Scientific Investigations Report 2008-5217

Variability in Lotic Communities in Three Contrasting Stream

Environments in the Santa Ana River Basin, California, 1999-2001

National Water-Quality Assessment Program

U.S. DEPARTMENT OF THE INTERIOR

U.S. GEOLOGICAL SURVEY
Photography:

Daniel Pickard, retrieved with permission, March 23, 2006, from

http://www.dfg.ca.gov/cabw/Lab/inverthome.html

Front cover description and credits:

Photography:

Philadelphia Academy of Natural Sciences,

Phycology Section, Patrick Center for Environmental Research,

retrieved with permission, June 23, 2006, from

http://diatom.acnatsci.org/AlgaeImage/ImageIM002408

Chironomidas Hydropsychidal Hydroptilidae

Cocconeis

placentula

Description of invertebrates and algae

Aquatic invertebrates Freshwater algae

Santa Ana River

below Prado Dam 

(photo credit: 

Carmen A. Burton, 

U.S. Geological

Survey, taken 

January 8, 1998)

Santa Ana River at

 Metropolitan Water

District’s pipeline

crossing near

Arlington 

(photo credit: 

Carmen A. Burton, 

U.S. Geological

Survey, taken 

January 7, 1998)

South Fork of

Santa Ana River

(photo credit: 

Carmen A. Burton, 

U.S. Geological

Survey, taken 

January 6, 1998)

Photograph: Photograph: Photograph:

Scientific Investigations Report 2008-5217

Variability in Lotic Communities in Three Contrasting Stream

Environments in the Santa Ana Basin, California, 1999-2001

National Water-Quality Assessment Program

U.S. DEPARTMENT OF THE INTERIOR

U.S. GEOLOGICAL SURVEY
Variability in Lotic Communities in Three 

Contrasting Stream Environments in the 

Santa Ana River Basin, California, 

1999–2001

By Carmen A. Burton

National Water-Quality Assessment Program

Scientific Investigations Report 2008–5217

U.S. Department of the Interior

U.S. Geological Survey
U.S. Department of the Interior

DIRK KEMPTHORNE, Secretary

U.S. Geological Survey

Mark D. Myers, Director

U.S. Geological Survey, Reston, Virginia: 2009

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Suggested reference:

Burton, C.A., 2009, Variability in lotic communities in three contrasting stream environments in the Santa Ana River 

Basin, California, 1999–2001: U.S. Geological Survey Scientific Investigations Report 2008-5217, 77 p. Available at 

http://pubs.usgs.gov/sir/2008/5217/
iii

FOREWORD

The U.S. Geological Survey (USGS) is committed to providing the Nation with credible scientific 

information that helps to enhance and protect the overall quality of life and that facilitates effective 

management of water, biological, energy, and mineral resources (http://www.usgs.gov/). Information 

on the Nation’s water resources is critical to ensuring long-term availability of water that is safe 

for drinking and recreation and is suitable for industry, irrigation, and fish and wildlife. Population 

growth and increasing demands for water make the availability of that water, now measured in terms 

of quantity and quality, even more essential to the long-term sustainability of our communities and 

ecosystems.

The USGS implemented the National Water-Quality Assessment (NAWQA) Program in 1991 to 

support national, regional, State, and local information needs and decisions related to water-quality 

management and policy (http://water.usgs.gov/nawqa). The NAWQA Program is designed to answer: 

What is the condition of our Nation’s streams and ground water? How are conditions changing over 

time? How do natural features and human activities affect the quality of streams and ground water, 

and where are those effects most pronounced? By combining information on water chemistry, 

physical characteristics, stream habitat, and aquatic life, the NAWQA Program aims to provide 

science-based insights for current and emerging water issues and priorities. From 1991-2001, the 

NAWQA Program completed interdisciplinary assessments and established a baseline understanding 

of water-quality conditions in 51 of the Nation’s river basins and aquifers, referred to as Study Units 

(http://water.usgs.gov/nawqa/studyu.html). 

Multiple national and regional assessments are ongoing in the second decade (2001–2012) of the 

NAWQA Program as 42 of the 51 Study Units are reassessed. These assessments extend the findings 

in the Study Units by determining status and trends at sites that have been consistently monitored for 

more than a decade, and filling critical gaps in characterizing the quality of surface water and ground 

water. For example, increased emphasis has been placed on assessing the quality of source water 

and finished water associated with many of the Nation’s largest community water systems. During 

the second decade, NAWQA is addressing five national priority topics that build an understanding 

of how natural features and human activities affect water quality, and establish links between 

sources of contaminants, the transport of those contaminants through the hydrologic system, and 

the potential effects of contaminants on humans and aquatic ecosystems. Included are topics on 

the fate of agricultural chemicals, effects of urbanization on stream ecosystems, bioaccumulation of 

mercury in stream ecosystems, effects of nutrient enrichment on aquatic ecosystems, and transport 

of contaminants to public-supply wells. These topical studies are conducted in those Study Units 

most affected by these issues; they comprise a set of multi-Study-Unit designs for systematic national 

assessment. In addition, national syntheses of information on pesticides, volatile organic compounds 

(VOCs), nutrients, selected trace elements, and aquatic ecology are continuing. 

The USGS aims to disseminate credible, timely, and relevant science information to address practical 

and effective water-resource management and strategies that protect and restore water quality. 

We hope this NAWQA publication will provide you with insights and information to meet your needs, 

and will foster increased citizen awareness and involvement in the protection and restoration of our 

Nation’s waters. 

The USGS recognizes that a national assessment by a single program cannot address all 

water-resource issues of interest. External coordination at all levels is critical for cost-effective 

management, regulation, and conservation of our Nation’s water resources. The NAWQA Program, 

therefore, depends on advice and information from other agencies—Federal, State, regional, 

interstate, Tribal, and local—as well as nongovernmental organizations, industry, academia, and 

other stakeholder groups. Your assistance and suggestions are greatly appreciated.

Matthew C. Larsen

Associate Director for Water
iv
v

Contents

Abstract ..........................................................................................................................................................1

Introduction ....................................................................................................................................................2

Study Design...................................................................................................................................................3

Description of Study Area ...................................................................................................................3

Data Collection and Analysis..............................................................................................................3

Site Selection ...............................................................................................................................3

Sample Collection........................................................................................................................5

Data Analysis................................................................................................................................6

Variability of Benthic Algae, Macroinvertebrates, and Fish...................................................................7

Benthic Algae........................................................................................................................................7

Macroinvertebrates..............................................................................................................................8

Fish ..................................................................................................................................................11

Variability in Habitat and Water Quality ..................................................................................................14

Relationship of Biological Variability to Habitat Variability...................................................................15

Benthic Algae......................................................................................................................................15

Macroinvertebrates............................................................................................................................16

Implications of Variability to Biomonitoring or Water Management Issues......................................18

Summary and Conclusions.........................................................................................................................21

References ...................................................................................................................................................21

Appendixes ...................................................................................................................................................24

Figures

Figure 1. Map showing location of study area, ecology sites, landuse, and ecoregions 

within the study area........................................................................ 4

Figure 2. Cluster dendrogram showing the results of an unweighted group average 

linkage cluster analysis of benthic algae data collected from four sites (SF, UPH, 

MWD, and PRD) in the Santa Ana River Basin, California, 1999–2001 ............... 8

Figure 3. Cluster dendrogram showing the results of an unweighted group average linkage 

cluster analysis of macroinvertebrate data collected from four sites (SF, UPH, 

MWD, and PRD) in the Santa Ana River Basin, California, 1999–2001 ............... 11

Figure 4. Cluster dendrogram showing the results of an unweighted group average linkage 

cluster analysis of fish data collected from four sites (SF, UPH, MWD, and PRD) 

in the Santa Ana River Basin, California, 1999–2001 .................................... 14

Figure 5. Graphs showing the relationships of the coefficient of variation of selected 

habitat variables to the coefficient of variation of selected benthic algae metrics 

collected at three sites (SF, MWD, and PRD) in the Santa Ana River Basin, 

California, 1999–2001 ........................................................................ 16

Figure 6. Graphs showing the relationships of the coefficient of variation of selected 

habitat variables to the coefficient of variation of selected macroinvertebrate 

metrics collected at three sites (SF, MWD, and PRD) in the Santa Ana River 

Basin, California, 1999–2001 ............................................................... 18
vi

Tables

Table 1. Sites sampled for benthic algae, macroinvertebrates, fish, and habitat 

 assessment during the summers of 1999, 2000, and 2001 in the Santa Ana

 River Basin, California .................................................................. 5

Table 2. Physical habitat variables measured and method of measurement, during the

 summers of 1999, 2000, and 2001, at four sites in the Santa Ana River Basin, 

 California ................................................................................. 6

Table 3. Coefficients of variation for benthic algae metrics that showed significant 

 differences between sites, Santa Ana River Basin, California, 1999–2001 ...... 9

Table 4. Coefficients of variation for benthic macroinvertebrate metrics that showed

 significant differences among three sites, Santa Ana River Basin, California, 

 1999–2001 ................................................................................. 12

Table 5. Coefficients of variation of habitat variables for the three summers of 

 1999−2001 for three sites in the Santa Ana River Basin, California ............... 15

Table 6. Benthic algae metric coefficients of variation that show a positive or negative

 association with the coefficient of variation of at least one habitat variable ... 17

Table 7. Macroinvertebrate metric coefficient of variations that show a positive or 

 negative association with the coefficient of variation of at least one habitat 

 variable.................................................................................... 19

Appendix tables

Appendix 1. Values for environmental variables measured during summers of 1999, 2000, 

 and 2001 at four sites in the Santa Ana River Basin, California .................. 25

Appendix 2. Benthic algae taxa collected from four sites in the Santa Ana River Basin, 

 California, 1999−2001 .................................................................. 27

Appendix 3. Benthic algae taxa and their densities from richest-targeted habitat samples

 collected from four sites in the Santa Ana River Basin, California, 1999−2001 ... 36

Appendix 4. Benthic algae taxa and their densities from depositional-targeted habitat 

 samples collected from four sites in the Santa Ana River Basin, California, 

 1999−2001 ................................................................................. 42

Appendix 5. Benthic algae metrics calculated from qualitative multihabitat, richest-

 targeted habitat, and depositional-targeted habitat samples collected from 

 four sites in the Santa Ana River Basin, California, 1999−2001 .................. 49

Appendix 6. Macroinvertebrate taxa collected from four sites in the Santa Ana River 

 Basin, California, 1999−2001 ............................................................ 54

Appendix 7. Macroinvertebrate taxa from richest-targeted habitat samples collected 

 from four sites in the Santa Ana River Basin, California, 1999−2001............... 63

Appendix 8. Macroinvertebrate metrics calculated from qualitative and richest-targeted 

 samples from four sites in the Santa Ana River Basin, California, 1999−2001 ... 70

Appendix 9. Data from fish collected from four sites during the summers 1999−2001 in 

 the Santa Ana River Basin, California ................................................ 76
vii

Abbreviations and Acronyms

(Clarification or additional information given in parentheses)

ANOVA analysis of variance

CV coefficient of variation

DTH depositional-targeted habitat

EPT sum of Ephemeroptera, Plecoptera, and Trichoptera

FFG functional feeding groups

IDAS Invertebrate Data Analysis System (USGS)

P significance level

PRD Santa Ana River below Prado Dam

QMH qualitative multihabitat

RTH richest-targeted habitat

SF South Fork of the Santa Ana River near Angeles Oaks

UPH Santa Ana River at upper powerhouse near Running Springs

Organizations

EPA U.S. Environmental Protection Agency

MWD Santa Ana River at Metropolitan Water District’s pipeline crossing near Arlington

NAWQA National Water-Quality Assessment (USGS)

NWQL National Water Quality Laboratory (USGS)

SAWPA Santa Ana Watershed Project Authority

USGS U.S. Geological Survey

Units of Measurement

cm centimeter (1 cm = 0.3937 in)

ft foot (feet)

in. inch

km kilometer (1 km = 0.6214 mi)

km2 square kilometer

m meter (1 m = 3.281 ft)

m2 square meter

mi mile

mi2 square mile

mm millimeter (10–3 meter)

μm micrometer (10–6 meter)

Notes

Temperature in degrees Celsius (°C) may be converted to degrees Fahrenheit (°F) as follows:

 °F = (1.8 × °C) + 32

Vertical coordinate information is referenced to the North American Vertical Datum of 1988 

(NAVD 88).

Horizontal coordinate information is referenced to the North American Datum of 1983 (NAD 

83).

Altitude, as used in this report, refers to distance above the vertical datum.

Specific conductance is given in microsiemens per centimeter at 25 degrees Celsius (μS/cm at 

25 °C).
Abstract 

Biotic communities and environmental conditions 

can be highly variable between natural ecosystems. The 

variability of natural assemblages should be considered in the 

interpretation of any ecological study when samples are either 

spatially or temporally distributed. Little is known about biotic 

variability in the Santa Ana River Basin. In this report, the 

lotic community and habitat assessment data from ecological 

studies done as part of the U.S. Geological Survey’s National 

Water-Quality Assessment (NAWQA) program are used for a 

preliminary assessment of variability in the Santa Ana Basin.

Habitat was assessed, and benthic algae, benthic 

macroinvertebrate, and fish samples were collected at four 

sites during 1999–2001. Three of these sites were sampled 

all three years. One of these sites is located in the San 

Bernardino Mountains, and the other two sites are located in 

the alluvial basin. Analysis of variance determined that the 

three sites with multiyear data were significantly different for 

41 benthic algae metrics and 65 macroinvertebrate metrics 

and fish communities. Coefficients of variation (CVs) were 

calculated for the habitat measurements, metrics of benthic 

algae, and macroinvertebrate data as measures of variability. 

Annual variability of habitat data was generally greater at the 

mountain site than at the basin sites. The mountain site had 

higher CVs for water temperature, depth, velocity, canopy 

angle, streambed substrate, and most water-quality variables. 

In general, CVs of most benthic algae metrics calculated 

from the richest-targeted habitat (RTH) samples were greater 

at the mountain site. In contrast, CVs of most benthic algae 

metrics calculated from depositional-targeted habitat (DTH) 

samples were lower at the mountain site. In general, CVs 

of macroinvertebrate metrics calculated from qualitative 

multihabitat (QMH) samples were lower at the mountain 

site. In contrast, CVs of many metrics calculated from RTH 

samples were greater at the mountain site than at one of the 

basin sites. Fish communities were more variable at the basin 

sites because more species were present at these sites.

Annual variability of benthic algae metrics was related 

to annual variability in habitat variables. The CVs of benthic 

algae metrics related to the most CVs of habitat variables 

included QMH taxon richness, the RTH percentage richness, 

RTH abundance of tolerant taxa, RTH percentage richness of 

halophilic diatoms, RTH percentage abundance of sestonic 

diatoms, DTH percentage richness of nitrogen heterotrophic 

diatoms, and DTH pollution tolerance index. The CVs of 

macroinvertebrate metrics related to the most CVs of habitat 

variables included the RTH trichoptera, RTH EPT, RTH 

scraper richness, RTH nonchironomid dipteran abundance 

(in percent), and RTH EPA (U.S. Environmental Protection 

Agency) tolerance, which is based on abundance. Many of the 

CVs of habitat variables related to CVs of macroinvertebrate 

metrics were the same habitat variables that were related 

to the CVs of benthic algae metrics. On the basis of these 

results, annual variability may have a role in the relationship 

of benthic algae and macroinvertebrates assemblages with 

habitat and water quality in the Santa Ana Basin. This report 

provides valuable baseline data on the variability of biological 

communities in the Santa Ana Basin.

Variability in Lotic Communities in Three Contrasting 

Stream Environments in the Santa Ana River Basin, 

California, 1999–2001

By Carmen A. Burton
2 Variability in Lotic Communities, Three Contrasting Stream Environments, Santa Ana River Basin, Calif., 1999–2001

Introduction 

Biotic communities and habitat conditions are known 

to be highly heterogeneous in natural ecosystems. This 

heterogeneity is observed at multiple spatial scales ranging 

from river systems to microhabitats within stream reaches. 

Variability of natural assemblages should be considered in the 

interpretation of any ecological study when samples are either 

spatially or temporally distributed. 

Variance of community composition or habitat can be a 

factor with ecological relevance (Palmer and others, 1997). 

Many papers (some cited by Palmer and others, 1997) suggest 

three reasons why studying variance in biotic communities 

or habitat may aid in understanding stream ecosystems. First, 

factors that affect ecological processes may be identified by 

a close examination of individual data points that contribute 

to variance. Second, changes in variance with spatial scale 

may lead to a better understanding of stream ecosystems. 

And third, identification of domains, areas of scale where the 

variance of a factor does not change (Wiens, 1989), also may 

lead to better understanding of stream ecosystems.

Effects of variability in benthic algae or habitat have 

not been studied extensively. However, Cardinale and others 

(2002) found that increased habitat heterogeneity resulted in 

increased primary productivity of stream algae. Large spatial 

variability was observed in some marine algae within similar 

habitats at the local scale (Wahl, 2001). On the other hand, 

variability in benthic macroinvertebrate assemblages has 

been studied for many years. Needham and Usinger (1956) 

studied the macroinvertebrate genera in a riffle in Prosser 

Creek, near Truckee, California, and found that most genera 

preferred moderate depths and velocities. In more recent 

studies, variation in macroinvertebrates was found at scales as 

small as groups (patches) of stones (Barmuta, 1990; Downes 

and others, 1993; Palmer and others, 2000). For example, 

in a northern Virginia stream, the spatial arrangement of 

patches or microhabitats was correlated to macroinvertebrate 

abundance (Palmer and others, 2000). In central Texas, a 

greater abundance of most macroinvertebrates was found 

toward the heads of riffles (Brown and Brown, 1984), which 

contrasts with the findings in Prosser Creek by Needham 

and Usinger (1956). In northern New Hampshire, benthic 

macroinvertebrate richness increased and macroinvertebrate 

variability decreased with increasing habitat heterogeneity 

(Brown, 2003). In two rivers with different channel forms 

in New Zealand, seasonal variation in species composition 

was lower in the river that had the less stable streambed 

substrate (Fowler and Death, 2000). Spatial variation in 

macroinvertebrates also occurs at larger scales, such as 

between streams or ecoregions, for macroinvertebrate richness 

metrics (Li and others, 2001). All these studies indicate a 

relationship between macroinvertebrate variability and habitat.

Several studies indicate that variation in fish assemblages 

is correlated to environmental variables or variation in these 

variables. Herbert and Gelwick (2003) explained variation 

in fish assemblages in a Texas stream by instream structure, 

hydrologic and physicochemical factors, and drainage 

features. In Minnesota and North Dakota, some species of 

fish were correlated with low variability in physical and 

chemical variables (Koel and Peterka, 2003). In central 

Europe, Slavik and Bartos (2001) observed decreased variation 

in fish assemblages in response to anthropogenic increases 

in variation in the physical environment, specifically for 

dissolved oxygen. Fayram and others (2005) observed higher 

variability of index of biotic integrity scores for cold-water 

fish in smaller Wisconsin streams compared with larger 

streams.

Because factors affecting variability of biota depend on 

scale (Andrew and others, 2003; Heino and others, 2003; Li 

and others 2001; Wiens, 1989), scale needs to be considered 

when changes in biological communities are assessed over 

space. This could partially explain why findings of different 

studies do not always agree (Wiens, 1989). 

Few studies of biological communities have been 

conducted in the Santa Ana River Basin. The U.S. Forest 

Service has collected biological data pertaining to forest lands, 

especially data on fish populations. The Santa Ana Watershed 

Project Authority (SAWPA) funded a study to determine 

the attainable uses of the Santa Ana River, especially in 

the inland basin. The U.S. Fish and Wildlife Service, the 

California Department of Fish and Game, and SAWPA are 

involved in a study to devise strategies to aid the endangered 

Santa Ana sucker. Very few studies of macroinvertebrates or 

benthic algae have been conducted in the basin and none have 

addressed the issues of spatial or annual variability.

The U.S. Geological Survey (USGS) incorporated 

ecological studies as part of the National Water-Quality 

Assessment (NAWQA) program (Gilliom and others, 1995). 

The Santa Ana Basin is one of more than 50 major river basins 

in the United States (U.S.) included in the NAWQA program. 

One purpose of these studies is to use the condition of aquatic 

biological communities as an indicator of the physical and 

chemical condition of water and hydrologic systems in the 

U.S. (Gilliom and others, 1995). The data from the Santa Ana 

NAWQA study was used for a preliminary assessment of 

variability in the Santa Ana Basin.

The purposes of this report are to assess (1) annual 

variability at each site for various biological measures, (2) the 

relationship of variability in biological measures to habitat 

and water quality variability, and (3) implications of any such 

relationship for biomonitoring or water management issues 

in the Santa Ana Basin. In addition, biological community 

information and habitat assessment data are listed in the 

appendixes.
Study Design 3

Study Design

Description of Study Area

The Santa Ana River Basin is the largest stream system 

in southern California, encompassing almost 6,900 km2

(2,670 mi 2) of densely populated coastal area (fig. 1). The 

river begins in the San Bernardino Mountains (which reach 

altitudes exceeding 3,000 m (10,000 ft)) and flows more than 

160 km (100 mi) to the Pacific Ocean. The watershed is home 

to almost 4.8 million people, and the population is expected 

to reach 7 million by the year 2025 (Santa Ana Watershed 

Project Authority, accessed June 9, 2003).

The basin is divided between two ecoregions, the 

Southern California Mountains ecoregion and the Southern 

and Central California Chaparral and Oak Woodlands 

ecoregion (U.S. Environmental Protection Agency, accessed 

September 3, 2004). Most of the urban and agricultural land 

uses occur in the alluvium-filled valleys and coastal plains 

of the Southern and Central California Chaparral and Oak 

Woodlands ecoregion (fig. 1). 

The basin has a Mediterranean climate, characterized 

by hot, dry summers and cool, wet winters. Average annual 

precipitation ranges from about 25 to 60 cm (10 to 24 in.) 

in the coastal plains and inland valleys, and from 60 to 120 

cm (24 to 48 in.) in the San Gabriel and San Bernardino 

Mountains (U.S. Army Corps of Engineers, 1994). This 

study started at the beginning of a drought period with annual 

precipitation well below the norm (Belitz and others, 2004).

The hydrologic system of the basin has been greatly 

altered. At higher elevations in the mountains, the streams 

are relatively unaltered except for intense recreational use 

and some diversions for hydroelectric power production on 

the Santa Ana River. At the transition from the mountains 

to the valley, most streams are diverted directly to public 

drinking-water supplies or to ground-water-recharge facilities. 

As a result of these alterations to the system and the natural 

Mediterranean climate, streams generally do not flow onto the 

valley floor, except during large stormflows that exceed the 

capacity of the diversions.

Flow is re-established in many low-elevation valley 

streams by various combinations of urban runoff, ground 

water, or discharges from wastewater treatment plants. These 

streams are composed of 70–100 percent treated wastewater 

(Mendez and Belitz, 2002). All of the base-flow of the river 

is diverted to a ground-water-recharge facility several miles 

downstream of Prado Dam. During the period of this study 

(summer 1999 to summer 2001), precipation was less than the 

30-year average. Streamflows in many tributaries to the Santa 

Ana River were generally near historical lows during baseflow conditions. 

Data Collection and Analysis

Site Selection

The Santa Ana Basin study design for NAWQA included 

seven surface-water fixed sites as part of a surface-water 

network. These sites were chosen to either represent stream 

water-quality conditions resulting from a specific land use or 

to represent stream water-quality conditions resulting from 

a combination of land uses and other influences. Ecology 

studies were not carried out at three of the fixed sites because 

the channels were completely or partially concrete-lined. The 

four remaining sites ranged from high in the San Bernardino 

Mountains near the headwaters of the Santa Ana River to just 

below Prado Dam (fig. 1). These four sites are listed in table 1.

The first site is located on the South Fork of the 

Santa Ana River near Angeles Oaks in the San Bernardino 

Mountains (hereinafter, SF). It is an alpine site located in the 

Southern California Mountains ecoregion (U.S. Environmental 

Protection Agency, accessed Sept. 3, 2004). The stream 

channel consists mostly of bedrock, boulders, and cobbles. 

Land use is undeveloped forest, mainly pines. 

The second site is located on the Santa Ana River at 

the upper powerhouse near Running Springs (hereinafter, 

UPH). This site is located near the base of the San Bernardino 

Mountains in the Southern California Mountains ecoregion 

(fig. 1). The stream channel consists mostly of large boulders 

and cobbles. Land use is mostly undeveloped chaparral forest 

with willows, cottonwoods, and alders in the riparian corridor. 

This site is located upstream of the Seven Oaks Dam, which 

was under construction during the period of this study. The 

water quality from this site is similar to that measured at a 

USGS gage located near the Seven Oaks Dam, which was part 

of the NAWQA surface-water network.

The third site is located upstream of the Metropolitan 

Water District’s pipeline crossing of the Santa Ana River 

in the inland basin (hereinafter, MWD). This site is located 

within the Southern and Central California Chaparral and Oak 

Woodlands ecoregion (fig. 1). The river at this site is a broad, 

shallow, sand channel constricted by bedrock outcrops on both 

banks. Baseflow is primarily treated wastewater supplemented 

with ground water forced upward by the bedrock outcrops. 

The riparian vegetation was primarily Arundo donax (an 

invasive, non-native cane), with small amounts of cattails, 

rushes, willows, and cottonwoods. The A. donax was removed 

during the second and third years of the study. Outside of the 

riparian corridor, land use is primarily urban.
4 Variability in Lotic Communities, Three Contrasting Stream Environments, Santa Ana River Basin, Calif., 1999–2001

The fourth site is located on the Santa Ana River below 

Prado Dam (hereinafter, PRD). This site is also located in 

the Southern and Central California Chaparral and Oak 

Woodlands ecoregion (fig. 1). The stream channel consists of 

mainly cobbles and gravel. Prado Dam is operated for flood 

control and a permanent pool is not maintained behind the 

dam. Baseflow is primarily treated wastewater. Upstream of 

Prado Dam, a series of wetlands were constructed to act as a 

treatment facility for the removal of nitrate from the Santa Ana 

River.

Pacific Ocean

Santa

Chino Cr Cucamonga Cr

San Jacinto

River

Santa

 Ana

 Ana

River

River

COASTAL

BASIN

INLAND

BASIN

SAN JACINTO

BASIN

San Jacinto Mts

San Gabriel Mts

San Bernardino Mts

San

Bernardino

County

Riverside County

San

Bernardino

Santa Ana

Anaheim Orange County

Orange County

Riverside

Santa Ana Mts

Los Angeles County

Chino Hills

EXPLANATION

Land use

Lakebed-Intermittently flooded

Agricultural

Urban

Santa Ana surface-water

 basin study area boundary

Subbasin boundary

Ecoregion boundary

Undeveloped-< 50 people

 per square mile

Southern California Mountains

Mountains ecoregion

Southern California

ecoregion

Southern and Central

California

Chaparral an d

Oak

Woodlands ecoregion

Ecological site

Santa Ana River

at upper powerhouse

South Fork

Santa Ana River

at MWD crossing

Santa Ana River

below Prado Dam

Los Angeles

San Diego

California

0 10 20 MILES

0 10 20 KILOMETERS

45’ 30’ 15’

Ecoregion data from U.S. Environmental Protection

Agency Level III Ecoregions, 2004

Base from U.S. Geological Survey digital elevation

data, 1999, Albers Equal-Area Conic Projection.

Population density data from 1990 U.S. Census.

Land use data from 1993 Southern California

Association of Governments (SCAG).

34 00’

34 15’

33 45’

118 00’ 117 00’ 116 45’

Santa Ana 

River Basin

San

Francisco

Figure 1. Location of study area, ecology sites, landuse, and ecoregions within the study area.
Study Design 5

Sample Collection

Benthic algae, benthic macroinvertebrate, and fish 

community data were collected and stream habitat assessed 

at all sites during low-flow conditions (July to August) from 

1999 to 2001 (table 1) to minimize variability resulting from 

seasonality. Three sites, PRD, MWD, and SF were sampled 

each year; one site, UPH, was sampled for macroinvertebrates 

and benthic algae in 1999, and fish and habitat conditions 

were assessed in 1999 and 2000. All sampling activity was 

conducted within a reach of stream defined as 20 times 

the mean channel width and within the range of 150 m to 

1,000 m long. Habitat conditions were assessed along 11 

transects in the reach as described by Fitzpatrick and others 

(1998). Habitat variables, such as channel width, velocity and 

substrate variables, and their method of collection, are listed in 

table 2.

Water-quality samples were collected monthly at PRD 

(1999–2001) and MWD (1999–2000) as part of the surfacewater fixed-site network for NAWQA (Gilliom and others, 

1995; Kent and Belitz, 2004). Water-quality samples were 

collected monthly at SF for the first year (1999) and then 

quarterly for the next two years. Water-quality samples were 

collected at the UPH site once in August 2000, but were 

collected monthly at the USGS gage located about 2 mi 

downstream for all three years. Only samples collected during 

the summer months (June–September) were used for analysis 

to minimize seasonal effects in variability. Water samples were 

analyzed for major ions, nutrients, and organic carbon at the 

USGS’s National Water Quality Laboratory (NWQL).

Benthic algae samples were collected according to 

NAWQA protocols (Porter and others, 1993; Moulton and 

others, 2002) and are briefly summarized below. Three 

types of samples were collected, one qualitative and two 

quantitative. Qualitative benthic algae samples were collected 

from each microhabitat available in the reach using a variety 

of methods. The subsamples from each microhabitat were 

composited in a single container. 

The quantitative benthic algae samples were collected 

from five representative areas in each of two different types 

of microhabitats: depositional-targeted habitat or DTH 

(which refers to the habitat in the stream where sediments 

are deposited) and the richest-targeted habitat or RTH (which 

refers to the habitat where the highest number of taxa is 

expected to be found). DTH benthic algae samples were 

collected from the surficial (5–7 mm) layer of epipelic (silt 

or mud) or epipsammic (sand) microhabitat at five locations 

within the reach. One-half of a 47-mm Petri dish was gently 

pushed upside down into the sediment. A stainless-steel 

spatula was slipped underneath the Petri dish to seal the algae 

subsample inside the Petri dish. The five subsamples were 

composited in a single container. 

