertiary channels, which functioned as 3rd- or 4th-order streams in 1854 had all 

but disappeared by 1946, when the river was confined primarily to a single channel. The authors 

speculate that the functional feeding groups of invertebrate and fish communities would have 

been more like lower order streams in these lost channels. Most of the channel changes 

occurred prior to the construction of dams for flood control. 

Geographic location: EPA Region10; Oregon; Willamette Valley; Mountains; 

Willamette River Basin, eco3, mountains 

Keywords: phab; fish; macroinvertebrates; snag removal; agriculture; dams; habitat loss; 

change detection 

176
Author: Sedell, J.R.; Luchessa, K.J.

Year of Conference: 1981 

Title: Using the historical record as an aid to salmonid habitat enhancement 

Reference Type: Conference Proceedings 

Editor: Armantrout, N.B. 

Conference Name: Symposium on Acquisition and Utilization of Aquatic Habitat Inventory 

Information 

Conference Location: Portland, Oregon 

Publisher: American Fisheries Society, Bethesda, Maryland (1982) 

Pages: 210-223 

Value of reference: This paper discusses historical conditions in numerous basins of 

Washington and Oregon and is therefore more of a general observation of prevailing conditions 

in multiple basins, as compared to the historical condition. It presents an historical perspective 

that the authors suggest can help provide a needed rationale for rehabilitation of wild salmonid 

stocks, including creation of new habitat, restoring damaged habitat, and protecting good 

habitat. 

The basic premise is that historical information can assist in our understanding of how far many 

river systems deviate from a pre-settlement condition (i.e., optimum habitat requirements for 

salmonids), specifically with respect to habitat complexity created by large wood and debris 

dams. 

Results relevant to EMAP: Historically, streams in lowlands of the Willamette Valley and Puget 

Sound consisted of a network of sloughs, islands, beaver ponds, and drift dams with no main 

channel. Using historical documentation, the authors found that debris dams in many basins of 

western Oregon and Washington were once very common, often damming 20% or more of a 

stream's length. In many lowlands, a high degree of interaction of the stream with its flood plain 

was common. For example, over a quarter of the area of the Skagit River lowlands were beaver 

marsh, sloughs, and wet grass meadows. 

Large volumes of wood influenced both low and high gradient channels; many rivers were 

completely blocked by drift jams for 100-1500 m in the mid 1800s. The historical record shows 

that even in big rivers, large wood contributed to in-channel structure. Salmon were once 

abundant under these conditions. For example, using published material for the Siuslaw River, 

estimated runs in the 1890s would have been about 27,500 chinook and 218,750 coho salmon. 

However, the habitat is no longer present to support those run sizes, even though they are 

being set as goals. 

Channelization and clearing of large wood and debris to facilitate river transport began in the 

mid 1800s and continued into the 20th century to create easier access to spawning areas. 

Management alternatives to debris clearing in high-gradient reaches is discussed and supported 

by the historical record and current literature findings. 

 

Geographic location: Washington, Oregon, EPA region 10, eco1, eco2, eco3, numerous 

basins, mountains 

Keywords: phab, large wood, debris dams, anadromous fish, logging, channelization, habitat 

degradation

177
Abstract: Historically, wild anadromous fish stocks evolved with stream systems that were 

obstructed by fallen trees, beaver dams, and vegetation growing in and beside the channels. 

River systems as large as 7th order had large numbers of fallen trees in their channels and 

often were obstructed by drift jams that were up to 1500 m long. The main river channels 

contained abundant gravels and fine sediments. Habitat complexity was great because of scour 

around boulders and fallen trees, and the presence of numerous and extensive stable side 

channels and sloughs. These pristine streams interacted intensively with their flood plains. 

Historical records document over 100 years of "diligent" stream and river cleanup. Primary 

activities included removal of boulders, large woody debris, and other obstructions from 

channels. We believe that historical documentation of the ways unmanaged streams interacted 

with the streamside forest allows us to know how far we have deviated from the optimum habitat 

requirements for various salmonids. Until we understand the structure of undisturbed habitats 

that wild stocks develop within, and the sequence of changes that have occurred in those 

habitats, our present protection and enhancement efforts will lack both a rational context and 

effective direction.

178
Author: Sedell, J. R.; Reeves, G. H.; Hauer, F. R.; Stanford, J. A.; Hawkins, C. P. 

Year: 1990 

Title: Role of refugia in recovery from disturbances: Modern fragmented and disconnected river 

systems 

Reference Type: Journal Article

Journal: Environmental Management 

Volume: 14 

Pages: 711-724 

Value of reference: The reference does not describe reference condition per se (except for a 

short description of changes on the Willamette River (see Results below), but it does give a 

useful table of attributes of refugia at various spatial scales. These attributes are the same as 

those natural features composing a reference stream reach, segment, or watershed. The 

authors see this classification system as being applicable to both the conservation of existing 

minimally disturbed systems as well as the recognition of isolated natural features within 

disturbed systems.

Results relevant to EMAP: The authors compile a list of stream refugia attributes at various 

spatial scales (channel unit, reach, segment, watershed). 

Between 1854 and 1967 the Willamette River, Oregon, became increasingly isolated from its 

floodplain as a result of channelization and agricultural modification of riparian forests. In 1854, 

the riparian forest was in contact with >250 km of river edge on oxbow lakes and cutoff sloughs. 

By 1967 the length of river edge had been systematically decreased to 64 km, a reduction of 

74%. Much of the change in riparian forest interaction was completed by 1910 owing to snag 

removal and river navigation improvements (revetments). 

The implication of these changes are that the ability of alluvial reaches to provide refugia, retain 

sediments and organic materials and to determine the quantity of organic inputs has been 

greatly reduced.

Geographic location: Willamette River, Oregon, EPA Region 10, eco3, mountains 

Keywords: phab, riparian vegetation, river ecosystems, refugia, groundwater, reference 

condition, human disturbance 

Abstract: Habitats or environmental factors that convey spatial and temporal resistance to biotic 

communities that have been impacted by biophysical disturbances may be called refugia. Most 

refugia in rivers are characterized by extensive coupling of the main channel with adjacent 

streamside forests, floodplain features, and groundwater. These habitats operate at different 

spatial scales, from localized particles to channel units such as pools and riffles, to reaches and 

longer sections, and at the basin level. A spatial hierarchy of different physical components of a 

drainage network is proposed to provide a context for different refugia. Examples of refugia 

operating at different spatial scales, such as pools, large woody debris, floodplains, below 

dams, and catchment basins are discussed. We hope that the geomorphic context proposed for 

examining refugia habitats will assist in the conservation of pristine areas and attributes of river 

systems and also allow a better understanding of rehabilitation needs in rivers that have been 

extensively altered. 

179
Author: Shaffer, H. Bradley; Fisher, Robert N.; Davidson, Carlos 

Year: 1998 

Title: The role of natural history collections in documenting species declines. 

Reference Type: Journal Article

Journal: Trends in Ecology and Evolution 

Volume: 13 

Issue: 1 

Pages: 27-30 

Value of reference: This article summarizes ways in which museum collections and related 

data repositories have been used as a source of historical information in documenting changes 

in the presence or absence of species. Although museum data often represent an imperfect 

match to current sampling programs, they can still provide the critical information necessary to 

identify declines, and should comprise one of the standard databases in conservation biology.

Results relevant to EMAP: Museum and other historic locality archives offer a rich source of 

material for the analysis of species declines; however, assessments of changes in abundance 

over time are very problematic, and should be interpreted with great caution. 

Judiciously using museum collections as a source of historical data, changes in the 

presence/absence of individual species and communities can successfully be evaluated across 

a wide range of plant and animal taxa in habitats ranging from single-species temperate habitats 

to complex tropical systems. 

This article is a helpful tool and includes a good bibliography.

Geographic location: Article not specific to one geographic area, however the article does list 

several studies from California (e.g., Fisher, R.N and Shaffer, H.B., 1996, The decline of 

amphibians in California's great central valley, Conservation Biology 10, 1387-1397, in this 

bibliography) as examples of studies using museum specimens or other archival records as 

historical data to document species decline. 

Keywords: historic condition, phab, museum collections, fish, amphibians, species decline 

Abstract: Efforts to document the decline of extant populations require a historical record of 

previous occurrences. Natural history museums contain such information for most regions of the 

world. at least at a coarse spatial scale. Museum collections have been successfully used to 

analyze declines in a wide range of plants and animals, at spatial scales ranging from single 

localities to large biotic and political regions. Natural history museum collections, when properly 

analyzed, can be an invaluable tool in documenting changes in biodiversity during the past 

century. 

180
Author: Sheldon, A.L. 

Year: 1979 

Title: Stonefly (Plecoptera) records from the basin ranges of Nevada and Utah 

Reference Type: Journal Article

Journal: The Great Basin Naturalist 

Volume: 39 

Issue: 3 

Pages: 289-292 

Value of reference: Since macroinvertebrate information is limited, this record of the 

distribution of Plecoptera in streams on Nevada's mountain ranges in the 1979 may have value 

to EMAP if combined with other papers such as Stewart et al. (1974) on distribution and past 

dispersal of southwestern U.S. Plecoptera. 

Distributional records are given for 40 stonefly species on 15 isolated mountain ranges mostly in 

Nevada (1 included in Utah). 

Stewart, K.W., R.W. Baumann, and B.P. Stark. 1974. The distribution and past dispersal of 

southwestern United States Plecoptera. Transactions of the American Entomological Society 

99:507-546.

Results relevant to EMAP: This list of Plecoptera species sampled in 1979 may be compared 

with species sampled 25 yrs later for EMAP. 

