Long Term Resource Monitoring Program

Technical Report 

2005-T004

May 2005

Spatial Structure and Temporal Variation

of Fish Communities in the Upper Mississippi River System
Long Term Resource Monitoring Program Technical Reports

provide Long Term Resource Monitoring Program 

partners with scientific and technical support.

All reports in this series receive anonymous peer review.

Mention of trade names or commercial products does not constitute endorsement

or recommendation for use by the U.S. Department of the Interior, U.S. Geological Survey.
Spatial Structure and Temporal Variation

of Fish Communities in the Upper Mississippi River System

by

John H. Chick, Brian S. Ickes, Mark A. Pegg, Valerie A. Barko,

Robert A. Hrabik, and David P. Herzog

U.S. Geological Survey

Upper Midwest Environmental Sciences Center

2630 Fanta Reed Road

La Crosse, Wisconsin 54603

May 2005
Suggested citation:

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

of fish communities in the Upper Mississippi River System. U.S. Geological Survey, Upper Midwest Environmental Sciences 

Center, La Crosse, Wisconsin, May 2005. LTRMP Technical Report 2005-T004. 15 pp.

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

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

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

703-767-9050).
iii

Page

Contents

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

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

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

Methods ............................................................................................................ 2

Analyses ...................................................................................................... 4

Results ............................................................................................................... 5

Community Composition ................................................................................. 5

Community Structure ....................................................................................... 6

Community Structure—Environmental Relationships ................................................ 7

Discussion ......................................................................................................... 8

Implications for LTRMP ................................................................................. 14

Acknowledgments ............................................................................................. 14

References ...................................................................................................... 14

Tables

1. Habitat variables routinely collected from each electrofishing site for the Long Term Resource 

Monitoring Program ....................................................................................... 3

2. Common and scientific names for 19 fishes found only in the lower regional trend areas

(Pool 26, La Grange Pool, and Open River Reach). ................................................... 6

3. Presence/absence data for 31 fishes contributing to compositional differences among the three 

lower regional trend areas. ................................................................................. 7

4. Mean catch-per-unit-effort (square root catch/15 min) of 14 species of fish accounting for more

 than 90% of the dissimilarity among the groups A (Pool 8), B (Pools 4 and 13), C (Pool 26

and La Grange Pool), and D (Open River Reach). ................................................... 9

Number Page
iv

Number Page

Figures

1. Map of the Upper Mississippi River System showing the six regional trend areas (Pools 4, 8, 

13, and 26, La Grange Pool, and Open River Reach) for the Long Term Resource Monitoring 

Program ...................................................................................................... 2

2. Nonmetric multidimensional scaling ordination of fish community composition data (presence/

absence) for the Upper Mississippi River System collected by the Long Term Resource 

Monitoring Program, 1994–2002 ........................................................................ 6

3. Nonmetric multidimensional scaling ordination of fish community structure data (square root 

catch/15 min) for the Upper Mississippi River System collected by the Long Term Resource 

Monitoring Program, 1994-2002 ........................................................................ 8

4. Nonmetric multidimensional scaling ordination of fish community structure data (square root 

catch/15 min) for the Upper Mississippi River System collected by the Long Term Resource 

Monitoring Program, 1994-2002 ........................................................................ 8

5. Nonmetric multidimensional scaling ordination of fish community structure data (square root 

catch/15 min) for the Upper Mississippi River System collected by the Long Term Resource 

Monitoring Program, 1994–2002 ........................................................................ 9

6. Nonmetric multidimensional scaling ordination of fish community structure data and indexed by 

multiple gears, for the Upper Mississippi River System collected by the Long Term Resource 

Monitoring Program, 1994–2002 ..................................................................... 10

7. Nonmetric multidimensional scaling ordination of fish community structure data, indexed by 

multiple gears, and averaged by year across all resource trend areas for the Upper Mississippi 

River System collected by the Long Term Resource Monitoring Program, 1994–2002 ...... 10

8. Nonmetric multidimensional scaling ordination of fish community structure data, indexed by 

multiple gears, and averaged by year across all resource trend areas for the Upper Mississippi 