The RTH benthic algae samples were collected from 

rocks at all stream reaches, except for MWD where the 

sample was collected from woody snags. Rocks or snags 

were selected from five areas within a reach at each site. The 

top-rock scrape method was used except for the sample at 

UPH. This sample was collected from the top of rocks using 

the SG-92 benthic algae sampler as described by Porter and 

others (1993). These methods remove the benthic algae from 

the rock surface by scrubbing with a small brush. AT MWD, 

submerged woody snags (5 to 10 snags) were collected and 

scraped, and the area measured as described by Moulton 

and others (2002). The subsamples from each area were 

composited in a single container.

Sample

 identification USGS station no. Station name Total basin area (mi2

)

Ecology sampling 

dates

SF99 341014116494801 South Fork of the Santa Ana River 7 July 21−22, 1999

SF00 July 10−11, 2000

SF01 July 23−25, 2001

UPH99 340843117032501 Santa Ana River at upper powerhouse 154 July 19−20, 1999

UPH00 Sept. 15 and 21, 20001

MWD99 11066460 Santa Ana River at MWD crossing 825 July 26−27, 1999

MWD00 July 11−12, 2000

MWD01 July 26−27, 2001

PRD99 11074000 Santa Ana River below Prado Dam 1,439 July 28−29, 1999

PRD00 July 13−14, 2000

PRD01 July 29−Aug. 2, 2001

1 Sampled fish and habitat only.

Table 1. Sites sampled for benthic algae, macroinvertebrates, fish, and habitat assessment during the summers of 1999, 2000, and 2001 

in the Santa Ana River Basin, California.

[mi2, square mile; MWD, Metropolitan Water District; no., number; USGS, U.S. Geological Survey]
6 Variability in Lotic Communities, Three Contrasting Stream Environments, Santa Ana River Basin, Calif., 1999–2001

All three types of composited benthic algae samples were 

preserved in 4-percent formalin. Benthic algae was identified 

and(or) enumerated at the National Academy of Sciences in 

Philadelphia, Pennsylvania, according to Charles and others 

(2002).

Benthic macroinvertebrate samples also were collected 

according to NAWQA protocols (Cuffney and others, 1993; 

Moulton and others, 2002). Two types of samples were 

collected, qualitative and semiquantitative. The qualitative 

multihabitat (QMH) macroinvertebrate samples were collected 

using a D-frame kick net equipped with a 210-μm mesh net. 

All habitat types present at each site were sampled. 

The semiquantitative macroinvertebrate samples were 

RTH samples collected from five representative areas of 

riffles at PRD, UPH, and SF. Woody snags were used for RTH 

samples at MWD because riffles were not present at this site. 

Samples were collected using a modified slack sampler (mesh 

size 425 μm) with an area of 0.25 m2

. These five subsamples 

were composited in a single container. The RTH and QMH 

samples were preserved with 10-percent formalin and sent to 

the Biological Unit of the NWQL for identification and(or) 

enumeration according to Moulton and others (2000).

Fish community data were collected following NAWQA 

protocols (Meador and others, 1993; Moulton and others, 

2002). Fish were collected using a Smith-Root Model 12B 

backpack electrofisher. Additional fish were collected at 

PRD by seining. Fish were identified to species, weighed, 

measured, and checked for external anomalies, then returned 

to the stream.

Data Analysis

Habitat variables were summarized as mean and 

standard deviation for each year at each site. Water-quality 

data from samples collected from June to September in each 

year were summarized as mean and standard deviation. 

Discharge and water temperature were summarized using 

data from continuous monitors when possible; otherwise, 

discrete samples were used. Data for habitat and waterquality variables can be found in appendix 1. To assess the 

annual habitat variability, coefficients of variation (CV) were 

calculated from the annual means of habitat variables at sites 

with multiyear data.

Variable (units) Method of measurement Equipment used

Reach length (m) Mid-channel distance from top to bottom of sampling reach Measuring tape

Reach water-surface gradient Vertical drop from top to bottom of sampling reach Surveying level and rod

Wetted channel width (m) Width of wetted channel at 11 equidistant transects Measuring tape

Bankful width (m) Channel width from top of left bank to top of right bank, 

measured at each of 11 equidistant transects

Measuring tape

Depth (m) Depth at thalweg (deepest point) and two additional evenly 

spaced points, measured at each of 11 equidistant transects

Calibrated wading rod

Water velocity (ft/s) Velocity at thalweg and two additional evenly spaced points, 

measured at each of 11 equidistant transects

Marsh-McBirney 

electronic flow meter

Shape index Calculated1 na

Canopy angles (degrees) Degrees of open sky, measured from the midpoint of each of 

11 equidistant transects

Clinometer

Riparian canopy closure (percent) Percentage of canopy at the left and right banks, measured at 

each of 11 equidistant transects

Densiometer

Geomorphic channel units (percent) Percentage of reach distance consisting of pool, riffle, and run Measuring tape

Streambed substrate2 Dominant substrate at thalweg and two additional evenly 

spaced points, measured at each of 11 equidistant transects

Visual estimate

Heterogeneity index Calculated3 na

1 w/(dd/dmax) at 11 equidistant transects, where w = wetted channel width, d = mean depth of water along transect, and dmax = maximum depth of water along 

transect. 

2

The dominant streambed substrate was characterized as: 1, concrete; 2, silt, mud, or detritus; 3, sand (>0.063−2 mm); 4, fine/medium gravel (>2−16 mm); 5, 

coarse gravel (>16−32 mm); 6, very coarse gravel (>32−64 mm); 7, small cobble (>64−128 mm); 8, large cobble (>128−256 mm); 9, small boulder (>256−512 

mm); 10, large boulder, irregular bedrock, irregular hardpan, or irregular artificial surface (Fitzpatrick and others, 1998).

3 Geometric mean of the coefficients of variation for shape index, water velocity, riparian canopy closure, and streambed substrate.

Table 2. Physical habitat variables measured and method of measurement, during the summers of 1999, 2000, and 2001, at four sites in 

the Santa Ana River Basin, California.

[ft/s, feet per second; m, meter; mm, millimeter; na, not applicable; >, greater than]
Variability of Benthic Algae, Macroinvertebrates, and Fish 7

Benthic algae and macroinvertebrate species lists were 

constructed using all taxa collected in all sample types. 

Benthic algae were identified to species in most cases. Benthic 

algae taxa and their densities, where applicable, can be found 

in appendixes 2, 3, and 4. To assess similarity in taxa among 

sites and years, the taxa lists for QMH, RTH, and DTH data 

for all sites were analyzed using an unweighted group average 

linkage clustering analysis of percentage of similarities. 

Metrics were calculated using autecological and tolerance 

information (Van Dam and others, 1994; Bahls, 1993; LangeBertalot, 1979). Metrics calculated from the benthic algae data 

can be found in appendix 5. 

Benthic macroinvertebrates were generally identified to 

genus. Ambiguous individuals identified at a higher taxonomic 

level (usually family) were distributed among the lower taxa 

(usually genera) in accordance with the relative abundance 

of each genus when more than half of the individuals were 

identified at the lower level. Otherwise, data were aggregated 

at the higher level of taxonomy. Benthic macroinvertebrates 

and their densities, where applicable, can be found in 

appendixes 6 and 7. To assess similarity in taxa among sites 

and years, the taxa lists for QHM, RTH, and DTH data for 

all sites were analyzed using an unweighted group average 

linkage clustering analysis of percentage of similarities. The 

taxa data also were summarized as biological metrics using the 

Invertebrate Data Analysis System (IDAS) program developed 

by the USGS (Cuffney, 2003). The metrics calculated from 

macroinvertebrate data can be found in appendix 8.

Analysis of variance (ANOVA) was used to determine 

which benthic algae and macroinvertebrate metrics were 

significantly different (P < 0.05) between the three sites with 

multiyear data. CVs were calculated for each metric that was 

significantly different between sites. The CV was used as a 

measure of temporal variance to compare sites with multiyear 

data. Biplots were used to examine the relationships between 

the CVs of benthic algae or macroinvertebrate metrics and 

the CVs of habitat variables. Metrics of benthic algae or 

macroinvertebrates that were not present at all three sites were 

not used in comparisons involving variance.

Fish data were summarized as relative abundance of 

fish species and the mean and range of the weight and length 

of individuals measured for each species. Appendix 9 gives 

the summary of fish data. Fish abundance data for all sites 

were analyzed using an unweighted group average linkage 

clustering analysis of percentage of similarities among fish 

samples.

Variability of Benthic Algae, 

Macroinvertebrates, and Fish

Benthic Algae

The cluster dendrogram of benthic algae data indicates 

that, for each site, the 2000 and 2001 samples were more 

similar to each other compared with the 1999 sample (fig. 2). 

This pattern was observed with QMH, RTH, and DTH 

samples. This may be a result of a storm that occurred in the 

mountains two weeks before sampling in 1999. The higher 

flows from the storm may have disturbed the benthic algae, 

especially those in depositional zones. Some benthic algae 

species, such as stalked diatoms (Gomphonema) (Burkholder, 

1996; Kutka and Richards, 1996; Peterson, 1996) or prostrate 

diatoms with mucilaginous forms (Achnanthes, Cocconeis) 

(Goldsborough and Robinson, 1996; Hill, 1996; Kutka and 

Richards, 1996), recover more quickly from high flows. 

Higher abundances of these types of diatoms in the 1999 

samples support the hypothesis that the storm was responsible 

for the differences. 

Of the 116 metrics calculated, CVs were calculated for 

the 41 metrics (table 3) that were significantly different among 

sites. In general, CVs of most benthic algae metrics calculated 

from the RTH samples were higher at SF than at MWD or 

PRD (table 3). In contrast, CVs of most metrics calculated 

from DTH samples were lower at SF. MWD generally had 

the highest CVs for metrics from DTH samples. CVs of most 

metrics that were calculated for both RTH and DTH samples 

were in the same ranges (<30, 30–100, >100). This suggests 

that, in general, annual variability was not strongly related to 

different microhabitats (pools vs. riffles or woody snags).

 Differences in annual variability may be a result of 

comparing the smaller SF site with the larger MWD and PRD 

sites (Vannote and others, 1980). Only four RTH metrics 

and two DTH metrics had CVs greater than 100 percent, 

indicating relatively low annual variation at all three sites for 

most benthic algae metrics. This may be a result of the study 

occurring during drought years (Belitz and others, 2004).
8 Variability in Lotic Communities, Three Contrasting Stream Environments, Santa Ana River Basin, Calif., 1999–2001

Macroinvertebrates

The cluster dendrogram of benthic macroinvertebrate data 

indicates that the similarities between samples for each site is 

much higher than was observed in the benthic algae samples, 

suggesting little effect from the 1999 storm (fig. 3). Of the 

167 metrics calculated for macroinvertebrates, CVs were 

calculated for the 65 metrics (table 4) that were significantly 

different among sites.

Differences in annual variation among sites were 

observed for both richness and abundance metrics in the 

Santa Ana River Basin. In general, CVs of macroinvertebrate 

metrics calculated from QMH samples were lower at SF than 

at MWD or PRD. In contrast, CVs of many metrics calculated 

from RTH samples were higher at SF than at MWD. PRD 

and SF had about the same number of high values for metrics 

from RTH samples; this is similar to the trend that was 

observed for benthic algae. MWD generally had lower CVs 

for RTH richness metrics than PRD, but had higher CVs for 

RTH abundance metrics. The higher CVs for abundance at 

MWD may be due to the unstable sand streambed. However, 

in a New Zealand study, Fowler and Death (2000) found 

less monthly variability at the site with the most unstable 

streambed substrate. They attributed this to the fewer number 

of species present at that site. In contrast, MWD had higher 

taxa richness than PRD during this study. The differences in 

temporal variability between this study (annual) and the New 

Zealand study (monthly) may have been due to the different 

temporal scales. Similar to algae, the CVs for almost all of 

the macroinvertebrate metrics were relatively low. Only six 

metrics, mainly abundance metrics, had CVs greater than 

100 percent. This suggests that during the period of this study, 

annual variability in macroinvertebrate assemblages was low 

for all three sites. This low variability may be the result of 

fewer scouring events from stormflows because of the drought. 

PRD99

MWD99

PRD00

PRD01

MWD01

MWD00

SF99

SF00

SF01

UPH99

-20 0 20 40 60 80 100

PERCENT SIMILARITY

Figure 2. Cluster dendrogram showing the results of an unweighted group average linkage cluster analysis of benthic algae data 

collected from four sites (SF, UPH, MWD, and PRD) in the Santa Ana River Basin, California, 1999–2001. 

See table 1 for sample codes.
Variability of Benthic Algae, Macroinvertebrates, and Fish 9

Table 3. Coefficients of variation for benthic algae metrics that showed significant differences between sites, Santa Ana River 

Basin, California, 1999-2001.—Continued

[Coefficients of variation are given in percent; significance is at P<0.05. CV, coefficient of variation ; MWD, Metropolitan Water District; QMH, qualitative 

habitat; RTH, richest targeted habitat; DTH, depositional habitat; nd, not detected]

Metric

CV for 

South Fork of 

Santa Ana River

CV for 

Santa Ana River 

and MWD Crossing

CV for 

Santa Ana River 

below Prado Dam

Metrics from QMH data

Taxon richness 3.4 10.6 9.5

Phylum richness 26.6 21.7 34.6

Metrics from RTH data

Simpson's diversity index 15.2 1.1 4.3

Taxon richness 13.3 12.5 7.1

Taxon abundance 60.9 138.2 60.5

Diatom richness 16.1 10.6 3.8

Blue-green algae abundance 173.2 122.2 173.2

Obligative nitrogen autotrophic diatom richness (in percent) 70.3 98.2 37.9

Halophobic (fresh) diatom richness (in percent) 9.7 nd 5.1

Sestonic diatom richness (in percent) nd 9.7 59.3

Motile diatom richness (in percent) 12.5 7.9 11.7

Tolerant taxon richness (in percent) 38.0 15.6 12.7

Intolerant taxon richness (in percent) 14.5 55.5 20.9

Nitrogen heterotrophic diatom abundance (percent) 69.9 35.5 37.6

Facultative nitrogen autotroph abundance (in percent) 7.9 22.1 0.9

Halophilic diatom abundance (percent) 127.5 12.1 22.0

Halophobic (fresh-brackish) diatom abundance (in percent) 3.8 3.7 10.2

Sestonic diatom abundance (in percent) nd 37.9 39.7

Motile diatom abundance (percent) 67.5 4.1 11.0

Bahl's tolerance index based on abundance 5.8 10.5 5.3

Tolerant taxon abundance (in percent) 51.0 5.7 6.0

Intolerant taxon abundance (in percent) 19.3 108.2 15.7

Siltation index 60.6 12.8 5.2

Pollution tolerance index 8.1 20.6 6.0

Table 3. Coefficients of variation for benthic algae metrics that showed significant differences between sites, Santa Ana River Basin, 

California, 1999-2001.

[Coefficients of variation are given in percent; significance is at P<0.05. CV, coefficient of variation ; MWD, Metropolitan Water District; QMH, qualitative 

habitat; RTH, richest targeted habitat; DTH, depositional habitat; nd, not detected]
10 Variability in Lotic Communities, Three Contrasting Stream Environments, Santa Ana River Basin, Calif., 1999–2001

Table 3. Coefficients of variation for benthic algae metrics that showed significant differences between sites, Santa Ana River 

Basin, California, 1999-2001.—Continued

[Coefficients of variation are given in percent; significance is at P<0.05. CV, coefficient of variation ; MWD, Metropolitan Water District; QMH, qualitative 

habitat; RTH, richest targeted habitat; DTH, depositional habitat; nd, not detected]

Metric

CV for 

South Fork of 

Santa Ana River

CV for 

Santa Ana River 

and MWD Crossing

CV for 

Santa Ana River 

below Prado Dam

Metrics from DTH data

Simpson's diversity index 5.5 9.1 3.8

Nitrogen heterotrophic diatom richness (in percent) 29.5 9.3 8.8

Obligative nitrogen autotrophic diatom richness (in percent) 25.5 72.2 51.7

Eutrophic diatom richness (in percent) 9.9 8.8 4.4

Halophilic diatom richness (in percent) 13.5 21.8 28.6

Alkaline diation richness (in percent) 1.8 3.5 3.1

Sestonic diatom richness (in percent) 173.2 173.2 23.4

Motile diatom richness (in percent) 5.4 8.7 8.5

Intolerant taxon richness (in percent) 12.7 17.4 30.8

Facultative nitrogen autotroph abundance (in percent) 1.1 48.7 31.7

Obligative nitrogen autotroph abundance (in percent) 22.1 38.3 81.9

Eutrophic diatom abundance (in percent) 25.6 6.0 11.4

Halophobic (fresh-brackish) diatom abundance (in percent) 80.0 173.2 102.8

Motile diatom abundance (in percent) 22.7 16.1 11.0

Bahl's tolerance index based on abundance 5.7 15.6 5.4

Siltation index 11.4 34.6 14.4

Pollution tolerance index 17.2 22.9 6.6
Variability of Benthic Algae, Macroinvertebrates, and Fish 11

The difference in CV between SF and MWD or PRD 

for a particular metric is generally greater than the difference 

in CV between MWD and PRD. This trend may be partially 

a result of ecoregion differences because SF is located 

in a different ecoregion than MWD and PRD. It is also 

possible that differences in stream size may also be a partial 

explanation for differences in variability between SF and the 

basin sites, as was suggested for benthic algae.

Fish

The cluster dendrogram for fish data shows that the 

samples from each site were generally similar, indicating low 

annual variability (fig. 4). However, fish samples from SF and 

UPH were less variable from year to year than the samples 

from PRD and MWD. The main reason for the low variability 

at SF and UPH is the low number of species (1 or 2) present 

compared with several species found at either MWD or PRD. 

For this reason, variability between sites or between years 

was not further investigated. More detailed information on 

the distribution of fish in the basin can be found in Brown and 

others (2005).

20 36 52 68 84 100

PERCENT SIMILARITY

MWD99

MWD01

MWD00

PRD99

PRD00

PRD01

UPH99

SF99

SF00

SF01

4

Figure 3. Cluster dendrogram showing the results of an unweighted group average linkage cluster 

analysis of macroinvertebrate data collected from four sites (SF, UPH, MWD, and PRD) in the Santa Ana 

River Basin, California, 1999–2001. See table 1 for sample codes.
12 Variability in Lotic Communities, Three Contrasting Stream Environments, Santa Ana River Basin, Calif., 1999–2001

Table 4. Coefficients of variation for benthic macroinvertebrate metrics that showed significant differences among three sites, 

Santa Ana River Basin, California, 1999–2001.—Continued

[Coefficients of variation are given in percent. Significance is at P < 0.05; CV, coefficient of variation; EPA, Environmental Protection Agency; EPT, sum 

of Ephemeroptera, Plecoptera, and Trichoptera; MWD, Metropolitan Water District; nd, not detected; QMH, qualitative multihabitat; RTH, richest-targeted 

habitat]

Metric

CV for

South Fork of

Santa Ana River

CV for

Santa Ana River

at MWD Crossing

CV for

Santa Ana River 

below Prado Dam

Metrics from QMH data

Taxon richness 7.7 8.9 15.6

Ephemeroptera richness 15.8 25.0 21.7

Trichoptera richness 20.8 21.7 0.0

EPT richness 11.3 8.7 12.4

EPT/Chironmid richness 12.1 23.3 11.1

Diptera richness 9.2 7.5 9.4

Chironomid richness 13.3 15.8 5.6

Nonchironomid dipteran richness 19.9 10.2 50.0

Noninsect richness 0.0 17.3 20.0

Nonmidge dipterans and noninsect richness 12.1 4.7 24.7

Odonate richness nd 0.0 114.6

Ephemeroptera richness (percent) 14.4 33.3 8.2

Trichoptera richness (percent) 20.9 16.1 16.8

EPT richness (percent) 3.6 16.6 4.5

Diptera richness (percent) 1.8 11.7 7.2

Chironomid richness (percent) 10.7 15.1 13.7

Noninsect richness (percent) 7.6 9.6 6.2

Nonmidge dipterans and noninsect richness (percent) 10.3 5.3 11.5

Oligochaete richness (percent) 7.6 44.8 16.7

Average EPA tolerance value based on richness 2.2 2.2 1.6

Filterer richness 20.0 0.0 25.0

Gatherer richness 14.0 14.5 17.6

Scraper richness 21.7 43.3 0.0

Filterer richness (percent) 13.1 7.1 15.3

Scraper richness (percent) 18.0 46.0 17.0

Metrics from RTH data

Taxon richness 5.1 13.9 30.7

Ephemeroptera richness 19.9 17.3 34.6

Trichoptera richness 39.0 0.0 0.0

EPT richness 12.5 10.8 15.7

EPT/Chironmid richness 11.6 50.2 23.4

Orthoclad richness 20.0 0.0 49.5

Odonate richness nd 0.0 nd

Coleoptera richness 173.2 100.0 nd

EPT richness (percent) 16.2 10.2 44.1

Odonate richness (percent) nd 14.7 nd

Table 4. Coefficients of variation for benthic macroinvertebrate metrics that showed significant differences among three sites, Santa 

Ana River Basin, California, 1999–2001.

[Coefficients of variation are given in percent. Significance is at P < 0.05; CV, coefficient of variation; EPA, Environmental Protection Agency; EPT, sum of 

Ephemeroptera, Plecoptera, and Trichoptera; MWD, Metropolitan Water District; nd, not detected; QMH, qualitative multihabitat; RTH, richest-targeted habitat]
Variability of Benthic Algae, Macroinvertebrates, and Fish 13

Table 4. Coefficients of variation for benthic macroinvertebrate metrics that showed significant differences among three sites, 

Santa Ana River Basin, California, 1999–2001.—Continued

[Coefficients of variation are given in percent. Significance is at P < 0.05; CV, coefficient of variation; EPA, Environmental Protection Agency; EPT, sum 

of Ephemeroptera, Plecoptera, and Trichoptera; MWD, Metropolitan Water District; nd, not detected; QMH, qualitative multihabitat; RTH, richest-targeted 

habitat]

Metric

CV for

South Fork of

Santa Ana River

CV for

Santa Ana River

at MWD Crossing

CV for

Santa Ana River 

below Prado Dam

Noninsect richness (percent 34.6 34.2 15.4

Oligochaete richness (percent) 37.7 24.3 32.5

Taxon abundance 35.0 19.5 48.1

Ephemeroptera abundance 33.9 21.3 111.7

Nonchironomid diptera abundance 74.5 21.8 39.7

Nonmidge dipterans and noninsect abundance 3.9 110.9 46.3

Mollusc and crustacean abundance 173.2 nd 155.4

Oligochaete abundance 76.1 17.8 35.1

Ephemeroptera abundance (percent) 25.1 41.4 79.3

Trichoptera abundance (percent) 36.5 44.5 12.7

Tanytarsinii abundance (percent) 51.0 173.2 91.9

Nonchironomid dipteran abundance (percent) 46.2 31.3 80.4

Nonmidge dipterans and noninsect abundance 

(percent)

19.9 118.7 41.3

Coleoptera abundance (percent) 173.2 93.7 nd

Mollusc and crustacean abundance (percent) 173.2 nd 166.0

Average EPA tolerance value based on richness 8.5 5.7 1.6

EPA tolerance value (average, abundance-weighted) 12.7 5.5 5.1

Percentage of most abundant taxon 2.1 60.0 14.0

Percentage of two most abundant taxon 10.2 32.6 4.3

Simpson’s diversity index 2.7 7.9 43.1

Predator richness 37.8 17.3 50.0

Scraper richness 21.7 43.3 43.3

Shredder richness 21.7 50.0 0.0

Filterer richness (percent) 34.6 14.7 15.1

Scraper richness (percent) 20.1 62.2 23.4

Predator abundance 33.4 41.4 45.8

Gatherer abundance 41.7 13.6 42.8

Predator abundance (percent) 22.7 48.7 85.9

Gatherer abundance (percent) 19.8 27.5 45.3

Filterer abundance (percent) 34.2 22.8 14.7
14 Variability in Lotic Communities, Three Contrasting Stream Environments, Santa Ana River Basin, Calif., 1999–2001

Variability in Habitat and Water Quality 

Differences in CV between sites were observed for many 

habitat and water-quality variables. Annual variability was 

greater at SF than at the basin sites for most of the habitat 

and water-quality variables (table 5). SF had higher CVs for 

water temperature, depth, velocity, canopy angle, streambed 

substrate, and most water-quality variables. The CVs for 

these variables ranged from 10 to 105 percent. In general, the 

CVs at SF were higher than those for wilderness streams in 

Idaho (Robinson and others, 2000). This suggests the physical 

environment was more dynamic at SF than at the Idaho 

streams. The CV for the heterogeneity index was low (three 

percent) suggesting little change in channel complexity during 

the three years.

The multiyear CVs (table 5) for the habitat and waterquality variables, such as channel width, water temperature, 

and specific conductance, for PRD and MWD were generally 

low (frequently less than 30 percent). The CVs for riparian 

canopy closure and the heterogeneity index were higher 

at MWD. This increase was due to the removal of Arundo 

donax, an invasive cane species, which began during summer 

2000. As a result, shading at the channel margins was greatly 

reduced during the last two years of the study.

PERCENT SIMILARITY

SF99

SF00

SF01

UPH99

UPH00

MWD99

MWD00

MWD01

PRD99

PRD01

PRD00

-20 0 20 40 60 80 100

Figure 4. Cluster dendrogram showing the results of an unweighted group average linkage cluster analysis of fish data collected from 

four sites (SF, UPH, MWD, and PRD) in the Santa Ana River Basin, California, 1999–2001. 

See table 1 for sample codes.
Relationship of Biological Variability to Habitat Variability 15

Relationship of Biological Variability 

to Habitat Variability

Benthic Algae

Many studies have shown that benthic algae assemblages 

are correlated to a variety of environmental variables (Leland, 

1995; DeNicola, 1996; Hill and others, 2000; Sherwood and 

others, 2000; Kennen and Ayers, 2002). In the Santa Ana 

River Basin, many benthic algae metrics were associated with 

habitat and water-quality variables (Burton and others, 2005). 

However, it may be just as important to investigate the role 

variability may have in the interaction of benthic algae and 

habitat as suggested by Palmer and others (1997).

Associations of CVs of benthic algae metrics with the 

CVs of habitat variables suggest a relationship between the 

variability in benthic algae metrics and habitat variables (see 

fig. 5 for examples). Of the 41 benthic algae metrics that were 

significantly different among sites, the CVs of 22 showed a 

relationship with the CV of at least one habitat variable. One 

QMH metric, four RTH metrics, and two DTH metrics were 

related to the CVs of three habitat variables (table 6). The 

QMH metric is taxon richness. The RTH metrics included 

percentage richness and abundance of tolerant taxa (tolerant 

taxa as defined by Lange-Bertelot [1979]), percentage richness 

of halophobic diatoms, and percentage abundance of sestonic 

diatoms. The DTH metrics included percentage richness of 

nitrogen heterotrophic diatoms and the pollution tolerance 

index. The habitat variables that were related most often to 

benthic algae metrics included water temperature, water depth, 

streambed substrate, the percentage of the reach consisting of 

run, specific conductance, and concentrations of chloride and 

orthophosphate. 

Variable CV for South Fork 

of Santa Ana River

CV for Santa Ana River 

at MWD Crossing

CV for Santa Ana River 

below Prado Dam

Discharge 46.8 19.6 11.6

Water temperature 15.4 5.9 5.2

Reach gradient 0.9 0.0 40.3

Wetted channel width 24.6 26.5 25.5

Bankfull width 21.6 25.9 24.5

Depth 44.3 37.9 39.3

Velocity 100.8 35.2 63.9

Shape index 17.7 22.2 7.2

Canopy angle 105.4 7.5 57.0

Riparian canopy closure 12.9 63.6 16.1

Streambed substrate1 40.5 3.4 38.9

Run 66.4 0.0 9.1

Riffle 5.4 0.0 18.1

Pool 55.4 0.0 93.0

Heterogeneity index2 3.3 139.5 40.9

Specific conductance 9.8 2.6 2.0

Oxygen, dissolved 8.0 9.5 4.8

Chloride, dissolved 41.8 5.1 3.8

Nitrite + nitrate, dissolved 15.4 12.1 7.4

Orthophosphate, dissolved 66.1 7.2 15.5

Total organic carbon 53.3 16.0 38.0

Table 5. Coefficients of variation of habitat variables for the three summers of 1999−2001 for three sites in the Santa Ana River Basin, 

California.

[CV, coefficient of variation; mm, millimeter; MWD, Metropolitan Water District; >, greater than]

1

The streambed substrate size was characterized as: 1, concrete; 2, silt, mud, or detritus; 3, sand (>0.063−2 mm); 4, fine/medium gravel (>2−16 mm); 

5, coarse gravel (>16−32 mm); 6, very coarse gravel (>32−64 mm); 7, small cobble (>64−128 mm); 8, large cobble (>128−256 mm); 9, small boulder 

(>256−512 mm); 10, large boulder, irregular bedrock, irregular hardpan, or irregular artificial surface (Fitzpatrick and others, 1998).

2

The heterogeneity index is the geometric mean of the coefficient of variation of shape index, riparian canopy closure, stream velocity, and streambed 

substrate.
16 Variability in Lotic Communities, Three Contrasting Stream Environments, Santa Ana River Basin, Calif., 1999–2001

This study suggests that variability of benthic algae 

metrics is related to variability of habitat variables in the Santa 

Ana River Basin. However, ecoregion differences and the 

stream size also may have effects. This study included three 

sites with only three years of data. Additional studies that 

would include more sites over a longer time period would be 

needed to better understand the relationship between benthic 

algae variability and the variability of habitat. Also, this 

study addresses temporal variability on only an annual scale. 

Variability on shorter (seasonal) or longer (decadal) temporal 

scales may also occur. 

Macroinvertebrates

Many studies have shown that macroinvertebrate 

assemblages are correlated to a variety of environmental 

variables (Brown and Brown, 1984; Barmuta, 1990; Fore 

and others, 1996; Leland and Fend, 1998; Brown and May, 

2000). Brown and Brown (1984) showed correlations of 

macroinvertebrate assemblages with streambed substrate size, 

velocity, depth, dissolved oxygen, and water temperature. 