Stonefly (Plecoptera) species are listed by family with a record of mountain range and county 

where collected.

Geographic location: EPA Region 9, central basin and range, Nevada, Utah, eco13, xeric 

Keywords: macroinvertebrates, animal taxonomy and geography, entomology, stonefly, 

Plecoptera 

181
Author: Shepard, B.B.; Sanborn, B.; Ulmer, L.; Lee, D.C. 

Year: 1997 

Title: Status and risk of extinction for westslope cutthroat trout in the upper Missouri River 

basin, Montana 

Reference Type: Journal Article

Journal: North American Journal of Fisheries Management 

Volume: 17 

Pages: 1158-1172 

Value of reference: Although this article focuses on calculating probabilities and risk of 

extinction of westslope cutthroat trout in multiple basins in Montana, it does contain some 

historical information about distribution in the upper Missouri River, including Figure 1: map 

showing sub-basins in Montana believed to have supported westslope cutthroat trout at the time 

of European settlement (Behnke 1992, this bibliography). The authors examined evidence from 

the historical record to estimate the length of streams and rivers once occupied by the trout. 

144 sub-basins on federal lands were assessed and rated according to the estimated extinction 

risk for westslope cutthroat as: very high, high, and moderate. 

Results relevant to EMAP: There is some disagreement in the historical record as to the 

historical range of the trout. For this analyses, the authors assumed that it originally occupied 

the entire Missouri River drainage down to, and including, the Musselshell River and the upper 

Milk River basin, but not the upper Sun River basin 

The abundance and distribution of westslope cutthroat trout have declined substantially 

throughout their historical range. Trout that are at least 90% genetically pure (based on 

allozyme electrophoresis) now occupy less than 5% of the original 93,000 km of stream habitat 

they historically occupied in the upper Missouri River basin in Montana. Remaining populations 

are restricted to isolated headwater habitats, many of which are impacted. Factors suggested 

as contributing to decline were grazing, mining, fishing, genetic introgression, and competition 

with nonnative species. 

Each current population of the trout occupied relatively small habitat fragments in headwaters 

(<35 km of continuous stream length), and each was isolated either physically or biologically. 

Most (71%) of the 144 populations assessed had a very high predicted risk of extinction; 19% 

had a high risk, and 10% had a moderate risk. The conclusion was that westslope cutthroat 

trout populations inhabiting federal lands within the upper Missouri basin are at serious risk of 

extinction under current conditions. 

Geographic location: Montana, upper Missouri River basin, eco43, eco42, eco17, EPA region 

8, mountains 

Keywords: fish, westslope cutthroat trout, habitat fragmentation, nonnative species, grazing, 

mining, fishing, genetic introgression 

Abstract: Westslope cutthroat trout Oncorhynchus clarki lewisi now occupy less than 5% of the 

subspecies' historical range within the upper Missouri River drainage in Montana. We assessed 

the risk of extinction for 144 known populations inhabiting streams within federally managed 

lands in the upper Missouri River basin using a Bayesian viability assessment procedure that 

estimates probability of persistence based on subjective evaluation of population survival and 

reproductive rates as influenced by environmental conditions. We first customized this model 

using estimates of demographic parameters from the literature and field data. Each population 

182
was classified into one of three risk groups based on their Bayesian probability of persistence 

over 100 years (p100). Most (71%) of the 144 populations had a very high predicted risk of 

extinction (p100 ≤ 50%), 19% exhibited a high risk (50% < p100 ≤80%), and 10% had a 

moderate risk (80 < p100 ≤ 95%). Higher average predictions of plop were consistently 

associated with populations inhabiting watersheds with lower levels of management activities. 

Analysis of variance and a matrix of information divergence measures indicated that livestock 

grazing, mineral development, angling, and the presence of nonnative fish had the greatest 

association with both estimated population parameters and persistence probabilities. Of 26 

major sub-basins within the upper Missouri River drainage, 16 support at least one known 

westslope cutthroat trout population on federal lands, and 14 of these 16 support at least one 

population with an estimated p100 value of 0.5 or greater. Results of our analysis have led to 

action by citizens of Montana, prompting state and federal managers to develop a conservation 

and restoration program for this subspecies in the upper Missouri River basin. 

183
Author: Silkensen, G. 

Year: 1993 

Title: South Platte River observations: Historical clues to the evolution of a river's ecology 

Reference Type: Book Section

Editor: Woodring, R. C. 

Book Title: Defining ecological and sociological integrity for the South Platte River basin. 

City: Fort Collins, Colorado 

Publisher: Colorado Water Resources Research Institute 

Pages: 41-53 

Series Title: Information Series No. 72 

Value of reference: The author compiles multiple views of the pre-settlement South Platte 

River written by the first explorers to the region.

Results relevant to EMAP: In the mid-19th Century large stretches of the South Platte River 

valley in northeastern Colorado were treeless, and described by phrases such as "a miserable 

country" of "alkali soils" and "unvaried sterility". The earliest observations of the South Platte 

reveal a river which could be a raging torrent one year, and a dry sand bed the next. P. 42. 

Today the hydrography is evened out by diversion of water from the upper Colorado River; an 

average total of nearly 400,000 acre-feet/year of water is imported into the South Platte basin. 

This is approximately 30% of the South Platte's annual native runoff. Nearly 95% of this water 

originates in the Colorado River basin. The North Platte basin supplies most of the balance. P. 

51 

Short descriptions of observations made during expeditions in 1820 and 1842, addressing 

variability in amount of riparian vegetation on tributaries and relative to the Rocky Mountains, as 

well as two descriptions of the confluence of the North and South Platte (pages 43 and 44), are 

included.

Geographic location: Colorado, EPA Region 8, xeric, eco25, eco26, South Platte River 

Keywords: riparian vegetation, phab, hydrology, runoff, agriculture 

Abstract: The South Platte River begins high in the Colorado Rockies, emerging from the 

foothills of the front range southwest of Denver. From here the river flows in a general 

northeasterly direction across Colorado's high plains before leaving the state and entering 

Nebraska. During the 19th Century, that portion of the river which traverses the high plains was 

explored by both Stephen H. Long and Charles C. Fremont. The river also became one of the 

primary routes (the Denver Road) to the Colorado gold fields during the 1859 Pikes Peak gold 

rush, and later for pioneers, settlers, and the railroads. Eventually the river's water was stored 

and used to irrigate crops in the South Platte valley. Throughout Colorado history, the river has 

been both praised and cursed. Early descriptions have ranged from "treeless", " sandy", 

"barren", to " a beautiful river in whom the thirsty finds a true friend." Many 19th Century 

explorers, gold-seeking fifty-niners, pioneers, and farmers encountered the South Platte River 

and described it in detail. These descriptions, albeit unintentionally, often provide clues to the 

ecological nature of the South Platte River as it began to evolve during the last half of the 19th 

Century. 

184
Author: Skinner, J. E. 

Year: 1962 

Title: An historical review of the fish and wildlife resources of the San Francisco Bay area 

Reference Type: Report

City: Sacramento, CA 

Institution: The Resources Agency of California and California Department of Fish and Game 

Pages: 57-71 

Report Number: Water Projects Branch Report No.1 

Value of reference: The reference provides a view of the extent of the fishing effort on the 

Sacramento-San Joaquin River system during the years of commercial fishing and salmon 

canneries. Although the river system was considered degraded in the late 1800s, the salmon 

catch data provide a good benchmark for assessing salmon losses since then.

Results relevant to EMAP: A table in Appendix C-2 and a bar graph show the salmon catch 

data for the gillnet fishery on the lower Sacramento-San Joaquin River for the years 1864-1957. 

The numbers do not include the portion of the catch consumed locally or that were caught 

above the city of Sacramento. The gillnet catch peaked at over 10,000,000 pounds in 1880 and 

1910; and it exceeded 1,000,000 pounds every year until 1910, after which the catch amounts 

became more variable. 

The Wakeman report in 1870 surveyed the fisheries of the tributaries of San Francisco Bay and 

described the disturbed condition of streams due to the logging operations, saw mills, and flour 

mills located on them. The inference from his description is that the coastal streams had once 

been very productive of silver salmon (Oncorhynchus kisutch) and steelhead trout (Salmo 

gairdnerii), but at the time of the 1870 survey they were already degraded. 

Map IV Fold out map in back of book. Historical salmon migration routes and probable 

distribution. 

Appendix F comprises two tables: a "List of selected freshwater fishes of the San Francisco Bay 

area" and "Some initial introductions of freshwater food and game fishes now occurring in the 

San Francisco Bay area". The majority of the introductions occurred in the late 1800's, 

beginning in 1872 with eastern brook trout (Salvelinus fontinalis). Of the anadromous fishes, 

silver salmon were limited to coastal streams until 1956 when they were introduced into the 

Sacramento River system.

Geographic location: California, San Francisco Bay basin, Sacramento River, San Joaquin 

River, eco6, eco7, Central Valley, EPA Region 9, xeric 

Keywords: fish, chinook salmon, silver salmon, fishing, urban, logging, dams, nonnative 

species 

185
Author: Stalnaker, C.B.; Holden, P.B. 

Year: 1973 

Title: Changes in native fish distribution in the Green River system, Utah-Colorado 

Reference Type: Journal Article

Journal: Proceedings of the Utah Academy of Science, Arts, and Letters 

Volume: 50 

Pages: 25-32 

Value of reference: This article provides descriptive summaries of the historical distribution and 

relative abundance of seven indigenous species common to the main tributaries of the upper 

Colorado basin and reports fish distribution following impoundment by the Flaming Gorge dam. 