River System collected by the Long Term Resource Monitoring Program, 1994–2002 ...... 11

9. Nonmetric multidimensional scaling ordination of fish community structure data, indexed by 

multiple gears, and averaged by year across all resource trend areas for the Upper Mississippi 

River System collected by the Long Term Resource Monitoring Program, 1994–2002 ...... 12

10. Nonmetric multidimensional scaling ordination of fish community structure data (square root 

catch/15 min) for the Upper Mississippi River System collected in day electrofishing samples

by the Long Term Resource Monitoring Program, 1994–2002 .................................... 13
v

Preface

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

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

of Engineers’ Environmental Management Program. The LTRMP is implemented by the Upper 

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

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

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

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

Memorandum of Agreement.

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

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

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

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

with information for maintaining the UMRS as a sustainable large river ecosystem given its multuse 

character. The long-term goals of the Program are to understand the system, determine resource trends 

and effects, develop management alternatives, manage information, and develop useful products.

This report supports Task 2.2.8 as specified in Goal 2, Monitor Resource Change, of the LTRMP 

Operating Plan (U.S. Fish and Wildlife Service 1993). This report was developed with funding 

provided by the LTRMP.
Spatial Structure and Temporal Variation

of Fish Communities in the Upper Mississippi River System

by

John H. Chick1, Brian S. Ickes2, Mark A. Pegg3, Valerie A. Barko4,

Robert A. Hrabik4, and David P. Herzog4

1

Illinois Natural History Survey, Great Rivers Field Station

8450 Montclair Avenue, Brighton, Illinois 62012 2

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

2630 Fanta Reed Road, La Crosse, Wisconsin 54603 3

Illinois Natural History Survey, Illinois River Biological Station

704 North Schrader, Havana, Illinois 62644 4

Missouri Department of Conservation, Open River and Wetlands Field Station

3815 E. Jackson Blvd., Jackson, Missouri 63755

Abstract: Variation in community composition (presence/absence data) and structure (relative abundance) of 

Upper Mississippi River fishes was assessed using data from the Long Term Resource Monitoring Program 

collected from 1994 to 2002. Community composition of fishes varied more in space than through time. 

We found substantial variation in community composition across two spatial scales: large-scale differences 

between upper and lower river reaches and small-scale differences among individual regional trend areas 

(RTA). Community structure (relative abundance data) of fishes also varied more through space than through 

time. We found substantial variation in fish community structure at three spatial scales: (1) large-scale 

differences between upper and lower river reaches, (2) differences among individual RTA, and (3) differences 

among habitat strata, with backwaters having a distinct community structure relative to the main channel and 

side channels. When averaged across all RTA, fish community structure in 1994 and 1995 was distinct from 

all other years, possibly as a result of the 1993 Flood. Fish community structure observations for each RTA 

and year correlated with the environmental variables measured at each sample site. A canonical approach 

revealed that the combination of Secchi depth, water temperature, current velocity, and vegetation abundance 

had the greatest correlation with community structure.

Key words: fish communities, LTRMP, ordination, spatial scale, Upper Mississippi River System

and trends of UMRS natural resources, (3) assist 

in the development and evaluation of management 

alternatives, and (4) manage and provide access 

to resulting data, information, and products (U.S. 

Army Corps of Engineers 1997). A critical tool for 

achieving these goals is standardized monitoring 

of four key ecosystem components—water quality, 

aquatic vegetation, aquatic macroinvertebrates, 

and fish—at five regional trend areas (RTA) on 

the Mississippi River and one RTA on the Illinois 

River. Central to the objectives of LTRMP are 

the ability to detect long-term trends for these 

key components, and the ability to correlate these 

Introduction

The Long Term Resource Monitoring Program 

(LTRMP) was authorized by the Water Resources 

Development Act of 1986 as an element of the 

U.S. Army Corps of Engineers’ Environmental 

Management Program. The primary mission of 

the LTRMP is to provide river managers and the 

public with ecological information necessary to 

maintain the Upper Mississippi River System 

(UMRS) as a viable multiuse ecosystem. Four 

long-term goals have been established for the 

LTRMP: (1) increase understanding of how the 

river ecosystem operates, (2) monitor the status 
2

trends with environmental variables to gain 

insight into possible cause-and-effect relations.

