Long Term Resource Monitoring Program

Technical Report 

2005-T002

February 2005

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Spatial, Temporal, and Environmental Trends of Fish Assemblages 

within Six Reaches of the Upper Mississippi River System
Long Term Resource Monitoring Program Technical Reports

provide Long Term Resource Monitoring Program 

partners with scientific and technical support.

All reports in this series receive anonymous peer review.

Mention of trade names or commercial products does not constitute endorsement

or recommendation for use by the U.S. Department of the Interior, U.S. Geological Survey.
Spatial, Temporal, and Environmental Trends of Fish Assemblages

within Six Reaches of the Upper Mississippi River System

by

Valerie A. Barko, Brian S. Ickes, David P. Herzog, Robert A. Hrabik,

John H. Chick, and Mark A. Pegg

U.S. Geological Survey

Upper Midwest Environmental Sciences Center

2630 Fanta Reed Road

La Crosse, Wisconsin 54603

February 2005
Suggested citation:

Barko, V. A., B. S. Ickes, D. P. Herzog, R. A. Hrabik, J. H. Chick, and M. A. Pegg. 2005. Spatial, temporal, and environmental 

trends of fish assemblages within six reaches of the Upper Mississippi River System. U.S. Geological Survey, Upper Midwest 

Environmental Sciences Center, La Crosse, Wisconsin, February 2005. Technical Report LTRMP 2005-T002. 27 pp.

Additional copies of this report may be obtained from the National Technical Information Service, 5285 Port Royal Road, 

Springfield, VA 22161 (1-800-553-6847 or 703-487-4650). Also available to registered users from the Defense Technical 

Information Center, Attn: Help Desk, 8725 Kingman Road, Suite 0944, Fort Belvoir, VA 22060-6218 (1-800-225-3842 or 

703-767-9050).
iii

Contents

Preface ......................................................................................................... v

Introduction ................................................................................................... 1

Materials and Methods .................................................................................... 2

Field Methods .......................................................................................... 2

Statistical Methods—Ordination ..................................................................... 3

Results and Discussion .................................................................................... 8

Assemblage Structure ................................................................................. 8

Ordination—Environmental Gradients/fish Assemblages ....................................... 8

Ordination—Temporal Shifts in Assemblages ................................................... 12

Ordination—Assemblage/strata Relations by Reach ............................................. 12

Ordination—Sampling Period ........................................................................ 21

Conclusions and Recommendations ..................................................................... 21

Acknowledgments .......................................................................................... 23

References ................................................................................................... 24

Page

Number

Tables

 1. Abundance of each fish species (adult/young-of-the-year) collected by the Long Term

Resource Monitoring Program in the Upper Mississippi River System from 1993 to 2001

using daytime electrofishing, mini-fyke netting, and small and large hoop netting ......... 4

 2. Summary statistics and number of samples (N) for environmental variables measured

during fish sampling in the Upper Mississippi River System from 1993 to 2001

at six sampling reaches .............................................................................. 9

 3. Amount of variation of each environmental variable explained within the six sampling

reaches of the Upper Mississippi River System based on partial canonical correspondence 

analyses ................................................................................................ 10
iv

Number Page

Figures

 1. Geographic representation of the six Upper Mississippi River System Long Term

 Resource Monitoring Program sites sampled from 1993 to 2001 ........................... 3

 2. Partial canonical correspondence analysis (pCCA) of environmental gradients and

species for the Upper Mississippi River System, given gear, year, and period ............... 11

 3. Partial canonical correspondence analysis (pCCA) of year and adult individuals for the

Upper Mississippi River System, given gear, period, and physical habitats .................. 13

 4. Partial canonical correspondence analysis (pCCA) of year and young-of-the-year

individuals for the Upper Mississippi River System, given gear, period, and

physical habitat ....................................................................................... 14

 5. Partial canonical correspondence analysis (pCCA) of strata and young-of-the-year

individuals for the Upper Mississippi River System, given period, gear, and year ......... 15

 6. Partial canonical correspondence analysis (pCCA) of strata and adult individuals for

the Upper Mississippi River System, given gear, period, and year ........................... 18

 7. Partial canonical correspondence analysis (pCCA) of sampling periods 1, 2 , and 3

for the Upper Mississippi River System, given gear, year, and physical habitats ............ 22
v

Preface

The Long Term Resource Monitoring Program (LTRMP) was authorized under the Water Resources 

Development Act of 1986 (Public Law 99-662) as an element of the U.S. Army Corps of Engineers’ 

Environmental Management Program. The LTRMP is being implemented by the Upper Midwest 

Environmental Sciences Center, a U.S. Geological Survey science center, in cooperation with 

the five Upper Mississippi River System (UMRS) States of Illinois, Iowa, Minnesota, Missouri, 

and Wisconsin. The U.S. Army Corps of Engineers provides guidance and has overall Program 

responsibility. The mode of operation and respective roles of the agencies are outlined in a 1988 

Memorandum of Agreement.

The UMRS encompasses the commercially navigable reaches of the Upper Mississippi River, as 

well as the Illinois River and navigable portions of the Kaskaskia, Black, St. Croix, and Minnesota 

Rivers. Congress has declared the UMRS to be both a nationally significant ecosystem and a 

nationally significant commercial navigation system. The mission of the LTRMP is to provide 

decision makers with information for maintaining the UMRS as a sustainable large river ecosystem 

given its multiple-use character. The long-term goals of the Program are to understand the system, 

determine resource trends and effects, develop management alternatives, manage information, and 

develop useful products.

This multiyear report supports Tasks 2.2.8 and 2.3.2 as specified in Goal 2, Monitor Resource 

Change, of the LTRMP Operating Plan (U.S. Fish and Wildlife Service 1993). This report was 

developed with funding provided by the LTRMP.
Spatial, Temporal, and Environmental Trends of Fish Assemblages

within Six Reaches of the Upper Mississippi River System

by

Valerie A. Barko1, Brian S. Ickes2, David P. Herzog1, Robert A. Hrabik1,

John H. Chick3, and Mark A. Pegg4

1

Missouri Department of Conservation, Open Rivers and Wetlands Field Station 

3815 E. Jackson Blvd., Jackson, Missouri 63755 2

U.S. Geological Survey, Upper Midwest Environmental Sciences Center

2630 Fanta Reed Road, La Crosse, Wisconsin 54603 3

Illinois Natural History Survey, Great Rivers Field Station

8450 Montclair, Brighton, Illinois 62012 4

Illinois Natural History Survey, Illinois River Biological Station

704 N. Schrader Avenue, Havana, Illinois 62644

Abstract: We investigated differences in adult and young-of-the-year (YOY) fishes within each of the six Long 

Term Resource Monitoring Program study areas, using monitoring data from 1993 to 2001. Our objective was 

to investigate the relative roles of seasonal, annual, in situ, and physical habitat factors in explaining assemblage 

structure patterns within the Long Term Resource Monitoring Program study areas. Adult and YOY assemblage 

structure within each reach was dominated by one to three numerically abundant species. The percent of the total 

abundance for which these species accounted was 10–88% and varied among age classes and study areas. Physical 

habitat classes were only weakly associated with differences in fish assemblage patterns within each study area. 

The amount of variation in fish abundance explained by physical habitats varied among the reaches. Differences 

among physical habitat classes accounted for 3–23% of the variation in the adult fish assemblage and for 3–20% of 

the difference in the YOY fish assemblage within each reach of our study area. Factors associated with interannual 

differences in environmental conditions were strongly correlated to patterns in assemblage structure within each of 

the six study areas. This was particularly true for YOY assemblages. Such a result would not have been attainable 

without long-term standardized data. Little is known regarding YOY assemblage patterns and dynamics in large 

river systems and long-term data sets are vital for continued investigation. The influence of environmental gradients 

on fish assemblage structure varied among the six study areas and explained 9–31% of the variation in assemblage 

structure. In the northern four reaches, water velocity was one of the primary factors associated with differences 

in fish assemblage structure. In the Unimpounded Reach (Upper Mississippi River) and Illinois River study areas, 

river elevation was one of the primary factors associated with differences in assemblage structure. Depth of gear 

deployment was influential in explaining differences in assemblage structure patterns in all reaches except the 

Upper Mississippi River Pool 4 and the Illinois River study areas. In all study areas, the amount of variation in fish 

abundance patterns explained by sampling period was relatively low. However, assemblage structure differed among 

sampling periods. In the northern reaches, sampling periods 2 and 3 were the most similar. 

Key words: fishes; Illinois River, impounded, long-term, LTRMP, Mississippi River, ordination, unimpounded, YOY

Introduction

Large river systems worldwide have been 

subjected to anthropogenic disturbances 

throughout the last century (Petts et al. 1989; 

Dynesius and Nilsson 1994). These changes 

include channelization, the creation of wing 

dikes and levees, dredging, loss of low velocity 

physical habitats, exotic species introductions, 

agricultural pollution, and the creation of locks 

and dams (Gehrke et al. 1995; Williams et al. 

1996). As a result, North America’s temperate 
2

freshwater ecosystems are being depleted of 

species as rapidly as tropical forests (Ricciardi 

and Rasmussen 1999), and this loss has been 

exacerbated by landscape-level disturbances (i.e., 

erosion, sedimentation, river regulation, degraded 

water quality, etc.).

Natural floodplain rivers are among the most 

biologically productive and diverse ecosystems 

(Tockner and Standforth 2002). They are also 

among the most disturbed ecosystems, especially 

in north temperate regions (Welcomme 1979). 

Large floodplain rivers are generally regarded 

as having diverse physical habitat maintained 

by natural flows, providing the variety of lentic 

and lotic environments that support diverse fish 

faunas (Poff et al. 1997). This diversity, both 

biological and physical, may exist because of the 

channel-floodplain complex and the annual cycle 

of flooding (i.e., flood-pulse concept; Junk et al. 

1989). Whereas the flood-pulse concept has yet 

to be validated in large temperate rivers, studies 

in Europe (Welcomme 1995) and North America 

(Hesse et al. 1993) indicate similar processes 

between temperate and tropical rivers. Riverfloodplain connectivity and habitat heterogeneity 

are maintained by natural hydrologic regimes 

and environmental gradients (Sparks et al. 