It cites publications dating from the 1890s to the early 1960s (pre-impoundment), documenting 

declines before closure of the dam. It then reports changes in abundance and distribution in the 

mid-1960s following closure of the dam and in 1973. It thus provides several historical points of 

reference for tracking the changes in populations of these 7 species (Colorado squawfish, 

roundtail chub, bonytail chub, humpback chub, humpback sucker, bluehead sucker, 

flannelmouth sucker). 

Results relevant to EMAP: Minckley and Deacon (1968; in this bibliography) document the 

decrease in native fishes in the lower Colorado River basin. Subsequently, the upper Colorado 

River basin was the last available habitat for the large river endemic fishes. All species were 

historically reported to be common to abundant in the upper Colorado basin except the 

humpback chub. Prior to closure of the dam, declines were already being reported for some of 

these species, but the roundtail chub, bonytail chub, bluehead sucker, and flannelmouth sucker 

still seemed to be doing well at least in some portions of their range. 

After closure of the Flaming Gorge dam, stream physical habitat in the first 65 miles 

downstream (above the mouth of the Yampa River) changed drastically. None of the 7 native 

species investigated were still reproducing, and all species except the flannelmouth sucker, 

bluehead sucker, and roundtail chub were eliminated from that area. Growth rates of the 

bonytail chub, roundtail chub, and Colorado squawfish had decreased greatly. Introduced 

rainbow and brown trout had replaced the large native fishes in that stretch of river. The 

humpback chub, Colorado squawfish, bonytail chub, and humpback sucker were considered 

rare and possibly endangered at the time of publication (1973).

Geographic location: Utah, Colorado, Green River basin, EPA region 8, xeric, eco18, eco20, 

eco21 

Keywords: fish, nonnative species, dams, habitat fragmentation 

186
Author: Starnes, W.C. 

Year: 1995 

Title: Colorado River Basin Fishes 

Reference Type: Electronic Source

Producer: U.S. Department of Interior, National Biological Service 

Access Year: 2005 

Access Date: May 18 

Value of reference: Web site summarizes the changes in fish species richness between the 

1800s and present, including the increase in nonnative species. Tributaries and sections of the 

river are listed along with the species richness in the 1800s and the changes in richness that 

occurred throughout the 20th century, notably the introduction of numerous species, creating 

higher species richness (sometimes more than double the historical levels) but lower native 

species diversity (Table 2). Gives list of native fish taxa of the river basin, including status of 

jeopardized species (Table 1). Summary also discusses the use of baseline data describing 

unaltered native fauna and determining, to the extent possible, the true extent of diversity of 

native fish. 

Results relevant to EMAP: Historically, the lower basin (downstream of the Arizona/Utah 

border) had the greatest diversity of taxa (44), while the upper basin contained 14 species; the 

number of native species has drastically declined since the 1800s in every portion of the basin, 

while the number of introduced species has increased, and in many cases, far surpassed the 

native richness (Table 2). 

Presently, 40 of the 49 native species are considered either possibly or actually jeopardized or 

are extinct (see Table 1 for status by species). Impacts to fish include impoundments, irrigation 

diversions, diking, channelization, pollutants, habitat destruction, grazing, dewatering, and 

competition with nonnative species (at least 72 nonnative fish taxa have been introduced to the 

CO River system); genetic integrity is compromised by hybridization between native and 

nonnative species. 

The situation complicates the use of biodiversity as an indicator of ecological integrity of the 

ecosystem. 

Geographic location: Colorado River basin, xeric, eco20, eco22, eco14, eco81 eco23, 

Colorado, Utah, Arizona, EPA Region 8, EPA Region 9 

Keywords: fish, dams, agriculture, water diversion, diking, channelization, pollutants, habitat 

destruction, grazing, dewatering, nonnative species, species diversity 

URL: http://biology.usgs.gov/s+t/noframe/e063.htm 

187
Author: Steedman, R. J.; Whillans, T. H.; Behm, A. P.; Bray, K. E.; Cullis, K. I.; Holland, M. M.; 

Stoddart, S. J.; White, R. J. 

Year: 1996 

Title: Use of historical information for conservation and restoration of Great Lakes aquatic 

habitat 

Reference Type: Journal Article

Journal: Canadian Journal of Fisheries and Aquatic Sciences 

Volume: 53 

Issue: Suppl. 1 

Pages: 415-423 

Value of reference: Though the specific information applies to the Great Lakes, the conceptual 

background and application of the approach to management is universal. The section "Why is it 

important to consider historical information?" is among the most thorough presentations of the 

utility of historical information encountered.

Results relevant to EMAP: Why is it important to consider historical information? 

(Section headings) 

1. Those who ignore history are doomed to repeat the worst of it. 

2. Historical information is frequently required during the specification of targets for ecosystem 

restoration. 

3. Historical information can be used to modify values and beliefs as they relate to habitat. 

4. By its very nature, information about natural ecosystem processes needs to be interpreted in 

a context that is long term and retrospective. 

5. Humans are not very good at perceiving slow processes or rare events without the help of 

scientists or historians. 

6. In culture, religion, and science, humans have often preferred to seek out and preserve 

stability in the natural world and to filter human perceptions through models grounded on 

stability or steady-state dynamics. 

7. Human perceptions and expectations are influenced by the highly modified and simplified 

state of most contemporary landscapes. 

8. The present is the history of the future.

Geographic location: Not applicable 

Keywords: historic fish abundance, historical information, retrospective analysis, aquatic habitat 

management 

Abstract: We provide a rationale and methodological overview for historical (retrospective) 

study of Great Lakes aquatic habitats and biota. Historical information has significant potential 

to direct aquatic habitat management in the Great Lakes, particularly in setting restoration goals. 

Although the use of historical information has been opportunistic (it is limited by the preservation 

of information in specific forms) and generally of low resolution(it is generally semiquantitative at 

best), the products of these analyses have been compelling (they have changed attitudes and 

expectations of people) and surprising (many of the conclusions of historical analysis were not 

predictable from other sources). 

188
Author: Suckley, G. 

Year: 1860 

Title: Report upon the fishes collected on the survey 

Reference Type: Book Section 

Editor: U.S. War Department 

Book Title: Reports of Explorations and Surveys to ascertain the most practicable and 

economical route for a railroad from the Mississippi River to the Pacific Ocean, made under the 

direction of the Secretary of War, in 1853-4. 

City: Washington, D.C. 

Publisher: Government Printing Office 

Volume: 12 

Pages: 307-368 

Value of reference: This is an original early source that describes the massive numbers of 

various species of salmon in river basins of the Pacific Northwest in the mid-19th century. It 

offers first-hand descriptions and drawings of the species encountered. Notes on abundance, 

general distribution, and migration distances to inland rivers and streams are spread throughout 

the document. It is somewhat laborious to sift through to glean pertinent information, but it is 

worthwhile in its documentation of true pre-settlement conditions. Taxonomy may be difficult to 

pair with modern names, but should be possible for a fish biologist with the descriptions and 

drawings included in the document. Most is descriptive information, but it provides a good 

perspective, which could be very useful as a supplement to later, more quantitative summaries 

in reconstructing historical conditions. 

Results relevant to EMAP: A range of descriptive information can be extracted from this 

document, including fish distribution, general abundance, species present, distance ascended 

upriver to spawn, habits, descriptions, early Native American fishing and usage, and other 

natural history anecdotes. A variety of baseline information can be extracted that may not be 

reported in later documentation. The reference should be consulted for details. The information 

is relevant for any historical reconstruction of pre-settlement conditions.

Geographic location: Pacific Northwest, Oregon, Washington, Columbia River basin, Puget 

Sound, EPA Region 10, eco1, eco2, eco3, eco4, eco9, eco10, eco11, mountains, xeric 

Keywords: fish, historical data, primary source, baseline information 

URL: http://www.cprr.org/Museum/Pacific_RR_Surveys/ 

189
Author: Swift, C. C.; Haglund, T. R.; Ruiz, M.; Fisher, R. N. 

Year: 1993 

Title: The status and distribution of the freshwater fishes of southern California 

Reference Type: Journal Article

Journal: Bulletin of the Southern California Academy of Sciences 

Volume: 92 

Issue: 3 

Pages: 101-167 

Value of reference: This is one of the few references encountered that cover the fishes of 

southern California. The article describes native and exotic species, their ranges, and changes 

in their status (qualitative) between early settlement times and the present.

Results relevant to EMAP: In southern California 38 native freshwater fish taxa have been 

extirpated or severely reduced in number since European settlement. 

Coastal areas were once well watered with an extensive stream system, springs, and marshes. 

After settlement, channel modifications and lowering of the water table altered stream habitats 

toward more desert-like conditions. The lowland areas are so highly modified today (e.g., 

concrete-lined channels) that they are practically uninhabitable for resident species and those 

that migrate between the headwater areas and the coast. 40% of the freshwater fishes of the 

Los Angeles basin were extirpated after the second World War following the completion of a 

large flood control project. 

The article includes detailed distribution maps for selected species that separate records into 

pre-1970 and post-1970.