Fishes are one of the most important goods 

and services that rivers provide to humans. 

Upper Mississippi River fishes are the subject 

of commercial and recreational fisheries, both 

of which contribute substantially to local 

economies. For example, recreation on the Upper 

Mississippi River alone has been estimated to 

provide 18,000 jobs and generate $1.2 billion in 

our economy per year and recreational fishing 

is a key component of this economic activity 

(Carlson et al. 1995; Sparks et al. 1998). Fish 

communities are frequently used as indicators of 

ecological integrity for large-river ecosystems 

because of their diversity and their response 

to environmental variation at multiple scales 

(Gammon and Simon 2000; Schiemer 2000; 

Schmutz et al. 2000). Therefore, the ability 

to detect variation in the 

composition and structure of 

fish communities is a desirable 

feature of long-term monitoring 

programs in large-river 

ecosystems.

We used LTRMP fish data 

from 1994 to 2002 to examine 

shifts in the composition 

(presence/absence of species) 

and structure (relative abundance 

of species) of fish communities 

in the UMRS. Our analyses of 

community composition relied 

on presence/absence data from 

a combination of five gears: 

day electrofishing, large and 

small hoop nets, fyke nets, and 

mini-fyke nets (Gutreuter et 

al. 1995). To assess patterns 

in fish community structure, 

we relied on data from day 

electrofishing, and we also 

developed a multigear index 

of community structure and 

analyzed this to complement 

the information gained from the 

more conservative analysis of 

day electrofishing data alone. 

Finally, we used multivariate 

correlation techniques to 

assess whether any patterns of the measured 

environmental variables were correlated with 

observed fish community patterns.

Methods

We analyzed fish data collected by the 

LTRMP from 1994 to 2002 (1993 was excluded 

from these analyses because of incomplete 

data collection). This program monitors fish 

communities in six RTA in the Upper Mississippi 

River System: Pools 4, 8, 13, and 26, La Grange 

Pool of the Illinois River, and an open river 

reach (Open River Reach; Figure 1). We relied 

on two sets of data for our analyses: (1) day 

electrofishing catch-per-unit-effort (CPUE; 

number collected per 15 min), which has been 

shown to have power to detect changes for 

the greatest number of species relative to all 

Figure 1. Map of the Upper Mississippi River System showing the six regional 

trend areas (Pools 4, 8, 13, and 26, La Grange Pool, and Open River Reach) in light 

grey for the Long Term Resource Monitoring Program.
3

in diameter by 2.5 cm), and the mesh size was 

2.5 cm. Large and small hoop nets were baited 

with 3 kg of soybean cake and were deployed for 

48 hours. Hoop nets were set so that the open end 

(first hoop) was facing downstream in water of 

sufficient depth to submerge all of the throats. 

Fyke and mini-fyke nets were Wisconsin-type 

trap nets comprised of three sections: (1) a 

rectangular frame, (2) a cab section within the 

frame comprised of six hoops that led to the cod 

end, and (3) a lead, which was a bar of mesh 

that extended from the frame to the shoreline. 

For fyke nets, the lead was 15 m long and 1.3 m 

high, the frame was 1.8 × 6 m, the cab was 

formed from 0.9-m steel hoops, and the mesh 

size was 1.8 cm. For mini-fyke nets, the lead was 

4.5 m long and 0.6 m high, the frame was 1.2 × 

3 m, the cab was formed by two 0.6-m diameter 

hoops, and the mesh size was 3 mm. Fyke and 

mini-fyke nets were set with the lead extended 

perpendicular to the shoreline. Water depth at the 

frame had to be sufficient to submerge the throats 

and nets were fished for 24 hours.

For all collection methods, a series of standard 

physical and chemical measurements were 

made at the initiation of sampling (Table 1). 