1990; Ward 1998). However, altered hydrologic 

regimes, habitat modifications, exotic species 

invasions, and pollution are resulting in 

floodplain degradation and may prove to lower 

species diversity (Heiler et al. 1995; Theiling 

1996; Pegg and Pierce 2002).

The Upper Mississippi River System (UMRS) 

is probably the most biologically productive and 

economically important large floodplain river 

system in the United States (Patrick 1998; U.S. 

Geological Survey 1999). Fishes inhabiting the 

UMRS occupy a broad range of macrohabitats, 

including the navigation channel (Dettmers et 

al. 2001). However, fish:habitat relations and 

assemblages across environmental gradients are 

just beginning to be explored (Pegg and Pierce 

2001, 2002; Braaten and Guy 2002; Barko and 

Herzog 2003; Barko et al. 2004b).

Whereas a wealth of biological data is available 

on the Mississippi River (Patrick 1998), most 

studies conducted were largely area specific and 

not standardized. As navigation expanded on the 

UMRS, concerns grew over the sustainability of 

the ecosystem. Consequently, the Environmental 

Management Program was created in 1986 in 

response to these concerns (Lubinski 1999). The 

Environmental Management Program includes 

a biological monitoring program for the UMRS 

known as the Long Term Resource Monitoring 

Program (LTRMP; Jackson et al. 1981; U.S. 

Fish and Wildlife Service 1993). Although the 

state of Illinois has maintained a longer Illinois 

River monitoring program (Bertrand 1997), 

the LTRMP is the largest systemic monitoring 

program in the basin. Understanding how fish 

assemblages are similar or different within the 

LTRMP study areas is critical for evaluating 

past and present stressors on fish resources 

throughout the UMRS, while understanding 

how assemblages respond to ecosystem changes 

over time is critically important for adaptive 

management of the UMRS.

Using LTRMP data, we investigated fish 

assemblages within five reaches of the UMR 

and one reach of the Illinois River to better 

understand patterns in assemblage structure 

and identify trends. The objectives of this study 

were to assess associations between fish species 

abundance, sampling periods, sampling years, 

environmental variables, and five physical habitat 

classes using ordination techniques.

Materials and Methods

Field Methods

We used data collected from 1993 to 2001 in 

five reaches of the UMR and one reach of the 

Illinois River (La Grange Pool; river mile [RM] 

80–158) by the LTRMP (Gutreuter et al. 1995). 

Mississippi River study areas included Pool 4 

(excluding Lake Pepin; RM 752–797), Pool 8 

(RM 679–703), Pool 13 (RM 523–557), Pool 26 

(RM 202–242), and the Unimpounded Reach 

(RM 29–80; Figure 1). Fishes were sampled 

annually from June 15 to October 30 in three 

annual sampling periods (1: June 15–July 31; 

2: August 1–September 15; 3: September 16–

October 30) using a stratified random sampling 

design developed by Gutreuter et al. (1995). At 

each site, measurements of water temperature, 
3

Secchi transparency, depth of gear deployment, 

water velocity, and conductivity were made 

prior to fish sampling. Water temperature was 

measured to the nearest 0.1oC and conductivity 

was measured in μS/cm using a Labcomp digital 

conductivity meter. A Marsh-McBirney flow 

meter (model 201 D; Frederick, MD) was used to 

measure water velocity to the nearest 0.01 m/s. 

Depth of gear deployment was measured to the 

nearest 0.1 m using boat-mounted sonar. River 

elevation was obtained from the U.S. Geological 

Survey for each day of sampling.

Data collected from five physical habitat 

classes and four sampling gears common to all 

six study areas were used for analysis. Physical 

habitat was classified and stratified based on 

geomorphic features and included side channel 

border, backwater contiguous, main channel 

border, main channel border wing dike, and 

impounded (Gutreuter et al. 1995). Collection 

methods included active (daytime electrofishing) 

and passive (mini-fyke netting, small 

and large hoop netting) techniques. 

See Gutreuter et al. (1997a–c) and 

Burkhardt et al. (1997, 1998, 2000, 

2001, 2004a,b) for annual gear 

allocations within and among the six 

study areas.

Statistical Methods—Ordination

We separated young-of-the-year 

(YOY) fishes from adult fishes using 

reported lengths for each species 

(Carlander 1969, 1977; Becker 

1983; Etnier and Starnes 1993; 

Morrow and Kirk 1995; Pflieger 

1997; Gido et al. 2000) following the 

methodology of Barko et al. (2004a) 

because adult and YOY fishes appear 

to exhibit different responses to 

physical habitats and environmental 

conditions in this system (Barko and 

Herzog 2003; Barko et al. 2004a,b). 

Hybrid individuals, larval fishes, and 

unidentified fishes were removed 

from the data set prior to analysis. 

We conducted separate ordination 

analyses for each study area, using 

all four gears combined, to enable 

us to identify reach-related trends 

and determine whether the fish assemblages 

responded similarly to environmental and 

temporal variability. Ordination methods used 

in analysis included detrended correspondence 

(DCA), canonical correspondence (CCA), partial 

canonical correspondence (pCCA), and stepwise 

pCCA, with methodology following Barko 

et al. (2004b). All analyses were performed 

using CANOCO v. 4.5 (ter Braak and Šmilauer 

2002). An estimate of the amount of variation 

explained by each ordination analysis is provided 

by the sum of all canonical eigenvalues (Lepš 

and Šmilauer 2003). Caution must be used in 

interpretation, however, because the amount 

of variation explained is not equivalent to an 

r2 value. For visual clarity, we only display 

abundant taxa (e.g., species weights ≥1) on 

ordination biplots by species codes listed in 

Table 1. Discussions on biplot interpretation can 

Unimpounded 

Reach

Figure 1. Geographic representation of the six Upper Mississippi River 

System Long Term Resource Monitoring Program sites sampled from 1993

to 2001.
4

Table 1. Abundance of each fish species (adult/young-of-the-year) collected by the Long Term Resource Monitoring Program in the Upper Mississippi River daytime electrofishin g, mini-fyke netting, and small and large hoop netting. Numerically dominant species (>10% of total catch) are in bold by reach.Family name Common name-species code Scientific name Pool 4 Pool 8 Pool 13 Pool 26 Petromyzontidae Chestnut lamprey-CNLP Ichthyomyzon castaneus 6/0 33/3 3/0 3/0 

Silver lamprey-SVLP Ichthyomyzon unicuspis 11/1 53/0 12/0 2/0 American brook lamprey-ABLP Lampetra appendix 2/0 0/0 0/0 0/0 

Acipenseridae Lake sturgeon-LKSG Acipenser fulvescens 1/0 0/0 0/0 0/0 

Shovelnose sturgeon-SNSG Scaphirhynchus platorynchus 0/0 2/0 12/0 1/0 

Polyodontidae Paddlefish-PDFH Polyodon spathula 0/0 0/0 0/0 2/0 Lepisosteidae Spotted gar-STGR Lepisosteus oculatus 0/0 0/0 1/0 36/6 

Longnose gar-LNGR Lepisosteus osseus 13/16 127/142 46/30 17/21 Shortnose gar-SNGR Lepisosteus platostomus 11/2 242/33 242/78 938/148 

Amiidae Bowfin-BWFN Amia calva 141/0 177/3 153/5 36/0 Hiodontidae Goldeye-GDEY Hiodon alosoides 0/0 0/0 1/0 25/140 

Mooneye-MNEY Hiodon tergisus 59/1 44/6 23/25 13/58 

Anguillidae American eel-AMEL Anguilla rostrata 4/0 0/0 0/0 3/0 Clupeidae Skipjack herring-SJHR Alosa chrysochloris 0/1 0/0 0/0 225/137 

Gizzard shad-GZSD Dorosoma cepedianum 4,950/4,822 4,802/4,295 5,189/9,889 17,121/34,384 Threadfin shad-TFSD Dorosoma petenense 0/0 0/0 0/0 64/183 

Cyprinidae Central stoneroller-CLSR Campostoma anomalum 0/0 0/0 1/0 0/11 

Goldfish-GDFH Carassius auratus 0/0 0/0 0/0 5/1 Grass carp-GSCP Ctenopharyngodon idella 0/0 0/0 0/0 24/38 Red shiner-RDSN Cyprinella lutrensis 0/0 0/0 0/0 243/54 Spotfin shiner-SFSN Cyprinella spiloptera 1.282/1.179 9,487/11,105 959/293 472/2.616 Blacktail shiner-BTSN Cyprinella venusta 0/0 0/0 0/0 0/0 Common carp-CARP Cyprinus carpio 3,751/92 3,972/1,820 4,249/1,277 12,969/257 Western silvery minnow-WSMW Hybognathus argyritis 0/0 0/0 0/0 7/0 Brassy minnow-BSMW Hybognathus hankinsoni 0/0 1/1 0/0 0/0 Mississippi silvery minnow-SVMW Hybognathus nuchalis 0/0 2/14 9/1 74/137 Plains minnow-PNMW Hybognathus placitus 0/0 0/0 0/0 0/0 Silver carp-SVCP Hypophthalmichthys molitrix 0/0 0/0 0/0 15/0 Bighead carp-BHCP Hypophthalmichthys nobilis 0/0 0/0 0/0 113/8 Striped shiner-SPSN Luxilus chrysocephalus 0/0 0/0 0/0 0/0 Speckled chub-SKCB Macrhybopsis aestivalis 1/0 0/0 2/0 4/4 Silver chub-SVCB Macrhybopsis storeriana 38/1 33/0 229/104 115/76 
5

Table 1. Abundance of each fish species (adult/young-of-the-year) collected by the Long Term Resource Monitoring Program in the Upper Mississippi River Sdaytime electrofishin Family name Common name-species code Scientific name Pool 4 Pool 8 Pool 13 Pool 26 