Geographic location: xeric, eco6, eco8, southern California, Los Angeles basin, Region 6 

Keywords: fish, distribution, habitat degradation, water diversion, channelization, dams, 

nonnative species, urban, pollution 

Abstract: The fresh and low salinity waters of southern California include the Owens, Mohave, 

Colorado, and coastal drainages south of Monterey Bay to the Mexican border. The youthful 

topography presents a strong dichotomy between steep rocky streams abruptly meeting 

relatively flat deserts or coastal plains. Little or no intermediate, foothill habitat exists. Thirtyeight native freshwater and 23 estuarine fishes have been recorded from this area. In addition, 

at least 100 species have been introduced, with widely varying success. Since the late 1940's 

and 1950's the native fishes of the Owens, Colorado, and Mohave drainages have been in 

jeopardy or extirpated in California. At the same time, the lowland fishes in coastal drainages 

still remain in a few isolated areas, but are so reduced that special protection is needed. Only 

one estuarine species, Eucyclogobius newberryi, is threatened. Some tropical estuarine species 

of extreme southern California were last collected 50 to 80 years ago, and are very rare or 

extirpated here. If the remaining elements of the fish fauna are to survive, immediate action is 

needed to preserve the remaining habitat and to restore areas within the native range. 

190
Author: Tabor, V.M. 

Year: 1998 

Title: Endangered and threatened wildlife and plants: Final rule to list the Topeka shiner as 

endangered 

Reference Type: Report

City: Manhattan, KS 

Institution: U.S. Department of Interior, Fish and Wildlife Service 

Report Number: Federal Register: 69008-69021, 50 CRF Part 17 

Value of reference: This document provides justification and background for listing the Topeka 

shiner as an endangered species. It provides a summary of the species' historical distribution in 

6 states, including one--South Dakota--in the EMAP-West region. The reasons for decline of 

the species are summarized in detail. 

Results relevant to EMAP: The Topeka shiner was historically widespread and abundant 

throughout low order tributary streams in portions of 6 states of the central prairie region. 

Stream basins within the range historically occupied by Topeka shiners within the EMAP-West 

region include the Big Sioux, Vermillion, and James basins in South Dakota. The species 

occupied open pools in small streams with cool, clear water. Many such streams reportedly 

existed throughout the species' geographic range. 

The number of known occurrences of Topeka shiner populations has been reduced by 

approximately 80%, with 50% of this decline occurring within the last 25 years. It now inhabits 

less than 10% of its original geographic range. The species now primarily exists as isolated and 

fragmented populations. Some recent capture sites in each of the historical basins in South 

Dakota, including a few new localities, are given in the document. The species has been 

extirpated in many of its historical river basins, primarily in Kansas, Missouri, Iowa, and 

Nebraska. 

Intensive agricultural development and grazing, leading to increased sedimentation and 

eutrophication, has the greatest impact on the Topeka shiner. Other impacts include the 

maintenance of altered waterways, dewatering of streams, tributary impoundment, and 

channelization.

Geographic location: South Dakota, EPA region 8, eco34, eco42, eco46, plains, Big Sioux 

basin, Vermillion basin, James basin 

Keywords: fish, endangered status, agriculture, grazing, water diversion, dams, channelization, 

habitat degradation 

191
Author: Taft, Oriane W.; Haig, Susan M. 

Year: 2003 

Title: Historical wetlands in Oregon's Willamette Valley: implications for restoration of winter 

waterbird habitat 

Reference Type: Journal Article

Journal: Wetlands 

Volume: 23 

Issue: 1 

Pages: 51-64 

Value of reference: This reference is a good synthesis of the pre-settlement condition and 

extent of the Willamette River, associated wetlands, oxbows, marshes, etc. and how land use 

practices have extensively altered the habitat to bring it to its current condition. The study used 

a combination of primary sources: expedition journals, explore/naturalist logs, missionary 

writings, early settler-farmer diaries, promotionists’ reports, and government documents; 

Secondary sources include habitat maps, geomorphology studies, anthropological research, 

and prior work on the historical Willamette River and its floodplain to compile a view of the "presettlement" habitat of the Willamette Valley.

Results relevant to EMAP: This report investigated the historical Willamette Valley at the time 

of Euro-American settlement (ca. 1840) and attempts to determine the pre-settlement spatial 

extent of the river and wetlands in the valley. 

This is a good source for establishment of pre-settlement habitat condition of the Willamette 

Valley and the river/ wetlands structure. It also helps document habitat change after agricultural 

development in the valley. 

Paper presents a good historical overview and changes to the Willamette River system due to 

land use practices and development; includes an extensive bibliography.

Geographic location: Oregon, Willamette River, Willamette Valley, Pacific Northwest, EPA 

region 10, eco3 

Keywords: phab, agricultural landscape, fire, historical wetlands, Kalapuya, land use, 

shorebirds, pre-settlement condition, wading birds, waterfowl, wetland loss, wetland prairie 

Abstract: Before agricultural expansion in the 19th century, river valleys of North America 

supported expanses of wetland habitat. In restoring these landscapes, it is important to 

understand their historical condition and biological function. Synthesizing historical primary 

accounts (from explorers, travelers, settlers, and farmers) with contemporary knowledge of 

these wetland systems, we developed a profile of the wetlands and their use by non-breeding 

waterbirds (e.g., waterfowl, wading birds, and shorebirds) within the Willamette Valley, Oregon, 

ca. 1840. We found evidence for three types of wetlands used by non-breeding waterbirds in 

fall, winter, and spring: emergent wetlands, riverine wetlands, and wetland prairie. The most 

extensive wetland type was wetland prairie, which functioned as fall/winter habitat for 

waterbirds, but only while native Kalapuyans managed the region with fire. Since the mid-1800s, 

four species, in particular, have decreased their use of the Willamette Valley: trumpeter swan 

(Cygnus buccinator), snow goose (Chen caerulescens), sandhill crane (Grus canadensis), and 

long-billed curlew (Numenius americanus). Information suggests that ca. 1840, waterbirds and 

their habitats were more abundant in the Willamette Valley than today. Restoration of the 

Willamette Valley landscape is warranted, and today's agricultural wetlands-former wetland 

192
prairie-hold highest restoration potential. 

URL: http://www.bioone.org/bioone/?request=get-abstract&issn=0277-

5212&volume=023&issue=1&page=0051 

193
Author: Tait, C. K.; Li, J. L.; Lamberti, G. A.; Pearsons, T. N.; Li, H. W. 

Year: 1994 

Title: Relationships between riparian cover and the community structure of high desert streams 

Reference Type: Journal Article

Journal: Journal of the North American Benthological Society 

Volume: 13 

Issue: 1 

Pages: 45-56 

Value of reference: Tait et al. recreate studies done in western Oregon and Washington in the 

semiarid Blue Mountains of eastern Oregon to examine how the absence of riparian canopy 

affects fish and macroinvertebrate communities. Though the mention of pre-settlement 

conditions is brief, the assumption is that there was once much more riparian vegetation present 

along Blue Mountain streams, that agriculture and grazing have greatly reduced the amount of 

vegetation and shading along those streams, and that stream communities have been 

dramatically altered as a result. 

Results relevant to EMAP: The hypothesis of the study is that extensive destruction of riparian 

stream cover by human activity has affected the structure of Blue Mountain streams by 

increasing incident radiation and altering water temperature regimes. Canopy removal in 

coolwater streams often has been associated with increased salmonid abundance or biomass in 

western Washington and Oregon. In this study, densities of steelhead trout (Oncorhynchus 

mykiss) and sculpin (Cottus sp.) decreased significantly with greater incident radiation and 

higher stream temperatures. 

Sites with considerable upstream vegetative cover, maintained cooler summer temperatures 

than unshaded reaches or canopied sites with limited extent of upstream riparian vegetation. 

Water temperatures in open reaches at study sites often exceeded 30 degrees C, well beyond 

the normal range of tolerance for salmonids and cottids. Study sites with high light levels were 

dominated by the large caddisfly larvae Dicosmoecus, that feeds on thick beds of filamentous 

algae. This armored caddisfly escapes predation by the warmwater fish populating the open 

study reaches and sequesters a significant portion of the energy entering the stream that would 

otherwise be transferred to predators. 

"Warm water species of fish, such as redside shiners, bridgelip suckers, northern squawfish, 

and chiselmouth chub, were positively related to solar input (r = 0.82, p = 0.025), but unrelated 

to temperature (r = 0.63, p = 0.13)." These warmwater species would normally not enter 

tributaries of the size sampled in this study. "In contrast, cool-adapted rainbow trout and Paiute 

sculpin showed a strong negative correlation (r = -0.97, p = 0.0004) with temperature and a 

negative but insignificant correlation (r = -0.47, p = 0.29) with incident light."

Geographic location: xeric, mountains, eastern Oregon, John Day River basin, eco11, EPA 

Region 10 

Keywords: riparian vegetation, macroinvertebrates, periphyton, fish, salmonids, sculpins, 

cyprinids, open canopy, stream ecology, benthic community structure, trophic interactions, 

agriculture, grazing 

Abstract: Many studies on cool, forested streams have shown that removal of riparian canopy 

leads to higher incident radiation, blooms in algal and macroinvertebrate populations, and 

concomitant increases in salmonid abundance. In warm, high-elevation desert streams, 

194
however, an open canopy may not increase salmonid density. Our seven study reaches on 3rd 

order tributaries of the John Day River in eastern Oregon included riparian areas ranging from 

denuded, heavily grazed stream banks to intact conifer forest. Average summer solar inputs to 

these sites varied from 165 to 2230 megajoules/sq m, and stream temperatures were influenced 

by the density and extent of canopy. Densities of steelhead trout (Oncorhynchus mykiss) and 

sculpin (Cottus spp.) decreased significantly with greater incident radiation and higher stream 

temperatures, although many warmwater cyprinids increased in abundance in unshaded sites. 