Water depth was recorded from a depth-finder, 

and Secchi depth was recorded to the nearest 

centimeter. Water temperature was measured to 

the nearest 0.1°C, conductivity was measured 

in μS/cm using a YSI Conductivity Meter 

(YSI, Inc., Yellow Springs, OH), and current 

velocity was measured to the nearest 0.01 m/s. 

Additionally, qualitative assessments of percent 

the collection methods used in the LTRMP 

(Lubinski et al. 2001); and (2) a combination of 

total catch data from day electrofishing, large 

and small hoop nets, fyke nets, and mini-fyke 

nets to provide more complete data on species 

composition and community structure. Collection 

methodology are published elsewhere (Gutreuter 

et al. 1995) and will be only briefly summarized 

below. For all gears, data were collected using a 

stratified random design, where the main channel 

borders, side channels, contiguous backwaters, 

and impounded areas constitute unique strata. 

Sites are selected at random from each stratum, 

allowing for the computation of poolwide 

averages that are weighted by the total area of 

each stratum within each RTA.

Day electrofishing was conducted using pulsedDC output with two ring anodes, and the boat 

hull served as the cathode. Two dippers collected 

fishes, and voltage and amperage were adjusted 

for water temperature and conductivity to achieve 

a power output of 3,000 W. Day electrofishing 

was conducted continuously along shorelines for 

15 min at each sample site.

Large and small hoop nets were set in paired 

deployments. Large hoop nets were 4.8 m long 

and included seven fiberglass hoops. The first 

hoop was 1.2 m in diameter and successive hoops 

decreased in diameter incrementally by 2.5 cm. 

Two throats were attached, one to the second 

hoop and one to the fourth hoop, and the mesh 

size was 3.7 cm in diameter. Small hoop nets 

were 3 m long, had seven hoops (first hoop was 

0.6 m in diameter, successive hoops decreased 

Table 1. Habitat variables routinely collected from each electrofishing site for the Long Term Resource Monitoring 

Program (Gutreuter et al. 1995).

Habitat factor Units Explanation

Secchi cm

Conductivity μS/cm

Flow (surface velocity) m/s

Water temperature °C

Depth m

Vegetation coverage 0, 1, 2, 3 0 = 0% coverage; 1 = 1-19% coverage 2 = 20-49% coverage;

3 = 50% coverage

Vegetation density 0, 1, 2 0 = no vegetation; 1 = sparse; 2 = dense

Substrate 1, 2, 3, 4 1 = silt; 2 = silt/clay/little sand 3 = sand/mostly sand;

4 = gravel/rock/hard clay

Woody structure presence/absence presence/absence of woody structure

Revetment presence/absence presence/absence of shoreline revetment

Inlet/outlet presence/absence presence/absence on an inlet/outlet channel to a backwater lake

Flooded terrestrial vegetation presence/absence presence/absence of flooded terrestrial vegetation
4

aquatic vegetation coverage and density, substrate 

type, and other habitat factors were recorded 

(Table 1).

Analyses

We analyzed variation of community 

composition through space and time using 

presence/absence data from a combination of day 

electrofishing, large and small hoop nets, fyke 

nets, and mini-fyke nets. Because some species 

were not well sampled by any of these gears, we 

eliminated any species where <20 individuals 

were collected when summed across all RTA 

and years. This resulted in analyses being 

conducted on presence/absence data from a total 

of 100 fishes. Hybrids and fishes not identified 

to species were eliminated from these analyses. 

Presence/absence data were summarized for 

each RTA and year, and a similarity matrix 

was constructed based on Euclidean distance. 

All analyses were performed using the Primer 

version 5 software package (Primer-E Ltd 2001).

We used Analysis of Similarity (ANOSIM) 

to test for significant variation among RTA and 

years. Analysis of similarity is analogous to 

univariate Analysis of Variance (ANOVA) which 

tests for significant differences among groups. 