Golden shiner-GDSN Notemigonus crysoleucas 19/45 79/806 95/887 0/27 Emerald shiner-ERSN Notropis atherinoides 10,148/33,720 6,606/9,184 10,190/7,450 6,454/6,385 River shiner-RVSN Notropis blennius 620/3 2,880/1,790 2,700/6,686 683/1,105 Bigeye shiner-BESN Notropis boops 0/0 0/0 0/0 1/4 Ghost shiner-GTSN Notropis buchanani 0/0 0/0 0/0 0/1 Spottail shiner-STSN Notropis hudsonius 289/2 600/185 539/120 14/13 Silverband shiner-SBSN Notropis shumardi 0/0 0/0 0/0 102/285 Sand shiner-SNSN Notropis stramineus 3/16 2/13 0/3 3/38 Weed shiner-WDSN Notropis texanus 15/1 1398/470 0/0 0/0 Mimic shiner-MMSN Notropis volucellus 34/1,221 1,002/3,062 120/3,5679 0/0 Channel shiner-CNSN Notropis wickliffi 0/0 0/0 49/2,584 52/8,481 Pugnose minnow-PGMW Opsopoeodus emiliae 110/682 1,257/4,002 84/142 0/0 Suckermouth minnow-SMMW Phenacobius mirabilis 0/0 0/0 0/1 4/4 Southern redbelly dace-SRBD Phoxinus erythrogaster 0/0 0/0 0/2 0/0 Bluntnose minnow-BNMW Pimephales notatus 12/24 4/6 3/58 4/16 Fathead minnow-FHMW Pimephales promelas 7/0 37/2 8/21 0/0 Bullhead minnow-BHMW Pimephales vigilax 1,177/365 9,868/3,167 2,099/293 1,424/301 Creek chub-CKCB Semotilus atromaculatus 0/0 0/0 0/0 1/1 

Catostomidae River carpsucker-RVCS Carpiodes carpio 59/1 54/4 305/1,374 387/208 

Quillback-QLBK Carpiodes cyprinus 187/130 45/707 26/34 2/20 Highfin carpsucker-HFCS Carpiodes velifer 0/0 2/0 101/0 0/0 White sucker-WTSK Catostomus commersoni 37/3 3/6 4/0 0/1 Blue sucker-BUSK Cycleptus elongatus 16/0 14/5 4/0 8/4 Northern hog sucker-NHSK Hypentelium nigricans 1/0 5/0 2/0 0/0 Smallmouth buffalo-SMBF Ictiobus bubalus 393/2 962/231 1,760/26 3,863/256 Bigmouth buffalo-BMBF Ictiobus cyprinellus 51/10 41/19 160/13 352/138 Black buffalo-BKBF Ictiobus niger 0/0 0/0 11/0 276/2 Spotted sucker-SPSK Minytrema melanops 404/3 724/48 241/0 0/0 Silver redhorse-SVRH Moxostoma anisurum 1,009/12 1,783/127 18/2 0/0 River redhorse-RVRH Moxostoma carinatum 308/0 239/0 0/0 0/0 Golden redhorse-GDRH Moxostoma erythrurum 325/3 925/9 31/2 7/5 Shorthead redhorse-SHRH Moxostoma macrolepidotum 1,504/175 3,855/569 588/126 113/10 

Ictaluridae Black bullhead-BKBH Ameiurus melas 1/0 8/0 32/14 26/0 

Continued.
6

Table 1. Abundance of each fish species (adult/young-of-the-year) collected by the Long Term Resource Monitoring Program in the Upper Mississippi River Sdaytime electrofishin Family name Common name-species code Scientific name Pool 4 Pool 8 Pool 13 Pool 26 

Yellow bullhead-YLBH Ameiurus natalis 3/0 12/0 48/1 10/3 Brown bullhead-BNBH Ameiurus nebulosus 0/0 3/4 0/0 11/0 Blue catfish-BLCF Ictalurus furcatus 0/0 0/0 0/0 462/7 Channel catfish-CNCF Ictalurus punctatus 271/2 2,725/9 1,787/39 7,837/301 Stonecat-STCT Noturus flavus 1/0 2/2 4/6 2/0 Tadpole madtom-TPMT Noturus gyrinus 10/1 84/80 123/69 3/2 Freckled madtom-FKMT Noturus nocturnus 0/0 0/0 0/0 5/0 Flathead catfish-FHCF Pylodictis olivaris 65/1 217/29 199/2 578/2 

Esocidae Grass pickerel-GSPK Esox americanus vermiculatus 0/0 0/0 0/1 0/3 

Northern pike-NTPK Esox lucius 161/45 180/113 39/19 1/0 

Umbridae Central mudminnow-CMMW Umbra limi 0/0 8/8 0/12 0/0 Salmonidae Brown trout-BNTT Salmo trutta 0/0 0/1 0/0 0/0 Percopsidae Trout-perch-TTPH Percopsis omiscomaycus 7/2 6/2 0/0 0/0 Aphredoderidae Pirate perch-PRPH Aphredoderus sayanus 0/0 2/1 0/0 2/2 Gadidae Burbot-BRBT Lota lota 3/3 11/5 0/0 0/0 Fundulidae Starhead topminnow-SHTM Fundulus dispar 0/0 0/0 0/0 1/0 

Blackstripe topminnow-BTTM Fundulus notatus 0/0 0/0 0/0 7/0 Blackspotted topminnow-BPTM Fundulus olivaceus 0/0 0/0 0/0 0/0 

Poeciliidae Western mosquitofish-MQTF Gambusia affinis 0/0 0/0 0/0 1,170/6,573 Atherinidae Brook silverside-BKSS Labidesthes sicculus 5/29 146/253 52/1,170 28/39 

Inland silverside-IDSS Menidia beryllina 0/0 0/0 0/0 0/0 

Gasterosteidae Brook stickleback-BKSB Culaea inconstans 0/0 5/6 2/0 0/0 Percichthyidae White perch-WTPH Morone americana 0/0 0/0 0/0 0/0 

White bass-WTBS Morone chrysops 446/930 234/1,519 194/2,403 546/3,090 Yellow bass-YWBS Morone mississippiensis 0/0 0/6 7/28 2/21 Striped bass-SDBS Morone saxatilis 0/0 0/0 0/0 0/0 

Centrarchidae Rock bass-RKBS Ambloplites rupestris 620/4 1,222/34 45/0 0/0 

Green sunfish-GNSF Lepomis cyanellus 53/0 717/38 9/0 302/1 Pumpkinseed-PNSD Lepomis gibbosus 67/0 345/111 721/425 0/0 Warmouth-WRMH Lepomis gulosus 0/0 62/23 78/21 79/40 Orangespotted sunfish-OSSF Lepomis humilis 4/0 1,200/64 2,336/530 2,480/354 Bluegill-BLGL Lepomis macrochirus 4,588/283 24,868/291 20,023/3,191 5,144/338 Longear sunfish-LESF Lepomis megalotis 0/0 0/0 0/0 0/0 

Continued.
7

Table 1. Abundance of each fish species (adult/young-of-the-year) collected by the Long Term Resource Monitoring Program in the Upper Mississippi River Sdaytime electrofishin Family name Common name-species code Scientific name Pool 4 Pool 8 Pool 13 Pool 26 

Redear sunfish-RESF Lepomis microlophus 0/0 0/0 0/0 1/0 Smallmouth bass-SMBS Micropterus dolomieu 1,316/7 2,302/33 81/0 4/0 Spotted bass-STBS Micropterus punctulatus 0/0 0/0 0/0 0/0 Largemouth bass-LMBS Micropterus salmoides 1,755/0 5,487/304 3,345/1,558 683/33 White crappie-WTCP Pomoxis annularis 79/23 81/11 571/234 198/97 Black crappie-BKCP Pomoxis nigromaculatus 633/76 1,709/415 1,040/167 499/154 

Percidae Crystal darter-CLDR Ammocrypta asprella 0/3 0/0 0/0 0/0 

Western sand darter-WSDR Ammocrypta clara 0/1 15/10 0/0 0/0 Mud darter-MDDR Etheostoma asprigene 4/4 70/140 52/139 1/8 Bluntnose darter-BNDR Etheostoma chlorosomum 0/0 0/0 3/0 0/0 Iowa darter-IODR Etheostoma exile 0/0 5/3 0/0 0/0 Fantail darter-FTDR Etheostoma flabellare 0/0 1/0 0/0 0/0 Johnny darter-JYDR Etheostoma nigrum 68/22 736/623 131/203 0/0 Orangethroat darter-OTDR Etheostoma spectabile 0/0 0/0 0/0 0/0 Banded darter-BDDR Etheostoma zonale 1/0 1/0 0/0 0/0 Yellow perch-YWPH Perca flavescens 943/77 615/236 104/19 0/0 Logperch-LGPH Percina caprodes 157/286 540/1,000 142/241 28/24 Blackside darter-BSDR Percina maculata 0/0 3/0 0/0 0/0 Slenderhead darter-SHDR Percina phoxocephala 3/3 52/55 3/1 10/2 Dusky darter-DYDR Percina sciera 0/0 0/0 0/0 0/0 River darter-RRDR Percina shumardi 3/17 11/98 11/554 5/61 Sauger-SGER Stizostedion canadense 352/151 517/214 390/116 179/146 Walleye-WLYE Stizostedion vitreum 224/199 193/191 77/207 3/9 

Sciaenidae Freshwater drum-FWDM Aplodinotus grunniens 654/92 1,002/1,018 1,095/7,448 2,191/3,711  Total 39,495/44,794 96,757/48,784 63,013/86,023 68,775/70,605 

Continued.
8

be found in Legendre and Legendre (1998) or 

Lepš and Šmilauer (2003).

Results and Discussion

Assemblage Structure

In all four gears combined, we collected 

740,994 fishes comprising 122 species in 

7,838 sampling episodes (i.e., Pool 4 = 714, 

Pool 8 = 1,885, Pool 13 = 1,546, Pool 26 = 1,701, 

Unimpounded Reach = 1,206, and Illinois River 

= 786; Table 1). Pool 8 had the most adult fish 

(67% of total catch), followed by Pool 26 (49%), 

Pool 4 (47%), Unimpounded Reach (44%), 

Pool 13 (42%), and the Illinois River reach 

(38%). The numerically abundant component 

of the adult and YOY assemblage (e.g., species 

accounting for >10% of total catch) differed 

among the age classes and reaches. In Pool 4, 

there were three numerically abundant adult 

species, emerald shiner (Notropis atherinoides; 

26%), gizzard shad (Dorosoma cepedianum; 

13%), and bluegill (Lepomis macrochirus; 

12%), which accounted for 51% of the total 

adult abundance. Emerald shiner and gizzard 

shad comprised 86% of the YOY abundance 

(75% and 11%, respectively). In Pool 8, there 

were two numerically abundant adult species, 

bluegill (26%) and bullhead minnow (Pimephales 

vigilax; 10%), and two numerically abundant 

YOY species, emerald shiner (19%) and spotfin 

shiner (Cyprinella spiloptera; 23%). In Pool 13, 

there were also two numerically abundant adult 

species, bluegill (32%) and emerald shiner 

(16%), and two YOY species, gizzard shad 

(12%) and mimic shiner (Notropis volucellus; 

41%). The numerically abundant component 

of the adult assemblage were gizzard shad 

(25%), common carp (Cyprinus carpio; 19%), 

and channel catfish (Ictalurus punctatus; 11%), 

whereas the numerically abundant component of 

the YOY assemblage were gizzard shad (49%) 

and channel shiner (Notropis wickliffi; 12%). 