Periphyton standing crop (g ash-free dry mass/m2

) closely tracked solar inputs and was, in turn, 

strongly positively correlated with biomasses of total invertebrates and of grazers. Collector, 

shredder, and predator biomasses, and numerical abundances of all invertebrate groups, did 

not change with canopy density. The abundances of chironomids and baetids were unrelated to 

increases in light or algal resources, in contrast to studies in Cascades and Coast Range 

streams where irruptions of these taxa occurred in canopy openings. In our streams the largebodied caddisfly Dicosmoecus accounted for the higher total invertebrate biomass observed in 

exposed sites. These insects composed 55-96% of the total biomass in open reaches, but only 

0-1.4% in the three most shaded sites. Increases in total invertebrate biomass with increasing 

light levels or periphyton were not observed when Dicosmoecus were removed from the 

analysis. Dicosmoecus are consumed infrequently by juvenile trout or other small fish species 

common in John Day tributaries; consequently, extensive openings in the canopy appear to 

produce few advantages to upper trophic levels in these streams. 

195
Author: Thurow, R.F.; Lee, D.C.; Rieman, B.E. 

Year: 1997 

Title: Distribution and status of seven native salmonids in the interior Columbia River basin and 

portions of the Klamath River and Great Basins

Reference Type: Journal Article

Journal: North American Journal of Fisheries Management

Volume: 17 

Issue: 4 

Pages: 1094-1110 

Value of reference: This paper presents individual and composite distributions and status of 

seven native salmonids: bull trout, westslope cutthroat trout, Yellowstone cutthroat trout, 

redband trout, steelhead, ocean type chinook salmon and stream type chinook salmon. It 

describes their potential historical range, loss of historical range, and factors that have 

influenced current distribution and status. This is a detailed summary of seven salmonids, 

which are addressed similarly but in less detail in a broader summary by Lee and others 1997 

(this bibliography). 

Results relevant to EMAP: Results are summarized for each species and for the area as a 

whole with respect to all species combined. Tabular (Table 1) and mapped results of historical 

and current distributions and predicted strong populations (Figures 2-7). 

Known or predicted occurrence as a percentage of subwatersheds in the historical range: Bull 

trout--6%; Yellowstone cutthroat trout--66%; westslope cutthroat trout--85%; redband trout--64% 

(combined occupancy by sympatric and allopatric forms); steelhead--46%; chinook salmon 

stream type--28%; chinook salmon ocean type--29%. 

Although some of the taxa remain in most of their potential range, declines in abundance, 

reductions in distribution, and fragmentation into smaller patches are apparent for all species 

examined. Four of seven taxa are present in less than 50% of their historical range. Less than 

38% of subwatersheds supported two or more taxa. Less than 0.01% supported strong 

populations of three salmonids and only 3% supported two. 

A literature review of the human impacts that have contributed to declines (provided in the 

discussion) addresses introduction of nonnative species, habitat degradation, habitat 

fragmentation and inaccessibility caused by dams, overfishing, and genetic dilution in hatchery 

programs. 

Geographic location: Oregon, Washington, Idaho, EPA region 10, Columbia River basin, 

Klamath River basin, eco80, eco9, eco11, eco10, eco15, eco16, eco12, mountains, xeric 

Keywords: fish, salmonids, habitat degradation, nonnative species, dams, fishing, hatchery 

programs

Abstract: We summarized presence, absence, current status, and potential historical 

distribution of seven native salmonid taxa - bull trout Salvelinus confluentus, Yellowstone 

cutthroat trout Oncorhynchus clarki bouvieri, westslope cutthroat trout O. c. lewisi, redband trout 

and steelhead O. mykiss gairdneri, stream type (age-1 migrant) chinook salmon O. 

tshawytscha, and ocean type (age-0 migrant) chinook salmon - in the interior Columbia River 

basin and portions of the Klamath River and Great basins. Potential historical range was defined 

as the likely distribution in the study area prior to European settlement. Data were compiled 

196
from existing sources and surveys completed by more than 150 biologists. Within the potential 

range of potamodromous salmonids, status was unknown in 38-69% of the area, and the 

distribution of anadromous salmonids was unknown in 12-15%. We developed models to 

quantitatively explore relationships among fish status and distribution, the biophysical 

environment, and land management, and used the models to predict the presence of taxa in 

unsampled areas. The composition, distribution, and status of fishes within the study area is 

very different than it was historically. Although several of the salmonid taxa are distributed 

throughout most of their potential range, declines in abundance and distribution and 

fragmentation into smaller patches are apparent for all forms. None of the salmonid taxa have 

known or predicted strong populations in more than 22% of their potential ranges, with the 

exception of Yellowstone cutthroat trout. Both forms of chinook salmon are absent from more 

than 70% and steelhead from more than 50% of their potential ranges, and all are approaching 

extirpation in portions of their remaining ranges. If current distributions of the taxa are useful 

indicators, many aquatic systems are remnants of what were larger and more complex, diverse, 

and connected systems. Because much of the ecosystem has been altered, areas supporting 

strong populations or multiple species will be critical for conservation management. Moreover, 

restoration of a broader matrix of productive habitats also will be necessary to allow fuller 

expression of phenotypic and genotypic diversity in native salmonids. 

Notes: Lee and others 1997 (this bibliography) present an extensive assessment of changes in 

status of 46 fish species in the interior Columbia basin and portions of Klamath and Great 

basins. 

Rieman and others 1997 describe bull trout in more detail: 

Rieman, B.E., D.C. Lee, and R.F. Thurow. 1997. Distribution, status, and likely future trends of 

bull trout within the Columbia River and Klamath River basins. North American Journal of 

Fisheries Management 17:1111-1125.

197
Author: U.S. Department of Agriculture, Forest Service. 

Year: 1996 

Title: Status of the interior Columbia basin: summary of scientific findings 

Reference Type: Report

City: Portland, OR 

Institution: U.S. Department of Agriculture, Forest Service, Pacific Northwest Research Station 

and U.S. Department of the Interior, Bureau of Land Management 

Pages: 144 

Report Number: Gen. Tech. Rpt. PNW-GTR-385 

Value of reference: Though the results of the assessment are general and presented for the 

entire region, there are several useful maps and tables that summarize historical and present 

day distributions of key salmonids in the Columbia Basin.

Results relevant to EMAP: A Basin-wide analysis of riparian vegetation found a widespread 

decline in shrublands in the riparian zones. In the overstory, cottonwood and aspen have also 

declined significantly in the last 100 years. 

Map of historic salmonid distribution in the Columbia Basin for six species of salmon and map of 

current key salmonid presence. 

Table of Historical and Occupied Range and Habitat Status for key salmonids within the Basin 

assessment area. 

Geographic location: Columbia Basin, eco10, eco15, eco16, eco12, eco11, eco80, Oregon, 

Idaho, Washington, northern Great Basin, Blue Mountains, Columbia Plateau, EPA Region 10, 

mountains, xeric 

Keywords: fish, ecosystem assessment, ecosystem management, ecosystem integrity, risk 

analysis, salmonids, historical, riparian vegetation 

Abstract: The Status of the Interior Columbia Basin is a summary of the scientific findings from 

the Interior Columbia Basin Ecosystem Management Project. The Interior Columbia Basin 

includes some 145 million acres within the northwestern United States. Over 75 million acres of 

this area are managed by the Forest Service or the Bureau of Land Management. A framework 

for ecosystem management is described that assumes the broad purpose is to maintain the 

integrity of ecosystems over time and space. An integrated scientific assessment links 

landscape, aquatic, terrestrial, social, and economic characterizations to describe the 

biophysical and social systems. Ecosystem conditions within the Basin have changed 

substantially within the last 100 years. The status of ecosystems is described in terms of current 

conditions and trends under three broadly defined management options. The scientific 

information brought forward will be used in decision making, and may potentially amend Forest 

Service and Bureau of Land Management plans within the Basin. The information highlighted 

here represents an integrated view of biophysical and socioeconomic elements at a scale never 

before attempted. The risks and opportunities are characterized in the broad context of the 

Basin for managers and the public to use as a foundation for discussion about future 

management. 

URL: http://www.fs.fed.us/pnw/pubs/summary/gtr_385a.pdf 

198
Author: U.S. Department of Interior 

Year: 1994 

Title: Endangered and Threatened Wildlife and Plants: Designation of Critical Habitat for the 

Threatened Spikedace (Meda fulgida) 

Reference Type: Report

Publisher: Federal Register 

Volume: 59 

Issue: 45 

Pages: 10906-10915 

Value of reference: This is a policy document, but it briefly summarizes the historical and 

present range, habitat needs, and status of the spikedace as background for designating critical 

habitat.

Results relevant to EMAP: The spikedace is found in moderate to large perennial streams 

where it inhabits shallow riffles with sand, gravel, and rubble substrates and moderate to swift 

currents. Recurrent flooding is important to maintain habitat and the species' competitive edge 

over nonnative fish species. 

The spikedace was first collect in 1851 from the San Pedro river in Arizona. Historically it was 

common throughout much of the Verde, Agua Fria, Salt, San Pedro, San Francisco, and Gila 

(upstream from Phoenix) River systems in both main stem and moderate gradient perennial 

tributaries up to 1900 m elevation. 

Due to habitat destruction and competition and predation by nonnative fish, its range and 

abundance have been severely reduced, and it is now restricted to only 9% of its historic range 

of 2600 km of stream.

Geographic location: Arizona, xeric, mountains, eco22, eco23, eco79, eco81, EPA region 9, 

Verde River, San Pedro River, Gila River, Salt River, San Francisco River, Agua Fria 

Keywords: fish, nonnative species, habitat degradation, flooding, flow alteration 

199
Author: U.S. Department of Interior 

Year: 1994 

Title: Endangered and Threatened Wildlife and Plants; Designation of Critical Habitat for the 

Threatened Loach Minnow (Tiaroga cobitis) 

Reference Type: Report

Publisher: Federal Register 

Volume: 59 

Issue: 45 

Pages: 10898-10906 

Value of reference: This is a policy document, but it briefly summarizes the historical and 

present range, habitat needs, and status of the loach minnow as background for designating 

critical habitat. 