Unlike ANOVA, however, ANOSIM is based 

on a similarity matrix rather than raw data, and 

significance is based on comparisons of this 

matrix to random permutations of the matrix 

(Clarke and Warwick 1994). Two test statistics 

are provided by ANOSIM, an R statistic that 

reflects the amount of dissimilarity associated 

with each factor (analogous to the R2 statistic 

from ANOVA) and a P value that indicates 

whether R (range -1 to 1) is significantly 

different from zero. Both R and P are important 

to consider because it is possible for R to 

be significantly different from zero but still 

inconsequentially small (Clarke and Warwick 

1994). Our analyses tested for variation of the 

fish community among RTA when averaged 

across all years and variation among years 

when averaged across all RTA. Nonmetric 

multidimensional scaling (NMDS) was used 

to identify groupings of observations, and a 

similarity breakdown (SIMPER procedure in 

Primer; Primer-E Ltd 2001) was used to identify 

the species contributing to the dissimilarity 

among the groups identified with NMDS. 

Variation in community structure was 

analyzed from day electrofishing CPUE data 

and from standardized total catch data from the 

combination of day electrofishing, large and 

small hoop nets, fyke nets, and mini-fyke nets. 

For day electrofishing, we limited the species 

used to a group of 16 for which electrofishing 

had power ≥0.80 to detect a 20% interannual 

abundance change in at least one habitat stratum 

of at least one RTA based on the Lubinski et al. 

(2001) power analysis. This conservative criteria 

was adopted to help ensure that the patterns of 

relative abundance used in these analyses reflect 

true ecological patterns rather than sampling 

artifacts. Hybrids and fishes not identified to 

species were omitted from these analyses.

Because of the large size of the UMRS and its 

physical complexity, no single gear effectively 

samples the entire UMRS fish community. Thus, 

we chose to include data from five gear types 

(day electrofishing, large and small hoop nets, 

fyke nets, and mini-fyke nets) simultaneously 

to permit the broadest definition of the UMRS 

fish community as possible. However, each gear 

differed notably in its selectivity characteristics 

(Ickes and Burkhardt 2002), potentially 

complicating our approach. Our solution 

capitalized on the highly standardized nature of 

the LTRMP sampling protocols. Within a RTA, 

proportional gear allocations were constant 

over time (years). Although the individual gears 

used in our analyses differ in their selectivity, 

the combined selectivity of the five gear types 

remains constant over time within a river reach. 

By placing data from each gear on the same 

scale (standardization) and calculating separate 

multigear indexes for each study reach and year, 

we ensure that no single gear overly influenced 

our results while allowing the broadest definition 

of community as possible. Furthermore, the use 

of poolwide estimates of mean CPUE weighted 

by habitat strata should minimize differences in 

abundance estimates arising from variation of 

gear allocation among RTA.

Annual mean CPUE estimates were compiled 

for each collected species from all RTA, years, 

and gear types. For each gear, we limited the 

species used in these analyses to those for 
5

which power ≥0.80 to detect a 20% interannual 

abundance change in at least one habitat stratum 

of at least one RTA (Lubinski et al. 2001). Under 

this criteria, a total of 37 fishes were included 

in these analyses. We arranged data from each 

gear in a matrix with species (n = 37) comprising 

the rows and RTA (n = 6) and year (n = 10) 

combinations comprising the columns. We 

then calculated a total catch for each row (i.e., 

summed CPUE across species) and calculated 

the grand mean total catch (GMTC) for each 

gear type. To place CPUE data from each gear 

on the same relative scale, we divided CPUE 

from each species, RTA, and year combination 

by the appropriate GMTC for that particular 

gear. This standardization places all observations 

on the same scale (proportion of GMTC) 

while maintaining all of the species abundance 

relations within a RTA-year combination and 

all differences among RTA-year combinations 

within a species. Finally, we summed the 

standardized mean CPUE estimates for all 

five gear types together for each RTA and year 

combination resulting in a 37 × 60 matrix, 

to arrive at a multigear index of community 

structure.

We used ANOSIM to test for variation 

in community structure (day electrofishing 

CPUE and multigear index) among RTA when 

averaged across years and for variation among 

years when averaged across RTA. We used 

NMDS to identify groupings of observations. 