Gizzard shad (25%) and channel catfish (14%) 

were the numerically abundant fishes of the 

Unimpounded Reach adult assemblage whereas 

freshwater drum (Aplodinotus grunniens; 36%), 

gizzard shad (32%), and channel shiner (12%) 

were the numerically abundant fishes of the YOY 

assemblage. Gizzard shad (27%), common carp 

(18%), and bluegill (13%) were the numerically 

abundant adult species in the Illinois River, 

whereas gizzard shad alone accounted for 88% 

of the YOY abundance. Of the 10 numerically 

abundant species listed above, 7 (emerald shiner, 

gizzard shad, bluegill, bullhead minnow, common 

carp, channel catfish, and freshwater drum) 

are considered fluvial generalists (Kingsolving 

and Bain 1993; Galat et al. In press; Barko et 

al. 2004b). Collectively, these seven fluvial 

generalists accounted for 64% of the total UMR 

fish abundance. The remaining three species 

are considered fluvial specialists (Barko et al. 

2004b).

Ordination—Environmental Gradients/fish 

Assemblages

The six environmental variables measured 

concurrently with fish sampling (Table 2) 

had varied effects on fish assemblages. These 

variables explained 23% of the variation in fish 

abundance in Pool 4, 23% of the variation in fish 

abundance in Pool 8, 17% of the variation in fish 

abundance in Pool 13, 31% of the variation in 

fish abundance in Pool 26, 30% of the variation 

in fish abundance in the Unimpounded Reach, 

and 9% of the variation in fish abundance in the 

Illinois River reach (Table 3). Because of shared 

variance among the variables, percentages listed 

in Table 3 may not sum to equal the overall 

percentages listed above. Water velocity was 

one of the primary factors (i.e., explained the 

most variation and had the longest arrow[s] 

on the ordination biplots) associated with 

differences in fish assemblage structure in the 

northern four study areas (Figure 2). In the 

Unimpounded Reach and the Illinois River reach, 

river elevation was one of the primary factors 

associated with differences in fish assemblage 

structure (Figure 2). Depth of gear deployment 

was influential in explaining differences in 

assemblage structure patterns in all study areas 

except Pool 4 and the Illinois River (Figure 2). 

Secchi transparency was most influential in 

Pool 4, whereas conductivity was most influential 

in the Illinois River reach (Figure 2).
9

Table 2. Summary statistics and number of samples (N) fo r environmental variables measured during fish sampling in the Upper Mississipp River (UMR) System reaches (see Figure 1).

Secchi (cm) Water temperature (°C) 

Field station N Min Max Mean Std Min Max Mean Std MIllinois River 786 5 80 21 10 7.5 35.0 23.9 5.0 0Unimpounded Upper 

Mississippi River 1,206 1 69 24 12 7.9 31.9 24.9 4.5 0

Pool 26 1,701 7 85 33 14 10.8 54.1 24.9 5.6 0Pool 13 1,546 8 120 37 13 7.2 33.0 22.9 5.1 0Pool 8 1,885 5 150 60 19 4.5 30.4 21.4 5.2 0Pool 4 714 10 183 65 27 6.8 30.0 21.3 4.9 0

Current velocity (m/s) Conductivity (μS/cm) 

Field station N Min Max Mean Std Min Max Mean Std MIllinois River 786 0.02 0.67 0.09 0.10 12 1018 613 136 42Unimpounded Upper 

Mississippi River 1,206 0.02 1.53 0.22 0.19 199 768 531 69 31

Pool 26 1,701 0.02 1.25 0.23 0.26 148 1031 443 71 42Pool 13 1,546 0.02 1.07 0.17 0.20 232 545 402 44 58Pool 8 1,885 0.02 1.40 0.17 0.17 114 569 397 65 63Pool 4 714 0.02 0.95 0.14 0.16 35 755 393 121 66
10

Table 3. Amount of variation of each en vironmental variable explained within the six sampling reaches of the Upper Mississippi River (UMR) bc orrespondence analyses. Data were collected annually from 1993 to 2001 and variance shared among the variables was not examined.

Secchi (cm) Water temperature (°C) 

Field station % variation F-statistic P-value % variation F-statistic P -value % variation Illinois River 1.0 5.3 0.002 2.0 6.0 0.002 <1.0 Unimpounded Upper 

Mississippi River 3.0 6.9 0.001 3.0 7.4 0.001 15.0 

Pool 26 4.0 16.1 0.002 3.0 12.2 0.002 15.0 Pool 13 2.0 5.6 0.002 1.0 2.7 0.002 2.0 Pool 8 4.0 6.8 0.002 <1 2.5 0.002 12.0 Pool 4 11.0 22.5 0.002 1.0 3.0 0.002 3.0 

Current velocity (m/s) Conductivity (μS/cm) 

(f

Field station % variation F-statistic P-value % variation F-statistic P -value % variation Illinois River 1.0 4.0 0.002 3.0 9.9 0.002 2.0 Unimpounded Upper 

Mississippi River 3.0 8.71 0.001 <1.0 2.0 0.006 6.0 

Pool 26 6.0 22.5 0.002 1.0 4.8 0.002 2.0 Pool 13 11.0 28.1 0.002 <1.0 1.8 0.002 <1.0 Pool 8 9.0 20.0 0.002 1.0 3.9 0.002 2.0 
11

Figure 2. Partial ca nonical correspondence analysis (pCCA) of environmental gradients and species for the Upper Mississippi Riveyear, and period. Eigenva lues were as follows: Pool 4 (Axis 1 eigenvalue = 0.115, Axis 2 eigenvalue = 0.069); Pool 8 (Axis 1 eigenvaleigenvalue = 0.046); Pool 13 (Axis 1 eigenvalue = 0.107, Axis 2 eigenvalue = 0.028): Pool 26 (Axis 1 eigenvalue = 0.186, Axis 2 eigenvUnimpounded Reach (Axis 1 eigenvalue = 0.194, Axis 2 eigenvalue = 0.049): Illinois River (Axis 1 eigenvalue = 0.047, Axis 2 eigenval

-0.6 1.0

-0.81.0

secchi temp

depth

current

cond

ELEV

pCCA Axis 1

pCCAAxis2

Pool 4

-0.6 1.0

-0.81.0

secchi

temp

depth

current

cond

ELEV

pCCA Axis 1

pCCAAxis2

Pool 8

-0.6 

-0.81.0

te

cond

E

pCCAAxis2

-0.6 1.0

-0.81.0

secchi

temp

depth

current

cond

ELEV

pCCA Axis 1

pCCAAxis2

Pool 26

-0.6 1.0

-0.81.0

secchi

temp

depth

current

cond

ELEV

pCCA Axis 1

pCCAAxis2

Unimpounded Reach

-0.6 

-0.81.0

temp

current

ELEV

p

pCCAAxis2
12

Ordination—Temporal Shifts in Assemblages

Between 1993 and 2001, the fish assemblages 

of the UMRS were subjected to floods of varying 

magnitude, as well as the introduction of exotic 

species, such as silver carp (Hypophthalmichthys 

molitrix) and bighead carp (H. nobilis; Chick 

and Pegg 2002). The effects of the 1993 flood 

seem to have resonated through 1994 and 1995, 

probably because it was an unusual summer 

flood and among the highest recorded floods 

throughout the system (Gutreuter et al. 1999; 

Figures 3 and 4). In the lower reaches of the 

UMRS, this was classified as a 500-year flood 

with record setting duration and discharge 

(Parrett et al. 1993). However, the extent of 

the influence of interannual variability on 

assemblage structure varied between age classes 

(i.e., YOY and adult) and among the study areas 

(Figures 3 and 4). For adults, sample years 

explained the most variation in the Unimpounded 

study area (12.2%; F = 3.7; P = 0.0005) 

followed by Pools 8 (11%; F = 17.5; P = 0.002) 

and 26 (11%; F = 5.6; P = 0.0005), Pools 4 

(9%; F = 2.9; P = 0.0005) and 13 (9%; F = 3.8; 

P = 0.005), and the Illinois River study area (8%; 

F = 12.2; P = 0.002). For YOY assemblages, 

sample year explained the most variation in 

Pool 13 (50%; F = 7.4; P = 0.0005), followed 

by Pool 4 (34%; F = 2.9; P = 0.0005), Pool 8 

(32%; F = 15.1; P = 0.002), the Unimpounded 

study area (27%; F = 14.4; P = 0.002), Pool 26 

(19%; F = 4.1; P = 0.0005), and the Illinois 

River study area (13%; F = 3.7; P = 0.0005). 

Interannual variability appears to influence 

YOY assemblage structure in the UMR to a 

greater extent than adult assemblage structure, 

especially in the upper study areas. For both 

adult and YOY assemblages, patterns were not 

strong, but temporal variability was evident 

based on the separation of the sample years in 

ordination space (Figures 3 and 4). In Pool 26 

and the Unimpounded reach, Axis 1 separated 

the years 1994, 1995, and 1996 from the other 

years indicating the adult assemblage present 

in the early years of sampling differed from the 

assemblage present in the later years in these 

lower UMR study areas (Figure 3). Within all 

study areas except the Unimpounded Reach, 

the YOY assemblage structure has shifted over 

time because Axis 1 separates the earlier sample 

years (1993–1998) from the later sample years 

(1999–2001; Figure 4). The underlying cause 

of the shift in abundance is unknown. Although 

some general patterns emerged, 9 years may 

not be enough time to identify the response of 

the fish assemblage to interannual variability 

within the system. Many species are long-lived 

and responses to changes in the system are not 

instantaneous and may not appear for several 

generations. Conversely, these findings may also 

suggest that temporal variability within the UMR 

may not affect assemblages as much as regional 

variability (e.g., localized variability within each 

reach) because assemblages and age classes did 

not respond to each year similarly within and 

among the study reaches.