Results relevant to EMAP: The loach minnow was first collected in 1851 from the San Pedro 

River in Arizona. Historically, it was locally common throughout much of the Verde, Salt, San 

Pedro, San Francisco, and Gila (upstream from Phoenix) River systems in suitable habitat in 

both main stem and tributaries up to 2200 m elevation. The historical range was estimated as 

2600 km of river. 

This species needs recurrent flooding to maintain a substrate free of embedded sediments and 

to maintain conditions that allow it to better compete with nonnative fish species. Due to flow 

alterations, habitat destruction, and competition and predation by nonnative fish species, its 

range and abundance have been severely reduced, and it is now restricted to only 17% of its 

historic range. It is included o the State lists of threatened and endangered species in Arizona 

and New Mexico. 

Geographic location: Arizona, San Pedro River, Blue River, White River, Verde River, Gila 

River, EPA region 9, eco22, eco23, eco79, eco81, xeric, mountains 

Keywords: fish, nonnative species, habitat degradation, flooding, flow alteration 

200
Author: U.S. Geological Survey 

Year: 2004 

Title: Pre-settlement wildlife and habitat of Montana: An overview ( Pre-settlement Habitat and 

Wildlife literature) 

Reference Type: Electronic Source

Producer: U.S. Geological Survey; Northern Prairie Wildlife Research Center 

Access Year: 2005 

Access Date: June 24 

Value of reference: A bibliography of books, papers, and documents pertaining to presettlement habitat and wildlife of Montana and adjacent lands. References cover the Great 

Plains and include information on the following: Natural history, exploration, history of 

settlement, ecology, species inventories, expedition accounts, etc.

Results relevant to EMAP: A good source to locate available pre-settlement literature and 

references. This web site includes listings of many early exploration accounts and 

observations, which may be the only source for pre-settlement conditions of the Great Plains. 

Stream conditions and species inventories may be limited, however some baseline information 

can be gleaned from some of these references.

Geographic location: Montana, North Dakota, South Dakota, Wyoming, Colorado, Iowa, Great 

plains, mountains, plains, eco25, eco21, eco43, eco17, eco42, eco41, eco15, eco44, eco27, 

EPA region 7, EPA region 8 

Keywords: phab, pre-settlement, literature survey, early expeditions, species inventories, fish, 

ecology, historic condition 

URL: http://www.npwrc.usgs.gov/resource/literatr/presettl/books.htm 

201
Author: Valdez, R.A.; Muth, R.T. 

Year of Conference: 2005 

Title: Ecology and conservation of native fishes in the upper Colorado River basin 

Reference Type: Conference Proceedings

Editor: Rinne, J.N.; Hughes, R.M.; Calamusso, B. 

Conference Name: Historical Changes in Large River Fish Assemblages of the Americas 

Conference Location: Bethesda, MD 

Publisher: American Fisheries Society 

Volume: 45 

Pages: 157-204 

Value of reference: Although the focus of this chapter is on current status and ecology of the 

fishes (see Table 1), the section 'Current Status and Ecology' includes summaries of the 

historical status and distribution for the following species: Colorado Pikeminnow, Humpback 

Chub, Bonytail, Razorback Sucker, Roundtail Chub, Flannelmouth Sucker, Bluehead Sucker, 

Mountain Sucker, and Colorado River Cutthroat Trout. 

The relative abundance in different parts of a river and its tributaries is described in text format, 

with references to many of the original historical ichthyological reports, some of which are cited 

in this bibliography. 

A section on 'threats to native fishes' is also included, describing the primary causes of decline 

of the native fish species. 

Results relevant to EMAP: Historical distribution and abundance is described for a number of 

species, for example: "The Colorado pikeminnow...was once widespread and abundant in warm 

main-stem rivers and tributaries...Wild populations of Colorado pikeminnow are presently found 

only in the upper basin in about 25% of historic range basin-wide"; "Razorback sucker was 

historically common to abundant in most warm regions of the Colorado River system during the 

19th and 20th centuries....the species now exists naturally in only a few locations"; "Roundtail 

chub in the upper basin remains as 15 populations in about 55% of its historic habitat...[it] was 

once common in 5 tributary rivers where it is now nearly eliminated." 

Threats to native fishes are discussed: flow regulation and diversion, degraded water quality. 

nonnative fish, and physical habitat destruction, alteration, and fragmentation. 

Geographic location: Colorado River basin, Colorado, Wyoming, Utah, EPA region 8, xeric, 

mountains, eco20, eco22, eco23, eco21, eco18, eco19 

Keywords: fish, historical status and distribution, water diversion, dams, nonnative fish, habitat 

degradation and fragmentation 

202
Author: Van Steeter, M. M.; Pitlick, J. 

Year: 1998 

Title: Geomorphology and endangered fish habitats of the upper Colorado River. 1. Historic 

changes in stream flow, sediment load, and channel morphology 

Reference Type: Journal Article 

Journal: Water Resources Research 

Volume: 34 

Issue: 2 

Pages: 287-302 

Value of reference: The authors examine the changes in channel morphology and sediment 

load of a segment of the upper Colorado River near Grand Junction, Colorado between 1900 

and 1995 and relate it to the habitat requirements of a native fish, the Colorado squawfish.

Results relevant to EMAP: Flow records were divided into a predevelopment period (1900-

1949) and compared to a post-development period (1950-1995) since most of the reservoirs 

were built upstream after 1950. Dams, irrigation withdrawals, and interbasin transfers have 

significantly altered the natural flow regimes of the upper Colorado and Gunnison rivers. Peak 

discharges in reaches used by endangered native fishes are 29-40% lower than they were in 

the past. Reservoirs affect the way runoff is distributed throughout the year; yearly average 

discharge is similar to that in the past, but the spring peak flows are much reduced. 

Sediment loads are similar to those in the past; however, since high flows are less common, the 

rivers have lost their capacity to carry the sediment. In the last 40 years or so, there is a 

tendency for sediment to build up in the channel, causing it to become narrower and less 

complex. 

The rivers' declining ability to carry sediment affects native fish because the substrate is not 

regularly cleaned of silt and sand by peak flows. This has limited the reproductive success of 

the Colorado squawfish. The silting of the channel also favors nonnative (competitive) fish such 

as the channel catfish. There has also been significant habitat loss for native fish as 

backwaters, bars, and islands have been reduced. Analysis of aerial photographs indicates that 

between 1937 and 1993 the main channel of the Colorado River has narrowed by an average of 

20 m and about 1/4 of the area formed by side channels and backwaters has been lost.

Geographic location: eco20, Region 8, Colorado, upper Colorado River, Gunnison River, xeric 

Keywords: fish, Colorado squawfish, sediment, dams, habitat degradation, nonnative species, 

phab, channel geomorphology, historic change, hydrologic variability, peak discharge 

Abstract: The hydrologic, geomorphic, and ecologic effects of reservoir operation are thought to 

be key factors in the decline of native fishes in the upper Colorado River basin. The present 

paper examines the extent to which changes in stream flow and sediment loads have affected 

alluvial reaches of the Colorado River near Grand Junction, Colorado. The analysis shows that 

since 1950, annual peak discharges of the Colorado River and its major tributary, the Gunnison 

River, have decreased by 29-38%. The total volume of runoff delivered to the study area has 

not changed significantly over the period of record, but the annual hydrograph has been 

modified greatly by reductions in peak flows and augmentation of base flows. Annual 

suspended sediment loads of the Colorado River and Gunnison River have likewise decreased. 

This was particularly apparent during the period from 1964 to 1978, when annual sediment 

loads were 40-65% less than the long-term average. Analysis of aerial photographs indicates 

203
that between 1937 and 1993 the main channel of the Colorado River has narrowed by an 

average of 20 m and about 1/4 of the area formed by side channels and backwaters has been 

lost. 

204
Author: Varley, J. D.; Gresswell, R. E. 

Year: 1988 

Title: Ecology, status, and management of the Yellowstone cutthroat trout 

Reference Type: Book Section

Editor: Gresswell, R. E. 

Book Title: Status and management of interior stocks of cutthroat trout. 

City: Bethesda, Maryland 

Publisher: American Fisheries Society 

Pages: 13-24 

Value of reference: The authors compare historical and present Yellowstone cutthroat trout 

distribution and discuss the factors implicated in its decline.

Results relevant to EMAP: Yellowstone cutthroat trout once inhabited about 24,000 km of 

stream in Montana, Wyoming, Idaho, and a corner of Utah. Today they exist in an estimated 

2400 km of stream in and around Yellowstone and Grand Teton National Parks. 

The Yellowstone cutthroat trout presently occurs mainly in headwater streams, but historically, 

the fish had a greater elevational distribution. Its historic elevational range extended from 275 m 

to 3200 m. The fish were common in large rivers such as the Snake River above Shoshone 

Falls and the main stem Yellowstone River at Miles City, Montana. 

Yellowstone cutthroat declines are attributed mainly to stream dewatering, grazing-related 

riparian vegetation loss, and the introduction of nonnative species.