Correlations of specific conductance with macroinvertebrates 

assemblages have also been found (Leland and Fend, 1998; 

Brown and May, 2000). Higher abundance and richness of 

different types of functional feeding groups (FFG) have been 

observed in riffles (high velocity) even though more detritus 

(food) was available in pools (low velocity) with different 

substrate sizes (Barmuta, 1990). Similar relationships have 

also been observed in the Santa Ana River Basin (Brown 

and others, 2005; Burton and others, 2005). However, as 

with benthic algae, it may be just as important to investigate 

the interaction of habitat variability and variability in 

macroinvertebrate assemblages. 

Of the 65 macroinvertebrate metrics that showed 

significant differences between sites, the CVs of 44 

macroinvertebrate metrics showed a relationship with the 

CV of at least one habitat variable (see fig. 6 for examples). 

The CVs of six RTH metrics showed a relationship with the 

CVs of more than two habitat variables (table 7). The RTH 

metrics included the sum of Ephemeroptera, Plecoptera, 

and trichoptera (EPT) and scraper richness, percentage 

abundance of trichoptera and nonchironomid dipteran, and 

U.S. Environmental Protection Agency (EPA) tolerance 

(as described in Barbour and others, 1999), which is based 

on abundance. The habitat variables with CVs related to 

the most CVs of macroinvertebrate metrics included water 

temperature, water depth, riparian canopy closure, streambed 

substrate, percentage of the reach consisting of run, specific 

conductance, and orthophosphate concentrations. 

CV SPECIFIC CONDUCTANCE

10

15

20

25

30

35

40

CV ORTHOPHOSPHATE

2

4

6

8

10

12

0 2 4 6 8 10 12 0 10 20 30 40 50 7060

CV WATER TEMPERATURE

0

10

20

30

40

50

60

70

4 6 8 10 12 14 16

CV OF RTH SILTATION INDEX

CV WATER DEPTH

2

4

6

8

10

12

37 38 39 40 41 42 43 44 45

CV OF QMH TAXA RICHNESS

CV OF RTH TOLERANT TAXA RICHNESS

CV OF QMH TAXA RICHNESS

PRD

PRD

SF

SF

PRD

SF

MWD

MWD

MWD

PRD

SF

RTH MWD

Figure 5. The relationships of the coefficient of variation of selected habitat variables to the coefficient of variation of selected benthic 

algae metrics collected at three sites (SF, MWD, and PRD) in the Santa Ana River Basin, California, 1999–2001.

See table 1 for sample codes and list of Abbreviations and Acronyms for definitions.
Relationship of Biological Variability to Habitat Variability 17

Table 6. Benthic algae metric coefficients of variation that show a positive or negative association with the coefficient of variation of 

at least one habitat variable.—Continued

[(+), suggests a positive association with the algae metric; (–), suggests a negative association with the algae metric. CV, coefficient of variation; 

DTH, depositional-targeted habitat; QMH, qualitative multihabitat; RTH, richest-targeted habitat; mm, milimeter; nd, not detected]

QMH and RTH algae metric CVs and associated habitat variable CVs 

QMH taxon richness Halophobic (fresh) diatom richness (percent) Sestonic diatom abundance 

(percent)

Depth (–) Wetted channel width (–) Water temperature (–)

Run (–) Canopy angle (+) Specific conductance (–)

Orthophosphate, dissolved (–) Total organic carbon (+) Chloride, dissolved (–)

QMH phylum richness Tolerant taxon richness 

(percent)

Motile diatom abundance 

(percent)

Oxygen, dissolved (–) Water temperature (+) Run (+)

Specific conductance (+) Orthophosphate, dissolved (+)

Chloride, dissolved (+)

Simpson’s diversity index Nitrogen heterotrophic diatom abundance (percent) Tolerant taxon abundance (percent)

Depth (+) Run (+) Water temperature (+)

Orthophosphate, dissolved (+) Specific conductance (+)

Chloride, dissolved (+)

Taxon abundance Halophilic diatom abundance (percent) Siltation index

Riparian canopy closure (+) Run (+) Water temperature (+)

 Streambed substrate1

 (–) Orthophosphate, dissolved (+) Specific conductance (+)

Blue-green algae abundance Halophobic (fresh-brackish) diatom abundance 

(percent)

Riparian canopy closure (–) Wetted channel width (+)

Streambed substrate (+)

DTH algae metric CVs and associated habitat variable CVs 

Nitrogen heterophic diatom 

richness (percent)

Sestonic diatom richness (percent) Siltation index

Water temperature (+) Reach gradient (–) Riparian canopy closure (+)

Specific conductance (+)

Chloride, dissolved (+)

Obligative nitrogen autotrophic 

diatom richness (percent)

Facultative nitrogen autotroph abundance (percent) Pollution tolerance index

Velocity (–) Bankfull width (+) Shape index (+)

Canopy angle (–) Riffle (–)

Oxygen, dissolved (+)

Alkaline diation richness (percent) Halophobic (fresh-brackish) diatom 

 abundance (percent)

Depth (–) Heterogeneity index2

 (+)

Table 6. Benthic algae metric coefficients of variation that show a positive or negative association with the coefficient of variation of 

at least one habitat variable.

[(+), suggests a positive association with the algae metric; (–), suggests a negative association with the algae metric. CV, coefficient of variation; 

DTH, depositional-targeted habitat; QMH, qualitative multihabitat; RTH, richest-targeted habitat; mm, millimeter; nd, not detected]

1

The streambed substrate size was characterized as: 1, concrete; 2, silt, mud, or detritus; 3, sand (>0.063−2 mm); 4, fine/medium gravel (>2−16 mm); 

5, coarse gravel (>16−32 mm); 6, very coarse gravel (>32−64 mm); 7, small cobble (>64−128 mm); 8, large cobble (>128−256 mm); 9, small boulder 

(>256−512 mm); 10, large boulder, irregular bedrock, irregular hardpan, or irregular artificial surface (Fitzpatrick and others, 1998).

2

 The heterogenieity index is the geometric mean of the coefficient of variation of the shape index, the riparian closure, stream velocity, and streambed 

substrate.
18 Variability in Lotic Communities, Three Contrasting Stream Environments, Santa Ana River Basin, Calif., 1999–2001

This study suggests that annual variability of habitat 

variables may be related to variability of macroinvertebrate 

metrics in the Santa Ana River Basin. However, it is also 

possible that ecoregion differences and stream size may have 

effects on macroinvertebrate variability. As noted previously, 

this study included three sites with only three years of 

data. Additional studies would be needed to better define 

this relationship. More sites over a longer time period are 

necessary to better understand the role of variability in the 

relationship between habitat and macroinvertebrates and at 

what scales these relationships exist. Studies using individual 

taxa, in addition to metrics, may need to be investigated to 

determine some of these relationships.

Implications of Variability to 

Biomonitoring or Water Management 

Issues

Aquatic ecosystems are naturally dynamic and vary 

over space and time. This report shows the annual variability 

for habitat, water quality, and biological communities. The 

differences in biological communities at small and large 

temporal scales need to be documented in the Santa Ana River 

to determine if observed changes in communities are within 

the range of natural variability or if human activities may 

be the cause. This information would be important for any 

biomonitoring program that evaluates whether the ecosystem 

is improving or degrading in quality.

The effects of physical variability on aquatic life are 

important considerations for water management and stream 

improvement projects. Biological communities are composed 

of species adapted for some measure of variability in the 

hydrologic system during their life cycle. However, large 

differences in flow, such as floods, at the wrong time can 

have a detrimental effect on aquatic organisms. Streams with 

homogeneous habitat will not provide preferred habitat or 

necessary food resources for some species. Concrete channels 

with shallow flow may be highly productive for algae and 

can reduce nitrate concentrations (Kent and others, 2005), but 

such channels usually provide habitat for few species of algae, 

macroinvertebrates, or fish (Brown and others, 2005; Burton 

and others, 2005). 

PRD

SF

PRD

SF

MWD

PRD

SF

MWD

PRD

SF

MWD

MWD

0

-5

5

10

15

20

25

CV OF SPECIFIC CONDUCTANCE

0 2 4 6 8 10 12

4

6

8

10

12

14

CV OF WATER TEMPERATURE

4 6 8 10 12 14 16

CV OF RTH EPA TOLERANCE

VALUES BASED ON ABUNDANCE

20

30

40

50

60

70

80

90

CV OF SHAPE INDEX

6 8 10 12 14 16 18 20 22 24

CV OF RTH NONCHIRONOMID DIPTERRAN

ABUNDANCE, IN PERCENT

0 10 20 30 40 50 7060

2

4

6

8

10

12

14

16

18

CV OF RIPARIAN CANOPY CLOSURE

CV OF QMH EPT RICHNESS,

IN PERCENT

CV OF QMH NONINSECT RICHNESS

QMH

RTH

Figure 6. The relationships of the coefficient of variation of selected habitat variables to the coefficient of variation of selected 

macroinvertebrate metrics collected at three sites. (SF, MWD, and PRD) in the Santa Ana River Basin, California, 1999–2001. 

CV, coefficient of variation; EPA, U.S. Environmental Protection Agency; EPT, sum of Ephemeroptera, Plecoptera, and Trichoptera; 

RTH, richest-targeted habitat; DTH, depositional-targeted habitat; QMH, qualitative multihabitat.
Implications of Variability to Biomonitoring or Water Management Issues 19

Table 7. Macroinvertebrate metric coefficient of variations that show a positive or negative association with the coefficient of 

variation of at least one habitat variable.—Continued

[(+), suggests a positive association with the macroinvertebrate metric; (–), suggests a negative association with the macroinvertebrate metric. CV, coefficient 

of variation; EPA, Environmental Protection Agency; EPT, sum of Ephemeroptera, Plecoptera, and Trichoptera; QMH, qualitative multihabitat; RTH, richesttargeted habitat; mm, milimeter]

QMH macroinvertebrate metric CVs and associated habitat variable CVs 

Ephemeroptera richness Nonmidge dipterans and noninsect 

richness

Chironomid richness (percent)

Bankfull width (+) Shape index (–) Bankfull width (+)

Riffle (+)

Trichoptera richness Odonate richness Noninsect richness (percent)

Reach gradient (–) Reach gradient (+) Pool (–)

Chironomid richness Trichoptera richness (percent) Oligochaete richness (percent)

Shape index (+) Run (+) Heterogeneity index2

 (+)

Riffle (–) Orthophosphate, dissolved (+)

Nonchironomid dipteran richness EPT richness (percent) EPA tolerance value (average, richnessweighted)

Shape index (–) Riparian canopy closure (+) Reach gradient (–)

Riffle (+) Streambed substrate1

 (–)

Noninsect richness Diptera richness (percent) Scraper richness (percent)

Water temperature (–) Velocity (–) Streambed substrate (–)

Specific conductance (–) Canopy angle (–)

RTH macroinvertebrate metric CVs and associated habitat variable CVs 

Taxon richness Coleoptera richness Taxon abundance

Nitrite + nitrate, dissolved (–) Nitrite + nitrate, dissolved (+) Pool (+)

Trichoptera richness Noninsect richness (percent) Nonchironomid diptera abundance

Water temperature (+) Reach gradient (–) Bankfull width (–)

Specific conductance (+)

Chloride, dissolved (+)

EPT richness Odonate richness (percent) Nonmidge dipterans and noninsect 

abundance

Shape index (–) Riparian canopy closure (+) Wetted channel width (+)

Riffle (+) Streambed substrate (–) Total organic carbon (–)

Oxygen, dissolved (–)

EPT/Chironmid richness Oligochaete richness (percent) Mollusc and crustacean abundance

Heterogeneity index (+) Wetted channel width (–) Riparian canopy closure (–)

Total organic carbon (+) Streambed substrate (+)

Table 7. Macroinvertebrate metric coefficient of variations that show a positive or negative association with the coefficient of 

variation of at least one habitat variable.

[(+), suggests a positive association with the macroinvertebrate metric; (–), suggests a negative association with the macroinvertebrate metric. CV, coefficient of 

variation; EPA, Environmental Protection Agency; EPT, sum of Ephemeroptera, Plecoptera, and Trichoptera; QMH, qualitative multihabitat; RTH, richesttargeted habitat; mm, milimeter]
20 Variability in Lotic Communities, Three Contrasting Stream Environments, Santa Ana River Basin, Calif., 1999–2001

Table 7. Macroinvertebrate metric coefficient of variations that show a positive or negative association with the coefficient of 

variation of at least one habitat variable.—Continued

[(+), suggests a positive association with the macroinvertebrate metric; (–), suggests a negative association with the macroinvertebrate metric. CV, coefficient 

of variation; EPA, Environmental Protection Agency; EPT, sum of Ephemeroptera, Plecoptera, and Trichoptera; QMH, qualitative multihabitat; RTH, richesttargeted habitat; mm, milimeter]

RTH macroinvertebrate metric CVs and associated habitat variable CVs —Continued

Oligochaete abundance Mollusc and crustacean abundance 

(percent)

Scraper richness

Bankfull width (–) Riparian canopy closure (–) Water temperature (–)

Depth (+) Streambed substrate (+) Specific conductance (–)

Chloride, dissolved (–)

Trichoptera abundance (percent) EPA tolerance value (average, richnessweighted)Shredder richness

Shape index (+) Nitrite + nitrate, dissolved (+) Pool (–)

Riffle (–)

Oxygen, dissolved (+)

Tanytarsinii abundance (percent) EPA tolerance value (average, abundanceweighted)Filterer richness (percent)

Heterogeneity index (+) Water temperature (+) Water temperature (+)

Specific conductance (+) Chloride, dissolved (+)

Chloride, dissolved (+)

Nonchironomid dipteran abundance 

(percent)

Percentage of most abundant taxon Scraper richness (percent)

Shape index (–) Heterogeneity index (+) Riparian canopy closure (+)

Riffle (+) Streambed substrate (–)

Oxygen, dissolved (–)

Nonmidge dipterans and noninsect 

abundance (percent)

Predator richness Gatherer abundance

Heterogeneity index (+) Pool (+) Streambed substrate (+)

Coleoptera abundance (percent) Predator abundance (percent)

Nitrite + nitrate, dissolved (+) Nitrite + nitrate, dissolved (–)

1

The streambed substrate size was characterized as: 1, concrete; 2, silt, mud, or detritus; 3, sand (>0.063−2 mm); 4, fine/medium gravel (>2−16 mm); 

5, coarse gravel (>16−32 mm); 6, very coarse gravel (>32−64 mm); 7, small cobble (>64−128 mm); 8, large cobble (>128−256 mm); 9, small boulder 

(>256−512 mm); 10, large boulder, irregular bedrock, irregular hardpan, or irregular artificial surface (Fitzpatrick and others, 1998).

2

The heterogenieity index is the geometric mean of the coefficient of variation of the shape index, the riparian closure, stream velocity, and streambed 

substrate.
References 21

Summary and Conclusions

Understanding variability of natural assemblages is 

important in the interpretation of any ecological study. Data 

from an ecological study conducted during the summers 

1999–2001 by the Santa Ana River Basin study unit of the 

USGS’s NAWQA program were used to do a preliminary 

assessment of variability in the Santa Ana River Basin. 

Twenty-two habitat and water-quality variables were measured 

at three sites in the basin. The appendixes list the 233 taxa of 

benthic algae, 144 taxa of macroinvertebrates, and 16 taxa 

of fish that were collected. Significant differences in benthic 

algae metrics, macroinvertebrate metrics, and fish assemblages 

and variability were observed among the three sites. Annual 

variability in most habitat and water-quality variables was 

higher at the alpine site located in the mountains (SF) than at 

the basin sites (MWD and PRD). In general, annual variability 

in RTH benthic algae metrics was higher at SF, but annual 

variability in DTH metrics was lower. Annual variability 

in RTH macroinvertebrate metrics was higher at SF and 

PRD than at MWD. In contrast, annual variability in QMH 

macroinvertebrate metrics was lower at SF than at MWD or 

PRD. Annual variability in fish assemblages was higher at 

MWD and PRD primarily because of the higher number of 

species present at these sites. The CVs of seven benthic algae 

metrics and six macroinvertebrate metrics were correlated to 

the CVs of many of the habitat variables measured.

The variability of physiochemical variables is likely to 

have a role in structuring the annual variability of aquatic 

communities in the Santa Ana River Basin. However, some of 

the differences observed in habitat and aquatic communities 

between sites may be attributed to differences in ecoregions or 

stream size rather than variability. Although the data collected 

have a limited temporal scope, this report provides valuable 

baseline data on the variability of biological communities in 

the Santa Ana River Basin. Additional sampling at more sites 

over several years to address variability would be needed 

to better understand the variability in the composition of 

biological communities in the Santa Ana River Basin.

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and Alvestad, Rachel, 2000, Streambed landscapes—

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24 Variability in Lotic Communities, Three Contrasting Stream Environments, Santa Ana River Basin, Calif., 1999–2001

Appendixes
Appendixes 25

Appendix 1. Values for environmental variables measured during summers of 1999, 2000, and 2001 at four sites in the Santa Ana River Basin, California.—Continued[See table 1 for explanation of sample identification. Values are mean ± standard deviation unless n = 1; °C, degrees Celsius; E, estimated; ft/s, feet per second; ft3/s, cubic feet per second; m, meter; mg/L, 

milligrams per liter; mi, mile; mm, millimeter; n, sample size; mS/cm, microsiemens per centimeter; >, greater than; <, less than; —, no data]

Sample identification

Variable SF99 SF00 SF01 UPH99 UPH00 MWD99 MWD00 MWD01 PRD99 PRD00 PRD01

Discharge (ft3/s) 3.8 3.0 1.31 10.2 2.5 ± 1.2 99 ± 16 76 ± 8 74 ± 8 210 ± 31 189 ± 18 191 ± 11

Water temperature (°C) 12.2 ± 1.2 10.1 ± 1.7 10.9 ± 1.5 22 19.6 ± 3.0 21.8 ± 1.4 22.4 ± 1.0 25.0 ± 4.2 23.7 ± 1.4 24.2 ± 1.2 24.4 ± 

1.0

Reach length (m) 150 150 150 200 200 900 900 900 540 540 540

Reach gradient 0.082 0.083 0.084 0.0401 0.039 0.003 0.003 0.003 0.003 0.001 0.003

Wetted channel width (mean) 

(m, n = 11)

3.4 ± 0.7 3.2 ± 0.8 2.9 ± 0.8 8.0 ± 3.6 7.5 ± 2.5 59.7 ± 11.4 42.4 ± 7.4 46.0 ± 13.5 17.8 ± 4.2 17.0 ± 4.4 18.7 ± 

5.3

Bankfull width 

(m, n = 11)

4.2 ± 0.6 3.9 ± 0.9 3.9 ± 1.0 19.4 ± 5.2 7.8 ± 2.5 64.1 ± 10.7 60.0 ± 14.3 63.4 ± 22.5 21.8 ± 4.2 22.0 ± 4.7 20.5 ± 

6.9

Depth (m, n = 33) 0.17 ± 0.07 0.16 ± 0.07 0.15 ± 0.08 0.26 ± 0.14 0.19 ± 0.11 0.13 ± 0.05 0.12 ± 0.04 0.12 ± 0.05 0.75 ± 0.27 0.64 ± 0.25 0.66 ± 

0.29

Velocity (ft/s, n = 33) 1.10 ± 1.00 1.20 ± 1.18 0.64 ± 0.63 0.67 ± 0.73 0.37 ± 0.38 1.32 ± 0.43 1.44 ± 0.39 1.23 ± 0.55 1.95 ± 1.26 2.33 ± 1.45 2.02 ± 

1.32

Shape index (n = 11) 12.4 ± 11.9 12.0 ± 11.7 8.8 ± 3.8 12.2 ± 9.0 20.3 ± 13.1 143 ± 131 96 ± 55 103 ± 65 14.4 ± 5.4 13.4 ± 5.1 15.5 ± 

5.2

Canopy angle (degrees, 

n = 11)

9 ± 16 20 ± 15 16 ± 17 112 ± 33 88 ± 29 152 ± 6 142 ± 8 147 ± 16 64 ± 42 61 ± 29 56 ± 35

Riparian canopy closure 

(percent, n = 22)

92 ± 12 94 ± 7 91 ± 16 24 ± 21 78 ± 28 82 ± 20 70 ± 19 14 ± 172 88 ± 16 87 ± 19 100 ± 1

Streambed substrate3 (n = 33) 7.0 ± 2.2 5.8 ± 3.1 6.2 ± 2.6 7.9 ± 2.0 8.3 ± 0.5 3.0 ± 0.2 3.0 ± 0 3.0 ± 0 5.5 ± 2.5 5.8 ± 2.2 6.8 ± 2.2

Run (percent) 4 8 16 30 33 100 100 100 82 74 69

Riffle (percent) 76 83 76 60 55 0 0 0 18 22 26

Pool (percent) 20 8 8 9 13 0 0 0 0 4 6

Heterogeneity index4 43.4 44.9 42.0 64.4 35.1 25.7 1.4 2.4 37.5 37.2 15.9

Appendix 1. Values for environmental variables measured during summers of 1999, 2000, and 2001 at four sites in the Santa Ana River Basin, California.[See table 1 for explanation of sample identification. Values are mean ± standard deviation unless n = 1; °C, degrees Celsius; E, estimated; ft/s, feet per second; ft3/s, cubic feet per second; m, meter; mg/L, 

milligrams per liter; mi, mile; mm, millimeter; n, sample size; mS/cm, microsiemens per centimeter; >, greater than; <, less than; —, no data]
26 Variability in Lotic Communities, Three Contrasting Stream Environments, Santa Ana River Basin, Calif., 1999–2001 Appendix 1. Values for environmental variables measured during summers of 1999, 2000, and 2001 at four sites in the Santa Ana River Basin, California.—Continued [See table 1 for explanation of sample identification. Values are mean ± standard deviation unless n = 1; °C, degrees Celsius; E, estimated; ft/s, feet per second; ft3/s, cubic feet per second; m, meter; mg/L, milligrams per liter; mi, mile; mm, millimeter; n, sample size; mS/cm, microsiemens per centimeter; >, greater than; <, less than; —, no data] Sample identification Variable SF99 SF00 SF01 UPH99 UPH00 MWD99 MWD00 MWD01 PRD99 PRD00 PRD01 Specific conductance (μS/cm, n = 6) 66 ± 4 71 ± 2 78 ± 11 253 282 899 ± 115 932 ± 215 856 ± 15 961 ± 115 966 ± 6.55 974 ± 335 Oxygen, dissolved (mg/L, n = 6) 8.5 ± 0.8 9.3 ± 0.6 8.9 ± 0.6 8.1 8.4 ± 0.4 8.1 ± 0.6 7.4 ± 0.5 6.6 ± 0.6 8.2 ± 0.3 8.2 ± 0.4 8.1 ± 0.4 Chloride, dissolved (mg/L, n = 4) 0.75 ± .44 0.62 ± 0.07 0.69 ± 0.20 5.6 ± 0.56 8.4 ± 1.36 77.2 ± 2.7 83.6 ± 2.2

— 105 ± 2.2 108 ± 3.4 112 ± 3.0

Nitrite + nitrate, dissolved 

(mg/L, n = 4)

<0.05 ± 0 <0.05 ± 0 E 0.04 ± 

0.01

0.092 ± 

0.0256

E0.054 ± 

0.0396

6.6 ± 0.92 6.0 ± 0.50

— 5.5 ± 0.35 5.3 ± 0.32 5.1 ± 

0.45

Orthophosphate, dissolved 

(mg/L, n = 4)

E 0.008 ± 

0.008

E 0.009 ± 

0.007

<0.02 ± 0 E 0.018 ± 

0.0116

<0.01 ± 06 0.79 ± 0.05 0.83 ± 0.06

— 0.93 ± 0.20 0.85 ± 0.10 0.78 ± 

0.03

Total organic carbon 

(mg/L, n = 4)

2.1 ± 1.6 1.5 ± 0.8

—

—

— 3.0 

± 0.5 2.4 

± 0.1

— 3.0 

± 0.5 6.7 

± 0.9 8.2 

± 1.2

1Reach gradient for UPH99 determined from bottom of thalweg instead of water surface.2Lower percentage of riparian canopy closure is a result of Arundo donax removal.3The streambed substrate size was characterized as: 1, concrete; 2, silt, mud, or detritus; 3, sand (>0.063−2 mm); 4, fine/medium gravel (>2−16 mm); 5, coarse gravel (>16−32 mm); 6, very coarse gravel 

(>32−64 mm); 7, small cobble (>64−128 mm); 8, large cobble (>128−256 mm); 9, small boulder (>256−512 mm); 10, large boulder, irregular bedrock, irregular hardpan, or irregular artificial surface (Fitzpatrick and others, 1998).

4The heterogeneity index is the geometric mean of the coefficient of variation of shape index, riparian canopy closure, stream velocity, and streambed substrate.5Values are from continuous monitoring, June to September. 6Values are from gaging station 11051500 located about 2.5 mi downstream.
Appendixes 27

Appendix 2. Benthic algae taxa collected from four sites in the Santa Ana River Basin, California, 1999−2001.—Continued[Under sample identification, a “0” represents taxa was not present in the sample and a “1” represents taxa was present in the sample]

Scientific name

Number of 

samples with 

an

occurrence

Sample identification

SF99 SF00 SF01 UPH99 MWD99 MWD00 MWD01 PRD99 PRD00 PRD01

Total taxa per sample 57 59 61 71 67 72 84 93 82 89

Chlorophyta (green algae)Closterium lunula (Möller) Nitzsch 2 0 0 0 0 1 0 1 0 0 0

Scenedesmus acuminatus (Lagerheim) Chodat 1 0 0 0 0 0 0 0 1 0 0

Scenedesmus acutus Meyen 2 0 0 0 1 0 0 0 1 0 0

Scenedesmus ecornis (Ralfs) Chodat 1 0 0 0 0 0 0 0 1 0 0

Scenedesmus quadricauda (Turpin) Brébisson 4 0 0 0 0 1 1 1 1 0 0

Scenedesmus spinosus Chodat 1 0 0 0 0 0 0 0 1 0 0

Spirogyra sp. 2 0 0 0 0 1 0 0 1 0 0

Stigeoclonium lubricum (Dillwyn) Kützing 1 0 0 0 0 1 0 0 0 0 0

Chrysophyta (diatoms)Achnanthes cf. grischuna CLASON Wüthrich 4 1 0 0 1 1 0 0 1 0 0

Achnanthes conspicua Mayer 1 0 0 0 1 0 0 0 0 0 0

Achnanthes sp. 1 ANS WRC 1 1 0 0 0 0 0 0 0 0 0

Achnanthidium exiguum (Grunow) Czarnecki 9 1 0 1 1 1 1 1 1 1 1

Achnanthidium exiguum var. heterovalvum (Krasske) 

Czarnecki

1 0 0 0 0 0 1 0 0 0 0

Achnanthidium minutissimum (Kützing) Czarnecki 6 0 1 1 0 0 1 1 0 1 1

Achnanthidium pyrenaicum (Hustedt) Kobayasi 1 0 0 1 0 0 0 0 0 0 0

Adlafia bryophila (Petersen) Lange-Bertalot 2 0 0 0 1 1 0 0 0 0 0

Adlafia minuscula (Grunow) Lange-Bertalot 2 1 0 0 1 0 0 0 0 0 0

Amphora copulata (Kützing) Schoeman and Archibald 4 0 1 1 0 0 1 0 0 1 0

Amphora holsatica Hustedt 1 0 0 0 0 0 1 0 0 0 0

Amphora montana Krasske 1 0 0 0 0 0 0 0 1 0 0

Amphora ovalis (Kützing) Kützing 3 0 1 1 0 0 1 0 0 0 0

Amphora pediculus (Kützing) Grunow 10 1 1 1 1 1 1 1 1 1 1

Amphora sp. 1 ANS WRC 2 0 0 0 0 0 1 1 0 0 0

Amphora veneta Kützing 6 0 0 0 0 1 1 1 1 1 1

Anabaena oscillarioides Bory 1 0 0 0 0 0 0 0 1 0 0

Asterionella formosa Hassal 2 0 0 0 0 0 0 0 1 0 1

Aulacoseira ambigua (Grunow) Simonsen 3 0 0 0 0 0 0 0 1 1 1

Aulacoseira granulata (Ehrenberg) Simonsen 3 0 0 0 0 0 0 0 1 1 1

Bacillaria paradoxa Gmelin 5 0 0 0 0 0 1 1 1 1 1

Appendix 2. Benthic algae taxa collected from four sites in the Santa Ana River Basin, California, 1999−2001.[Under sample identification, a “0” represents taxa was not present in the sample and a “1” represents taxa was present in the sample]
28 Variability in Lotic Communities, Three Contrasting Stream Environments, Santa Ana River Basin, Calif., 1999–2001 Appendix 2. Benthic algae taxa collected from four sites in the Santa Ana River Basin, California, 1999−2001.—Continued [Under sample identification, a “0” represents taxa was not present in the sample and a “1” represents taxa was present in the sample] Scientific name Number of samples with an occurrence Sample identification SF99 SF00 SF01 UPH99 MWD99 MWD00 MWD01 PRD99 PRD00 PRD01 Caloneis bacillum (Grunow) Cleve 5 1 0 1 1 1 0 0 0 0 1 Chamaepinnularia bremensis (Hustedt) Lange- Bertalot

1 0 0 0 1 0 0 0 0 0 0

Characium pringsheimii Braun 1 0 0 0 0 0 0 0 1 0 0

Chroococcus limneticus Lemmermann 1 0 0 0 0 0 1 0 0 0 0

Cladophora glomerata (Linnaeus) Kützing 3 0 0 0 1 1 0 0 1 0 0

Cocconeis fluviatilis Wallace 1 0 0 1 0 0 0 0 0 0 0

Cocconeis neodiminuta Krammer 5 1 1 1 0 0 1 0 0 0 1

Cocconeis pediculus Ehrenberg 4 1 0 0 1 0 1 1 0 0 0

Cocconeis placentula Ehrenberg 1 0 0 0 1 0 0 0 0 0 0

Cocconeis placentula var. euglypta (Ehrenberg) Cleve 6 1 1 1 1 1 0 0 1 0 0

Cocconeis placentula var. lineata (Ehrenberg) 