Ordination—Assemblage/strata Relations 

by Reach

The physical habitats sampled by the LTRMP 

were separated in ordination space within all 

study areas based on fish abundance patterns; 

however, the amount of separation varied within 

and among the age classes and study areas 

(Figures 5 and 6). For adults, physical habitats 

explained the most variation in Pool 8 (23%; 

F = 61.33; P = 0.002), followed by Pool 4 (22%; 

F = 19.1; P = 0.0005), Pools 26 (19%; F = 60.55; 

P = 0.002) and 13 (19%: F = 16.1; P = 0.0005), 

Illinois River reach (12%; F = 47.2; P = 0.002), 

and the Unimpounded reach (3%; F = 4.07; 

P = 0.002). For YOY assemblages, physical 

habitats explained the most variation in Pool 

8 (20%; F = 12.3; P = 0.002), Pool 26 (17%; 

F = 17.8; P = 0.002), Pool 13 (15%; F = 4.3; 

P = 0.0005), Pool 4 (10%; F = 2.3; P = 0.017), 

Illinois River reach (3%; F = 3.4; P = 0.0005), 

and the Unimpounded Reach (3%; F = 2.4; 

P = 0.002). The magnitude of association 

between abundance and particular physical 

habitat was also low for many species, which 

may indicate: (1) an unstable fauna represented 

by a few dominant generalists, suggesting that 

the UMRS is degraded and could be moving 

toward a system dominated by tolerant species 

(Kingsolving and Bain 1993), (2) physical 

habitat classes defined by the LTRMP are 
13

-0.4 0.6

-0.30.4y1993

y1994

y1995

y1996

y1997

y1998 y1999

y2000

y2001 p

CCAAxis1

pCCA Axis 2

Pool 4

-0.4 0.6

-0.30.4

y1993

y1994

y1995

y1996

y1997

y1998

y1999

y2000

y2001

pCCA Axis 1

pCCAAxis2

Pool 8

-0.4 

-0.30.4

y1993

y1

y1995

y1996

y1998 y1

pCCA 

pCCAAxis2

-0.4 0.6

-0.30.4

y1993 y1994

y1995

y1997 y1996

y1998 y1999 y2000

y2001 Pool 26

pCCA Axis 1

pCCAAxis2

-0.4 0.6

-0.30.4

y1993

y1994

y1995 y1996

y1997

y1998

y1999

y2000

y2001

pCCA Axis 1

pCCAAxis2

Unimpounded Reach

-0.4 

-0.30.4

y1993

y1996

y1

y

y2000

y2001

pCCA 

pCCAAxis2

Figure 3. P artial canonical correspondence analysis (pCCA) of year and adult individuals for the Upper Mississippi River (UMR), given gear, period, and Eigenvalues were as follows: Pool 4 (Axis 1 eigenvalue = 0.030, Axis 2 eigenvalue = 0.019); Pool 8 (Axis 1 eigenvalue = 0.040, Axis 2 eigenvalue = 0.022); Peigenvalue = 0.027, Axis 2 eigenvalu e = 0.024); Pool 26 (Axis 1 eigenvalue = 0.045, Axis 2 eigenvalue = 0.024); Unimpounded Reach (Axis 1 eigenvalue = 0eigenvalue = 0.018); Illinois River (Axis 1 eigenvalue = 0.028, Axis 2 eigenvalue = 0.014). 
14

-1.0 1.0

-0.60.8

y1993

y1994

y1996 y1995 y1997

y1998

y1999

y2000

y2001

Pool 4

pCCA Axis 1

pCCAAxis2

-1.0 1.0

-0.60.8

y1993

y1994

y1995

y1996 y1997

y1998

y1999y2000

y2001

Pool 8

pCCA Axis 1

pCCAAxis2

-1.0 

-0.60.8

y1993 y1994

y1995 y1996

y1997

y1998

pCCA A

pCCAAxis2

-1.0 1.0

-0.60.8

y1993

y1994

y1995

y1996

y1997 y1998

y1999

y2000

y2001

Pool 26

pCCA Axis 1

pCCAAxis2

-1.0 1.0

-0.60.8

y1993

y1994

y1995 y1996 y1997

y1998

y1999

y2000

y2001

Unimpounded Reach

pCCA Axis 1

pCCAAxis2

-1.0 

-0.60.8

y1993

y1994

y1996

y1998

y1999

y2001

pCCA 

pCCAAxis2

Figure 4. Partial canonical correpsondence analysis (pCCA) of year and young-of-the-year individuals for the Upper Mississippi River, given gear, perioEigenvalues were as follows: Pool 4 (Axis 1 eigenvalue = 0.123, Axis 2 eigenvalue = 0.064); Pool 8 (Axis 1 eigenvalue = 0.136), Axis 2 eigenvalue = 0.063); eigenvalue = 0.281, Axis 2 eigenvalu e = 0.085); Pool 26 (Axis 1 eigenvalue = 0.069, Axis 2 eigenvalue = 0.038); Unimpounded Reach (Axis 1 eigenvalue = 0eigenvalue = 0.051); Illinois River (Axis 1 eigenvalue = 0.038, Axis 2 eigenvalue = 0.031). 
15

����������

����������

Figure 5. Partial canonical correspondence analysis (pCCA) of strata and young-of-the-year individuals for the

Upper Mississippi River System, given period, gear, and year. (A) Species scores for abundant species from Pool 4 (Axis 1 

eigenvalue = 0.080, Axis 2 eigenvalue = 0.012); (B) Pool 8 (Axis 1 eigenvalue = 0.092, Axis 2 eigenvalue = 0.054);
16

�����������

�����������

(C) Pool 13 (Axis 1 eigenvalue = 0.083, Axis 2 eigenvalue = 0.051); (D) Pool 26 (Axis 1

eigenvalue = 0.102, Axis 2 eigenvalue = 0.035);

Figure 5. Continued.
17

-1.0 2.0

-1.0 2.0

jCARP jCNCF

jCNSN jERSN

jFWDM

jGDEY

jGZSD

jLNGR

jRVCS

jRVSN

jSBSN

jSGER

jSJHR

jSVCB jTFSD

jWTBS

jWTCP

SCB

MCBU

MCBW

pCCA Axis 1

p

C

CA

Axis

2

���������������������

-1.5 2.0

-1.0

2.0

jCARP

jERSN

jFWDM

jGZSD jSGER

jSJHR jTFSD

jWTBS

BWC

SCB

MCBU

pCCA Axis 1

p

C

CA

Axis

2

������������������

Figure 5. Continued. (E) Unimpounded Reach (Axis 1 eigenvalue = 0.008, Axis 2 eigenvalue = 0.010); (F) Illinois River (Axis 1 

eigenvalue = 0.029, Axis 2 eigenvalue = 0.004). See Table 1 for species codes. Backwater contiguous 

(BWC), impounded (IMP), main channel border unstructured (MCBU), main channel border wing dam 

(MCBW), and side channel border (SCB).
18

-2 4

-1 5

aBKCP aBHMW

aBLGL

aBMBF

aBWFN

aCARP aCNCF

aERSN

aFHCF

aFWDM aGDRH

aGZSD

aJYDR

aLGPH

aLMBS

aNTPK

aPGMW

aPNSD

aQLBK aRKBS

aRVCS

aRVRH

aSFSN aRVSN

aSGER

aSHRH

aSMBF

aSMBS

aSPSK

aSTSN

aSVRH

aWLYE

aWTBS

aWTCP

aYWPH

BWC

SCB MCBU

MCBW

pCCA Axis 1

p

C

CA

Axis

2

����������

-1.5 2.5

-2.0 3.0

aBHMW

aBKCP

aBLGL

aBWFN

aCARP aCNCF

aERSN

aFHCF aGDRH aFWDM

aGNSF

aGZSD

aJYDR aLGPH

aLMBS

aLNGR

aMMSN

aNTPK aOSSF aPGMW aPNSD

aRKBS

aRVRH

aRVSN

aSFSN

aSGER

aSHRH

aSMBF

aSMBS

aSNGR

aSPSK

aSTSN

aSVRH

aWDSN

aWLYE

aWTBS

aYWPH BWC

SCB

MCBU

MCBW

IMP

pCCAAxis 1

p

C

CA

Axis

2

����������

Figure 6. Partial canonical correspondence analysis (pCCA) of strata and adult individuals for the Upper Mississippi River 

System, given gear, period, and year. (A) Species scores for abundant species from Pool 4 (Axis 1 eigenvalue = 0.139, Axis 2 

eigenvalue = 0.071); (B) Pool 8 (Axis 1 eigenvalue = 0.139, Axis 2 eigenvalue = 0.055); (C) Pool 13 (Axis 1 eigenvalue = 0.129, 

Axis 2 eigenvalue = 0.038); (D) Pool 26 (Axis 1 eigenvalue = 0.143, Axis 2 eigenvalue = 0.035); (E) Unimpounded Reach (Axis 1 

eigenvalue = 0.019, Axis 2 eigenvalue = 0.014); (F) Illinois River (Axis 1 eigenvalue = 0.103, Axis 2 eigenvalue = 0.012). See 