Geographic location: Region 8, Montana, Wyoming, Idaho, Utah, Yellowstone River basin, 

Snake River basin, mountains, eco17, eco43, eco12 

Keywords: fish, cutthroat trout, distribution, grazing, riparian vegetation, habitat degradation, 

nonnative species, water diversion 

Abstract: The Yellowstone cutthroat trout Salmo clarki bouvieri is the most abundant and widely 

dispersed subspecies of inland cutthroat trout. The historic range of the subspecies included the 

Yellowstone River drainage in Montana and Wyoming and portions of the Snake River drainage 

in Wyoming, Idaho, Nevada, Utah, and perhaps Washington. Introductions of nonnative fishes, 

environmental degradation, and human exploitation have severely reduced this range. The 

subspecies is estimated to presently exist in a genetically pure form in about 85% of the historic 

lake habitat but only in about 10% of the estimated original stream range. Additionally, 

Yellowstone cutthroat trout populations have been established outside the historic range in at 

least seven western states and two Canadian provinces. High landing rates and angler success, 

coupled with the fish's relatively large mean length, make the Yellowstone cutthroat trout a 

valuable recreational resource; however, vulnerability to angling has often led to overharvest of 

wild stocks. Current management of the Yellowstone subspecies includes wild trout programs 

for native and introduced populations and maintenance stocking from hatchery brood stocks. 

Genetic integrity, habitat management, and special angling regulations are important elements 

that influence the success of these programs. The status of the Yellowstone cutthroat trout is 

encouraging, but future management must emphasize protection of the full range of genetic 

diversity.

205
Author: Warren, G.K. 

Year: 1856 

Title: Explorations in the Dacota Country, in the year 1855 

Reference Type: Report

City: Washington, D.C. 

Institution: U.S. Senate 

Report Number: Executive Document No. 76, 34th Congress, 1st Session. 

Value of reference: This primary source provides physical descriptions of several river basins 

in the plains, including the Missouri, Little Missouri, Platte, Rapid, White, Big Shyenne, Big 

Sioux, Vermillion, and James. Appendix A gives accounts of the explorations of these areas in 

journal format, including additional habitat descriptions of stream widths, bank height, sediment 

composition, and riparian vegetation. Appendix B provides detailed descriptions of a smaller 

area under consideration for a military reserve in the vicinity of eastern Wyoming and western 

South Dakota. Appendix E is a geological summary, but also provides descriptions of riparian 

vegetation along rivers and streams, including the dominant trees, shrubs, and herbaceous 

riparian plants of the region, and a portion about travel through the badlands. This is a good 

source for early descriptions of riparian areas and landscapes of the plains region.

Results relevant to EMAP: Accounts describe the region encompassing southeast Wyoming, 

southern South Dakota, and northern Nebraska, including numerous descriptions of riparian 

habitats and stream physical characteristics throughout the exploration route. The majority of 

accounts mention the presence of grasses and woody plants such as cottonwood, willow, ash, 

oak, elm, boxelder, and wild plum. In places along streams where only grass was found, the 

accounts often include a mention of nearby wooded areas, upstream or downstream. Stream 

sediment type, width, depth, bank height, presence of fish (occasional mention) are also 

included in descriptions. 

In several locations of the exploration route, the author notes that trees (primarily 

cottonwood)were once more plentiful (based on signs of trees being cut), but they had been cut 

down for use by the "Indians". 

Geographic location: Wyoming, South Dakota, plains, EPA Region 8, Missouri River basin, 

Little Missouri River basin, Platte River basin, Rapid River basin, White River basin, Big 

Shyenne River basin, Big Sioux River basin, Vermillion River basin, and James River basin, 

eco43, eco17, eco42, eco46 

Keywords: phab, riparian vegetation, primary source, historical accounts, explorations 

206
Author: West, Elliott; Ruark, Greg 

Year: 2004 

Title: A long, long time ago ... Historical evidence of riparian forests in the Great Plains and how 

that knowledge can aid with restoration and management 

Reference Type: Journal Article

Journal: Journal of Soil and Water Conservation 

Volume: 59 

Issue: 5 

Pages: 105-110 

Value of reference: This article presents a differing point of view regarding the historical 

presence of large woody riparian areas along larger Great Plains streams and waterways. The 

author suggests that early historic accounts of the streams suggest that the original vegetation 

included large wooded riparian zones and that current thought (streams without woody 

vegetation) is based on post-settlement accounts which were after the woody vegetation had 

been removed by the increased demand on the resource due to the push for settlement and 

westward expansion. 

This article points out the importance of finding pre-settlement accounts and surveys when 

determining "natural" conditions. The author points out that much of the current historical 

baseline used to determine "normal conditions" is based on accounts that date back to the early 

20th century. In those reports trees were largely absent or thinly represented along water 

courses. No one should conclude from these records, that the absence of timber was natural. 

Rather the lack of trees was the consequence of some of the most rapid changes that the 

region has ever known. 

Results relevant to EMAP: Many of the larger streams of the Great Plains had a more 

extensive riparian woodland than had been commonly assumed. Riparian vegetation 

experienced substantial change during the mid to late 1800's due to human impacts. By 1900 

most of the trees and other woody vegetation along the rivers and streams in the Great Plains 

had been cut and removed by Indians, gold seekers, soldiers, railroad crews and settlers. 

These riparian zones were once heavily forested with wide bands of trees but are now occupied 

primarily by herbaceous plants or cropland. 

Looking at historical accounts from the pre- or early 1800's point to a more abundant woody 

riparian cover. This article highlights the importance of true pre-settlement reports and 

descriptions to determine "historic or reference condition", particularly in the Plains, which was 

altered early and dramatically.

Geographic location: Great Plains, Nebraska, Kansas, Colorado, Wyoming, eco25, eco27, 

eco43, plains, Platte River, North and South Platte rivers, Arkansas River, Solomon River, 

Republican River, EPA Region 7, EPA Region 8 

Keywords: phab, riparian zone, trees, human impact 

207
Author: Wissmar, R. C.; Smith, J. E.; McIntosh, B. A.; Li, H. W.; Reeves, G. H.; Sedell, J. R. 

Year: 1994 

Title: A history of resource use and disturbance in riverine basins of eastern Oregon and 

Washington (early 1800's-1990's) 

Reference Type: Journal Article

Journal: Northwest Science 

Volume: 68 

Issue: Special Issue 

Pages: 1-35 

Value of reference: A comprehensive look at the settlement and cumulative disturbance history 

of six river basins in eastern Oregon and Washington (the Okanogan, Methow, Yakima, Little 

Naches, John Day River, and Grand Ronde Rivers) and how 150 years of human use has 

affected fish populations and instream and riparian habitats. This paper is a companion to 

McIntosh et al. 1994 (in this bibliography), but it delves into the chronology of historical resource 

use in greater detail. 

Results relevant to EMAP: Wissmar et al. also discuss impacts to fish populations that are not 

as evident as those that are commonly reported, such as the effects of early diversions, 

ditching, and dredging for mining operations, changes to the pattern of snow accumulation and 

an earlier snowmelt caused by clear cutting, and fish response to high temperatures from a loss 

of shading in eastern Oregon streams. 

Earlier peak flows in the Upper Grande Ronde River may influence the survival of salmon 

smolts because fish outmigration is timed largely to peak flows. Early peak flows could force 

smolts to outmigrate too early and lower fish survival. The hydrograph of the John Day basin 

has changed significantly due partly to vegetative changes, with base flows increasing in all 

managed watersheds and remaining the same in wilderness areas. Prior to settlement, the John 

Day River basin supported substantial runs of spring and fall chinook salmon and steelhead and 

resident fish such as bull trout (Salvelinus confluentus). Currently salmon runs are suppressed, 

with fall chinook being nearly extinct (escapements < 100 fish), while spring chinook runs range 

from 2000 - 5000 and steelhead from 15,000 - 40,000 fish. 

Turbidity in some parts of the basin, such as Cottonwood Creek, a tributary to the North Fork, is 

notoriously high after storm events. The resulting siltation of stream beds decreases aquatic 

insect production and degrades spawning gravels. Lack of thermal cover also affects fish food 

availability. Exposed reaches with high solar radiation produce algae which changes the types 

of invertebrate prey base. Severe increases in water temperatures both summer and winter are 

critical limiting factors for salmonids over many portions of the John Day River basin. 

Geographic location: eco10, eco11, Columbia Plateau, Blue Mountains, North Cascades, 

Eastern Cascades Slopes and Foothills, eco77, eco9, Oregon, Washington, mountains, xeric, 

EPA Region 10 

Keywords: historical, fish, salmonids, human disturbance, temperature, sediments, logging, 

mining, grazing, dams, roads, water diversions 

Abstract: A historical review of human activities influencing streams and riparian ecosystems in 

eastern Washington and Oregon shows that cumulative effects of resource uses and 

management over the past two centuries are altering the health of many river basins. Past 

practices such as livestock grazing and forest harvest near riparian areas and streams became 

208
collectively significant over long time periods and are continuing today. Case histories for the 

Okanogan and Methow River basins (north central Washington), the Naches River (eastern 

Cascade Mountains), and the Grande Ronde and John Day River basins (eastern and north 

central Oregon) provide chronologies of events that shaped the present-day landscapes and 

socio-economic conditions of the region. Historic cumulative effects on stream and riparian 

ecosystems include livestock grazing and mining from the 1860's until about 1910. Timber 

harvest, roads, fire management, dams, irrigation, and fisheries increased in importance during 

the 20th Century. Management histories show minimal actions for reducing damage to stream 

and riparian ecosystems. Managers commonly perpetuate the notion that streams and riparian 

areas are difficult to manage because little is known about how these ecosystems function. 