Van Heurck

10 1 1 1 1 1 1 1 1 1 1

Cocconeis placentula var. pseudolineata Geitler 2 1 0 1 0 0 0 0 0 0 0

Craticula accomoda (Hustedt) Mann 2 0 0 0 0 0 0 0 1 0 1

Craticula cuspidata (Kützing) Mann 1 0 0 0 0 0 0 0 0 0 1

Craticula halophila (Grunow) Mann 2 0 0 0 0 1 0 0 0 0 1

Craticula molestiformis (Hustedt) Lange-Bertalot 2 0 0 0 0 0 1 0 1 0 0

Cryptomonas erosa Ehrenberg 1 0 0 0 0 0 0 0 1 0 0

Cyclotella atomus Hustedt 3 0 0 0 0 0 0 0 1 1 1

Cyclotella meneghiniana Kützing 6 0 0 0 0 1 1 1 1 1 1

Cyclotella pseudostelligera Hustedt 2 0 0 0 0 1 0 0 1 0 0

Cyclotella stelligera (Cleve and Grunow) Van Heurck 1 0 0 0 0 0 0 0 1 0 0

Cymbella affinis Kützing 2 0 1 0 1 0 0 0 0 0 0

Cymbella delicatula Kützing 1 0 0 0 0 0 0 0 0 1 0

Cymbella gracilis (Ehrenberg) Kützing 1 0 0 0 0 0 0 0 0 0 1

Cymbella sp. 6 ANS WRC 2 0 0 0 0 1 0 0 1 0 0

Cymbella tumida (Brébisson ex Kützing) Van Heurck 1 0 0 0 0 0 0 0 0 1 0

Denticula kuetzingii Grunow 2 0 0 0 0 0 0 1 0 0 1

Diadesmis confervacea Kützing 5 0 0 1 0 0 1 1 0 1 1

Diadesmis contenta (Grunow ex Van Heurck) Mann 1 1 0 0 0 0 0 0 0 0 0

Diadesmis perpusilla (Grunow) Mann 1 1 0 0 0 0 0 0 0 0 0

Diatoma mesodon (Ehrenberg) Kützing 3 1 1 1 0 0 0 0 0 0 0

Diatoma vulgaris Bory 2 0 0 0 1 0 0 1 0 0 0

Diploneis pseudovalis Hustedt 2 0 0 0 0 0 0 1 0 0 1
Appendixes 29

Appendix 2. Benthic algae taxa collected from four sites in the Santa Ana River Basin, California, 1999−2001.—Continued[Under sample identification, a “0” represents taxa was not present in the sample and a “1” represents taxa was present in the sample]

Scientific name

Number of 

samples with 

an

occurrence

Sample identification

SF99 SF00 SF01 UPH99 MWD99 MWD00 MWD01 PRD99 PRD00 PRD01

Diploneis puella (Schumann) Cleve 1 0 0 0 0 0 0 0 1 0 0

Encyonema minutum (Hilse) Mann 7 0 1 1 1 0 1 1 0 1 1

Encyonema muelleri (Hustedt) Mann 1 0 0 0 1 0 0 0 0 0 0

Encyonema prostratum (Berkeley) Kützing 1 0 1 0 0 0 0 0 0 0 0

Encyonema silesiacum (Bleisch) Mann 5 1 1 1 1 1 0 0 0 0 0

Encyonopsis microcephala (Grunow) Krammer 1 0 0 0 0 1 0 0 0 0 0

Epithemia sorex Kützing 2 0 0 1 1 0 0 0 0 0 0

Epithemia turgida (Ehrenberg) Kützing 1 0 0 0 1 0 0 0 0 0 0

Fallacia pygmaea (Kützing) Stickle and Mann 3 0 0 0 0 0 1 0 0 1 1

Fallacia tenera (Hustedt) Mann 1 0 0 0 0 0 0 0 1 0 0

Fistulifera saprophila (Lange-Bertalot and Bonik) 

Lange-Bertalot

1 0 0 0 0 0 0 1 0 0 0

Fragilaria bidens Heiberg 1 0 1 0 0 0 0 0 0 0 0

Fragilaria capucina Desmazières 4 0 1 1 1 0 0 0 1 0 0

Fragilaria capucina var. rumpens (Kützing) LangeBertalot 1 0 0 1 0 0 0 0 0 0 0

Fragilaria cf. bicapitata Mayer 2 1 0 0 1 0 0 0 0 0 0

Fragilaria crotonensis Kitton 3 0 0 0 0 0 0 1 0 1 1

Fragilaria pinnata var. lancettula (Schumann) Hustedt 2 1 0 0 0 0 0 0 1 0 0

Fragilaria vaucheriae (Kützing) Petersen 7 1 1 1 1 0 0 1 1 0 1

Frustulia amphipleuroides (Grunow) Cleve-Euler 3 1 1 1 0 0 0 0 0 0 0

Frustulia vulgaris (Thwaites) DeToni. 1 0 1 0 0 0 0 0 0 0 0

Geissleria acceptata (Hustedt) Lange-Bertalot and 

Metzeltin

5 1 1 1 1 1 0 0 0 0 0

Geissleria decussis (Hustedt) Lange-Bertalot and 

Metzeltin

6 0 1 1 1 1 1 1 0 0 0

Geissleria paludosa (Hustedt) Lange-Bertalot and 

Metzeltin

2 0 1 1 0 0 0 0 0 0 0

Gomphoneis herculeana (Ehrenberg) Cleve 1 0 0 1 0 0 0 0 0 0 0

Gomphonema aff. subclavatum ANS NAWQA EAM 2 0 1 0 0 0 1 0 0 0 0

Gomphonema affine Kützing 1 0 1 0 0 0 0 0 0 0 0

Gomphonema clevei Fricke 1 0 1 0 0 0 0 0 0 0 0

Gomphonema kobayasii Kociolek and Kingston 3 0 1 1 1 0 0 0 0 0 0

Gomphonema micropus Kützing 1 0 0 0 0 0 0 0 0 0 1

Gomphonema minutum (C.A. Agardh) C.A. Agardh 7 1 1 1 1 0 0 1 0 1 1
30 Variability in Lotic Communities, Three Contrasting Stream Environments, Santa Ana River Basin, Calif., 1999–2001 Appendix 2. Benthic algae taxa collected from four sites in the Santa Ana River Basin, California, 1999−2001.—Continued [Under sample identification, a “0” represents taxa was not present in the sample and a “1” represents taxa was present in the sample] Scientific name Number of samples with an occurrence Sample identification SF99 SF00 SF01 UPH99 MWD99 MWD00 MWD01 PRD99 PRD00 PRD01 Gomphonema olivaceum (Lyngbya) Kützing 1 0 0 0 1 0 0 0 0 0 0 Gomphonema parvulum (Kützing) Kützing 9 0 1 1 1 1 1 1 1 1 1 Gomphonema pumilum (Grunow) Reichett and Lange- Bert.

2 1 0 0 0 0 0 0 1 0 0

Gomphonema rhombicum Fricke 3 1 0 1 1 0 0 0 0 0 0

Gomphonema subclavatum (Grunow) Grunow 1 0 0 0 1 0 0 0 0 0 0

Gomphonema truncatum Ehrenberg 1 0 1 0 0 0 0 0 0 0 0

Gyrosigma attenuatum (Kützing) Rabenhorst 1 0 0 0 0 0 0 0 0 1 0

Gyrosigma nodiferum (Grunow) Reimer 2 0 0 0 0 0 0 0 0 1 1

Gyrosigma parkerii (Harrison) Elmore 1 0 0 0 0 0 0 0 0 1 0

Gyrosigma scalproides (Rabenhorst) Cleve 3 0 0 0 0 0 0 1 1 0 1

Gyrosigma spencerii (Quekett) Griff. and Henfr. 1 0 0 0 0 0 0 0 1 0 0

Hannaea arcus (Ehrenberg) Patrick 1 0 0 0 0 0 0 1 0 0 0

Hantzschia amphioxys (Ehrenberg) Grunow 1 0 0 1 0 0 0 0 0 0 0

Hippodonta capitata (Ehrenberg) Lange-Bertalot, 

Metzeltin and Witkowski

5 0 0 0 0 0 1 1 1 1 1

Karayevia clevei (Grunow) Kingston 1 0 0 0 1 0 0 0 0 0 0

Karayevia clevei var. rostrata (Hustedt) Kingston 1 0 0 0 1 0 0 0 0 0 0

Lemnicola hungarica (Grunow) Round and Basson 5 0 1 0 0 0 0 1 1 1 1

Luticola goeppertiana (Bleisch) Mann 6 0 0 0 0 1 1 1 1 1 1

Mayamaea atomus (Kützing) Lange-Bertalot 9 1 1 0 1 1 1 1 1 1 1

Melosira varians Agardh. 7 0 0 1 1 0 1 1 1 1 1

Meridion circulare var. constrictum (Ralfs) Van Heurck 1 0 0 1 0 0 0 0 0 0 0

Navicula antonii Lange Bertalot 4 0 0 1 1 1 0 0 0 1 0

Navicula biconica Patrick 7 0 1 1 1 1 1 1 0 0 1

Navicula canalis Patrick 1 0 0 0 0 0 0 0 0 1 0

Navicula capitatoradiata Germain 3 0 0 0 1 0 0 1 0 1 0

Navicula caterva Hohn and Hellerm. 2 0 0 0 0 1 1 0 0 0 0

Navicula cryptocephala Kützing 5 0 1 1 0 1 0 1 0 1 0

Navicula cryptotenella Lange-Bertalot in Kramm. and 

Lange-Bertalot

8 1 1 1 1 1 0 0 1 1 1

Navicula erifuga Lange-Bertalot 6 0 0 0 0 1 1 1 1 1 1

Navicula germainii Wallace 5 0 0 0 0 1 1 1 1 0 1

Navicula gregaria Donkin 10 1 1 1 1 1 1 1 1 1 1

Navicula incertata Hustedt 2 0 0 0 0 1 1 0 0 0 0

Navicula ingenua Hustedt 1 0 0 0 0 0 0 0 1 0 0
Appendixes 31

Appendix 2. Benthic algae taxa collected from four sites in the Santa Ana River Basin, California, 1999−2001.—Continued[Under sample identification, a “0” represents taxa was not present in the sample and a “1” represents taxa was present in the sample]

Scientific name

Number of 

samples with 

an

occurrence

Sample identification

SF99 SF00 SF01 UPH99 MWD99 MWD00 MWD01 PRD99 PRD00 PRD01

Navicula lanceolata (Agardh) Ehrenberg 4 0 0 1 1 0 0 1 0 1 0

Navicula longicephala Hustedt 1 0 0 0 0 0 0 0 0 0 1

Navicula menisculus Schumann 1 1 0 0 0 0 0 0 0 0 0

Navicula minima Grunow 10 1 1 1 1 1 1 1 1 1 1

Navicula perminuta Grunow 3 0 0 1 0 0 0 1 0 0 1

Navicula recens Lange-Bertalot 4 0 0 0 0 0 1 1 0 1 1

Navicula reichardtiana Lange-Bertalot 2 0 0 0 0 0 0 0 0 1 1

Navicula rhynchocephala Kützing 2 0 0 0 0 1 0 0 0 0 1

Navicula rostellata Kützing 5 0 0 0 0 1 1 1 0 1 1

Navicula sanctaecrucis Østrup 2 0 0 0 0 0 1 1 0 0 0

Navicula schroeteri var. escambia Patrick 3 0 0 0 0 0 0 1 0 1 1

Navicula sp. 1 ANS NAWQA EAM 2 0 1 0 0 0 0 0 0 1 0

Navicula subminuscula Manguin 6 0 0 0 0 1 1 1 1 1 1

Navicula submuralis Hustedt 1 0 0 0 0 0 1 0 0 0 0

Navicula symmetrica Patrick 5 0 0 0 0 1 0 1 1 1 1

Navicula tantula Hustedt 1 0 0 0 1 0 0 0 0 0 0

Navicula tenelloides Hustedt 5 0 1 0 0 0 0 1 1 1 1

Navicula tripunctata (O. F. Müll.) Bory 6 1 1 1 1 0 0 1 0 1 0

Navicula trivialis Lange-Bertalot 1 0 0 0 0 0 0 0 0 0 1

Navicula veneta Kützing 9 1 0 1 1 1 1 1 1 1 1

Navicula wildii Lange-Bertalot 1 0 0 0 0 0 0 1 0 0 0

Neidium binodis (Ehrenberg) Hust. 1 0 0 0 1 0 0 0 0 0 0

Neidium dubium (Ehrenberg) Cleve 1 0 1 0 0 0 0 0 0 0 0

Nitzschia acicularioides Hustedt 1 0 0 0 0 0 0 0 1 0 0

Nitzschia acicularis (Kützing) Smith 1 0 0 0 0 0 0 0 0 1 0

Nitzschia aequorea Hustedt 1 0 0 0 0 0 1 0 0 0 0

Nitzschia agnita Hustedt 1 0 0 0 0 0 0 0 1 0 0

Nitzschia amphibia Grunow 8 0 0 1 1 1 1 1 1 1 1

Nitzschia amphibioides Hustedt 1 0 0 0 0 0 0 1 0 0 0

Nitzschia angustiforaminata Lange-Bertalot 1 0 0 0 0 0 1 0 0 0 0

Nitzschia archibaldii Lange-Bertalot 4 0 0 0 0 0 1 1 0 1 1

Nitzschia bacillum Hustedt 1 0 0 0 0 0 0 0 1 0 0

Nitzschia capitellata Hustedt 5 0 0 0 0 1 1 0 1 1 1

Nitzschia cf. bacillum LAIRD Hustedt 3 1 0 0 1 1 0 0 0 0 0

Nitzschia clausii Hantzsch 1 0 0 0 0 0 0 0 0 0 1

Nitzschia communis Rabenhorst 2 0 0 0 0 0 0 0 1 0 1
32 Variability in Lotic Communities, Three Contrasting Stream Environments, Santa Ana River Basin, Calif., 1999–2001 Appendix 2. Benthic algae taxa collected from four sites in the Santa Ana River Basin, California, 1999−2001.—Continued [Under sample identification, a “0” represents taxa was not present in the sample and a “1” represents taxa was present in the sample] Scientific name Number of samples with an occurrence Sample identification SF99 SF00 SF01 UPH99 MWD99 MWD00 MWD01 PRD99 PRD00 PRD01 Nitzschia compressa var. vexans (Grunow) Lange- Bertalot

1 0 0 0 0 1 0 0 0 0 0

Nitzschia desertorum Hustedt 6 0 0 0 0 1 1 1 1 1 1

Nitzschia diserta Hustedt 1 0 0 0 0 0 0 0 1 0 0

Nitzschia dissipata (Kützing) Grunow 9 1 1 1 1 0 1 1 1 1 1

Nitzschia dissipata var. media (Hantzsch) Grunow 1 0 0 0 1 0 0 0 0 0 0

Nitzschia elegantula Grunow 2 0 0 0 0 1 0 0 1 0 0

Nitzschia filiformis (W. Smith) Van Heurck 2 0 0 0 0 0 0 1 0 1 0

Nitzschia flexoides Geitler 1 0 0 0 0 0 0 0 0 0 1

Nitzschia fonticola Grunow 8 0 0 1 1 1 1 1 1 1 1

Nitzschia fonticola var. pelagica Hustedt 1 0 0 0 0 0 0 0 1 0 0

Nitzschia frustulum (Kützing) Grunow 4 0 0 1 0 0 0 1 1 0 1

Nitzschia fruticosa Hustedt 2 0 0 0 0 1 0 0 1 0 0

Nitzschia gracilis Hantzsch ex Rabenhorst 1 0 0 0 0 0 0 0 1 0 0

Nitzschia hantzschiana Rabenhorst 1 0 0 0 0 0 0 0 0 0 1

Nitzschia inconspicua Grunow 10 1 1 1 1 1 1 1 1 1 1

Nitzschia intermedia Hantzsch ex Cl.eve et Grunow 2 0 0 0 0 0 0 0 1 0 1

Nitzschia lacuum Lange-Bertalot 1 0 0 0 0 1 0 0 0 0 0

Nitzschia levidensis var. salinarum Grunow 1 0 0 0 0 0 0 0 0 1 0

Nitzschia liebethruthii Rabenhorst 1 0 0 0 0 0 0 0 1 0 0

Nitzschia linearis (Agardh ex W. Smith) W. Smith 2 1 0 1 0 0 0 0 0 0 0

Nitzschia microcephala Grunow 3 0 0 0 1 1 0 0 1 0 0

Nitzschia palea (Kützing) Smith 7 0 1 0 0 1 1 1 1 1 1

Nitzschia paleacea Grunow in Van Heurck 1 0 0 0 0 0 0 0 1 0 0

Nitzschia perminuta (Grunow) Peragallo 3 0 0 0 0 0 1 1 0 1 0

Nitzschia pusilla Grunow 4 0 1 0 0 0 0 1 0 1 1

Nitzschia recta Hantzsch ex Rabenhorst 3 1 1 0 0 0 0 0 0 0 1

Nitzschia sigma (Kützing) W. Smith 4 0 0 0 0 0 1 1 0 1 1

Nitzschia sigmoidea (Nitzschia) W. Smith 3 0 1 1 0 0 0 1 0 0 0

Nitzschia sinuata var. delognei (Grunow) LangeBertalot

1 0 0 0 1 0 0 0 0 0 0

Nitzschia sociabilis Hustedt 5 0 0 0 0 0 1 1 1 1 1

Nitzschia solita Hustedt 3 0 0 0 0 1 0 1 1 0 0

Nitzschia supralitorea Lange-Bertalot 4 0 0 0 1 1 1 0 1 0 0

Nitzschia thermalis Kützing 1 0 0 0 0 0 0 0 1 0 0

Nitzschia tubicola Grunow in Cleve et Grunow 3 1 0 0 0 1 0 0 1 0 0
Appendixes 33

Appendix 2. Benthic algae taxa collected from four sites in the Santa Ana River Basin, California, 1999−2001.—Continued[Under sample identification, a “0” represents taxa was not present in the sample and a “1” represents taxa was present in the sample]

Scientific name

Number of 

samples with 

an

occurrence

Sample identification

SF99 SF00 SF01 UPH99 MWD99 MWD00 MWD01 PRD99 PRD00 PRD01

Nitzschia umbonata Lange-Bertalot 1 0 0 0 0 0 0 1 0 0 0

Nupela lapidosa (Krasske) Lange-Bertalot 1 0 0 0 0 0 0 1 0 0 0

Oedogonium sp. 1 0 0 0 1 0 0 0 0 0 0

Opephora olsenii M Moller 2 0 1 1 0 0 0 0 0 0 0

Oscillatoria limnetica Lemmermann 1 0 0 0 0 0 1 0 0 0 0

Parlibellus protracta (Grunow) Witkowski, LangeBertalot et Metzeltin 3 1 1 0 0 0 0 0 0 0 1

Pediastrum simplex (Meyen) Lemmermann 1 0 0 0 0 0 0 0 1 0 0

Phormidium formosum 1 0 0 0 0 0 0 0 1 0 0

Phormidium granulatum 1 0 0 0 1 0 0 0 0 0 0

Pinnularia divergentissima (Grunow) Cl. 1 0 0 0 0 0 0 0 0 1 0

Pinnularia subcapitata Greg. 1 0 0 0 1 0 0 0 0 0 0

Placoneis elginensis (Greg.) Cox 2 0 0 0 0 0 1 0 0 0 1

Placoneis pseudoanglica (Lange-Bertalot) Cox 1 0 0 0 0 0 0 0 0 1 0

Planothidium daui (Foged) Lange-Bertalot 2 1 0 1 0 0 0 0 0 0 0

Planothidium delicatulum (Kützing) Round et 

Bukhtiyarova

2 0 0 0 0 1 0 1 0 0 0

Planothidium frequentissimum (Lange-Bertalot) LangeBertalot 6 0 1 1 0 0 1 1 0 1 1

Planothidium granum (Hohn and Hellermann) LangeBertalot 1 0 1 0 0 0 0 0 0 0 0

Planothidium hauckianum (Grunow) Round and 

Bukhtiyarova

1 0 0 0 0 0 1 0 0 0 0

Planothidium lanceolatum (Brébisson ex Kützing) 

Lange-Bertalot

6 1 1 1 1 1 0 0 1 0 0

Planothidium rostratum (Østrup) Lange-Bertalot 2 1 1 0 0 0 0 0 0 0 0

Pleurosigma salinarum Grunow 1 0 0 0 0 0 0 0 0 1 0

Pleurosira laevis (Ehrenberg) Compere 4 0 0 0 0 0 1 1 0 1 1

Protoderma viride Kützing 1 0 0 0 0 1 0 0 0 0 0

Psammothidium bioretii (Germ.) Bukht. and Round 3 1 1 1 0 0 0 0 0 0 0

Psammothidium chlidanos (Hohn and Hellerman) 

Lange-Bertalot

1 0 0 1 0 0 0 0 0 0 0

Psammothidium helveticum (Hustedt) Bukhtiyarova and 

Round

1 1 0 0 0 0 0 0 0 0 0

Psammothidium rossii (Hustedt) Bukhtiyarova and 

Round

1 1 0 0 0 0 0 0 0 0 0
34 Variability in Lotic Communities, Three Contrasting Stream Environments, Santa Ana River Basin, Calif., 1999–2001 Appendix 2. Benthic algae taxa collected from four sites in the Santa Ana River Basin, California, 1999−2001.—Continued [Under sample identification, a “0” represents taxa was not present in the sample and a “1” represents taxa was present in the sample] Scientific name Number of samples with an occurrence Sample identification SF99 SF00 SF01 UPH99 MWD99 MWD00 MWD01 PRD99 PRD00 PRD01 Psammothidium subatomoides (Hustedt) Bukhtiyarova and Round

1 1 0 0 0 0 0 0 0 0 0

Pseudostaurosira brevistriata (Grunow in V.H.) 

Williams and Round

2 0 1 0 0 0 0 0 1 0 0

Reimeria sinuata (Greg.) Kociolek and Stoermer 8 1 1 1 1 1 0 1 0 1 1

Rhoicosphenia abbreviata (Agardh) Lange-Bertalot 9 1 1 1 1 0 1 1 1 1 1

Rhopalodia gibba (Ehr.) O. Müll. 1 0 0 0 1 0 0 0 0 0 0

Rossithidium pusillum (Grunow) Round and 

Bukhtiyarova

2 1 0 0 0 0 0 0 0 1 0

Sellaphora bacillum (Ehr.) Mann 1 0 0 0 1 0 0 0 0 0 0

Sellaphora pupula (Kütz.) Meresckowsky 7 0 0 1 0 1 1 1 1 1 1

Sellaphora seminulum (Grunow) Mann 10 1 1 1 1 1 1 1 1 1 1

Simonsenia delognei (Grunow) Lange-Bert. 1 0 0 0 0 1 0 0 0 0 0

Skeletonema potamos (Weber) Hasle 1 0 0 0 0 0 0 0 1 0 0

Staurosira construens (Ehrenberg) Williams and Round 2 0 0 0 0 0 1 1 0 0 0

Staurosira construens var. pumila (Grunow) Kingston 3 1 0 0 0 1 0 0 1 0 0

Staurosira construens var. subsalina (Hust.) Andresen 

and others

1 0 0 0 0 0 1 0 0 0 0

Staurosira construens var. venter (Ehr.) Hamilton 6 1 1 0 1 0 1 1 0 0 1

Staurosira elliptica (Schumann) Williams and Round 2 0 1 0 0 0 1 0 0 0 0

Staurosirella leptostauron (Ehrenberg) Williams and 

Round

1 0 0 1 0 0 0 0 0 0 0

Staurosirella pinnata (Ehrenberg) Williams and Round 4 1 1 0 1 0 0 0 1 0 0

Stephanodiscus hantzschii Grunow 2 0 0 0 0 0 0 0 1 1 0

Stephanodiscus medius Håkansson 1 0 0 0 0 1 0 0 0 0 0

Surirella angusta Kützing 4 0 0 0 0 0 1 1 0 1 1

Surirella brebissonii Kramm. and Lange-Bert. 3 0 0 0 0 0 0 1 0 1 1

Surirella minuta Bréb. 1 0 0 0 0 1 0 0 0 0 0

Surirella robusta Ehrenberg 4 0 0 0 0 0 0 1 1 1 1

Surirella tenera Greg. 1 0 0 0 0 0 0 0 1 0 0

Synedra parasitica (W. Sm.) Hust. 6 0 1 1 0 0 0 1 1 1 1

Synedra ulna (Nitz.) Ehr. 4 0 0 0 0 0 1 1 0 1 1

Synedra ulna var. contracta Østr. 2 0 0 0 1 0 0 0 1 0 0

Tabularia fasciculata (Ag.) Williams and Round 1 0 0 0 0 0 0 0 0 1 0

Tabularia tabulata (C. A. Ag.) Snoeijs 5 1 0 0 0 1 0 1 1 0 1

Terpsinoe musica Ehrenberg 1 0 0 0 0 0 0 1 0 0 0
Appendixes 35

Appendix 2. Benthic algae taxa collected from four sites in the Santa Ana River Basin, California, 1999−2001.—Continued[Under sample identification, a “0” represents taxa was not present in the sample and a “1” represents taxa was present in the sample]

Scientific name

Number of 

samples with 

an

occurrence

Sample identification

SF99 SF00 SF01 UPH99 MWD99 MWD00 MWD01 PRD99 PRD00 PRD01

Thalassiosira sp. 1 NAWQA DW SANA 1 0 0 0 0 0 0 0 0 0 1

Thalassiosira weissflogii (Grunow) Fryxell and Hasle 2 0 0 0 0 0 1 0 0 0 1

Tryblionella apiculata Greg. 6 0 0 0 0 1 1 1 1 1 1

Tryblionella calida (Grunow) Mann 3 0 0 0 0 0 1 1 0 1 0

Tryblionella compressa (Bailey) Poulin 1 0 0 0 0 0 0 0 0 1 0

Tryblionella levidensis W. Smith 2 0 0 0 0 0 1 0 0 0 1

Cyanophyta (blue-green algae)Blennothrix brebissonii (Kützing ex Gomont) 

Anagnostidis & Komárek

1 1 0 0 0 0 0 0 0 0 0

Homoeothrix janthina (Bornet et Flahault) Starmach 2 1 0 0 1 0 0 0 0 0 0

Lyngbya sp. 2 0 0 0 0 1 0 1 0 0 0

Nostoc commune Vaucher 1 0 0 0 1 0 0 0 0 0 0

Oscillatoria sp. 1 0 0 0 0 0 0 1 0 0 0

Unknown Cyanophyte Oscillatoriales (no sheath) 4 1 0 0 1 1 0 0 1 0 0

Unknown Cyanophyte Oscillatoriales (sheath) 5 1 0 0 0 1 1 0 1 1 0

EuglenophytaEuglena sp. 2 0 0 0 1 0 0 0 1 0 0

Trachelomonas hispida (Perty) Stein 1 0 0 0 0 1 0 0 0 0 0

Rhodophyta (red algae)Unknown Rhodophyte Florideophycidae (chantransia) 3 1 0 0 0 1 0 0 1 0 0
36 Variability in Lotic Communities, Three Contrasting Stream Environments, Santa Ana River Basin, Calif., 1999–2001 Appendix 3. Benthic algae taxa and their densities from richest-targeted habitat samples collected from four sites in the Santa Ana River Basin, California, 1999−2001.— Continued [Values are number of individuals per square centimeter] Scientific name Number of samples with an occurrence Sample identification SF99 SF00 SF01 UPH99 MWD99 MWD00 MWD01 PRD99 PRD00 PRD01 Total taxa per sample 31 26 34 38 33 26 32 45 42 39 Chlorophyta (green algae) Scenedesmus acutus Meyen 1 0 0 0 0 0 0 0 15,831 0 0 Scenedesmus quadricauda (Turpin) Brébisson 3 0 0 0 0 45,791 572,669 2,125 0 0 0 Stigeoclonium lubricum (Dillwyn) Kützing 1 0 0 0 0 177,439 0 0 0 0 0 Chrysophyta (diatoms) Achnanthes cf. grischuna CLASON Wüthrich 3 410 0 0 27,593 0 0 0 3,449 0 0 Achnanthidium exiguum (Grunow) Czarnecki 3 0 0 0 0 4,295 195,344 0 0 0 1,402 Achnanthidium minutissimum (Kützing) Czarnecki 4 0 1,162 10,745 0 0 195,344 1,284 0 0 0 Achnanthidium pyrenaicum (Hustedt) Kobayasi 1 0 0 546 0 0 0 0 0 0 0 Amphora pediculus (Kützing) Grunow 5 20 0 0 172,455 4,295 146,508 0 8,623 0 0 Amphora veneta Kützing 4 0 0 0 0 4,295 97,672 2,353 5,174 0 0 Aulacoseira ambigua (Grunow) Simonsen 1 0 0 0 0 0 0 0 0 25,470 0 Aulacoseira granulata (Ehrenberg) Simonsen 1 0 0 0 0 0 0 0 0 6,367 0 Bacillaria paradoxa Gmelin 1 0 0 0 0 0 0 0 1,725 0 0 Caloneis bacillum (Grunow) Cleve 2 39 0 0 13,796 0 0 0 0 0 0 Cocconeis neodiminuta Krammer 2 10 0 0 0 0 0 0 0 0 1,402 Cocconeis pediculus Ehrenberg 2 20 0 0 193,149 0 0 0 0 0 0 Cocconeis placentula Ehrenberg 1 0 0 0 55,185 0 0 0 0 0 0 Cocconeis placentula var. euglypta (Ehrenberg) Cleve 5 322 1,245 5,464 186,251 8,590 0 0 0 0 0 Cocconeis placentula var. lineata (Ehrenberg) Van Heurck 10 2,740 13,534 9,470 482,873 12,884 97,672 856 1,725 38,205 2,804 Cocconeis placentula var. pseudolineata Geitler 2 10 0 17,666 0 0 0 0 0 0 0 Cyclotella meneghiniana Kützing 3 0 0 0 0 0 0 0 77,606 25,470 2,804 Cyclotella pseudostelligera Hustedt 1 0 0 0 0 0 0 0 12,072 0 0 Cyclotella stelligera (Cleve and Grunow) Van Heurck 1 0 0 0 0 0 0 0 3,449 0 0 Cymbella affinis Kützing 1 0 0 0 462,178 0 0 0 0 0 0 Cymbella delicatula Kützing 1 0 0 0 0 0 0 0 0 216,492 0