Table 1 for species codes. Backwater contiguous (BWC), impounded (IMP), main channel border unstructured (MCBU), main 

channel border wing dam (MCBW), and side channel border (SCB).
19

-1.5 2.0

-2.0 3.0

aBHMW aBKCP

aBLGL

aBMBF aBWFN

aCARP

aCNCF aERSN

aFHCF

aFWDM

aGDSN

aGZSD

aJYDR

aLGPH

aLMBS

aOSSF

aPNSD

aRVCS aRVSN

aSGER aSFSN

aSHRH

aSMBF

aSMBS

aSNGR

aSPSK

aSTSN

aSVCB

aTPMT

aWLYE

aWTBS

aWTCP

BWC SCB

MCBU

MCBW

IMP

pCCA Axis 1

p

C

CA

Axis

2

�����������

�����������

Figure 6. Continued.
20

-1.0 2.0

-1.0 2.0

aBHMW aBKBF

aBKCP

aBLCF

aBLGL

aBMBF

aCARP

aCNCF aCNSN

aERSN

aFHCF

aFWDM

aGNSF

aGZSD

aOSSF aRDSN

aRVCS

aRVSN

aSMBF aSBSN

aSNGR

aTFSD aSTBS

aWTBS

aWTCP

SCB

MCBU

MCBW

pCCAAxis 1

p

C

CA

Axis

2

���������������������

-2.0 1.5

-1.0 1.5

aBHMW

aBKBF aBKCP

aBLGL

aBMBF aCARP

aCNCF

aERSN

aFHCF

aFWDM

aGNSF

aGSCP

aGZSD

aLMBS

aOSSF

aRDSN

aRVCS aSGER

aSHRH

aSJHR

aSMBF

aSNGR

aTFSD aWRMH

aWTBS

aWTCP

BWC

SCB

MCBU

pCCA Axis 1

p

CCA

Axis

2

������������������

Figure 6. Continued.
21

poor predictors of assemblage patterns, or 

(3) environmental conditions within these 

physical habitats are similar enough over the 

course of a sampling season that our approach 

did not discriminate their effects well. Baker et 

al. (1991) and Barko et al. (2004b) also reported 

low associations between fish species and 

Mississippi River physical habitats; patterns often 

indicative of a tolerant fauna. We are unsure 

if the low associations in the Unimpounded 

and Illinois River study areas are because of 

reduced habitat heterogeneity or merely reflect 

the disproportionate number of habitats sampled 

within the reaches (Unimpounded and Illinois 

River = 3; Pools 4, 8, 13, and 26 = 5).

Ordination—Sampling Period

In all reaches, the amount of variation 

explained by sampling period was relatively low. 

Sampling period explained the most variation 

in the Unimpounded study area (9%; F = 18.9; 

P = 0.002), Pool 8 (9%; F = 24.7; P = 0.002), and 

Pool 13 (9%; F = 11.7; P = 0.0005), followed by 

Pool 4 (7%; F = 11.9; P = 0.002), Pool 26 (6%; 

F = 16.4; P = 0.002) and the Illinois River study 

area (6%; F = 20.6; P = 0.002). Although the 

amount of variation in fish abundance explained 

was low, Axis 1 separated sampling period 1 

from sampling period 3 in all study areas, 

indicating that the assemblages present during 

these two periods were different (Figure 7). In 

Pools 4, 8, and 13 and along the same axis, the 

assemblage sampled in period 2 was more similar 

to the assemblage sampled in period 3 (because 

of their close proximity in ordination space) and 

sampling period 1 was the most unique based 

on assemblage structure (Figure 7). Conversely, 

in Pool 26, the Unimpounded and Illinois River 

study areas, the assemblage sampled in period 

2 was more similar to the assemblage sampled 

in period 1; hence, the assemblage sampled in 

period 3 was the most unique. In all study areas, 

Axis 2 separated sampling period 2 from the 

other sampling periods. Therefore, although 

sampling period 2 grouped with one of the other 

sampling periods along Axis 1, the assemblage 

sampled during period 2 provides additional 

structure information that is different from that 

provided by sampling periods 1 and 3.

Conclusions and Recommendations

Our analyses identified several factors 

associated with differences in fish assemblage 

patterns within each of six LTRMP study areas. 

Based on our findings, we make the following 

programmatic recommendations: 

1. The time series of LTRMP data is still 

relatively short and assessment of longterm trends in assemblage structure will 

require a longer time series. Our results 

suggest that some of the largest shifts in 

assemblage structure, particularly for YOY 

assemblages, were associated with flood 

years. However, the effects of floods on 

assemblage structure varied among the six 

study areas. The source of this variation is 

potentially related to how different sections 

of the river convey floodwaters and how 

accessible off-channel areas are to fishes 

during floods. Maintenance of standardized 

long-term monitoring data is necessary for 

arriving at a deeper understanding of how 

fish assemblages respond to the present 

day configuration of the UMRS, and how 

floods, acting across this physical template, 

affect the maintenance of diverse and persistent fish faunas. Such understanding will 

have direct applied and adaptive management benefits for managing the UMRS as a 

nationally significant system.

2. Whereas interannual factors, probably associated with flood responses, were important 

in explaining abundance patterns in the 

UMRS fish assemblages, spatial factors 

were generally found to be better predictors 

of differences in fish assemblages. This 

finding suggests that there is a strong spatial 

component in the way that UMRS fish 

assemblages are presently structured, and 

how these assemblages change over time. 

Additional research is needed to clarify 

how spatial factors influence assemblage 

structure.

3. Adult and YOY assemblage patterns 

differed in their response to environmental 

factors, interannual variability, and physical 

habitats. This suggests that future research 
22

-0.6 0.6

-0.20.2

P1

P2

P3

Pool 4

pCCA Axis 1

pCCAAxis2

-0.6 0.6

-0.20.2

P1

P2

P3

Pool 8

pCCA Axis 1

pCCAAxis2

-0.6 

-0.20.2

P2

P3

pCCA A

pCCAAxis2

-0.6 0.6

-0.20.2

P1

P2

P3

pCCA Axis 1

pCCAAxis2Pool 26

-0.6 0.6

-0.20.2

P1

P2

P3

pCCA Axis 1

pCCAAxis2Unimpounded

Reach

-0.6 

-0.20.2

P1

P2

pCCA 

pCCAAxis2

Figure 7. Partial canonical correspondence analysis (pCCA) of sampling periods 1 (P1), 2 (P2), and 3 (P3), for the Upper Mississippi River System, ghabitats. Eigenvalues were as follows: Pool 4 (Axis 1 eigenvalue = 0.058, Axis 2 eigenvalue = 0.016); Pool 8 (Axis 1 eigenvalue = 0.071, Axis 2 eigenveigenvalue = 0.069, Axis 2 eigenvalu e = 0.017); Pool 26 (Axis 1 eigenvalue = 0.045, Axis 2 eigenvalue = 0.017); Unimpounded Reach (Axis 1 eigenvalueigenvalue = 0.016); Illinois River (Axis 1 eigenvalue = 0.051, Axis 2 eigenvalue = 0.012). 
23

on UMRS fish assemblage dynamics should 

differentiate among life stages.

4. Program partners should use the results of 

this research and other recently completed 

research to develop and prioritize additional 

research topics. Many of the analyses 

completed over the last year, whereas 

quantitatively intense, are largely qualitative 

assessments.

5. Continued quantitative monitoring of the 

UMR fish assemblage will allow us to 

identify trends not visible with the 10 years 

of data presently available. Specifically, 

(1) will assemblages redistribute themselves 

within the river and reaches based on future 

habitat alterations and disturbances (e.g., 

increased navigation, climate change, 

altered hydrology, invasive species, habitat 

restoration, etc.); (2) will assemblages 

in impounded sections become skewed 

towards a lacusterine assemblage rather 

than a riverine assemblage; (3) how will 

species and assemblages respond to 

invasive introductions; (4) what environmental variables should the LTRMP be 

measuring in addition to the present suite 

to better explain fish assemblage patterns; 

and (5) does the UMR fish assemblage 

demonstrate persistence or stability over 

longer time frames and do different areas of 

the UMRS demonstrate different stability 

thresholds?

Acknowledgments

This study was supported by the U.S. Army 

Corps of Engineers, U. S. Geological Survey, 

Upper Midwest Environmental Center, 

Long Term Resource Monitoring Program, 

Minnesota Department of Natural Resources, 

Wisconsin Department of Natural Resources, 

Iowa Department of Natural Resources, 

Illinois Natural History Survey, and the 

Missouri Department of Conservation. We 

thank M. Stopyro, S. DeLain, D. Magnusen, 

M. Blohowiak, T. Thome, G. La Plante, L. 

Johnson, M. Russell, N. Frohnauer, J. Tepley, 

J. Stricker, and B. Schmidt for assistance with 

data collection in Pool 4. We thank A. Bartels, 

K. Mauel, E. Kramer, K. Hoff, J. Fischer, H. 

Langrehr, T. Dukerschein, L. Hodge-Richardson, 

M. Hargrove, B. Torrison, T. Clement, N. 

Frost, A. Schmidt, J. Zeigwied, J. Gutierrez, 

R. Greener, K. Callen, S. Hults, S. Skemp, P. 

Boma, B. Meier, and S. Weick for assistance with 

data collection in Pool 8. We thank S. Gritters, 

M. Steuck, M. Bowlers, E. Jones, J. Pence, K. 

Hanson, J. Martins, M. Boucher, D. Kirby, T. 

Boffeli, M. Daniels, M. Watters, M. Hubler, J. 

Hass, and J. Petersen for assistance with data 

collection in Pool 13. We thank E. Ratcliff, E. 

Gittinger, F. Cronin, D. Soergel, B. Kerans, 

J. Stone, R. Maher, J. Lamer, B. Lubinski, C. 

Theiling, and J. Utley for assistance with data 

collection in Pool 26. We thank M. Petersen, 

D. Ostendorf, J. Ridings, J. Crites, G. Lowes, J. 

Scott, D. Smith, K. Tilley, C. Beachum, B. Spane 

and J. Lopez for assistance with data collection 

in the Unimpounded UMR. We thank T. O’Hara, 

K. Irons, P. Raibley, T. Cook, M. McClelland, 

E. Harms, P. Crabtree, E. Hopps, M. Perfetti, M. 

Ward, M. Hoeker, E. Gittingher, K. Stephenson, 

J. Arnold, D. Hanson, C. Carlock, B. Black, R. 

Atchison, J. Woodley, M. Gorelitz, K. Emme, 

M. Cripps, M. McDermot, C. Wagner, B. Cross, 

S. Pierce, A. Heberlean, K. Cowen, M. Strode, 

J. Moore, D. Osland, M. Schroeder, J. Haas, 

D. Blodgett, C. Smith, S. Wickman, N. Willis, 

J. Stevens, J. Pierce, T. Koel, E. Duttlinger, 

M. Blikshteyn, L. Corradin, C. Heffren, L. 

Gittingher, N. LeRoy, J. Esarey, K. Elkin, D. 