Many agencies strive to develop procedures for treating the symptoms of degraded ecosystems 

while giving little consideration to the causes. Other agencies and public groups concerned with 

conflicting issues like water allocations and minimum instream flows for fish usually disagree 

with plans for resolving these issues. The continuous dissent by these parties only adds to the 

plight of fish as available water and habitats continue to decline. Alternatively, new basin-wide 

management strategies of federal and environmental organizations offer hope for improving the 

ecosystem biodiversity and population levels of fish and wildlife. Priorities include the protection, 

restoration, and monitoring of habitats and networks that connect stream and riparian 

ecosystems in degraded and intact watersheds. Intact watersheds (e.g., roadless and 

wilderness areas) function as critical habitats and refuge areas for fish and wildlife of adjoining 

ecosystems. 

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Editor: Yarrow, H. C.; Henshaw, H. W.; Cope, E. D. 

Year: 1875 

Title: Reports upon the zoological collections obtained from portions of Nevada, Utah, 

California, Colorado, New Mexico, and Arizona during the years 1871, 1872, 1873, and 1874 

Reference Type: Edited Book

Series Title: Geographical and geological explorations and surveys west of the 100th meridian 

in charge of first lieutenant George M. Wheeler 

City: Washington, D. C. 

Publisher: Government Printing Office 

Volume: 5 

Number of Volumes: 6 

Number of Pages: 1021 

Value of reference: This tome describes biota (fish) collected on a series of survey 

explorations made between 1871 and 1874 in 6 western states. The landscape descriptions in 

the mammals and birds chapters give glimpses of riparian vegetation. The chapter on fish 

(retained as hard copy) is valuable because it describes non-commercial cyprinids and suckers 

(including some line drawings).

Results relevant to EMAP: The descriptions of riparian growth along streams flowing through 

foothills and low mountains (at elevations as low as 2700 ft.) in arid regions (San Luis Valley, 

Colorado; Gila River, Arizona, smaller streams in Arizona) are notable in their continual mention 

of tall cottonwoods and heavy brush, so thick at times to "render progress at all times difficult, 

and occasionally well nigh impossible." 

Streams issuing from the base of the mountain normally disappeared in the "thirsty sands of the 

plains below", but even on the dry flats, the luxuriant vegetation which enclosed the banks did 

not disappear until the stream sank beneath the sand. 

The chapter on fish collected during the surveys lists species encountered and location, 

descriptions of individual fish with some body measurements, some general indications of 

abundance, and occasional anecdotes of fishing for subsistence or market.

Geographic location: Nevada, Utah, California, Colorado, New Mexico, Arizona, mountains, 

xeric, eco19, eco13, eco21, eco23, Provo River, San Pedro River, Gila River, EPA Region 8, 

EPA Region 9 

Keywords: fish, riparian vegetation, phab, historical survey 

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Author: Yoshiyama, R.M.; Fisher, R.W.; Moyle, P.B. 

Year: 1998 

Title: Historical abundance and decline of chinook salmon in the central valley region of 

California 

Reference Type: Journal Article

Journal: North American Journal of Fisheries Management 

Volume: 18 

Pages: 487-521 

Value of reference: This research reconstructs historical chinook salmon estimates (numbers 

and pounds) in two major drainages--San Joaquin and Sacramento Rivers, and discusses 

declines that may have begun as early as the 1850s, the factors causing those declines, and 

the general changes in ranges of the four major chinook runs over the last 70 years. It brings 

together many historical and current references and thus is a very thorough synthesis article 

that covers the history and status of Chinook salmon in the Central Valley. Paper also 

discusses the differential impacts on the 4 runs (spring, winter, fall, late-fall). 

Results relevant to EMAP: The Central Valley system contained a productive chinook 

resource before the 20th century; historical chinook runs for the Central Valley were estimated 

between 1 and 2 million spawners per year in the late 1800s, which was reduced by 

approximately 50-90% by the late 1900s (see Table 5). 

Harvest records estimate takings in 1856 at 450,000 fish (nearly 4000 per day); at an average 

weight of about fifteen pounds each, this amounts to 6,750,000 pounds (includes spring, 

summer, and winter run catches). Catches during 1875-1910 were often 5-10 million pounds 

annually, averaging at least 7,180,000 lb and exceeding 10 million pounds in 1880, 1883, 1909, 

and 1910 (see Table 2). 

A decrease in the abundance of salmon in the Sacramento River was noticed as early as 1851 

beginning with widespread mining. Factors causing declines over time are overfishing, 

destruction of habitat by hydraulic mining, dredge mining, railroad construction, logging, 

construction of dams, water diversions, and establishment of hatchery programs.

Geographic location: eco6, eco7, California, Central Valley, xeric, San Joaquin River, 

Sacramento River, EPA Region 9 

Keywords: fish, historical fish catch, historical fishery, fishing, mining, dams, water diversion, 

hatchery egg collecting 

Abstract: The Central Valley drainage of California formerly produced immense numbers of 

chinook salmon Oncorhynchus tshawytscha. Four seasonal runs occur in this system--fall, latefall, winter, and spring runs. Differences in life history timing and spatial distribution enabled the 

four runs to use the drainage to the fullest possible extent and once made it one of the richest 

regions in the world for chinook salmon production. Native American fishers within the central 

valley drainage harvested chinook salmon at estimated levels that reached 8.5 million pounds or 

more annually. Native harvests, therefore, were roughly comparable to the peak commercial 

harvests taken later by Euro-American fishers, but whether or not native fishing depressed the 

productive capacities of the salmon populations to any substantial degree is not known. The 

commercial chinook salmon fishery in CA started about 1850 in the San Francisco Bay and 

Sacramento-San Juaquin Delta region, where it formed the nucleus of the first major fishery 

conducted by Euro-American immigrants in the state. This fishery was one of the important 

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early industries that supported the Euro-American settlement of the Central Valley region. The 

salmon fishery remained centered there until the early 1900s, when ocean salmon fishing began 

to expand and eventually came to dominate the fishery. Annual catches by the early 

Sacramento-San Juaquin in-river fishery commonly reached 4-10 million pounds and generally 

were higher than the total statewide catches made during the most recent several decades. 

The historical abundances of Central Valley chinook salmon before large-scale commercial 

exploitation and depletion of the runs cannot be determined with certainty. However, on the 

basis of early commercial catch records, the maximal production levels of the central valley 

chinook salmon stocks in aggregate may be conservatively estimated to have reached 

approximately 1-2 million spawners annually. Although substantial investment has been made 

by the state of California in managing the chinook salmon resource since the early years of the 

commercial fishery, chinook salmon have declined over the decades to small fractions of their 

previous numbers. The decline of the central valley chinook salmon resource was caused by 

several factors: overfishing, blockage and degradation of streams by mining activities, and 

reduction of salmon habitat and stream flows by dams and water diversions. Differences 

between the four chinook salmon runs in life history timing and habitat requirements partly 

account for their different population histories; the winter run is now threatened with extinction, 

the spring run recently has approached a similarly imperiled state, and the late-fall run has been 

at moderately low population levels for the past two decades. Only the fall run, in aggregate, 

can be regarded as secure, but it too has undergone substantial reductions in abundance. Fallrun spawner numbers were especially low in the San Juaquin River basin in recent years, and in 

Sacramento River basin streams their numbers have been heavily influenced by production of 

hatchery fish. 

212
Author: Young, M.K. 

Year: 2003 

Title: Yellowstone Cutthroat Trout 

Reference Type: Electronic Source

Producer: American Fisheries Society, Montana Chapter 

Access Year: 2005 

Access Date: May 18 

Last Update Date: April 18, 2005 

Value of reference: Summary addresses a subspecies of cutthroat trout, historically wideranging and found in numerous basins in several states. The focus here is on the fish species 

of Montana, but historical accounts are given for the species entire range in the West. 

Estimates of percent range reductions are given by state, although these are complicated 

because the species is stocked and is actually now found in more waters than it was historically. 

Concerns about the genetic homogenization of various subspecies of cutthroat trout and among 

populations within the Yellowstone cutthroat trout subspecies due to introductions are 

discussed.

Results relevant to EMAP: Historically, Yellowstone cutthroat trout were believed to have 

occupied much of the Yellowstone River basin, including portions of the Clarks Fork of the 

Yellowstone River, Bighorn River, and Tongue River basins in Montana and Wyoming, and 

parts of the Snake River basin in Wyoming, Idaho, Utah, and Nevada (Behnke 1992 (in this 

bibliography)—Figure 1 shows the potential historical range in Montana). 

They have undergone substantial declines in distribution and abundance throughout their range. 

Populations in Utah and Nevada are limited to 102 basins; in Idaho, the trout occupied 43% of 

the historical range, in Wyoming 42% and in Montana, 32% (although more recent estimates 

suggest that only 10% of the historically occupied fluvial habitat in Montana still contains 

genetically pure populations). 

The greatest threat is competition with nonnative fish--brown trout, brook trout, lake trout--while 

a related concern is the widespread stocking of non-indigenous populations of YC-trout 

throughout the historical range, which tends to genetically homogenize populations; habitat 

issues are of lesser importance, but examples of the detrimental effects of habitat degradation, 

loss, and fragmentation on Yellowstone cutthroat trout are numerous--dewatering for irrigation, 

dams, reservoirs, channelization, grazing, logging, mining, road-building. 

Geographic location: Montana, mountains, eco 15, eco17, eco42, eco43, EPA Region 8, 

Yellowstone River basin, Bighorn River basin, Tongue River basin, Snake River basin 

Keywords: fish, historical distribution, agriculture, logging, dams, channelization, mining, roads, 

nonnative species, fishing 

Notes: Other species of concern in Montana are listed on the website and can be accessed 

electronically via the link provided in this entry. However, few present historical estimates or 

ranges. 

URL: http://www.fisheries.org/AFSmontana/SSCpages/yellowstone_cutthroat_trout.htm

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