Cymbella gracilis (Ehrenberg) Kützing 1 0 0 0 0 0 0 0 0 0 21,030

Cymbella sp. 6 ANS WRC 1 0 0 0 0 0 0 0 94,852 0 0

Appendix 3. Benthic algae taxa and their densities from richest-targeted habitat samples collected from four sites in the Santa Ana River Basin, California, 1999−2001.[Values are number of individuals per square centimeter]
Appendixes 37

Appendix 3. Benthic algae taxa and their densities from richest-targeted habitat samples collected from four sites in the Santa Ana River Basin, California, 1999−2001.—Continued[Values are number of individuals per square centimeter]

Scientific name

Number of 

samples 

with an

occurrence

Sample identification

SF99 SF00 SF01 UPH99 MWD99 MWD00 MWD01 PRD99 PRD00 PRD01

Cymbella tumida (Brébisson ex Kützing) Van Heurck 1 0 0 0 0 0 0 0 0 6,367 0

Denticula kuetzingii Grunow 1 0 0 0 0 0 0 1,070 0 0 0

Diadesmis confervacea Kützing 2 0 0 364 0 0 0 7,915 0 0 0

Diatoma mesodon (Ehrenberg) Kützing 2 0 249 2,914 0 0 0 0 0 0 0

Diploneis pseudovalis Hustedt 1 0 0 0 0 0 0 0 0 0 1,402

Encyonema minutum (Hilse) Mann 3 0 0 1,457 13,796 0 0 0 0 6,367 0

Encyonema muelleri (Hustedt) Mann 1 0 0 0 6,898 0 0 0 0 0 0

Encyonema silesiacum (Bleisch) Mann 2 10 0 0 89,676 0 0 0 0 0 0

Epithemia sorex Kützing 1 0 0 0 255,233 0 0 0 0 0 0

Epithemia turgida (Ehrenberg) Kützing 1 0 0 0 96,575 0 0 0 0 0 0

Fallacia pygmaea (Kützing) Stickle and Mann 1 0 0 0 0 0 0 0 0 0 1,402

Fistulifera saprophila (Lange-Bertalot and Bonik) 

Lange-Bertalot

1 0 0 0 0 0 0 12,407 0 0 0

Fragilaria capucina Desmazières 1 0 83 0 0 0 0 0 0 0 0

Fragilaria cf. bicapitata Mayer 1 0 0 0 13,796 0 0 0 0 0 0

Fragilaria crotonensis Kitton 1 0 0 0 0 0 0 0 0 0 4,907

Fragilaria pinnata var. lancettula (Schumann) 

Hustedt

1 10 0 0 0 0 0 0 0 0 0

Fragilaria vaucheriae (Kützing) Petersen 3 0 83 1,275 0 0 0 0 3,449 0 0

Frustulia amphipleuroides (Grunow) Cleve-Euler 1 0 0 728 0 0 0 0 0 0 0

Geissleria acceptata (Hustedt) Lange-Bertalot and 

Metzeltin

3 29 415 4,371 0 0 0 0 0 0 0

Geissleria paludosa (Hustedt) Lange-Bertalot and 

Metzeltin

2 0 83 182 0 0 0 0 0 0 0

Gomphonema clevei Fricke 1 0 3,072 0 0 0 0 0 0 0 0

Gomphonema kobayasii Kociolek and Kingston 3 0 415 911 200,047 0 0 0 0 0 0

Gomphonema minutum (C.A. Agardh) C.A. Agardh 5 49 249 1,821 55,185 0 0 0 0 12,735 0

Gomphonema parvulum (Kützing) Kützing 8 0 0 728 13,796 12,884 634,867 1,925 24,144 89,144 9,814

Gomphonema pumilum (Grunow) Reichett and 

Lange-Bertalot

2 176 0 0 0 0 0 0 8,623 0 0

Gomphonema rhombicum Fricke 3 351 0 2,914 393,196 0 0 0 0 0 0

Gomphonema subclavatum (Grunow) Grunow 1 0 0 0 6,898 0 0 0 0 0 0

Gomphonema truncatum Ehrenberg 1 0 83 0 0 0 0 0 0 0 0
38 Variability in Lotic Communities, Three Contrasting Stream Environments, Santa Ana River Basin, Calif., 1999–2001 Appendix 3. Benthic algae taxa and their densities from richest-targeted habitat samples collected from four sites in the Santa Ana River Basin, California, 1999−2001.— Continued [Values are number of individuals per square centimeter] Scientific name Number of samples with an occurrence Sample identification SF99 SF00 SF01 UPH99 MWD99 MWD00 MWD01 PRD99 PRD00 PRD01 Gyrosigma attenuatum (Kützing) Rabenhorst 1 0 0 0 0 0 0 0 0 19,102 0 Gyrosigma nodiferum (Grunow) Reimer 2 0 0 0 0 0 0 0 0 70,042 2,804 Gyrosigma scalproides (Rabenhorst) Cleve 1 0 0 0 0 0 0 0 0 0 21,030 Hippodonta capitata (Ehrenberg) Lange-Bertalot, Metzeltin and Witkowski

1 0 0 0 0 0 0 0 12,072 0 0

Karayevia clevei var. rostrata (Hustedt) Kingston 1 0 0 0 6,898 0 0 0 0 0 0

Lemnicola hungarica (Grunow) Round and Basson 1 0 0 0 0 0 0 428 0 0 0

Luticola goeppertiana (Bleisch) Mann 4 0 0 0 0 2,147 0 10,696 0 12,735 7,010

Mayamaea atomus (Kützing) Lange-Bertalot 5 0 0 0 0 143,876 976,719 1,711 1,725 6,367 0

Melosira varians Agardh 5 0 0 728 6,898 0 0 1,711 0 6,367 6,309

Navicula biconica Patrick 3 0 0 0 0 122,402 48,836 1,284 0 0 0

Navicula canalis Patrick 1 0 0 0 0 0 0 0 0 25,470 0

Navicula capitatoradiata Germain 1 0 0 0 0 0 0 0 0 6,367 0

Navicula caterva Hohn and Hellerm. 1 0 0 0 0 4,295 0 0 0 0 0

Navicula cryptotenella Lange-Bertalot. in Kramm. 

and Lange-Bertalot.

7 1,102 996 10,199 13,796 0 0 0 24,144 63,674 65,192

Navicula erifuga Lange-Bertalot 4 0 0 0 0 68,717 0 0 346,641 82,777 10,515

Navicula germainii Wallace 1 0 0 0 0 0 0 0 5,174 0 0

Navicula gregaria Donkin 6 0 83 728 0 8,590 0 0 24,144 38,205 701

Navicula lanceolata (Agardh) Ehrenberg 2 0 0 0 13,796 0 0 1,284 0 0 0

Navicula minima Grunow 5 185 0 1,639 0 17,179 439,524 0 0 0 1,402

Navicula perminuta Grunow 2 0 0 728 0 0 0 0 0 0 1,402

Navicula recens Lange-Bertalot 3 0 0 0 0 0 97,672 0 0 464,822 107,952

Navicula reichardtiana Lange-Bertalot 1 0 0 0 0 0 0 0 0 0 1,402

Navicula rostellata Kützing 2 0 0 0 0 0 0 0 0 25,470 1,402

Navicula schroeteri var. escambia Patrick 2 0 0 0 0 0 0 428 0 0 4,206

Navicula sp.1 ANS NAWQA DW 1 0 249 0 0 0 0 0 0 0 0

Navicula subminuscula Manguin 6 0 0 0 0 287,751 3,418,517 12,621 46,564 63,674 4,907

Navicula symmetrica Patrick 4 0 0 0 0 38,653 0 0 27,593 25,470 6,309

Navicula tenelloides Hustedt 2 0 83 0 0 0 0 0 10,347 0 0

Navicula tripunctata (O. F. Müll.) Bory 5 488 166 728 1,069,219 0 0 0 0 12,735 0

Navicula veneta Kützing 6 0 0 0 0 152,465 390,688 3,423 20,695 6,367 1,402
Appendixes 39

Appendix 3. Benthic algae taxa and their densities from richest-targeted habitat samples collected from four sites in the Santa Ana River Basin, California, 1999−2001.—Continued[Values are number of individuals per square centimeter]

Scientific name

Number of 

samples 

with an

occurrence

Sample identification

SF99 SF00 SF01 UPH99 MWD99 MWD00 MWD01 PRD99 PRD00 PRD01

Nitzschia acicularioides Hustedt 1 0 0 0 0 0 0 0 5,174 0 0

Nitzschia acicularis (Kützing) Smith 1 0 0 0 0 0 0 0 0 6,367 0

Nitzschia agnita Hustedt 1 0 0 0 0 0 0 0 3,449 0 0

Nitzschia amphibia Grunow 6 0 0 0 0 12,884 2,148,782 35,297 17,246 101,879 10,515

Nitzschia amphibioides Hustedt 1 0 0 0 0 0 0 856 0 0 0

Nitzschia archibaldii Lange-Bertalot 4 0 0 0 0 0 244,180 2,567 0 6,367 1,402

Nitzschia bacillum Hustedt 1 0 0 0 0 0 0 0 3,449 0 0

Nitzschia capitellata Hustedt 1 0 0 0 0 0 0 0 5,174 0 0

Nitzschia cf. bacillum LAIRD Hustedt 1 0 0 0 0 38,653 0 0 0 0 0

Nitzschia communis Rabenhorst 1 0 0 0 0 0 0 0 3,449 0 0

Nitzschia desertorum Hustedt 3 0 0 0 0 0 0 428 0 38,205 4,206

Nitzschia dissipata (Kützing) Grunow 6 0 83 11,838 0 0 146,508 0 13,797 89,144 12,618Nitzschia elegantula Grunow 1 0 0 0 0 2,147 0 0 0 0 0

Nitzschia fonticola Grunow 5 0 0 0 41,389 8,590 293,016 0 6,898 0 7,010

Nitzschia frustulum (Kützing) Grunow 4 0 0 728 0 0 0 428 20,695 0 1,402

Nitzschia inconspicua Grunow 9 10 0 1,275 6,898 85,896 2,539,469 5,562 46,564 19,102 56,780

Nitzschia linearis (Agardh ex W. Smith) W. Smith 2 20 0 5,646 0 0 0 0 0 0 0

Nitzschia palea (Kützing) Smith 6 0 0 0 0 304,930 1,611,586 10,910 141,416 216,492 14,020

Nitzschia perminuta (Grunow) Peragallo 2 0 0 0 0 0 195,344 2,567 0 0 0

Nitzschia pusilla Grunow 1 0 0 0 0 0 0 0 0 0 1,402

Nitzschia recta Hantzsch ex Rabenhorst 1 0 0 0 0 0 0 0 0 0 2,804

Nitzschia sigmoidea (Nitzschia) W. Smith 1 0 0 364 0 0 0 0 0 0 0

Nitzschia sinuata var. delognei (Grunow) 

Lange-Bertalot

1 0 0 0 48,287 0 0 0 0 0 0

Nitzschia sociabilis Hustedt 3 0 0 0 0 0 146,508 0 25,869 6,367 0

Nitzschia supralitorea Lange-Bertalot 1 0 0 0 0 141,728 0 0 0 0 0

Nitzschia tubicola Grunow in Cleve and Grunow 1 0 0 0 0 0 0 0 3,449 0 0

Opephora olsenii M Moller 2 0 415 4,735 0 0 0 0 0 0 0

Pinnularia subcapitata Greg. 1 0 0 0 6,898 0 0 0 0 0 0

Placoneis pseudoanglica (Lange-Bertalot) Cox 1 0 0 0 0 0 0 0 0 6,367 0

Planothidium frequentissimum (Lange-Bertalot)

Lange-Bertalot

3 0 166 3,096 0 0 48,836 0 0 0 0
40 Variability in Lotic Communities, Three Contrasting Stream Environments, Santa Ana River Basin, Calif., 1999–2001 Appendix 3. Benthic algae taxa and their densities from richest-targeted habitat samples collected from four sites in the Santa Ana River Basin, California, 1999−2001.— Continued [Values are number of individuals per square centimeter] Scientific name Number of samples with an occurrence Sample identification SF99 SF00 SF01 UPH99 MWD99 MWD00 MWD01 PRD99 PRD00 PRD01 Planothidium lanceolatum (Brébisson ex Kützing) Lange-Bertalot

6 273 415 546 13,796 8,590 0 0 8,623 0 0

Pleurosira laevis (Ehrenberg) Compere 2 0 0 0 0 0 0 642 0 0 1,402

Psammothidium chlidanos (Hohn and Hellermann) 

Lange-Bertalot

1 0 0 546 0 0 0 0 0 0 0

Reimeria sinuata (Greg.) Kociolek and Stoermer 5 39 498 911 165,556 0 0 0 0 6,367 0

Rhoicosphenia abbreviata (Agardh) Lange-Bertalot 6 107 498 1,093 131,065 0 0 0 0 12,735 12,618

Rhopalodia gibba (Ehrenberg) O. Müll. 1 0 0 0 13,796 0 0 0 0 0 0

Rossithidium pusillum (Grunow) Round and 

Bukhtiyarova

2 20 0 0 0 0 0 0 0 6,367 0

Sellaphora bacillum (Ehrenberg) Mann 1 0 0 0 6,898 0 0 0 0 0 0

Sellaphora pupula (Kützing) Meresckowsky 2 0 0 0 0 0 244,180 0 1,725 0 0

Sellaphora seminulum (Grunow) Mann 7 20 249 0 0 64,422 195,344 1,711 3,449 6,367 0

Simonsenia delognei (Grunow) Lange-Bertalot 1 0 0 0 0 2,147 0 0 0 0 0

Staurosira construens var. pumila (Grunow) Kingston 1 0 0 0 0 21,474 0 0 0 0 0

Staurosira construens var. venter (Ehrenberg) 

Hamilton

3 20 83 0 6,898 0 0 0 0 0 0

Staurosirella leptostauron (Ehrenberg) Williams and 

Round

2 0 249 2,185 0 0 0 0 0 0 0

Staurosirella pinnata (Ehrenberg) Williams and 

Round

1 0 0 0 0 0 0 0 3,449 0 0

Stephanodiscus hantzschii Grunow 1 0 0 0 0 0 0 0 0 6,367 0

Surirella minuta Brébisson. 1 0 0 0 0 4,295 0 0 0 0 0

Surirella robusta Ehrenberg 1 0 0 0 0 0 0 0 0 6,367 0

Synedra parasitica (W. Smith) Hust. 1 0 0 0 0 0 0 0 3,449 0 0

Synedra ulna (Nitzschia) Ehrenberg 3 0 0 0 0 0 97,672 4,706 0 0 1,402

Synedra ulna var. contracta Østrup 1 0 0 0 6,898 0 0 0 0 0 0

Tabularia fasciculata (Agardh) Williams and Round 1 0 0 0 0 0 0 0 0 6,367 0

Tabularia tabulata (C. A. Agardh) Snoeijs 5 10 0 0 0 19,327 0 856 18,970 0 2,103

Tryblionella apiculata Greg. 1 0 0 0 0 0 0 428 0 0 0

Tryblionella compressa (Bailey) Poulin 1 0 0 0 0 0 0 0 0 12,735 0
Appendixes 41

Appendix 3. Benthic algae taxa and their densities from richest-targeted habitat samples collected from four sites in the Santa Ana River Basin, California, 1999−2001.—Continued[Values are number of individuals per square centimeter]

Scientific name

Number of 

samples 

with an

occurrence

Sample identification

SF99 SF00 SF01 UPH99 MWD99 MWD00 MWD01 PRD99 PRD00 PRD01

Cyanophyta (blue-green algae)Blennothrix brebissonii (Kützing ex Gomont) 

Anagnostidis and Komárek

1 27,735 0 0 0 0 0 0 0 0 0

Homoeothrix janthina (Bornet and Flahault) Starmach 2 12,275 0 0 85,951,377 0 0 0 0 0 0

Lyngbya sp. 1 0 0 0 0 0 0 4,250 0 0 0

Nostoc commune Vaucher 1 0 0 0 1,484,615 0 0 0 0 0 0

Oscillatoria sp. 1 0 0 0 0 0 0 850 0 0 0

Phormidium granulatum 1 0 0 0 3,281,780 0 0 0 0 0 0

Unknown Cyanophyte Oscillatoriales (no sheath) 3 9,496 0 0 0 463,631 0 0 649,088 0 0

Unknown Cyanophyte Oscillatoriales (sheath) 3 36,131 0 0 0 818,510 4,772,243 0 0 0 0

EuglenophytaEuglena sp. 1 0 0 0 0 0 0 0 3,958 0 0

Rhodophyta (red algae)Unknown Rhodophyte Florideophycidae (chantransia) 2 23,856 0 0 0 0 0 0 87,073 0 0
42 Variability in Lotic Communities, Three Contrasting Stream Environments, Santa Ana River Basin, Calif., 1999–2001 Appendix 4. Benthic algae taxa and their densities from depositional-targeted habitat samples collected from four sites in the Santa Ana River Basin, California, 1999−2001.— Continued [Values are number of individuals per square centimeter] Scientific name Number of samples with an occurrence Sample identification SF99 SF00 SF01 UPH99 MWD99 MWD00 MWD01 PRD99 PRD00 PRD01 Total taxa per sample 38 28 42 40 39 42 59 62 45 58 Chlorophyta (green algae) Closterium lunula (Möller) Nitzsch 1 0 0 0 0 713,360 0 0 0 0 0 Scenedesmus acutus Meyen 1 0 0 0 0 0 0 0 11,440,899 0 0 Scenedesmus ecornis (Ralfs) Chodat 1 0 0 0 0 0 0 0 3,813,633 0 0 Scenedesmus quadricauda (Turpin) Brébisson 1 0 0 0 0 0 58,965 0 0 0 0 Chrysophyta (diatoms) Achnanthes cf. grischuna CLASON Wüthrich 4 6,746,216 0 0 4,741,228 2,358,052 0 0 201,653 0 0 Achnanthes conspicua Mayer 1 0 0 0 382,357 0 0 0 0 0 0 Achnanthes sp. 1 ANS WRC 1 210,819 0 0 0 0 0 0 0 0 0 Achnanthidium exiguum (Grunow) Czarnecki 4 0 0 0 38,236 0 220,383 234,717 100,827 0 0 Achnanthidium minutissimum (Kützing) Czarnecki

6 0 160,017 437,923 0 0 14,692 403,714 0 208,092 46,686

Achnanthidium pyrenaicum (Hustedt) 

Kobayasi

1 0 0 19,906 0 0 0 0 0 0 0

Adlafia minuscula (Grunow) Lange-Bertalot 1 210,819 0 0 0 0 0 0 0 0 0

Amphora copulata (Kützing) Schoeman and 

Archibald

2 0 0 0 0 0 29,384 0 0 52,023 0

Amphora ovalis (Kützing) Kützing 1 0 0 0 0 0 29,384 0 0 0 0

Amphora pediculus (Kützing) Grunow 9 843,277 0 29,858 3,058,857 138,709 58,769 18,777 403,308 104,046 16,674

Amphora sp. 1 ANS WRC 2 0 0 0 0 0 44,077 28,166 0 0 0

Amphora veneta Kützing 6 0 0 0 0 208,063 352,613 178,385 2,016,539 156,069 40,016

Asterionella formosa Hassal 2 0 0 0 0 0 0 0 201,653 0 16,674

Aulacoseira ambigua (Grunow) Simonsen 3 0 0 0 0 0 0 0 302,480 468,206 10,004

Aulacoseira granulata (Ehrenberg) Simonsen 3 0 0 0 0 0 0 0 1,008,269 208,092 13,339

Bacillaria paradoxa Gmelin 4 0 0 0 0 0 14,692 150,219 0 156,069 10,004

Caloneis bacillum (Grunow) Cleve 2 0 0 9,953 0 138,709 0 0 0 0 0

Chamaepinnularia bremensis (Hustedt) LangeBertalot

1 0 0 0 305,885 0 0 0 0 0 0

Cocconeis neodiminuta Krammer 3 632,457 8,206 9,953 0 0 0 0 0 0 0

Cocconeis pediculus Ehrenberg 2 0 0 0 0 0 29,384 103,276 0 0 0

Cocconeis placentula var. euglypta (Ehrenberg) 

Cleve

4 210,819 0 59,717 802,950 0 0 0 201,653 0 0

Appendix 4. Benthic algae taxa and their densities from depositional-targeted habitat samples collected from four sites in the Santa Ana River Basin, California, 1999−2001.[Values are number of individuals per square centimeter]
Appendixes 43

Appendix 4. Benthic algae taxa and their densities from depositional-targeted habitat samples collected from four sites in the Santa Ana River Basin, California, 1999−2001.—Continued[Values are number of individuals per square centimeter]

Scientific name

Number of 

samples 

with an

occurrence

Sample identification

SF99 SF00 SF01 UPH99 MWD99 MWD00 MWD01 PRD99 PRD00 PRD01

Cocconeis placentula var. lineata (Ehrenberg) 

Van Heurck

9 14,546,530 315,931 49,764 38,236 0 44,077 150,219 504,135 52,023 10,004

Cocconeis placentula var. pseudolineata Geitler 1 0 0 348,347 0 0 0 0 0 0 0

Craticula accomoda (Hustedt) Mann 2 0 0 0 0 0 0 0 100,827 0 6,669

Craticula halophila (Grunow) Mann 1 0 0 0 0 0 0 0 0 0 6,669

Craticula molestiformis (Hustedt) LangeBertalot 1 0 0 0 0 0 0 0 201,653 0 0

Cyclotella atomus Hustedt 2 0 0 0 0 0 0 0 0 156,069 6,669

Cyclotella meneghiniana Kützing 5 0 0 0 0 0 58,769 75,110 8,166,986 884,389 103,376

Cyclotella pseudostelligera Hustedt 1 0 0 0 0 0 0 0 2,016,539 0 0

Cymbella affinis Kützing 1 0 0 0 38,236 0 0 0 0 0 0

Cymbella delicatula Kützing 1 0 0 0 0 0 0 0 0 104,046 0

Cymbella sp. 6 ANS WRC 1 0 0 0 0 138,709 0 0 0 0 0

Denticula kuetzingii Grunow 2 0 0 0 0 0 0 56,332 0 0 3,335

Diadesmis confervacea Kützing 4 0 0 0 0 0 367,305 84,498 0 104,046 133,388

Diadesmis contenta (Grunow ex Van Heurck) 

Mann

1 210,819 0 0 0 0 0 0 0 0 0

Diatoma mesodon (Ehrenberg) Kützing 3 1,264,915 53,339 49,764 0 0 0 0 0 0 0

Diploneis pseudovalis Hustedt 1 0 0 0 0 0 0 9,389 0 0 0

Diploneis puella (Schumann) Cleve 1 0 0 0 0 0 0 0 201,653 0 0

Encyonema minutum (Hilse) Mann 3 0 0 9,953 38,236 0 14,692 0 0 0 0

Encyonema silesiacum (Bleisch) Mann 3 316,229 0 0 152,943 208,063 0 0 0 0 0

Encyonopsis microcephala (Grunow) Krammer 1 0 0 0 0 277,417 0 0 0 0 0

Fallacia pygmaea (Kützing) Stickle and Mann 2 0 0 0 0 0 0 0 0 52,023 13,339

Fragilaria bidens Heiberg 1 0 4,103 0 0 0 0 0 0 0 0

Fragilaria capucina Desmazières 3 0 8,206 0 114,707 0 0 0 201,653 0 0

Fragilaria capucina var. rumpens (Kützing) 

Lange-Bertalot

1 0 0 9,953 0 0 0 0 0 0 0

Fragilaria cf. bicapitata Mayer 1 1,475,735 0 0 0 0 0 0 0 0 0

Fragilaria crotonensis Kitton 2 0 0 0 0 0 0 0 0 52,023 140,058

Fragilaria pinnata var. lancettula (Schumann) 

Hustedt

2 737,867 0 0 0 0 0 0 201,653 0 0

Fragilaria vaucheriae (Kützing) Petersen 5 421,638 0 29,858 0 0 0 9,389 201,653 0 13,339

Frustulia amphipleuroides (Grunow) 

Cleve-Euler

1 0 0 4,976 0 0 0 0 0 0 0
44 Variability in Lotic Communities, Three Contrasting Stream Environments, Santa Ana River Basin, Calif., 1999–2001 Appendix 4. Benthic algae taxa and their densities from depositional-targeted habitat samples collected from four sites in the Santa Ana River Basin, California, 1999−2001.— Continued [Values are number of individuals per square centimeter] Scientific name Number of samples with an occurrence Sample identification SF99 SF00 SF01 UPH99 MWD99 MWD00 MWD01 PRD99 PRD00 PRD01 Geissleria acceptata (Hustedt) Lange-Bertalot and Metzeltin

5 4,532,614 32,824 278,678 76,471 138,709 0 0 0 0 0

Geissleria decussis (Hustedt) Lange-Bertalot et 

Metzeltin

6 0 4,103 14,929 191,178 346,772 29,384 75,110 0 0 0

Geissleria paludosa (Hustedt) Lange-Bertalot 

et Metzeltin

1 0 0 29,858 0 0 0 0 0 0 0

Gomphonema aff. subclavatum ANS NAWQA 

EAM

1 0 36,927 0 0 0 0 0 0 0 0

Gomphonema kobayasii Kociolek and 

Kingston

3 0 38,979 44,788 1,491,193 0 0 0 0 0 0

Gomphonema minutum (C.A. Agardh) 

C.A. Agardh

4 0 0 69,669 152,943 0 0 197,163 0 0 3,335

Gomphonema olivaceum (Lyngb.) Kütz. 1 0 0 0 38,236 0 0 0 0 0 0

Gomphonema parvulum (Kütz.) Kütz. 9 0 4,103 9,953 114,707 693,545 44,077 244,106 1,310,750 468,206 120,049

Gomphonema pumilum (Grunow) Reichett and 

Lange-Bertalot

1 948,687 0 0 0 0 0 0 0 0 0

Gomphonema rhombicum Fricke 2 421,638 0 24,882 0 0 0 0 0 0 0

Gyrosigma scalproides (Rabenhorst) Cleve 2 0 0 0 0 0 0 0 100,827 0 6,669

Hannaea arcus (Ehrenberg) Patrick 1 0 0 0 0 0 0 18,777 0 0 0

Hippodonta capitata (Ehrenberg) LangeBertalot, Metzeltin and Witkowski

2 0 0 0 0 0 0 37,555 0 52,023 0

Karayevia clevei (Grunow) Kingston 1 0 0 0 38,236 0 0 0 0 0 0

Lemnicola hungarica (Grunow) Round and 

Basson

4 0 0 0 0 0 0 18,777 100,827 52,023 3,335

Luticola goeppertiana (Bleisch) Mann 4 0 0 0 0 277,417 0 56,332 100,827 0 3,335

Mayamaea atomus (Kützing) Lange-Bertalot 6 0 4,103 0 76,471 0 14,692 56,332 604,961 0 3,335

Melosira varians Agardh 5 0 0 0 38,236 0 73,461 37,555 403,308 0 6,669

Meridion circulare var. constrictum (Ralfs) Van 

Heurek

1 0 0 4,976 0 0 0 0 0 0 0

Navicula antonii Lange Bertalot 2 0 0 9,953 802,950 0 0 0 0 0 0

Navicula cryptocephala Kützing 3 0 0 9,953 0 0 0 18,777 0 52,023 0

Navicula cryptotenella Lange-Bertalot in 

Kramm. and Lange-Bertalot

5 6,324,578 184,635 303,560 0 69,354 0 0 0 0 3,335

Navicula erifuga Lange-Bertalot 6 0 0 0 0 1,456,444 132,230 168,997 1,411,576 312,137 20,008

Navicula germainii Wallace 4 0 0 0 0 277,417 14,692 28,166 201,653 0 0
Appendixes 45

Appendix 4. Benthic algae taxa and their densities from depositional-targeted habitat samples collected from four sites in the Santa Ana River Basin, California, 1999−2001.—Continued[Values are number of individuals per square centimeter]

Scientific name

Number of 

samples 

with an

occurrence

Sample identification

SF99 SF00 SF01 UPH99 MWD99 MWD00 MWD01 PRD99 PRD00 PRD01

Navicula gregaria Donkin 10 843,277 14,361 29,858 114,707 346,772 14,692 150,219 806,616 364,160 16,674

Navicula lanceolata (Agardh) Ehrenberg 2 0 0 4,976 0 0 0 0 0 52,023 0

Navicula longicephala Hustedt 1 0 0 0 0 0 0 0 0 0 6,669

Navicula minima Grunow 7 2,002,783 8,206 0 2,867,678 0 14,692 75,110 100,827 52,023 0

Navicula perminuta Grunow 2 0 0 19,906 0 0 0 18,777 0 0 0

Navicula recens Lange-Bertalot 4 0 0 0 0 0 44,077 18,777 0 208,092 23,343

Navicula rhynchocephala Kützing 2 0 0 0 0 138,709 0 0 0 0 3,335

Navicula rostellata Kützing 4 0 0 0 0 69,354 514,228 112,664 0 52,023 0

Navicula sanctaecrucis Østrup 1 0 0 0 0 0 0 18,777 0 0 0

Navicula subminuscula Manguin 6 0 0 0 0 693,545 44,077 103,276 3,730,599 988,435 100,041

Navicula symmetrica Patrick 1 0 0 0 0 0 0 0 0 0 6,669

Navicula tenelloides Hustedt 1 0 0 0 0 0 0 0 0 52,023 0

Navicula tripunctata (O. F. Müll.) Bory 2 0 6,155 19,906 0 0 0 0 0 0 0

Navicula trivialis Lange-Bertalot 1 0 0 0 0 0 0 0 0 0 6,669

Navicula veneta Kützing 8 210,819 0 0 688,242 416,127 29,384 56,332 604,961 52,023 53,355