Gallagher, S. Whitney, K. Elderkin, M. Oest, 

A. Heintz, A.Williams, C. Ware, J. Dexter, 

A. Nealand, M. Irons, B. Ray, J. Merrick, D. 

Schoonover, J. Ellis, D. Schimmelphening for 

assistance with data collection in the Illinois 

River. We thank J. Sauer for providing Figure 1. 

We thank W. Popp, S. DeLain, T. Dukerschein, 

A. Bartels, M. Steuck, and M. Bowler for 

providing insight and discussion on their 

respective sampling reach. We thank C. Theiling, 

K. Cook, B. Johnson, J. Stewart, D. Ostendorf, 

and anonymous Iowa Department of Natural 

Resource biologists for providing a review of this 

report.
24

References

Baker, J. A., K. J. Killgore, and R. L. Kasul. 

1991. Aquatic habitat and fish communities 

in the Lower Mississippi River. Reviews in 

Aquatic Science 3:313–356.

Barko, V. A., and D. P. Herzog. 2003. 

Relationships among side channels, fish 

assemblages, and environmental gradients in 

the unimpounded Upper Mississippi River. 

Journal of Freshwater Ecology 18(3):377–381.

Barko, V. A., D. P. Herzog, R. A. Hrabik, and J. 

S. Scheibe. 2004a. Relationships between fish 

assemblages and main channel border mesohabitats in the unimpounded Upper Mississippi 

River. Transactions of the American Fisheries 

Society 133:371–384.

Barko, V. A., M. W. Palmer, D. P. Herzog, and 

B. Ickes. 2004b. Influential environmental 

gradients and spatiotemporal patterns of 

fish assemblages in the unimpounded Upper 

Mississippi River. American Midland 

Naturalist 152(2):369–385.

Becker, G. C. 1983. Fishes of Wisconsin. The 

University of Wisconsin Press, Madison.

Bertrand, B. A. 1997. Changes in the Mississippi 

River fishery along Illinois, 1976–1996. 

Journal of Freshwater Ecology 12(4):585–598.

Braaten, P. J., and C. S. Guy. 2002. Life history 

attributes of fishes along the latitudinal 

gradient of the Missouri River. Transactions of 

the American Fisheries Society 131:931–945.

Burkhardt, R. W., S. DeLain, A. Bartels, M. 

C. Bowler, E. J. Gittinger, E. Ratcliff, D. P. 

Herzog, K. S. Irons, and T. M. O’Hara. 2004a. 

2001 annual status report: A summary of fish 

data in six reaches of the Upper Mississippi 

River System. U.S. Geological Survey, Upper 

Midwest Environmental Sciences Center, 

La Crosse, Wisconsin. Web-based report 

LTRMP 2004-W002 available online at http://

www.umesc.usgs.gov/ reports_publications/

ltrmp/fish/2001/fish-srs.html. (Accessed 

December 2004.)

Burkhardt, R. W., S. DeLain, A. Bartels, M. 

C. Bowler, E. Ratcliff, D. P. Herzog, K. S. 

Irons, and T. M. O’Hara. 2004b. 2000 annual 

status report: A summary of fish data in six 

reaches of the Upper Mississippi River System. 

U.S. Geological Survey, Upper Midwest 

Environmental Sciences Center, La Crosse, 

Wisconsin. Web-based report LTRMP 2004-

W003 available online at http://www.umesc.

usgs.gov/ reports_publications/ltrmp/fish/2000/

fish-srs.html. (Accessed October 2004.)

Burkhardt, R. W., S. DeLain, E. Kramer, A. 

Bartels, M. C. Bowler, E. Ratcliff, D. P. 

Herzog, K. S. Irons, and T. M. O’Hara. 2001. 

1999 annual status report: A summary of fish 

data in six reaches of the Upper Mississippi 

River System. U.S. Geological Survey, Upper 

Midwest Environmental Sciences Center, 

La Crosse, Wisconsin. LTRMP 2001-P002. 

14 pp. + Chapters 1–6.

Burkhardt, R. W. S. DeLain, E. Kramer, A. 

Bartels, M. C. Bowler, F. A. Cronin, M. 

D. Petersen, D. P. Herzog, T. M. O’Hara, 

K. S. Irons. 2000. 1998 annual status 

report: a summary of fish data in six 

reaches of the Upper Mississippi River 

System. U.S. Geological Survey, Upper 

Midwest Environmental Sciences Center, 

La Crosse, Wisconsin. LTRMP 2000-P004. 

14 pp. + Chapters 1–6.

Burkhardt, R. W., M. Stopyro, E. Kramer, A. 

Bartels, M. C. Bowler, F. A. Cronin, D. W. 

Soergel, M. D. Petersen, D. P. Herzog, T. M. 

O’Hara, and K. S. Irons. 1998. 1997 annual 

status report: A summary of fish data in six 

reaches of the Upper Mississippi River System. 

U. S. Geological Survey, Environmental 

Management Technical Center, Onalaska, 

Wisconsin, June 1998. LTRMP 98-P008. 

15 pp. + Chapters 1–6.

Burkhardt, R. W., S. Gutreuter, M. Stopyro, 

A. Bartels, E. Kramer, M. C. Bowler, F. A. 

Cronin, D. W. Soergel, M. D. Petersen, D. 

P. Herzog, K. S. Irons, T. M. O’Hara, K. 

D. Blodgett, and P. T. Raibley. 1997. 1996 

Annual status report: a summary of fish data 
25

in six reaches of the Upper Mississippi River 

System. U.S. Geological Survey, Upper 

Midwest Environmental Sciences Center, 

La Crosse, Wisconsin. LTRMP 97-P011. 

15 pp. + Chapters 1–6.

Carlander, K. D. 1969. Handbook of freshwater 

fishery biology. Volume I. The Iowa State 

University Press, Ames. 752 pp.

Carlander, K. D. 1977. Handbook of freshwater 

fishery biology. Volume II. The Iowa State 

University Press, Ames. 431 pp.

Chick, J. H., and M. A. Pegg. 2002. Invasive 

carp in the Mississippi River Basin. Science 

292:2250–2251.

Dettmers, J. M., S. Gutreuter, D. H. Wahl, and D. 

A. Soluk. 2001. Patterns in abundance of fishes 

in the main channels of the Upper Mississippi 

River System. Canadian Journal of Fisheries 

and Aquatic Sciences 58:933–942.

Dynesius, M., and C. Nilsson. 1994. 

Fragmentation and flow regulation of river 

systems in the northern third of the world. 

Science 266:753–762.

Etnier, D. A., and W. L. Starnes. 1993. The fishes 

of Tennessee. The University of Tennessee 

Press, Knoxville.

Galat, D. L., C. R. Berry, W. M. Gardner, J. C. 

Hendrickson, G. E. Mestl, G. J. Power, C. 

Stone, and M. R. Winston. Spatiotemporal 

patterns and changes in Missouri River 

fishes. In J. N. Rinne, R. M. Hughs, and R. 

Calamusso, editors. Historical changes in 

fish assemblages of large American rivers. 

American Fisheries Society Symposium. (In 

press)

Gehrke, P. C., P. Brown, C. B. Schiller, D. 

B. Moffatt, and A. M. Bruce. 1995. River 

regulation and fish communities in the MurrayDarling River System, Australia. Regulated 

Rivers: Research & Management 11:363–375.

Gido, K. B., W. J. Matthews, and W. C. 

Wolfinbarger. 2000. Long-term changes 

in a reservoir fish assemblage: stability in 

an unpredictable environment. Ecological 

Applications 10:1517–1529.

Gutreuter, S., R. Burkhardt, and K. Lubinski. 

1995. Long Term Resource Monitoring 

Program procedures: Fish monitoring. 

National Biological Service, Environmental 

Management Technical Center, Onalaska, 

Wisconsin, July 1995. LTRMP 95-P002-1. 

42 pp. + Appendixes A–J 

Gutreuter, S., A. D. Bartles, K. Irons, and M. 

B. Sandheinrich. 1999. Evaluation of the 

flood-pulse concept based on statistical 

models of growth of selected fishes of the 

upper Mississippi River. Canadian Journal of 

Fisheries and Aquatic Sciences 56:2282–2291.

Gutreuter, S. R. W. Burkhardt, M. Stopyro, 

A. Bartels, E. Kramer, M. C. Bowler, F. A. 

Cronin, D. W. Soergel, M. D. Petersen, D. 

P. Herzog, K. S. Irons, T. M. O’Hara, K. D. 

Blodgett, and P. T.Raibley. 1997a. 1995 annual 

status report: a summary of fish data in six 

reaches of the Upper Mississippi River System. 

U.S. Geological Survey, Upper Midwest 

Environmental Sciences Center, La Crosse, 

Wisconsin. LTRMP 97-P009. 15 pp. + 

Chapters 1–6.

Gutreuter, S. R. W. Burkhardt, M. Stopyro, 

A. Bartels, E. Kramer, M. C. Bowler, F. A. 

Cronin, D. W. Soergel, M. D. Petersen, D. 

P. Herzog, K. S. Irons, T. M. O’Hara, K. 

D. Blodgett, and P. T.Raibley. 1997b. 1994 

Annual status report: a summary of fish data 

in six reaches of the Upper Mississippi River 

System. U.S. Geological Survey, Upper 

Midwest Environmental Sciences Center, 

La Crosse, Wisconsin. LTRMP 97-P007. 

15 pp. + Chapters 1–6.

Gutreuter, S. R. W. Burkhardt, M. Stopyro, 

A. Bartels, E. Kramer, M. C. Bowler, F. A. 

Cronin, D. W. Soergel, M. D. Petersen, D. 

P. Herzog, K. S. Irons, T. M. O’Hara, K. 

D. Blodgett, and P. T.Raibley. 1997c. 1993 

Annual status report: a summary of fish data 

in six reaches of the Upper Mississippi River 

System. U.S. Geological Survey, Upper 

Midwest Environmental Sciences Center, 
26

La Crosse, Wisconsin. LTRMP 97-P008. 

15 pp. + Chapters 1–6.

Heiler, G., T. Hein, F. Schiemer, and G. Bornette. 