Navicula wildii Lange-Bertalot 1 0 0 0 0 0 0 18,777 0 0 0

Neidium binodis (Ehrenberg) Hust. 1 0 0 0 76,471 0 0 0 0 0 0

Nitzschia acicularis (Kützing) Smith 1 0 0 0 0 0 0 0 0 52,023 0

Nitzschia agnita Hustedt 1 0 0 0 0 0 0 0 201,653 0 0

Nitzschia amphibia Grunow 8 0 0 19,906 76,471 554,835 176,307 600,876 5,847,966 728,321 260,107

Nitzschia archibaldii Lange-Bertalot 4 0 0 0 0 0 14,692 18,777 0 208,092 30,012

Nitzschia capitellata Hustedt 4 0 0 0 0 277,417 0 0 1,008,269 52,023 20,008

Nitzschia cf. bacillum LAIRD Hustedt 2 0 0 0 229,414 20,251,510 0 0 0 0 0

Nitzschia clausii Hantzsch 1 0 0 0 0 0 0 0 0 0 6,669

Nitzschia communis Rabenhorst 2 0 0 0 0 0 0 0 5,646,311 0 20,008

Nitzschia desertorum Hustedt 6 0 0 0 0 277,417 14,692 28,166 201,653 832,366 30,012

Nitzschia diserta Hustedt 1 0 0 0 0 0 0 0 806,616 0 0

Nitzschia dissipata (Kützing) Grunow 7 421,638 43,082 144,315 458,828 0 14,692 0 0 260,115 6,669

Nitzschia filiformis (W. Sm.) Van Heurek 1 0 0 0 0 0 0 9,389 0 0 0

Nitzschia fonticola Grunow 7 0 0 4,976 382,357 0 73,461 37,555 1,008,269 884,389 33,347

Nitzschia frustulum (Kützing) Grunow 3 0 0 0 0 0 0 93,887 1,209,924 0 13,339

Nitzschia fruticosa Hustedt 1 0 0 0 0 0 0 0 201,653 0 0

Nitzschia inconspicua Grunow 10 1,159,505 8,206 44,788 2,752,971 277,417 205,691 93,887 1,915,712 52,023 80,033

Nitzschia intermedia Hantzsch ex Cl. and 

Grunow

1 0 0 0 0 0 0 0 1,714,058 0 0
46 Variability in Lotic Communities, Three Contrasting Stream Environments, Santa Ana River Basin, Calif., 1999–2001 Appendix 4. Benthic algae taxa and their densities from depositional-targeted habitat samples collected from four sites in the Santa Ana River Basin, California, 1999−2001.— Continued [Values are number of individuals per square centimeter] Scientific name Number of samples with an occurrence Sample identification SF99 SF00 SF01 UPH99 MWD99 MWD00 MWD01 PRD99 PRD00 PRD01 Nitzschia lacuum Lange-Bertalot 1 0 0 0 0 138,709 0 0 0 0 0 Nitzschia liebethruthii Rabenhorst 1 0 0 0 0 0 0 0 201,653 0 0 Nitzschia linearis (Agardh ex W. Sm.) W. Sm. 1 0 0 34,835 0 0 0 0 0 0 0 Nitzschia microcephala Grunow 3 0 0 0 0 138,709 0 37,555 201,653 0 0 Nitzschia palea (Kützing) Smith 6 0 0 0 0 12,067,681 1,145,993 572,710 11,292,623 4,838,130 166,735 Nitzschia paleacea Grunow in Van Heurek 1 0 0 0 0 0 0 0 201,653 0 0 Nitzschia perminuta (Grunow) Peragallo 2 0 0 0 0 0 14,692 0 0 52,023 0 Nitzschia pusilla Grunow 3 0 0 0 0 0 0 18,777 0 1,196,527 200,082 Nitzschia recta Hantzsch ex Rabenhorst 1 316,229 0 0 0 0 0 0 0 0 0 Nitzschia sigma (Kütz.) W. Sm. 3 0 0 0 0 0 0 9,389 0 208,092 3,335 Nitzschia sigmoidea (Nitzschia) W. Sm. 1 0 12,309 0 0 0 0 0 0 0 0 Nitzschia sinuata var. delognei (Grunow) Lange-Bertalot

1 0 0 0 3,250,035 0 0 0 0 0 0

Nitzschia sociabilis Hustedt 2 0 0 0 0 0 0 18,777 201,653 0 0

Nitzschia solita Hustedt 2 0 0 0 0 0 0 18,777 201,653 0 0

Nitzschia supralitorea Lange-Bertalot 2 0 0 0 420,592 0 0 0 1,814,885 0 0

Nitzschia thermalis Kützing 1 0 0 0 0 0 0 0 604,961 0 0

Nitzschia tubicola Grunow in Cleve and 

Grunow

3 210,819 0 0 0 138,709 0 0 201,653 0 0

Nitzschia umbonata Lange-Bertalot 1 0 0 0 0 0 0 9,389 0 0 0

Nupela lapidosa (Krasske) Lange-Bertalot 1 0 0 0 0 0 0 46,943 0 0 0

Opephora olsenii M Moller 1 0 0 129,386 0 0 0 0 0 0 0

Parlibellus protracta (Grunow) Witkowski, 

Lange-Bertalot and Metzeltin

2 210,819 0 0 0 0 0 0 0 0 3,335

Planothidium daui (Foged) Lange-Bertalot 2 737,867 0 29,858 0 0 0 0 0 0 0

Planothidium delicatulum (Kützing) Round and 

Bukhtiyarova

2 0 0 0 0 138,709 0 18,777 0 0 0

Planothidium frequentissimum (Lange-Bertalot) 

Lange-Bertalot

6 0 100,524 238,867 0 0 58,769 431,880 0 52,023 13,339

Planothidium lanceolatum (Brébisson ex 

Kützing) Lange-Bertalot

5 12,859,975 0 144,315 2,829,443 416,127 0 0 1,008,269 0 0

Planothidium rostratum (Østrup) LangeBertalot

1 0 102,575 0 0 0 0 0 0 0 0

Pleurosira laevis (Ehrenberg) Compere 1 0 0 0 0 0 0 9,389 0 0 0
Appendixes 47

Appendix 4. Benthic algae taxa and their densities from depositional-targeted habitat samples collected from four sites in the Santa Ana River Basin, California, 1999−2001.—Continued[Values are number of individuals per square centimeter]

Scientific name

Number of 

samples 

with an

occurrence

Sample identification

SF99 SF00 SF01 UPH99 MWD99 MWD00 MWD01 PRD99 PRD00 PRD01

Psammothidium bioretii (Germ.) Bukhtiyarova 

and Round

3 421,638 18,464 29,858 0 0 0 0 0 0 0

Psammothidium helveticum (Hustedt) 

Bukhtiyarova and Round

1 210,819 0 0 0 0 0 0 0 0 0

Psammothidium subatomoides (Hustedt) 

Bukhtiyarova et Round

1 210,819 0 0 0 0 0 0 0 0 0

Pseudostaurosira brevistriata (Grunow in Van 

Heurek) Williams and Round

2 0 4,103 0 0 0 0 0 201,653 0 0

Reimeria sinuata (Greg.) Kociolek and 

Stoermer

5 1,370,325 20,515 39,811 879,421 208,063 0 0 0 0 0

Rhoicosphenia abbreviata (Agardh) LangeBertalot 6 737,867 6,155 79,622 76,471 0 0 9,389 0 0 3,335

Rossithidium pusillum (Grunow) Round and 

Bukhtiyarova

1 210,819 0 0 0 0 0 0 0 0 0

Sellaphora bacillum (Ehrenberg) Mann 1 0 0 0 38,236 0 0 0 0 0 0

Sellaphora pupula (Kütz.) Meresckowsky 6 0 0 0 0 485,481 88,153 234,717 705,788 104,046 10,004

Sellaphora seminulum (Grunow) Mann 9 210,819 12,309 0 76,471 277,417 58,769 150,219 1,209,924 260,115 56,690

Staurosira construens (Ehrenberg) Williams and 

Round

1 0 0 0 0 0 88,153 0 0 0 0

Staurosira construens var. pumila (Grunow) 

Kingston

2 1,054,096 0 0 0 762,899 0 0 0 0 0

Staurosira construens var. venter (Ehrenberg) 

Hamilton

2 210,819 0 0 0 0 102,846 0 0 0 0

Staurosirella leptostauron (Ehrenberg) 

Williams and Round

2 0 10,258 79,622 0 0 0 0 0 0 0

Staurosirella pinnata (Ehrenberg) Williams and 

Round

2 0 8,206 0 76,471 0 0 0 0 0 0

Stephanodiscus hantzschii Grunow 2 0 0 0 0 0 0 0 302,480 104,046 0

Surirella angusta Kützing 2 0 0 0 0 0 0 18,777 0 52,023 0

Surirella brebissonii Kramm. and LangeBertalot 2 0 0 0 0 0 0 9,389 0 0 3,335

Surirella tenera Greg. 1 0 0 0 0 0 0 0 403,308 0 0

Synedra parasitica (W. Sm.) Hust. 2 0 0 19,906 0 0 0 0 0 0 13,339

Synedra ulna (Nitzschia) Ehrenberg 3 0 0 0 0 0 14,692 75,110 0 0 3,335

Synedra ulna var. contracta Østr. 1 0 0 0 0 0 0 0 201,653 0 0

Tabularia tabulata (C. A. Agardh) Snoeijs 1 0 0 0 0 0 0 0 201,653 0 0
48 Variability in Lotic Communities, Three Contrasting Stream Environments, Santa Ana River Basin, Calif., 1999–2001 Appendix 4. Benthic algae taxa and their densities from depositional-targeted habitat samples collected from four sites in the Santa Ana River Basin, California, 1999−2001.— Continued [Values are number of individuals per square centimeter] Scientific name Number of samples with an occurrence Sample identification SF99 SF00 SF01 UPH99 MWD99 MWD00 MWD01 PRD99 PRD00 PRD01 Thalassiosira sp. 1 NAWQA DW SANA 1 0 0 0 0 0 0 0 0 0 36,682 Thalassiosira weissflogii (Grunow) Fryxell and Hasle

1 0 0 0 0 0 0 0 0 0 3,335

Tryblionella apiculata Greg. 6 0 0 0 0 138,709 29,384 28,166 201,653 156,069 6,669

Tryblionella calida (Grunow) Mann 1 0 0 0 0 0 44,077 0 0 0 0

Cyanophyta (blue-green algae)Nostoc commune Vaucher 1 0 0 0 78,713,503 0 0 0 0 0 0

Unknown Cyanophyte Oscillatoriales 

(no sheath) 

3 42,011,835 0 0 0 12,127,128 0 0 11,440,899 0 0

Unknown Cyanophyte Oscillatoriales (sheath) 2 18,623,803 0 0 0 29,961,139 0 0 0 0 0

EuglenophytaEuglena sp. 2 0 0 0 596,314 0 0 0 3,813,633 0 0

Trachelomonas hispida (Perty) Stein 1 0 0 0 0 713,360 0 0 0 0 0
Appendixes 49

Appendix 5. Benthic algae metrics calculated from qualitative multihabitat, richest-targeted habitat, and depositional-targeted habitat samples collected from four sites in the Santa Ana River Basin, California, 1999−2001.—Continued[EPA, Environmental Protection Agency; no., number; no./cm2, number of individuals per square centimeter]

Metric Sample identification

SF99 SF00 SF01 UPH99 MWD99 MWD00 MWD01 PRD99 PRD00 PRD01

Metrics from qualitative multihabitat (presence/absence) dataTaxon richness (no. of taxa) 57 59 61 72 71 73 86 99 82 89

Genus richness (no. of taxa) 50 36 45 36 33 33 48 34 35 45

Family richness (no. of taxa) 19 9 11 12 9 8 12 10 7 11

Phylum richness (no. of taxa) 5 3 5 6 3 2 3 2 1 2

Metrics from richest-targeted habitats (RTH)Simpson’s diversity index 0.785 0.681 0.923 0.180 0.877 0.873 0.892 0.827 0.900 0.880

Taxon richness (no. of taxa) 31 26 34 38 33 26 32 45 42 39

Taxon abundance (no./cm2) 115,983 24,906 109,269 95,015,334 3,113,772 19,995,700 135,579 1,856,234 1,910,223 420,596

Diatom richness (no. of taxa) 26 26 34 35 29 24 29 41 42 39

Green algae richness (no. of taxa) 0 0 0 0 2 1 1 1 0 0

Blue-green algae richness (no. of taxa) 4 0 0 3 2 1 2 1 0 0

Euglenoid algae richness (no. of taxa) 0 0 0 0 0 0 0 1 0 0

Red algae richness (no. of taxa) 1 0 0 0 0 0 0 1 0 0

Diatom richness (percent) 83.9 100.0 100.0 92.1 93.5 96.0 93.5 93.2 100.0 100.0

Green algae richness (percent) 0.0 0.0 0.0 0.0 6.5 4.0 3.2 2.3 0.0 0.0

Blue-green algae richness (percent) 12.9 0.0 0.0 7.9 6.1 3.8 6.3 2.2 0.0 0.0

Euglenoid algae richness (percent) 0.0 0.0 0.0 0.0 0.0 0.0 0.0 2.2 0.0 0.0

Red algae richness (percent) 3.2 0.0 0.0 0.0 0.0 0.0 0.0 2.2 0.0 0.0

Diatom abundance (no./cm2) 6,490 24,906 109,269 4,297,562 1,608,401 14,650,788 128,354 1,100,284 1,910,223 420,596

Green algae abundance (no./cm2) 0 0 0 0 223,230 572,669 2,125 15,831 0 0

Blue-green algae abundance (no./cm2) 85,637 0 0 90,717,772 1,282,141 4,772,243 5,100 649,088 0 0

Euglenoid algae abundance (no./cm2) 0 0 0 0 0 0 0 3,958 0 0

Red algae abundance (no./cm2) 23,856 0 0 0 0 0 0 87,073 0 0

Diatom abundance (percent) 5.6 100.0 100.0 4.5 51.7 73.3 94.7 59.3 100.0 100.0

Green algae abundance (percent) 0.0 0.0 0.0 0.0 7.2 2.9 1.6 0.9 0.0 0.0

Blue-green algae abundance (percent) 73.8 0.0 0.0 95.5 41.2 23.9 3.8 35.0 0.0 0.0

Euglenoid algae abundance (percent) 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.2 0.0 0.0

Red algae abundance (percent) 20.6 0.0 0.0 0.0 0.0 0.0 0.0 4.7 0.0 0.0

Nitrogen heterotrophic diatom richness 

(percent)

20.0 6.2 25.0 12.0 41.2 27.8 36.8 20.8 32.0 36.4

Facultative nitrogen autotrophic diatom 

richness (percent)

73.3 68.8 60.0 56.0 47.1 55.6 36.8 58.3 48.0 45.5

Appendix 5. Benthic algae metrics calculated from qualitative multihabitat, richest-targeted habitat, and depositional-targeted habitat samples collected from four sites in the Santa Ana River Basin, California, 1999−2001.[EPA, Environmental Protection Agency; no., number; no./cm2, number of individuals per square centimeter]
50 Variability in Lotic Communities, Three Contrasting Stream Environments, Santa Ana River Basin, Calif., 1999–2001 Appendix 5. Benthic algae metrics calculated from qualitative multihabitat, richest-targeted habitat, and depositional-targeted habitat samples collected from four sites in the Santa Ana River Basin, California, 1999−2001.—Continued [EPA, Environmental Protection Agency; no., number; no./cm2, number of individuals per square centimeter] Metric Sample identification SF99 SF00 SF01 UPH99 MWD99 MWD00 MWD01 PRD99 PRD00 PRD01 Obligative nitrogen autotrophic diatom richness (percent) 6.7 25.0 10.0 32.0 0.0 5.6 10.5 4.2 8.0 4.5 Nitrogen fixing diatom richness (percent) 0.0 0.0 0.0 10.3 0.0 0.0 0.0 0.0 0.0 0.0 Eutrophic diatom richness (percent) 77.8 73.7 86.4 78.6 100.0 89.5 85.7 89.3 86.7 81.5 Oligotrophic diatom richness (percent) 0.0 0.0 0.0 7.1 0.0 5.3 4.8 0.0 3.3 3.7 Halophilic diatom richness (percent) 10.0 5.3 17.4 10.0 30.0 21.1 38.1 31.3 19.4 34.5 Halophobic (fresh) diatom richness (percent) 5.0 5.3 4.3 3.3 0.0 0.0 0.0 3.1 3.2 3.4 Halophobic (fresh-brackish) diatom richness (percent) 90.0 89.5 78.3 86.7 70.0 78.9 61.9 65.6 77.4 58.6 Alkaline diatom richness (percent) 76.5 68.4 69.6 72.4 78.9 63.2 71.4 77.8 71.0 82.1 Acidiphilic diatom richness (percent) 0.0 0.0 0.0 3.4 0.0 0.0 0.0 0.0 0.0 3.6 Seston richness (percent) 0 0 0 0 4.3 5.0 4.17 8.8 12.9 3.1 Motile diatom richness (percent) 40.0 31.6 39.1 24.1 58.3 66.7 58.3 57.1 62.5 71.9 EPA tolerant species richness (percent) 22.2 37.5 50.0 27.3 80.0 58.3 70.0 53.3 54.5 66.7 EPA intolerant species richness (percent) 66.7 62.5 50.0 72.7 10.0 33.3 20.0 26.7 36.4 25.0 Nitrogen heterotrophic diatom abundance (percent) 5.0 1.3 8.0 0.8 29.6 45.2 62.0 31.9 25.6 51.9 Facultative nitrogen autotroph abundance (percent) 94.1 95.1 82.2 73.3 18.3 15.2 11.7 26.1 25.6 25.8 Obligative nitrogen autotroph abundance (percent) 0.9 3.5 8.6 25.9 0.0 1.5 3.5 2.0 21.3 11.4 Nitrogen fixing diatom abundance (percent) 0.0 0.0 0.0 9.0 0.0 0.0 0.0 0.0 0.0 0.0 Eutrotphic diatom abundance (percent) 76.5 85.1 65.3 91.9 100.0 97.1 95.3 96.0 85.8 74.5 Oligotrophic diatom abundance (percent) 0.0 0.0 0.0 0.4 0.0 1.5 2.4 0.0 13.4 5.6 Halophilic diatom abundance (percent) 0.5 0.4 4.2 5.8 26.5 23.5 20.9 59.5 37.9 50.0 Halophobic (fresh) diatom abundance (percent) 6.8 1.2 4.0 0.7 0.0 0.0 0.0 0.4 12.9 5.6 Halophobic (fresh-brackish) diatom abundance (percent) 92.7 98.3 91.8 93.6 73.5 76.5 79.1 40.1 49.2 44.4 Alkalinic diatom abundance (percent) 97.8 87.6 74.0 90.0 56.7 75.4 75.1 76.9 78.8 87.3 Acidophilic diatom abundance (percent) 0.0 0.0 0.0 0.2 0.0 0.0 0.0 0.0 0.0 5.6 Seston abundance (percent) 0 0 0 0 3.2 4.3 1.9 2.9 2.9 1.3

Motile diatom abundance (percent) 31.7 7.3 44.1 30.7 80.2 86.8 85.0 73.2 84.9 91.3
Appendixes 51

Appendix 5. Benthic algae metrics calculated from qualitative multihabitat, richest-targeted habitat, and depositional-targeted habitat samples collected from four sites in the Santa Ana River Basin, California, 1999−2001.—Continued[EPA, Environmental Protection Agency; no., number; no./cm2, number of individuals per square centimeter]

Metric Sample identification

SF99 SF00 SF01 UPH99 MWD99 MWD00 MWD01 PRD99 PRD00 PRD01

Bahl’s tolerance index based on abundance 2.7 2.9 2.6 3.0 1.4 1.5 1.7 1.8 1.9 2.0

EPA tolerant diatom abundance (percent) 41.9 22.6 15.6 1.6 94.1 86.0 95.9 72.4 79.1 70.7

EPA intolerant diatom abundance (percent) 57.2 77.4 84.4 98.4 0.8 10.1 2.7 20.4 19.8 26.1

Siltation index 27.8 6.7 31.0 27.8 70.9 77.0 59.5 71.9 68.3 75.8

Pollution tolerance index 2.4 2.8 2.8 3.0 1.1 1.6 1.7 1.6 1.7 1.8

Metrics from depositional-targeted habitats (DTH)Simpson’s diversity index 0.831 0.874 0.928 0.456 0.794 0.897 0.952 0.934 0.878 0.942

Taxon richness (no. of taxa) 38 28 42 40 39 42 59 62 45 58

Taxon abundance (no./cm2) 124,303,047 1,230,904 2,985,835 107,336,588 88,456,683 4,451,935 5,633,214 95,340,782 15,606,876 2,000,822

Diatom richness (no. of taxa) 36 28 42 38 35 41 59 58 45 58

Green algae richness (no. of taxa) 0 0 0 0 1 1 0 2 0 0

Blue-green algae richness (no. of taxa) 2 0 0 1 2 0 0 1 0 0

Euglenoid algae richness (no. of taxa) 0 0 0 1 1 0 0 1 0 0

Red algae richness (no. of taxa) 0 0 0 0 0 0 0 0 0 0

Diatom richness (percent) 94.7 100.0 100.0 95.0 89.7 100.0 100.0 96.7 100.0 100.0

Green algae richness (percent) 0.0 0.0 0.0 0.0 2.6 2.4 0.0 3.3 0.0 0.0

Blue-green algae richness (percent) 5.3 0.0 0.0 2.5 5.1 0.0 0.0 1.6 0.0 0.0

Euglenoid algae richness (percent) 0.0 0.0 0.0 2.5 2.6 0.0 0.0 1.6 0.0 0.0

Red algae richness (percent) 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0

Diatom abundance (no./cm2) 63,667,409 1,230,904 2,985,835 28,026,771 44,941,696 4,392,970 5,633,214 64,831,718 15,606,876 2,000,822

Green algae abundance (no./cm2) 0 0 0 0 713,360 58,965 0 15,254,532 0 0

Blue-green algae abundance (no./cm2) 60,635,638 0 0 78,713,503 42,088,267 0 0 11,440,899 0 0

Euglenoid algae abundance (no./cm2) 0 0 0 596,314 713,360 0 0 3,813,633 0 0

Red algae abundance (no./cm2) 0 0 0 0 0 0 0 0 0 0

Diatom abundance (percent) 51.2 100.0 100.0 26.1 50.8 100.0 100.0 81.0 100.0 100.0

Green algae abundance (percent) 0.0 0.0 0.0 0.0 0.8 1.3 0.0 19.0 0.0 0.0

Blue-green algae abundance (percent) 48.8 0.0 0.0 73.3 47.6 0.0 0.0 12.0 0.0 0.0

Euglenoid algae abundance (percent) 0.0 0.0 0.0 0.6 0.8 0.0 0.0 4.0 0.0 0.0

Red algae abundance (percent) 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0

Nitrogen heterotrophic diatom richness 

(percent)

15.8 23.5 13.6 29.2 25.0 29.6 29.4 28.6 24.3 25.0

Facultative nitrogen autotrophic diatom 

richness (percent)

63.2 47.1 68.2 54.2 45.0 55.6 52.9 45.7 59.5 60.0
52 Variability in Lotic Communities, Three Contrasting Stream Environments, Santa Ana River Basin, Calif., 1999–2001 Appendix 5. Benthic algae metrics calculated from qualitative multihabitat, richest-targeted habitat, and depositional-targeted habitat samples collected from four sites in the Santa Ana River Basin, California, 1999−2001.—Continued [EPA, Environmental Protection Agency; no., number; no./cm2, number of individuals per square centimeter] Metric Sample identification SF99 SF00 SF01 UPH99 MWD99 MWD00 MWD01 PRD99 PRD00 PRD01 Obligative nitrogen autotrophic diatom richness (percent) 21.1 29.4 18.2 16.7 15.0 7.4 2.9 5.7 8.1 2.5 Nitrogen fixing diatom richness (percent) 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 Eutrophic diatom richness (percent) 57.1 57.9 68.0 80.8 78.3 93.3 87.5 92.9 85.0 88.9 Oligotrophic diatom richness (percent) 4.8 0.0 4.0 0.0 0.0 3.3 2.5 0.0 5.0 0.0 Halophilic diatom richness (percent) 13.0 10.0 11.1 10.3 24.0 35.5 36.6 22.7 35.0 41.3 Halophobic (fresh) diatom richness (percent) 13.0 5.0 3.7 6.9 4.0 0.0 0.0 2.3 2.5 0.0 Halophobic (fresh-brackish) diatom richness (percent) 69.6 80.0 81.5 82.8 72.0 64.5 61.0 75.0 62.5 58.7 Alkaline diatom richness (percent) 65.0 63.2 65.4 64.3 75.0 73.3 70.0 75.6 77.5 80.4 Acidiphilic diatom richness (percent) 5.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 Seston richness (percent) 0.0 0.0 3.3 0.0 0.0 2.9 0.0 14.9 15.0 9.6 Motile diatom richness (percent) 40.9 36.8 40.0 42.3 73.1 61.8 70.5 59.6 70.0 62.0 EPA tolerant species richness (percent) 55.6 42.9 38.5 53.8 53.8 56.3 57.1 63.2 50.0 52.9 EPA intolerant species richness (percent) 44.4 57.1 53.8 46.2 23.1 31.3 23.8 15.8 21.4 29.4 Nitrogen heterotrophic diatom abundance (percent) 8.6 4.7 5.8 32.3 11.5 31.2 36.5 38.3 19.5 43.5 Facultative nitrogen autotroph abundance (percent) 82.8 82.5 81.1 48.6 14.2 28.0 41.2 20.4 36.7 39.2 Obligative nitrogen autotroph abundance (percent) 8.6 12.8 13.1 19.1 3.1 3.2 1.4 0.7 1.5 0.2 Nitrogen fixing diatom abundance (percent) 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 Eutrotphic diatom abundance (percent) 72.9 49.0 47.0 91.9 96.2 99.1 88.1 99.0 88.5 78.7 Oligotrophic diatom abundance (percent) 0.5 0.0 0.6 0.0 0.0 0.4 0.4 0.0 1.1 0.0 Halophilic diatom abundance (percent) 4.1 2.5 4.7 14.3 7.0 37.6 28.0 28.9 19.4 30.2 Halophobic (fresh) diatom abundance (percent) 15.2 5.9 2.9 20.6 5.5 0.0 0.0 0.3 0.7 0.0 Halophobic (fresh-brackish) diatom abundance (percent) 79.9 89.6 90.6 65.2 87.4 62.4 71.8 70.8 79.9 69.8 Alkalinic diatom abundance (percent) 88.5 69.1 60.4 88.1 65.3 48.5 54.5 65.7 48.6 58.9 Acidophilic diatom abundance (percent) 0.5 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 Seston abundance (percent) 0.0 0.0 0.3 0.0 0.0 1.7 0.0 34.0 6.8 9.5

Motile diatom abundance (percent) 25.6 29.9 39.6 53.6 89.9 73.4 65.9 66.2 81.0 68.7
Appendixes 53

Appendix 5. Benthic algae metrics calculated from qualitative multihabitat, richest-targeted habitat, and depositional-targeted habitat samples collected from four sites in the Santa Ana River Basin, California, 1999−2001.—Continued[EPA, Environmental Protection Agency; no., number; no./cm2, number of individuals per square centimeter]

Metric Sample identification

SF99 SF00 SF01 UPH99 MWD99 MWD00 MWD01 PRD99 PRD00 PRD01

Bahl’s tolerance index based on abundance 2.4 2.7 2.6 2.1 1.3 1.6 1.8 1.7 1.6 1.8

EPA tolerant diatom abundance (percent) 84.7 10.4 24.1 59.9 92.2 87.6 68.0 88.6 85.9 86.4

EPA intolerant diatom abundance (percent) 15.3 89.6 73.8 40.1 3.0 6.9 21.5 6.6 7.4 11.0

Siltation index 18.0 22.5 21.7 43.2 83.6 56.2 42.3 64.7 74.3 55.7

Pollution tolerance index 2.04 2.85 2.73 2.07 1.18 1.32 1.81 1.48 1.50 1.67
54 Variability in Lotic Communities, Three Contrasting Stream Environments, Santa Ana River Basin, Calif., 1999–2001 Appendix 6. Macroinvertebrate taxa collected from four sites in the Santa Ana River Basin, California, 1999−2001.—Continued [UPH was not sampled in 2000 or 2001. Under Sample identification, a “0” represents taxa was not present in the sample, and a “1” represents taxa was present in the sample] Taxon Number of samples with an occurrence Sample identification SF99 SF00 SF01 UPH99 MWD99 MWD00 MWD01 PRD99 PRD00 PRD01 Total taxa per sample 57 49 52 55 42 39 36 28 22 30 Platyhelminthes Turbellaria 6 1 1 1 0 1 0 1 1 0 0 Nemertea Enopla Hoplonemertea Tetrastmmatidae Prostoma sp. 1 0 0 0 0 1 0 0 0 0 0 Nematoda 4 1 1 1 1 0 0 0 0 0 0 Bryozoa 1 0 0 0 0 0 0 0 1 0 0 Mollusca Gastropoda Basomamatophor PhysidaePhysella sp. 7 0 0 0 1 1 1 1 1 1 1 Bivalvia Veneroida Corbiculidae Corbicula sp. 3 0 0 0 0 0 1 0 1 0 1 Sphaeriidae Pisidiinae Pisidium sp. 3 1 1 1 0 0 0 0 0 0 0 Annelida Oligochaeta Lumbriculida Lumbriculidae 2 0 0 0 1 0 0 0 0 0 1 Tubificida

 Naididae 7 0 0 0 1 1 1 1 1 1 1

 Tubificidae 8 1 1 1 0 1 0 1 1 1 1

Appendix 6. Macroinvertebrate taxa collected from four sites in the Santa Ana River Basin, California, 1999−2001.[UPH was not sampled in 2000 or 2001. Under Sample identification, a “0” represents taxa was not present in the sample, and a “1” represents taxa was present in the sample]
Appendixes 55

Appendix 6. Macroinvertebrate taxa collected from four sites in the Santa Ana River Basin, California, 1999−2001.—Continued[UPH was not sampled in 2000 or 2001. Under Sample identification, a “0” represents taxa was not present in the sample, and a “1” represents taxa was present in the sample]

Taxon

Number of 

samples 

with an

occurrence

Sample identification

SF99 SF00 SF01 UPH99 MWD99 MWD00 MWD01 PRD99 PRD00 PRD01

 Enchytraeida Enchytraeidae 4 1 1 1 0 1 0 0 0 0 0

Arthropoda Arachnida 6 1 1 1 0 1 1 1 0 0 0

 Malacostraca Decapoda Pleocyemata Astacidae

Pacifastacus sp. 2 0 0 0 0 0 1 1 0 0 0

 Amphipoda Gammaridea Hyalellidae

Hyalella sp. 3 0 0 0 0 0 1 0 0 1 1

 Collembola 1 0 0 0 0 0 1 0 0 0 0

 Insecta Ephemeroptera Furcatergalia Leptophlebiidae

Paraleptophlebia sp. 3 1 1 1 0 0 0 0 0 0 0

 Ephemerellidae

Caudatella sp. 3 1 1 1 0 0 0 0 0 0 0

Drunella sp. 4 1 1 1 1 0 0 0 0 0 0

Ephemerella sp. 2 1 1 0 0 0 0 0 0 0 0

Serratella sp. 2 1 0 0 1 0 0 0 0 0 0

 Leptohyphidae Tricorythodes sp. 5 0 0 0 1 1 1 1 0 0 1

 Pisciforma Ameletidae

Ameletus sp. 2 1 0 1 0 0 0 0 0 0 0

 Baetidae 8 1 1 1 1 0 0 1 1 1 1

Baetis sp. 8 1 1 1 1 1 1 1 0 0 1

Callibaetis sp. 3 0 0 0 1 0 1 1 0 0 0
56 Variability in Lotic Communities, Three Contrasting Stream Environments, Santa Ana River Basin, Calif., 1999–2001 Appendix 6. Macroinvertebrate taxa collected from four sites in the Santa Ana River Basin, California, 1999−2001.—Continued [UPH was not sampled in 2000 or 2001. Under Sample identification, a “0” represents taxa was not present in the sample, and a “1” represents taxa was present in the sample] Taxon Number of samples with an occurrence Sample identification SF99 SF00 SF01 UPH99 MWD99 MWD00 MWD01 PRD99 PRD00 PRD01 Camelobaetidius sp. 4 0 0 0 0 1 1 1 1 0 0 Diphetor sp. 2 0 1 0 1 0 0 0 0 0 0 Fallceon sp. 7 0 0 0 1 1 1 1 1 1 1 Setisura Heptageniidae Cinygmula sp. 2 1 1 0 0 0 0 0 0 0 0 Epeorus sp. 4 1 1 1 1 0 0 0 0 0 0 Ironodes sp. 3 1 1 1 0 0 0 0 0 0 0 Rhithrogena sp. 3 1 1 1 0 0 0 0 0 0 0 Odonata Zygoptera Coenagrionidae Hetaerina sp. 5 0 0 0 0 1 1 1 0 1 1 Argia sp. 4 0 0 0 0 1 1 1 0 0 1 Anisoptera Gomphidae 1 0 0 0 0 0 0 0 0 0 1 Progomphus sp. 3 0 0 0 0 1 1 1 0 0 0 Libellulidae Paltothemis sp. 1 0 0 0 1 0 0 0 0 0 0 Plecoptera Euholognatha Nemouridae Amphinemurinae Malenka sp. 1 1 0 0 0 0 0 0 0 0 0 Nemourinae Zapada sp. 2 1 0 1 0 0 0 0 0 0 0 Systellognatha Chloroperlidae Chloroperlinae Suwallia sp. 3 1 1 1 0 0 0 0 0 0 0 Peltoperlidae

 Peltoperlinae
Appendixes 57

Appendix 6. Macroinvertebrate taxa collected from four sites in the Santa Ana River Basin, California, 1999−2001.—Continued[UPH was not sampled in 2000 or 2001. Under Sample identification, a “0” represents taxa was not present in the sample, and a “1” represents taxa was present in the sample]

Taxon

Number of 

samples 

with an

occurrence

Sample identification

SF99 SF00 SF01 UPH99 MWD99 MWD00 MWD01 PRD99 PRD00 PRD01

Yoraperla sp. 3 1 1 1 0 0 0 0 0 0 0

 Perlidae Acroneuriinae Acroneuriini

Calineuria sp. 4 1 1 1 1 0 0 0 0 0 0

Hesperoperla sp. 4 1 1 1 1 0 0 0 0 0 0

 Perlodidae 1 1 0 0 0 0 0 0 0 0 0

 Hemiptera Heteroptera Belostomatidae 2 0 0 0 1 0 1 0 0 0 0

 Corixidae Corixinae Corixini

Corisella sp. 2 0 0 0 0 0 0 0 1 0 1

Sigara sp. 1 0 0 0 0 0 0 0 1 0 0

Trichocorixa sp. 3 0 0 0 0 0 0 0 1 1 1

 Gerridae

 Gerrinae 1 0 0 0 1 0 0 0 0 0 0

 Hebridae Hebrinae

Merragata sp. 3 0 0 0 0 1 1 1 0 0 0

 Veliidae Microveliinae

Microvelia sp. 2 0 0 0 1 0 1 0 0 0 0

 Rhagoveliinae

Rhagovelia sp. 5 0 0 0 0 1 1 1 0 1 1

 Trichoptera Spicipalpia Glossosomatidae 1 0 0 1 0 0 0 0 0 0 0

 Agapetinae

Agapetus sp. 1 0 0 0 1 0 0 0 0 0 0

 Hydroptilidae
58 Variability in Lotic Communities, Three Contrasting Stream Environments, Santa Ana River Basin, Calif., 1999–2001 Appendix 6. Macroinvertebrate taxa collected from four sites in the Santa Ana River Basin, California, 1999−2001.—Continued [UPH was not sampled in 2000 or 2001. Under Sample identification, a “0” represents taxa was not present in the sample, and a “1” represents taxa was present in the sample] Taxon Number of samples with an occurrence Sample identification SF99 SF00 SF01 UPH99 MWD99 MWD00 MWD01 PRD99 PRD00 PRD01 Hydroptilinae Hydroptila sp. 7 0 0 0 1 1 1 1 1 1 1 Oxyethira sp. 1 0 0 0 0 1 0 0 0 0 0 Rhyacophilidae Rhyacophila sp. 4 1 1 1 1 0 0 0 0 0 0 Annulipalpia Philopotamidae Philopotaminae Dolophilodes sp. 3 1 0 1 1 0 0 0 0 0 0 Hydropsychidae Arctopsychinae Parapsyche sp. 3 1 1 1 0 0 0 0 0 0 0 Hydropsychinae Ceratopsyche sp. 3 0 1 1 1 0 0 0 0 0 0 Hydropsyche sp. 8 1 0 0 1 1 1 1 1 1 1 Polycentropodidae Polycentropodinae Polycentropus sp. 1 0 0 0 1 0 0 0 0 0 0 Psychomyiidae Psychomyiinae Tinodes sp. 1 0 0 0 1 0 0 0 0 0 0 Integripalpia Apataniidae Apatania sp. 2 1 0 1 0 0 0 0 0 0 0 Brachycentridae Micrasema sp. 4 1 1 1 1 0 0 0 0 0 0 Lepidostomatidae Lepidostomatinae Lepidostoma sp. 2 0 1 0 1 0 0 0 0 0 0 Limnephilidae

 Dicosmoecinae

Cryptochia sp. 1 0 0 1 0 0 0 0 0 0 0
Appendixes 59

Appendix 6. Macroinvertebrate taxa collected from four sites in the Santa Ana River Basin, California, 1999−2001.—Continued[UPH was not sampled in 2000 or 2001. Under Sample identification, a “0” represents taxa was not present in the sample, and a “1” represents taxa was present in the sample]

Taxon

Number of 

samples 

with an

occurrence

Sample identification

SF99 SF00 SF01 UPH99 MWD99 MWD00 MWD01 PRD99 PRD00 PRD01

 Limnephilinae

Psychoglypha sp. 1 0 1 0 0 0 0 0 0 0 0

 Uenoidae Thremmatinae

Neophylax sp. 2 1 0 1 0 0 0 0 0 0 0

 Helicopsychidae

Helicopsyche sp. 2 0 0 0 1 0 1 0 0 0 0

 Lepidoptera Pyralidae Nymphulinae Argyactini

Petrophila sp. 2 0 0 0 1 0 1 0 0 0 0

 Coleoptera Myxophaga Hydroscaphidae

Hydroscapha sp. 1 0 0 0 0 1 0 0 0 0 0

 Adephaga Amphizoidae

Amphizoa sp. 1 0 1 0 0 0 0 0 0 0 0

 Dytiscidae Hydroporinae Bidessini

Liodessus sp. 1 0 0 0 0 0 1 0 0 0 0

 Hydroporini 2 0 1 0 1 0 0 0 0 0 0

 Haliplidae

Peltodytes sp. 1 0 0 0 0 1 0 0 0 0 0

 Polyphaga Staphylinidae 1 0 0 0 0 1 0 0 0 0 0

 Hydrophilidae

Ametor sp. 2 1 0 1 0 0 0 0 0 0 0

Enochrus sp. 3 0 0 0 1 1 0 1 0 0 0

Laccobius sp. 1 0 0 0 0 1 0 0 0 0 0
60 Variability in Lotic Communities, Three Contrasting Stream Environments, Santa Ana River Basin, Calif., 1999–2001 Appendix 6. Macroinvertebrate taxa collected from four sites in the Santa Ana River Basin, California, 1999−2001.—Continued [UPH was not sampled in 2000 or 2001. Under Sample identification, a “0” represents taxa was not present in the sample, and a “1” represents taxa was present in the sample] Taxon Number of samples with an occurrence Sample identification SF99 SF00 SF01 UPH99 MWD99 MWD00 MWD01 PRD99 PRD00 PRD01 Tropisternus sp. 3 0 0 0 0 1 1 1 0 0 0 Dryopidae Helichus sp. 1 0 0 0 1 0 0 0 0 0 0 Postelichus sp. 4 0 0 0 1 1 1 0 1 0 0 Elmidae 1 0 0 1 0 0 0 0 0 0 0 Microcylloepus sp. 1 0 0 0 0 1 0 0 0 0 0 Optioservus sp. 1 0 0 0 1 0 0 0 0 0 0 Zaitzevia sp. 1 0 0 0 1 0 0 0 0 0 0 Psephenidae Psephenus sp. 1 0 0 0 1 0 0 0 0 0 0 Diptera Nematocera Ceratopogonidae 1 0 0 1 0 0 0 0 0 0 0 Ceratopogoninae 1 0 1 0 0 0 0 0 0 0 0 Probezzia sp. 1 1 0 0 0 0 0 0 0 0 0 Dasyheleinae Dasyhelea sp. 2 0 0 0 1 0 0 1 0 0 0 Chironomidae Chironominae Chironomini Chironomus sp. 2 0 0 0 0 0 0 1 0 1 0 Cryptochironomus sp. 3 0 0 0 0 0 0 0 1 1 1 Dicrotendipes sp. 6 0 0 0 1 1 1 1 1 0 1 Endotribelos sp. 2 0 0 0 0 0 1 0 0 0 1 Microtendipes sp. 1 0 0 0 1 0 0 0 0 0 0 Nilothauma sp. 1 0 0 0 0 0 0 1 0 0 0 Paratendipes sp. 2 0 1 1 0 0 0 0 0 0 0 Phaenopsectra sp. 1 0 0 0 1 0 0 0 0 0 0 Polypedilum sp. 6 0 1 1 1 1 1 0 0 0 1 Saetheria sp. 3 0 0 0 0 1 1 1 0 0 0 Pseudochironomini Pseudochironomus sp. 6 0 0 0 1 1 1 1 1 1 0 Tanytarsini

Micropsectra sp. 3 1 1 1 0 0 0 0 0 0 0

Rheotanytarsus sp. 7 1 0 0 1 1 0 1 1 1 1
Appendixes 61

Appendix 6. Macroinvertebrate taxa collected from four sites in the Santa Ana River Basin, California, 1999−2001.—Continued[UPH was not sampled in 2000 or 2001. Under Sample identification, a “0” represents taxa was not present in the sample, and a “1” represents taxa was present in the sample]

Taxon

Number of 

samples 

with an

occurrence

Sample identification

SF99 SF00 SF01 UPH99 MWD99 MWD00 MWD01 PRD99 PRD00 PRD01

Tanytarsus sp. 3 0 0 0 1 0 0 0 1 1 0

 Diamesinae Diamesini

Pagastia sp. 4 1 1 1 1 0 0 0 0 0 0

Pseudodiamesa sp. 2 1 1 0 0 0 0 0 0 0 0

 Orthocladiinae

Brillia sp. 3 1 1 1 0 0 0 0 0 0 0

Cardiocladius sp. 1 0 0 0 1 0 0 0 0 0 0

Chaetocladius sp. 1 0 0 1 0 0 0 0 0 0 0

Corynoneura sp. 1 1 0 0 0 0 0 0 0 0 0

Cricotopus sp. 7 0 0 0 1 1 1 1 1 1 1

Eukiefferiella sp. 5 1 1 1 1 1 0 0 0 0 0

Euryhapsis sp. 1 1 0 0 0 0 0 0 0 0 0

Heleniella sp. 3 1 1 1 0 0 0 0 0 0 0

Limnophyes sp. 2 1 0 0 0 1 0 0 0 0 0

Nanocladius sp. 3 0 0 0 0 0 0 0 1 1 1

Orthocladius sp. 1 1 0 0 0 0 0 0 0 0 0

Parametriocnemus sp. 2 1 0 1 0 0 0 0 0 0 0

Paraphaenocladius sp. 1 1 0 0 0 0 0 0 0 0 0

Rheocricotopus sp. 8 0 1 1 0 1 1 1 1 1 1

Synorthocladius sp. 1 1 0 0 0 0 0 0 0 0 0

Thienemanniella sp. 1 1 0 0 0 0 0 0 0 0 0

Tvetenia sp. 3 1 1 1 0 0 0 0 0 0 0

 Prodiamesinae

Odontomesa sp. 1 0 1 0 0 0 0 0 0 0 0

Prodiamesa sp. 1 0 1 0 0 0 0 0 0 0 0

 Tanypodinae Macropelopiini

Brundiniella sp. 3 1 1 1 0 0 0 0 0 0 0

Macropelopia sp. 1 0 1 0 0 0 0 0 0 0 0

 Pentaneurini 2 0 1 1 0 0 0 0 0 0 0

Ablabesmyia sp. 2 0 0 0 0 0 0 0 1 0 1

Labrundinia sp. 1 0 0 0 0 1 0 0 0 0 0

Paramerina sp. 1 0 0 0 0 0 0 1 0 0 0

Pentaneura sp. 7 0 0 0 1 1 1 1 1 1 1

 Tanypodini
62 Variability in Lotic Communities, Three Contrasting Stream Environments, Santa Ana River Basin, Calif., 1999–2001 Appendix 6. Macroinvertebrate taxa collected from four sites in the Santa Ana River Basin, California, 1999−2001.—Continued [UPH was not sampled in 2000 or 2001. Under Sample identification, a “0” represents taxa was not present in the sample, and a “1” represents taxa was present in the sample] Taxon Number of samples with an occurrence Sample identification SF99 SF00 SF01 UPH99 MWD99 MWD00 MWD01 PRD99 PRD00 PRD01 Tanypus sp. 2 0 0 0 0 0 0 0 0 1 1 DixidaeDixa sp. 2 1 0 1 0 0 0 0 0 0 0 Psychodidae 3 1 1 1 0 0 0 0 0 0 0 Maruina sp. 1 0 0 0 1 0 0 0 0 0 0 Simuliidae 1 0 0 0 0 0 1 0 0 0 0 Prosimulium sp. 3 1 1 1 0 0 0 0 0 0 0 Simulium sp. 7 1 0 1 1 1 0 1 1 0 1 Thaumaleidae 1 0 0 1 0 0 0 0 0 0 0 Tipulidae Limoniinae Dicranota sp. 2 0 1 1 0 0 0 0 0 0 0 Limonia sp. 2 0 0 0 0 1 0 1 0 0 0 Brachycera Empididae Clinocerinae 1 1 0 0 0 0 0 0 0 0 0 Hemerodromiinae 2 0 1 1 0 0 0 0 0 0 0 Hemerodromia sp. 7 0 0 0 1 1 1 1 1 1 1 Neoplasta sp. 1 1 0 0 0 0 0 0 0 0 0 Ephydridae 2 0 0 0 0 0 1 0 1 0 0 Pelecorhynchidae Glutops sp. 3 1 1 1 0 0 0 0 0 0 0 Stratiomyidae Stratiomyinae Caloparyphus sp. 4 0 0 0 1 1 1 1 0 0 0 Euparyphus sp. 4 0 0 0 1 1 1 1 0 0 0 Tabanidae Tabanus sp. 1 0 0 0 0 0 1 0 0 0 0
Appendixes 63

Appendix 7. Macroinvertebrate taxa from richest-targeted habitat samples collected from four sites in the Santa Ana River Basin, California, 1999−2001.—Continued[Values are number of individuals per square meter. UPH was not sampled in 2000 or 2001]

Taxon

Number of 

samples with 

an occurrence

Sample identification

SF99 SF00 SF01 UPH99 MWD99 MWD00 MWD01 PRD99 PRD00 PRD01

Total taxa per sample 33 33 36 40 27 22 29 19 10 15

Platyhelminthes Turbellaria 4 0 34 0 0 35 0 42 14 0 0

Nemertea Enopla Hoplonemertea Tetrastmmatidae

Prostoma sp. 1 0 0 0 0 35 0 0 0 0 0

Nematoda 3 11 22 55 0 0 0 0 0 0 0

Bryozoa 1 0 0 0 0 0 0 0 14 0 0

Mollusca Gastropoda 1 0 0 0 0 0 0 0 14 0 0

 Basomamatophor Physidae

Physella sp. 1 0 0 0 601 0 0 0 0 0 0

Bivalvia Veneroida Corbiculidae

Corbicula sp. 2 0 0 0 0 0 0 0 18 0 2

 Sphaeriidae 1 0 11 0 0 0 0 0 0 0 0

Annelida Oligochaeta Lumbriculida Lumbriculidae 1 0 0 0 0 0 0 0 0 0 32

 Tubificida Naididae 7 0 0 0 47 330 408 242 136 103 162

 Tubificidae 5 0 0 1 0 0 0 42 15 41 65

 Enchytraeida Enchytraeidae 4 13 123 148 0 35 0 0 0 0 0

Arthropoda Arachnida 6 224 381 387 0 233 510 123 0 0 0

Appendix 7. Macroinvertebrate taxa from richest-targeted habitat samples collected from four sites in the Santa Ana River Basin, California, 1999−2001.[Values are number of individuals per square meter. UPH was not sampled in 2000 or 2001]
64 Variability in Lotic Communities, Three Contrasting Stream Environments, Santa Ana River Basin, Calif., 1999–2001 Appendix 7. Macroinvertebrate taxa from richest-targeted habitat samples collected from four sites in the Santa Ana River Basin, California, 1999−2001.—Continued [Values are number of individuals per square meter. UPH was not sampled in 2000 or 2001] Taxon Number of samples with an occurrence Sample identification SF99 SF00 SF01 UPH99 MWD99 MWD00 MWD01 PRD99 PRD00 PRD01 Insecta Ephemeroptera Furcatergalia Leptophlebiidae Paraleptophlebia sp. 1 0 11 0 0 0 0 0 0 0 0 Ephemerellidae Caudatella sp. 3 1,061 122 129 0 0 0 0 0 0 0 Drunella sp. 4 882 1,041 1,382 33 0 0 0 0 0 0 Ephemerella sp. 1 0 14 0 0 0 0 0 0 0 0 Serratella sp. 2 18 0 0 227 0 0 0 0 0 0 Leptohyphidae Tricorythodes sp. 4 0 0 0 117 1,491 1,224 1,297 0 0 0 Pisciforma Baetidae 1 0 0 0 0 0 0 0 14 0 0 Baetis sp. 7 739 493 1,898 691 0 0 84 0 40 170 Camelobaetidius sp. 3 0 0 0 0 1,588 736 162 0 0 0 Diphetor sp. 1 0 0 0 30 0 0 0 0 0 0 Fallceon sp. 5 0 0 0 0 893 799 1,293 0 20 56 Setisura Heptageniidae Cinygmula sp. 2 13 11 0 0 0 0 0 0 0 0 Epeorus sp. 4 186 34 92 166 0 0 0 0 0 0 Ironodes sp. 3 26 11 46 0 0 0 0 0 0 0 Rhithrogena sp. 3 2 11 46 0 0 0 0 0 0 0 Odonata Zygoptera Coenagrionidae Hetaerina sp. 3 0 0 0 0 35 9 4 0 0 0 Argia sp. 3 0 0 0 0 6 213 42 0 0 0 Anisoptera 1 0 0 0 23 0 0 0 0 0 0 Plecoptera Euholognatha

 Nemouridae Nemourinae
Appendixes 65

Appendix 7. Macroinvertebrate taxa from richest-targeted habitat samples collected from four sites in the Santa Ana River Basin, California, 1999−2001.—Continued[Values are number of individuals per square meter. UPH was not sampled in 2000 or 2001]

Taxon

Number of 

samples with 

an occurrence

Sample identification

SF99 SF00 SF01 UPH99 MWD99 MWD00 MWD01 PRD99 PRD00 PRD01

Zapada sp. 2 45 0 258 0 0 0 0 0 0 0

 Systellognatha Chloroperlidae Chloroperlinae

Suwallia sp. 1 0 56 0 0 0 0 0 0 0 0

 Peltoperlidae Peltoperlinae

Yoraperla sp. 3 45 190 55 0 0 0 0 0 0 0

 Perlidae Acroneuriinae Acroneuriini

Calineuria sp. 3 1 11 0 4 0 0 0 0 0 0

Hesperoperla sp. 3 11 11 0 2 0 0 0 0 0 0

 Perlodidae 1 11 0 0 0 0 0 0 0 0 0

 Hemiptera Heteroptera Hebridae Hebrinae

Merragata sp. 1 0 0 0 0 0 53 0 0 0 0

 Veliidae Rhagoveliinae

Rhagovelia sp. 1 0 0 0 0 0 53 0 0 0 0

 Trichoptera Spicipalpia Glossosomatidae 1 0 0 18 0 0 0 0 0 0 0

 Agapetinae

Agapetus sp. 1 0 0 0 29 0 0 0 0 0 0

 Hydroptilidae Hydroptilinae

Hydroptila sp. 7 0 0 0 346 1,522 6,695 1,820 67 202 32

 Rhyacophilidae

Rhyacophila sp. 3 24 34 37 0 0 0 0 0 0 0
66 Variability in Lotic Communities, Three Contrasting Stream Environments, Santa Ana River Basin, Calif., 1999–2001 Appendix 7. Macroinvertebrate taxa from richest-targeted habitat samples collected from four sites in the Santa Ana River Basin, California, 1999−2001.—Continued [Values are number of individuals per square meter. UPH was not sampled in 2000 or 2001] Taxon Number of samples with an occurrence Sample identification SF99 SF00 SF01 UPH99 MWD99 MWD00 MWD01 PRD99 PRD00 PRD01 Annulipalpia Philopotamidae Philopotaminae Dolophilodes sp. 2 1 0 0 1 0 0 0 0 0 0 Hydropsychidae Arctopsychinae Parapsyche sp. 2 0 90 398 0 0 0 0 0 0 0 Hydropsychinae Ceratopsyche sp. 2 0 0 9 53 0 0 0 0 0 0 Hydropsyche sp. 8 67 0 0 1,873 1,654 1,535 1,138 2,878 4,798 9,838 Polycentropodidae Polycentropodinae Polycentropus sp. 1 0 0 0 26 0 0 0 0 0 0 Psychomyiidae Psychomyiinae Tinodes sp. 1 0 0 0 164 0 0 0 0 0 0 Integripalpia Apataniidae Apatania sp. 2 13 0 166 0 0 0 0 0 0 0 Brachycentridae Micrasema sp. 4 132 325 258 46 0 0 0 0 0 0 Lepidostomatidae Lepidostomatinae Lepidostoma sp. 1 0 0 0 23 0 0 0 0 0 0 Uenoidae Thremmatinae Neophylax sp. 2 1 0 2 0 0 0 0 0 0 0 Helicopsychidae Helicopsyche sp. 1 0 0 0 138 0 0 0 0 0 0 Lepidoptera

 Pyralidae Nymphulinae
Appendixes 67

Appendix 7. Macroinvertebrate taxa from richest-targeted habitat samples collected from four sites in the Santa Ana River Basin, California, 1999−2001.—Continued[Values are number of individuals per square meter. UPH was not sampled in 2000 or 2001]

Taxon

Number of 

samples with 

an occurrence

Sample identification

SF99 SF00 SF01 UPH99 MWD99 MWD00 MWD01 PRD99 PRD00 PRD01

 Argyactini

Petrophila sp. 2 0 0 0 23 0 53 0 0 0 0

 Coleoptera Myxophaga Hydroscaphidae

Hydroscapha sp. 1 0 0 0 0 66 0 0 0 0 0

 Polyphaga Hydrophilidae

Enochrus sp. 1 0 0 0 0 0 0 42 0 0 0

Laccobius sp. 1 0 0 0 0 35 0 0 0 0 0

Tropisternus sp. 2 0 0 0 0 3 0 42 0 0 0

 Dryopidae

Helichus sp. 1 0 0 0 2 0 0 0 0 0 0

Postelichus sp. 2 0 0 0 1 6 0 0 0 0 0

 Elmidae 1 0 0 18 0 0 0 0 0 0 0

Optioservus sp. 1 0 0 0 70 0 0 0 0 0 0

Zaitzevia sp. 1 0 0 0 24 0 0 0 0 0 0

 Psephenidae

Psephenus sp. 1 0 0 0 2 0 0 0 0 0 0

 Diptera Nematocera Ceratopogonidae 1 0 0 37 0 0 0 0 0 0 0

 Ceratopogoninae 1 0 11 0 0 0 0 0 0 0 0

 Dasyheleinae

Dasyhelea sp. 2 0 0 0 46 0 0 42 0 0 0

 Chironomidae Chironominae Chironomini

Chironomus sp. 1 0 0 0 0 0 0 81 0 0 0

Dicrotendipes sp. 4 0 0 0 0 35 110 123 15 0 0

Endotribelos sp. 1 0 0 0 0 0 57 0 0 0 0

Microtendipes sp. 1 0 0 0 47 0 0 0 0 0 0

Nilothauma sp. 1 0 0 0 0 0 0 42 0 0 0

Saetheria sp. 3 0 0 0 0 136 331 365 0 0 0
68 Variability in Lotic Communities, Three Contrasting Stream Environments, Santa Ana River Basin, Calif., 1999–2001 Appendix 7. Macroinvertebrate taxa from richest-targeted habitat samples collected from four sites in the Santa Ana River Basin, California, 1999−2001.—Continued [Values are number of individuals per square meter. UPH was not sampled in 2000 or 2001] Taxon Number of samples with an occurrence Sample identification SF99 SF00 SF01 UPH99 MWD99 MWD00 MWD01 PRD99 PRD00 PRD01 Pseudochironomini Pseudochironomus sp. 6 0 0 0 47 101 220 1,216 15 21 0 Tanytarsini Micropsectra sp. 3 11 57 55 0 0 0 0 0 0 0 Rheotanytarsus sp. 6 11 0 0 658 0 0 246 15 42 240 Diamesinae Diamesini Pagastia sp. 4 22 114 498 24 0 0 0 0 0 0 Orthocladiinae Brillia sp. 3 13 11 44 0 0 0 0 0 0 0 Cardiocladius sp. 1 0 0 0 55 0 0 0 0 0 0 Chaetocladius sp. 1 0 0 66 0 0 0 0 0 0 0 Cricotopus sp. 7 0 0 0 82 583 893 2,280 706 1,005 206 Eukiefferiella sp. 5 142 103 22 217 51 0 0 0 0 0 Heleniella sp. 1 0 0 44 0 0 0 0 0 0 0 Nanocladius sp. 2 0 0 0 0 0 0 0 94 0 34 Parametriocnemus sp. 2 13 0 66 0 0 0 0 0 0 0 Paraphaenocladius sp. 1 13 0 0 0 0 0 0 0 0 0 Rheocricotopus sp. 5 0 11 0 0 0 128 356 24 0 34 Tvetenia sp. 3 77 217 88 0 0 0 0 0 0 0 Tanypodinae Macropelopiini Brundiniella sp. 1 0 0 55 0 0 0 0 0 0 0 Pentaneurini 5 0 23 18 117 101 0 0 0 0 34 Ablabesmyia sp. 1 0 0 0 0 0 0 0 15 0 0 Paramerina sp. 1 0 0 0 0 0 0 84 0 0 0 Pentaneura sp. 2 0 0 0 0 0 257 0 30 0 0 DixidaeDixa sp. 1 0 0 18 0 0 0 0 0 0 0 Psychodidae 2 0 11 18 0 0 0 0 0 0 0 Maruina sp. 1 0 0 0 23 0 0 0 0 0 0 Simuliidae 3 0 0 221 0 0 306 0 0 0 32 Prosimulium sp. 2 1 78 0 0 0 0 0 0 0 0 Simulium sp. 5 33 0 0 783 236 0 450 28 0 0 Thaumaleidae 1 0 0 18 0 0 0 0 0 0 0
Appendixes 69

Appendix 7. Macroinvertebrate taxa from richest-targeted habitat samples collected from four sites in the Santa Ana River Basin, California, 1999−2001.—Continued[Values are number of individuals per square meter. UPH was not sampled in 2000 or 2001]

Taxon

Number of 

samples with 

an occurrence

Sample identification

SF99 SF00 SF01 UPH99 MWD99 MWD00 MWD01 PRD99 PRD00 PRD01

 Tipulidae Limoniinae

Dicranota sp. 1 0 11 0 0 0 0 0 0 0 0

Limonia sp. 2 0 0 0 0 101 0 323 0 0 0

 Brachycera Empididae Hemerodromiinae 1 0 34 0 0 0 0 0 0 0 0

Hemerodromia sp. 7 0 0 0 47 563 257 135 107 81 32

Neoplasta sp. 1 34 0 0 0 0 0 0 0 0 0

 Pelecorhynchidae

Glutops sp. 1 0 0 18 0 0 0 0 0 0 0

 Stratiomyidae Stratiomyinae

Caloparyphus sp. 4 0 0 0 184 465 563 619 0 0 0

Euparyphus sp. 2 0 0 0 0 35 0 177 0 0 0
70 Variability in Lotic Communities, Three Contrasting Stream Environments, Santa Ana River Basin, Calif., 1999–2001 Appendix 8. Macroinvertebrate metrics calculated from qualitative and richest-targeted samples from four sites in the Santa Ana River Basin, California, 1999−2001

—

Continued.