1995. Hydrological connectivity and flood 

pulses as the central aspects for the integrity 

of a river-floodplain system. Regulated Rivers: 

Research & Management 11(3,4):351–362.

Hesse, L. W., C. B. Stalnaker, N. G. Benson, and 

Z. R. Zuboy. 1993. Restoration planning for 

the rivers of the Mississippi River ecosystem. 

National Biological Survey, Washington, D.C. 

Biological Report 19. 502 pp.

Jackson, G. A., C. E. Korschgen, P. A. Thiel, 

J. M. Besser, D. W. Steffeck, and M. H. 

Bockenhauer. 1981. A long term resource 

monitoring plan for the UMRS. Contract 

14-16-009-81-903. Upper Mississippi River 

Basin Commission, Bloomington, Minnesota. 

2 volumes.

Junk, W. J., P. Bayley, and R. E. Sparks. 1989. 

The flood pulse concept in river floodplain 

systems. Pages 110–127 in D. P. Dodge, editor. 

Proceedings of the International Large River 

Symposium. Canadian Special Publication of 

Aquatic Sciences 106.

Kingsolving, A. D., and M. B. Bain. 1993. 

Fish assemblage recovery along a riverine 

disturbance gradient. Ecological Applications 

3:531–544.

Legendre, P., and L. Legendre. 1998. Numerical 

ecology. 2nd edition. Elsevier Inc., 

Amsterdam, The Netherlands.

Lepš, J., and P. Šmilauer. 2003. Multivariate 

analyses of ecological data using CANOCO. 

Cambridge University Press, Cambridge.

Lubinski, K. 1999. Floodplain river ecology 

and the concept of river ecological health, 

Chapter 2. Pages 1–12 in K. Lubinski and C. 

Theiling, editors. Ecological status and trends 

of the Upper Mississippi River System 1998: a 

report of the Long Term Resource Monitoring 

Program. U.S. Geological Survey, Upper 

Midwest Environmental Sciences Center, 

La Crosse, Wisconsin. April 1999. LTRMP 99-

T001. 236 pp.

Morrow, J. V., and J. P. Kirk. 1995. Age and 

growth of grass carp in Lake Guntersville, 

AL. Pages 187–194 in Proceedings of the 

49th Annual Conference of the Southeastern 

Association of Fish and Wildlife Agencies, 

Nashville, Tennessee.

Parrett, C., N. B. Melcher, and R. W. James. 

1993. Flood discharges in the upper 

Mississippi River basin, 1993. In Floods in 

the upper Mississippi River Basin, 1993. U.S. 

Geological Survey Circular 1120-A.

Patrick, R. 1998. Rivers of the United States. The 

Mississippi River and tributaries. Volume 4, 

Parts A and B. John Wiley & Sons, New York.

Pegg, M. A., and C. L. Pierce. 2001. Growth rate 

responses of Missouri and Lower Yellowstone 

River fishes to a latitudinal gradient. Journal of 

Fish Biology 59:1529-1543.

Pegg, M. A., and C. L. Pierce. 2002. 

Classification of reaches in the Missouri 

and lower Yellowstone Rivers based on 

flow characteristics. River Research and 

Applications 18:31–42.

Petts, G. E., H. Möller, and A. L. Roux. 1989. 

Historical change of large alluvial rivers in 

western Europe. Wiley, Chichester. 355 pp.

Pflieger, W. L. 1997. The fishes of Missouri. 

Missouri Department of Conservation, 

Jefferson City, Missouri.

Poff, N. L., J. D. Allan, M. B. Bain, J. R. Karr, 

K. L. Prestegaard, B. D. Richter, R. E. Sparks, 

and J. C. Stromberg. 1997. The natural flow 

regime. Bioscience 47:769–784.

Ricciardi, A., and J. B. Rasmussen. 1999. 

Extinction rates of North American freshwater 

fauna. Conservation Biology 13:1220–1222.

Sparks, R. E., P. B. Bayley, S. L. Kohler, and L. 

L. Osborne. 1990. Disturbance and recovery 

of large floodplain rivers. Environmental 

Management 14:699–709.
27

ter Braak, C. J. F., and P. Šmilauer. 2002. 

CANOCO reference manual and CanoDraw 

for Window’s User’s guide: software for 

canonical community ordination (v. 4.5). 

Microcomputer Power, Ithaca, New York.

Theiling, C. H. 1996. An ecological overview 

of the Upper Mississippi River System: 

implications for postflood recovery and 

ecosystem management. Pages 3–28 in D. L. 

Galat, and A. G. Frazier, editors. Overview 

of river-floodplain ecology in the Upper 

Mississippi River Basin. Volume 3 of J. 

A. Kelmelis, editor. Science for floodplain 

management into the 21st century. U.S. 

Government Printing Office, Washington, D.C.

Tockner, K., and J. A. Standford. 2002. Riverine 

floodplains: present state and future trends. 

Environmental Conservation 29:308–330.

U.S. Fish and Wildlife Service. 1993. Operating 

plan for the Upper Mississippi River System 

Long Term Resource Monitoring Program. 

Environmental Management Technical Center, 

Onalaska, Wisconsin, revised September 1993. 

EMTC 91-P002R. 179 pp. (NTIS #PB94-

160199)

U.S. Geological Survey. 1999. Ecological 

status and trends of the Upper Mississippi 

River System 1998. A report of the Long 

Term Resource Monitoring Program. 

U.S. Geological Survey, Upper Midwest 

Environmental Sciences Center, La Crosse, 

Wisconsin. LTRMP 99-T001. 236 pp.

Ward, J. V. 1998. Riverine landscapes: 

biodiversity patterns, disturbance regimes, and 

aquatic conservation. Biological Conservation 

83:269–278.

Welcomme, R. L. 1979. Fisheries ecology 

of floodplain rivers. Longman Publishers, 

London. 317 pp.

Welcomme, R. L. 1995. Relationships between 

fisheries and the integrity of river systems. 

Regulated Rivers: Research & Management 

11:121–136.

Williams, L. R., C. S. Toepfer, and D. Martinez. 

1996. The relationship between fish 

assemblages and environmental gradients 

in an Oklahoma prairie stream. Journal of. 

Freshwater Ecology 11:459–468.

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ABSTRACT

Standard Form 298 (rev. 2-89)

Prescribed by ANSI Std. Z39-18

298-102

NSN 7540-01-280-5500

We investigated differences in adult and young-of-the-year (YOY) fishes within each of the six Long Term Resource Monitoring Program study areas, 

using monitoring data from 1993 to 2001. Our objective was to investigate the relative roles of seasonal, annual, in situ, and physical habitat factors in 

explaining assemblage structure patterns within the Long Term Resource Monitoring Program study areas. Adult and YOY assemblage structure within 

each reach was dominated by one to three numerically abundant species. The percent of the total abundance for which these species accounted was 

10–88% and varied among age classes and study areas. Physical habitat classes were only weakly associated with differences in fish assemblage patterns 

within each study area. The amount of variation in fish abundance explained by physical habitats varied among the reaches. Differences among physical 

habitat classes accounted for 3–23% of the variation in the adult fish assemblage and for 3–20% of the difference in the YOY fish assemblage within each 

reach of our study area. Factors associated with interannual differences in environmental conditions were strongly correlated to patterns in assemblage 

structure within each of the six study areas. This was particularly true for YOY assemblages. Such a result would not have been attainable without 

long-term standardized data. Little is known regarding YOY assemblage patterns and dynamics in large river systems and long-term data sets are vital for 

continued investigation. The influence of environmental gradients on fish assemblage structure varied among the six study areas and explained 9–31% 

of the variation in assemblage structure. In the northern four reaches, water velocity was one of the primary factors associated with differences in fish 

assemblage structure. In the Unimpounded Reach (Upper Mississippi River) and Illinois River study areas, river elevation was one of the primary factors 

associated with differences in assemblage structure. Depth of gear deployment was influential in explaining differences in assemblage structure patterns 

in all reaches except the Upper Mississippi River Pool 4 and the Illinois River study areas. In all study areas, the amount of variation in fish abundance 

patterns explained by sampling period was relatively low. However, assemblage structure differed among sampling periods. In the northern reaches, 

sampling periods 2 and 3 were the most similar.

fishes; Illinois River, impounded, long-term, LTRMP, Mississippi River, ordination, unimpounded, YOY

Release unlimited. Available from National Technical Information Service, 5285 Port Royal Road, Springfield, VA 

22161 (1-800-553-6847 or 703-487-4650. Available to registered users from the Defense Technical Information 

Center, Attn: Help Desk, 8725 Kingman Road, Suite 0944, Fort Belvoir, VA 22060-6218 (1-800-225-3842 or 

703-767-9050).

Unclassified Unclassified Unclassified

Valerie A. Barko1, Brian S. Ickes2, David P. Herzog1, Robert A. Hrabik1,

John H. Chick3, and Mark A. Pegg4

1

Missouri Department of Conservation, Open Rivers and Wetlands Field Station, 3815 E. Jackson Blvd., Jackson, 

Missouri 63755; 2U.S. Geological Survey, Upper Midwest Environmental Sciences Center, 2630 Fanta Reed Road, 

La Crosse, Wisconsin 54603; 3Illinois Natural History Survey, Great Rivers Field Station, 8450 Montclair, Brighton, 

Illinois 62012; 4Illinois Natural History Survey, Illinois River Biological Station,704 N. Schrader Avenue, Havana, 

Illinois 62644

U.S. Geological Survey

Upper Midwest Environmental Sciences Center

2630 Fanta Reed Road

La Crosse, Wisconsin 54603

27 pp.

2005-T002

Spatial, Temporal, and Environmental Trends of Fish Assemblages within Six Reaches of the Upper 

Mississippi River System

 February 2005
The Long Term Resource Monitoring Program (LTRMP) for the Upper Mississippi

River System was authorized under the Water Resources Development Act of 1986 as 

an element of the Environmental Management Program. The mission of the LTRMP

is to provide river managers with information for maintaining the Upper Mississippi 

River System as a sustainable large river ecosystem given its multiple-use character.

The LTRMP is a cooperative effort by the U.S. Geological Survey, the U.S. Army Corps

of Engineers, and the States of Illinois, Iowa, Minnesota, Missouri, and Wisconsin.