[EPT, sum of Ephemeroptera, Plecoptera, and Trichoptera; no., number; no./m2, number of individuals per square meter. UPH was not sampled in 2000 or 2001]

Metric Sample identification

SF99 SF00 SF01 UPH99 MWD99 MWD00 MWD01 PRD99 PRD00 PRD01

Metrics from qualitative (presence/absence) dataTaxon richness (no. of taxa) 57 49 52 55 43 39 36 28 22 30

Ephemeroptera richness (no. of taxa) 11 10 8 8 3 4 5 3 2 3

Plecoptera richness (no. of taxa) 7 4 5 2 0 0 0 0 0 0

Trichoptera richness (no. of taxa) 7 6 9 11 3 3 2 2 2 2

EPT richness (no. of taxa) 25 20 22 21 6 7 7 5 4 5

EPT/Chironmid richness (no. of taxa) 1.5 1.3 1.7 1.8 0.5 0.9 0.7 0.5 0.4 0.5

Diptera richness (no. of taxa) 25 21 22 18 16 14 16 13 11 13

Chironomid richness (no. of taxa) 17 15 13 12 11 8 10 10 10 11

Orthoclad richness (no. of taxa) 12 5 7 3 4 2 2 3 3 3

Tanytarsinii richness (no. of taxa) 2 1 1 2 1 0 1 2 2 1

Nonchironomid dipteran richness (no. of taxa) 8 6 9 6 5 6 6 3 1 2

Noninsect richness (no. of taxa) 5 5 5 3 8 6 6 5 4 6

Nonmidge dipterans and noninsect richness (no. of taxa) 13 11 14 9 13 12 12 8 5 8

Odonate richness (no. of taxa) 0 0 0 1 3 3 3 0 1 3

Coleoptera richness (no. of taxa) 1 2 2 7 8 3 2 1 0 0

Mollusc and crustacean richness (no. of taxa) 1 1 1 1 1 4 2 2 2 3

Gastropod richness (no. of taxa) 0 0 0 1 1 1 1 1 1 1

Bivalve richness (no. of taxa) 1 1 1 0 0 1 0 1 0 1

Corbicula richness (no. of taxa) 0 0 0 0 0 1 0 1 0 1

Amphipod richness (no. of taxa) 0 0 0 0 0 1 0 0 1 1

Oligochaete richness (no. of taxa) 2 2 2 2 3 1 2 2 2 3

Average EPA tolerance (richness-weighted) 3.7 3.9 3.7 4.4 6.1 5.8 5.9 6.0 6.1 6.0

Ephemeroptera richness (percent) 19.3 20.4 15.4 14.5 7.0 10.3 13.9 10.7 9.1 10.0

Plecoptera richness (percent) 12.3 8.2 9.6 3.6 0.0 0.0 0.0 0.0 0.0 0.0

Trichoptera richness (percent) 12.3 12.2 17.3 20.0 7.0 7.7 5.6 7.1 9.1 6.7

EPT richness (percent) 43.9 40.8 42.3 38.2 14.0 17.9 19.4 17.9 18.2 16.7

Diptera richness (percent) 43.9 42.9 42.3 32.7 37.2 35.9 44.4 46.4 50.0 43.3

Chironomid richness (percent) 29.8 30.6 25.0 21.8 25.6 20.5 27.8 35.7 45.5 36.7

Orthoclad richness (percent) 21.1 10.2 13.5 5.5 9.3 5.1 5.6 10.7 13.6 10.0

Tanytarsini richness (percent) 3.5 2.0 1.9 3.6 2.3 0.0 2.8 7.1 9.1 3.3

Nonmidge dipteran richness (percent) 14.0 12.2 17.3 10.9 11.6 15.4 16.7 10.7 4.5 6.7

Appendix 8. Macroinvertebrate metrics calculated from qualitative and richest-targeted samples from four sites in the Santa Ana River Basin, California, 1999−2001.[EPT, sum of Ephemeroptera, Plecoptera, and Trichoptera; no., number; no./m2, number of individuals per square meter. UPH was not sampled in 2000 or 2001]
Appendixes 71

Appendix 8. Macroinvertebrate metrics calculated from qualitative and richest-targeted samples from four sites in the Santa Ana River Basin, California, 1999−2001—

Continued.

[EPT, sum of Ephemeroptera, Plecoptera, and Trichoptera; no., number; no./m2, number of individuals per square meter. UPH was not sampled in 2000 or 2001]

Metric Sample identification

SF99 SF00 SF01 UPH99 MWD99 MWD00 MWD01 PRD99 PRD00 PRD01

Noninsect richness (percent) 8.8 10.2 9.6 5.5 18.6 15.4 16.7 17.9 18.2 20.0

Nonmidge dipterans and noninsect richness (percent) 22.8 22.4 26.9 16.4 30.2 30.8 33.3 28.6 22.7 26.7

Odonate richness (percent) 0.0 0.0 0.0 1.8 7.0 7.7 8.3 0.0 4.5 10.0

Coleoptera richness (percent) 1.8 4.1 3.8 12.7 18.6 7.7 5.6 3.6 0.0 0.0

Mollusc and crustacean richness (percent) 1.8 2.0 1.9 1.8 2.3 10.3 5.6 7.1 9.1 10.0

Gastropod richness (percent) 0.0 0.0 0.0 1.8 2.3 2.6 2.8 3.6 4.5 3.3

Bivalve richness (percent) 1.8 2.0 1.9 0.0 0.0 2.6 0.0 3.6 0.0 3.3

Corbicula richness (percent) 0.0 0.0 0.0 0.0 0.0 2.6 0.0 3.6 0.0 3.3

Amphipod richness (percent) 0.0 0.0 0.0 0.0 0.0 2.6 0.0 0.0 4.5 3.3

Oligochaete richness (percent) 3.5 4.1 3.8 3.6 7.0 2.6 5.6 7.1 9.1 10.0

Filterer richness (no. of taxa) 6 4 5 7 3 3 3 5 3 4

Gatherer richness (no. of taxa) 24 19 19 17 15 12 16 10 7 9

Omnivore richness (no. of taxa) 0 0 1 0 0 1 1 0 0 0

Parasite richness (no. of taxa) 1 1 1 1 0 0 0 0 0 0

Predator richness (no. of taxa) 12 14 12 11 14 12 10 7 7 10

Scraper richness (no. of taxa) 6 4 6 11 2 4 2 2 2 2

Shredder richness (no. of taxa) 4 4 4 5 5 3 2 2 1 2

Filterer richness (percent) 11.3 8.7 10.4 13.5 7.7 8.6 8.8 19.2 15.0 14.8

Gatherer richness (percent) 45.3 41.3 39.6 32.7 38.5 34.3 47.1 38.5 35.0 33.3

Omnivore richness (percent) 0.0 0.0 2.1 0.0 0.0 2.9 2.9 0.0 0.0 0.0

Parasite richness (percent) 1.9 2.2 2.1 1.9 0.0 0.0 0.0 0.0 0.0 0.0

Predator richness (percent) 22.6 30.4 25.0 21.2 35.9 34.3 29.4 26.9 35.0 37.0

Scraper richness (percent) 11.3 8.7 12.5 21.2 5.1 11.4 5.9 7.7 10.0 7.4

Shredder richness (percent) 7.5 8.7 8.3 9.6 12.8 8.6 5.9 7.7 5.0 7.4

Metrics from richest-targeted habitats (RTH)Taxon richness (no. of taxa) 33 33 36 40 27 22 29 19 10 15

Ephemeroptera richness (no. of taxa) 8 9 6 6 3 3 4 1 2 2

Plecoptera richness (no. of taxa) 5 4 2 2 0 0 0 0 0 0

Trichoptera richness (no. of taxa) 6 3 7 10 2 2 2 2 2 2

EPT richness (no. of taxa) 19 16 15 18 5 5 6 3 4 4

EPT/Chironmid richness (no. of taxa) 0.8 0.7 0.7 0.4 1.3 0.8 2.3 2.4 2.3 1.5

Diptera richness (no. of taxa) 11 12 16 13 11 10 15 10 4 7
72 Variability in Lotic Communities, Three Contrasting Stream Environments, Santa Ana River Basin, Calif., 1999–2001 Appendix 8. Macroinvertebrate metrics calculated from qualitative and richest-targeted samples from four sites in the Santa Ana River Basin, California, 1999−2001

—

Continued.

[EPT, sum of Ephemeroptera, Plecoptera, and Trichoptera; no., number; no./m2, number of individuals per square meter. UPH was not sampled in 2000 or 2001]

Metric Sample identification

SF99 SF00 SF01 UPH99 MWD99 MWD00 MWD01 PRD99 PRD00 PRD01

Chironomid richness (no. of taxa) 8 7 10 8 6 7 9 8 3 5

Orthoclad richness (no. of taxa) 5 4 6 3 2 2 2 3 1 3

Tanytarsinii richness (no. of taxa) 2 1 1 1 0 0 1 1 1 1

Nonchironomid dipteran richness (no. of taxa) 3 5 6 5 5 3 6 2 1 2

Noninsect richness (no. of taxa) 2 4 3 2 5 2 4 5 2 4

Nonmidge dipterans and noninsect richness (no. of taxa) 5 9 9 7 10 5 10 7 3 6

Odonate richness (no. of taxa) 0 0 0 1 2 2 2 0 0 0

Coleoptera richness (no. of taxa) 0 0 1 5 4 0 2 0 0 0

Mollusc and crustacean richness (no. of taxa) 0 1 0 1 0 0 0 2 0 1

Gastropod richness (no. of taxa) 0 0 0 1 0 0 0 1 0 0

Bivalve richness (no. of taxa) 0 1 0 0 0 0 0 1 0 1

Corbicula richness (no. of taxa) 0 0 0 0 0 0 0 1 0 1

Amphipod richness (no. of taxa) 0 0 0 0 0 0 0 0 0 0

Oligochaete richness (no. of taxa) 1 1 2 1 2 1 2 2 2 3

Ephemeroptera richness (percent) 24.2 27.3 16.7 15.0 11.1 13.6 13.8 5.3 20.0 13.3

Plecoptera richness (percent) 15.2 12.1 5.6 5.0 0.0 0.0 0.0 0.0 0.0 0.0

Trichoptera richness (percent) 18.2 9.1 19.4 25.0 7.4 9.1 6.9 10.5 20.0 13.3

EPT richness (percent) 57.6 48.5 41.7 45.0 18.5 22.7 20.7 15.8 40.0 26.7

Diptera richness (percent) 33.3 36.4 44.4 32.5 40.7 45.5 51.7 52.6 40.0 46.7

Chironomid richness (percent) 24.2 21.2 27.8 20.0 22.2 31.8 31.0 42.1 30.0 33.3

Orthoclad richness (percent) 15.2 12.1 16.7 7.5 7.4 9.1 6.9 15.8 10.0 20.0

Tanytarsini richness (percent) 6.1 3.0 2.8 2.5 0.0 0.0 3.4 5.3 10.0 6.7

Nonmidge dipteran richness (percent) 9.1 15.2 16.7 12.5 18.5 13.6 20.7 10.5 10.0 13.3

Noninsect richness (percent) 6.1 12.1 8.3 5.0 18.5 9.1 13.8 26.3 20.0 26.7

Nonmidge dipterans and noninsect richness (percent) 15.2 27.3 25.0 17.5 37.0 22.7 34.5 36.8 30.0 40.0

Odonate richness (percent) 0.0 0.0 0.0 2.5 7.4 9.1 6.9 0.0 0.0 0.0

Coleoptera richness (percent) 0.0 0.0 2.8 12.5 14.8 0.0 6.9 0.0 0.0 0.0

Mollusc and crustacean richness (percent) 0.0 3.0 0.0 2.5 0.0 0.0 0.0 10.5 0.0 6.7

Gastropod richness (percent) 0.0 0.0 0.0 2.5 0.0 0.0 0.0 5.3 0.0 0.0

Bivalve richness (percent) 0.0 3.0 0.0 0.0 0.0 0.0 0.0 5.3 0.0 6.7

Corbicula richness (percent) 0.0 0.0 0.0 0.0 0.0 0.0 0.0 5.3 0.0 6.7

Amphipod richness (percent) 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0
Appendixes 73

Appendix 8. Macroinvertebrate metrics calculated from qualitative and richest-targeted samples from four sites in the Santa Ana River Basin, California, 1999−2001—

Continued.

[EPT, sum of Ephemeroptera, Plecoptera, and Trichoptera; no., number; no./m2, number of individuals per square meter. UPH was not sampled in 2000 or 2001]

Metric Sample identification

SF99 SF00 SF01 UPH99 MWD99 MWD00 MWD01 PRD99 PRD00 PRD01

Oligochaete richness (percent) 3.0 3.0 5.6 2.5 7.4 4.5 6.9 10.5 20.0 20.0

Taxon abundance (no./m2) 3,897 3,718 6,694 7,091 10,371 15,413 12,913 4,218 6,351 10,967

Ephemeroptera abundance (no./m2) 2,927 1,747 3,594 1,262 3,972 2,760 2,836 14 60 226

Plecoptera abundance (no./m2) 113 269 314 6 0 0 0 0 0 0

Trichoptera abundance (no./m2) 238 448 888 2,699 3,176 8,230 2,959 2,945 5,000 9,870

EPT abundance (no./m2) 3,278 2,464 4,795 3,967 7,148 10,989 5,794 2,958 5,060 10,095

Dipteran abundance (no./m2) 370 683 1,289 2,331 2,406 3,123 6,539 1,050 1,148 611

Chironomid abundance (no./m2) 302 538 958 1,247 1,006 1,996 4,793 915 1,067 547

Orthoclad abundance (no./m2) 258 343 331 353 634 1,020 2,635 824 1,005 274

Tanytarsini abundance (no./m2) 22 57 55 658 0 0 246 15 42 240

Nonmidge dipteran abundance (no./m2) 68 146 331 1,084 1,399 1,127 1,746 135 81 64

Noninsect abundance (no./m2) 237 549 536 648 667 918 450 196 143 261

Nonmidge dipterans and noninsect abundance (no./m2) 2,066 2,045 2,196 331 224 325 1,732 305 694 867

Odonate abundance (no./m2) 0 0 0 23 41 222 46 0 0 0

Coleoptera abundance (no./m2) 0 0 18 98 110 0 84 0 0 0

Mollusc and crustacean abundance (no./m2) 0 11 0 601 0 0 0 32 0 2

Gastropod abundance (no./m2) 0 0 0 601 0 0 0 14 0 0

Bivalve abundance (no./m2) 0 11 0 0 0 0 0 18 0 2

Corbicula abundance (no./m2) 0 0 0 0 0 0 0 18 0 2

Amphipod abundance (no./m2) 0 0 0 0 0 0 0 0 0 0

Oligochaete abundance (no./m2) 13 123 149 47 365 408 285 150 143 258

Ephemeroptera abundance (percent) 75 47 54 18 38 18 22 0 1 2

Plecoptera abundance (percent) 3 7 5 0 0 0 0 0 0 0

Trichoptera abundance (percent) 6 12 13 38 31 53 23 70 79 90

EPT abundance (percent) 84 66 72 56 69 71 45 70 80 92

Dipteran abundance (percent) 10 18 19 33 23 20 51 25 18 6

Chironomid abundance (percent) 8 14 14 18 10 13 37 22 17 5

Orthoclad abundance (percent) 7 9 5 5 6 7 20 20 16 2

Tanytarsini abundance (percent) 1 2 1 9 0 0 2 0 1 2

Nonmidge dipteran abundance (percent) 2 4 5 15 13 7 14 3 1 1

Noninsect abundance (percent) 6 15 8 9 6 6 3 5 2 2

Nonmidge dipterans and noninsect abundance (percent) 20 13 17 8 4 3 24 8 19 13
74 Variability in Lotic Communities, Three Contrasting Stream Environments, Santa Ana River Basin, Calif., 1999–2001 Appendix 8. Macroinvertebrate metrics calculated from qualitative and richest-targeted samples from four sites in the Santa Ana River Basin, California, 1999−2001

—

Continued.

[EPT, sum of Ephemeroptera, Plecoptera, and Trichoptera; no., number; no./m2, number of individuals per square meter. UPH was not sampled in 2000 or 2001]

Metric Sample identification

SF99 SF00 SF01 UPH99 MWD99 MWD00 MWD01 PRD99 PRD00 PRD01

Odonate abundance (percent) 0 0 0 0 0 1 0 0 0 0

Coleoptera abundance (percent) 0 0 0 1 1 0 1 0 0 0

Mollusc and crustacean abundance (percent) 0 0 0 8 0 0 0 1 0 0

Gastropod abundance (percent) 0 0 0 8 0 0 0 0 0 0

Bivalve abundance (percent) 0 0 0 0 0 0 0 0 0 0

Corbicula abundance (percent) 0 0 0 0 0 0 0 0 0 0

Amphipod abundance (percent) 0 0 0 0 0 0 0 0 0 0

Oligochaete abundance (percent) 0 3 2 1 4 3 2 4 2 2

Average EPA tolerance (richness-weighted) 3.3 3.7 3.8 3.9 6.1 5.5 5.9 5.7 5.7 5.8

Average EPA tolerance (abundance-weighted) 2.2 2.5 2.8 4.8 5.0 5.3 5.5 4.6 4.5 4.2

Percentage of most abundant taxon 27.2 28.0 28.4 26.4 16.0 43.4 17.7 68.2 75.6 89.7

Percentage of two most abundant taxon 49.9 41.2 49.0 37.5 31.3 53.4 31.7 85.0 91.4 91.9

Simpson’s diversity 0.83 0.87 0.86 0.89 0.89 0.78 0.91 0.50 0.40 0.19

Filterer richness (no. of taxa) 5 3 3 6 2 2 3 4 2 4

Gatherer richness (no. of taxa) 11 11 14 12 10 8 15 8 4 6

Omnivore richness (no. of taxa) 0 0 1 0 0 0 0 0 0 0

Parasite richness (no. of taxa) 1 1 1 0 0 0 0 0 0 0

Predator richness (no. of taxa) 5 10 6 7 8 6 6 3 1 2

Scraper richness (no. of taxa) 6 4 6 10 1 2 1 2 1 1

Shredder richness (no. of taxa) 3 2 3 4 3 1 2 1 1 1

Filterer richness (percent) 16.1 9.7 8.8 15.4 8.3 10.5 11.1 22.2 22.2 28.6

Gatherer richness (percent) 35.5 35.5 41.2 30.8 41.7 42.1 55.6 44.4 44.4 42.9

Omnivore richness (percent) 0.0 0.0 2.9 0.0 0.0 0.0 0.0 0.0 0.0 0.0

Parasite richness (percent) 3.2 3.2 2.9 0.0 0.0 0.0 0.0 0.0 0.0 0.0

Predator richness (percent) 16.1 32.3 17.6 17.9 33.3 31.6 22.2 16.7 11.1 14.3

Scraper richness (percent) 19.4 12.9 17.6 25.6 4.2 10.5 3.7 11.1 11.1 7.1

Shredder richness (percent) 9.7 6.5 8.8 10.3 12.5 5.3 7.4 5.6 11.1 7.1

Filterer abundance (no./m2

) 245 414 488 3,462 1,890 1,841 1,834 2,939 4,840 10,112

Gatherer abundance (no./m2

) 2,110 1,277 3,071 1,654 4,266 3,721 4,891 327 204 496

Omnivore abundance (no./m2

) 0 0 18 0 0 0 0 0 0 0
Appendixes 75

Appendix 8. Macroinvertebrate metrics calculated from qualitative and richest-targeted samples from four sites in the Santa Ana River Basin, California, 1999−2001—

Continued.

[EPT, sum of Ephemeroptera, Plecoptera, and Trichoptera; no., number; no./m2, number of individuals per square meter. UPH was not sampled in 2000 or 2001]

Metric Sample identification

SF99 SF00 SF01 UPH99 MWD99 MWD00 MWD01 PRD99 PRD00 PRD01

Parasite abundance (no./m2) 11 22 55 0 0 0 0 0 0 0

Predator abundance (no./m2) 962 1,344 1,891 302 812 843 349 151 81 66

Scraper abundance (no./m2) 241 67 370 1,562 1,522 6,748 1,820 81 202 32

Shredder abundance (no./m2) 102 202 358 108 690 893 2,603 706 1,005 206

Filterer abundance (percent) 6.7 12.5 7.8 48.8 20.6 13.1 16.0 69.9 76.4 92.7

Gatherer abundance (percent) 57.5 38.4 49.1 23.3 46.5 26.5 42.5 7.8 3.2 4.5

Omnivore abundance (percent) 0.0 0.0 0.3 0.0 0.0 0.0 0.0 0.0 0.0 0.0

Parasite abundance (percent) 0.3 0.7 0.9 0.0 0.0 0.0 0.0 0.0 0.0 0.0

Predator abundance (percent) 26.2 40.4 30.2 4.3 8.8 6.0 3.0 3.6 1.3 0.6

Scraper abundance (percent) 6.6 2.0 5.9 22.0 16.6 48.0 15.8 1.9 3.2 0.3

Shredder abundance (percent) 2.8 6.1 5.7 1.5 7.5 6.4 22.6 16.8 15.9 1.9
76 Variability in Lotic Communities, Three Contrasting Stream Environments, Santa Ana River Basin, Calif., 1999–2001 Appendix 9. Data from fish collected from four sites during the summers 1999−2001 in the Santa Ana River Basin, California.—Continued [See table 1 for explanation of sample identification. UPH was not sampled in 2001. g, gram; mm, millimeter; na, not applicable; YOY, young of the year;

—, no data]

Sample 

identification Scientific name Common name Number collected Relative abundance (percent) Mean weight (g) Range weight (g) Mean standard length (mm) Range standard length (mm) Mean total length (mm) Range total length (mm)

SF991 Salmo trutta Brown trout 86 100.0 49.4 3.1−127 134 49−195 158 69−230

SF00 Salmo trutta Brown trout 114 100.0 46.1 5.9−176 129 65−218 155 80−261

SF01 Salmo trutta Brown trout 120 100.0 24.8 1.1−81 104 38−175 125 46−210

UPH991 Salmo trutta Brown trout 27 10.1 72.7 8.0−251 140 75−244 165 90−292

Oncorhynchus mykiss2 Rainbow trout 240 89.9 43.3 1.5−151 111 48−210 134 56−252

UPH001 Salmo trutta Brown trout 21 14.5 64.9 8.2−241 139 79−255 168 97−302

Oncorhynchus mykiss2 Rainbow trout 124 85.5 42.8 4.2−99 131 62−194 160 75−233

MWD99 Gila orcutti2 Arroyo chub 46 24.7 23.1 0.5−805 68 29−166 79 35−178

Catostomus santaanae2 Santa Ana sucker 11 5.9 13.9 0.5−23 85 30−110 100 36−126

Lepomis cyanellus Green sunfish 3 1.6 14.3 1.3−40 62 36−113 72 45−125

Gambusia affinis Western mosquitofish 53 28.5 0.8 0.2−2.0 13 13−44 37 17−54

Ameiurus natalis Yellow bullhead 63 33.9 10.2 0.6−68 59 30−153 71 36−178

Tilapia mossambica Mozambique tilapia 2 1.1 16.7 1.4−32 63 34−92 79 41−117

Pimephales promelas Fathead minnow 7 3.8 1.6 0.4−5.6 41 30−64 49 36−75

Cyprinus carpio Common carp 1 0.5 257.0 na 215 na 258 na

MWD00 Gila orcutti2 Arroyo chub 41 10.8 3.9 0.9−26 52 35−105 60 41−120

Catostomus santaanae2 Santa Ana sucker 72 19.0 2.3 1.0−5.9 50 39−66 59 46−80

Gambusia affinis Western mosquitofish 249 65.7 1.0 0.1

−1.9 35 20

−43 43 23

−58

Ameiurus natalis Yellow bullhead 14 3.7 12.6 0.7−73 71 29−155 84 34−181

Pimephales promelas Fathead minnow 2 0.5 1.2 0.9−1.4 42 38−46 50 45−55

Cyprinus carpio Common carp 1 0.3

— na 280 na 340 na

MWD01 Gila orcutti2 Arroyo chub 93 47.2 2.8 0.5−14 46 30−94 55 36−100

Catostomus santaanae2 Santa Ana sucker 14 7.1 8.9 0.8−31 65 34−115 79 40−140

Micropterus salmoides Largemouth bass 1 0.5 21.9 na 97 na 118 na

Gambusia affinis Western mosquitofish 38 19.3 0.9 0.1−2.3 33 18−44 40 23−53

Ameiurus natalis Yellow bullhead 46 23.4 21.9 1.1−112 85 35−175 101 37−112

Pimephales promelas Fathead minnow 5 2.5 1.7 1.2−2.4 44 40−50 53 47−60

PRD99 Lepomis macrochirus Bluegill 28 4.4 23.0 0.2−46 79 19−105 98 23−130

Ictalurus punctatus Channel catfish 6 0.9 85.2 32−167 173 130−225 214 163−282

Cyprinus carpio Common carp 86 13.4 280.3 7.9−1,933 193 66−450 237 81−550

Pimephales promelas Fathead minnow 246 38.3 1.0 0.5−3.0 37 19−55 45 22−65

Carassius auratus Goldfish 37 5.8 60.8 30−178 126 101−185 157 125−226

Lepomis cyanellus Green sunfish 3 0.5 14.0

— 77

— 92

—

Micropterus salmoides Largemouth bass 8 1.2 66.3 52−90 147 138−160 173 162−190

Cottus asper Prickly sculpin 1 0.2 26.0 na 105 na 121 na

Appendix 9. Data from fish collected from four sites during the summers 1999−2001 in the Santa Ana River Basin, California.[See table 1 for explanation of sample identification. UPH was not sampled in 2001. g, gram; mm, millimeter; na, not applicable; YOY, young of the year;

—, no data]
Appendixes 77

Appendix 9. Data from fish collected from four sites during the summers 1999−2001 in the Santa Ana River Basin, California.—Continued[See table 1 for explanation of sample identification. UPH was not sampled in 2001. g, gram; mm, millimeter; na, not applicable; YOY, young of the year; —, no data]

Sample 

identification Scientific name Common name Number collected Relative abundance (percent) Mean weight (g) Range weight (g) Mean standard length (mm) Range standard length (mm) Mean total length (mm) Range total length (mm)

Gambusia affinis Western mosquitofish 211 32.8 0.9 0.3−1.3 33 22−38 40 28−46

Ameiurus natalis Yellow bullhead 17 2.6 32.8 1.5−100 101 32−173 116 42−200

PRD00 Lepomis macrochirus Bluegill 11 1.7 16.6 0.6−38 66 25−99 83 31−124

Cyprinus carpio Common carp 71 11.3 80.4 3.2−928 107 49−320 135 60−420

Pimephales promelas Fathead minnow 268 42.5 1.2 0.6−2.6 40 34−51 50 41−62

Carassius auratus Goldfish 58 9.2 78.9 0.6−254 122 31−205 158 38−265

Lepomis cyanellus Green sunfish 27 4.3 17.1 0.3−36 71 25−100 88 29−123

Micropterus salmoides Largemouth bass 7 1.1 38.9 4.3−143 96 56−170 119 69−213

Poecilia latipinna Sailfin molly 3 0.5 1.8 1.3−2.6 39 37−42 48 45−52

Catostomus santaanae2 Santa Ana sucker 1 0.2 YOY na YOY na YOY na

Gambusia affinis Western mosquitofish 172 27.3 0.5 0.1−1.5 27 19−39 33 21−48

Ameiurus natalis Yellow bullhead 12 1.9 2.1 0.6−4.5 41 20−60 50 32−72

PRD01 Lepomis macrochirus Bluegill 3 1.6 53.2 1.5−81 88 32−120 110 41−145

Ictalurus punctatus Channel catfish 1 0.6 228.0 na 255 na 310 na

Cyprinus carpio Common carp 39 21.4 376.4 2.8−1,182 215 48−355 276 60−460

Pimephales promelas Fathead minnow 36 19.8 1.9 0.6−3.8 46 30−59 55 35−71

Carassius auratus Goldfish 23 12.6 127.6 17−266 146 80−200 188 105−260

Lepomis cyanellus Green sunfish 52 28.6 14.8 0.6−48 67 28−108 81 33−48

Micropterus salmoides Largemouth bass 13 7.1 62.4 2.6−500 102 48−270 124 55−330

Poecilia latipinna Sailfin molly 2 1.1 2.8 0.9−4.6 39 32−46 49 40−57

Gambusia affinis Western mosquitofish 6 3.3 1.1 0.4−1.6 33 30−36 41 36−45

Ameiurus natalis Yellow bullhead 7 3.8 54.3 1.9−103 119 40−175 140 46−205

1Fish data from one pass instead of two passes using a backpack electrofisher.2Native species.
Manuscript approved for publication, July 17, 2008

Prepared by the USGS Publishing Network,

Publishing Service Center, Sacramento, California

Susan Davis

 Phil Contreras

For more information concerning the research in this report, contact the

California Water Science Center Director,

U.S. Geological Survey, 6000 J Street

Sacramento, California 95619

http://ca.water.usgs.gov
nted on recycled paper

Burton, C.-Variability in Lotic Communities in Three Contrasting Stream Environments in the Santa Ana River Basin, California, 1999–2001-Scientific Investigations Report 2008–5217