Analysis of similarity and NMDS were based on 

Bray-Curtis similarity matrices. Two analyses 

were conducted examining different spatial 

scales. In the first, observations consisted 

of RTA-stratum-year combinations. In the 

second, observations consisted of RTA-year 

combinations. Furthermore, we examined 

temporal patterns across all RTA by averaging 

the standardized catch data from the multigear 

index across RTA for each year. For the analysis 

of day electrofishing data among RTA and years, 

a similarity breakdown was used to identify the 

species contributing most to the dissimilarity 

among groups. We did not conduct a similarity 

breakdown for the multigear index because the 

efficacy of this approach has not been examined 

on a species-by-species basis.

Finally, we used the electrofishing data to 

examine whether spatial and temporal variation 

in fish community structure corresponded with 

variation in the environmental factors collected 

from each sample site. The two categorical 

vegetation measures—percent cover and 

density (Table 1)—were multiplied to form 

one variable representing overall abundance of 

aquatic vegetation. We calculated a normalized 

(mean = 0, standard deviation = 1) Euclidean 

distance matrix from the habitat variables, and a 

Mantel test was used to determine whether this 

correlated with the Bray-Curtis similarity matrix 

from fish community structure data. A canonical 

Mantel test (BioEnv procedure in Primer; Clarke 

and Warwick 1994) was used to determine the 

combination of habitat variables that provided the 

greatest correlation with community data.

Results

Community Composition

We found notable spatial variation of 

community composition at two scales. 

Community composition varied significantly 

among river reaches (R = 0.92; P < 0.001) and 

years (R = 0.13; P = 0.019), but the relatively 

small R value associated with among year 

differences suggests that most of the dissimilarity 

among observations was due to spatial variation. 

Nonmetric multidimensional scaling revealed 

spatial groupings at two scales: upper and 

lower river reaches and individual RTA. The 

greatest variation was between upper and lower 

river reaches (Figure 2). Also, community 

composition overlapped substantially among the 

three upper RTA whereas the three lower RTA 

each formed separate and fairly distinct groups 

(Figure 2). Five fish species—burbot (Lota lota), 

spotted sucker (Minytrema melanops), weed 

shiner (Notropis texanus), western sand darter 

(Ammocrypta clara), and central mudminnow 

(Umbra limi)—were collected only in upper river 

reaches. Nineteen species were collected only in 

the lower river reaches (Table 2). The similarity 

breakdown showed that 31 species contributed 

more than 90% of the dissimilarity among the 

three lower RTA (Table 3).
6

Community Structure

We found notable variation in community 

structure at three spatial scales. Community 

structure of fishes collected using day 

electrofishing varied 

significantly among RTA 

(R = 0.840; P < 0.001) and 

stratum (R = 0.532; P < 0.001). 

Nonmetric multidimensional 

scaling revealed little overlap 

between upper and lower river 

reaches (Figure 3). Pool 8 was 

disassociated from the other 

upper RTA, and the Open 

River Reach was somewhat 

distinct from the other lower 

reaches. Pools 4 and 13 showed 

considerable overlap as did 

Pool 26 and La Grange Pool 

(Figure 3). When the samples 

are coded according to stratum, 

backwaters were fairly distinct 

from the main channel borders 

and side channels, which 

overlapped considerably 

(Figure 4). A total of 12 species 

accounted for more than 90% 

of the dissimilarity between 

backwaters and the main channel 

or side channels. Gizzard shad (Dorosoma 

cepedianum), bluegill (Lepomis macrochirus), 

largemouth bass (Micropterus salmoides), 

common carp (Cyprinus carpio), smallmouth 

buffalo (Ictiobus bubalus), black crappie 

(Pomoxis nigromaculatus), bullhead minnow 

(Pimephales vigilax), and freshwater drum 

(Aplodinotus grunniens) were more abundant 

in backwaters. Emerald shiner (Notropis 

atherinoides), spotfin shiner (Cyprinella 

spiloptera), white bass (Morone chrysops), and 

shorthead redhorse (Moxostoma macrolepidotum) 

were more abundant in the main channel borders 

and side channels.

We also found substantial variation in 

community structure among river reaches 

when annual poolwide averages of CPUE 

were analyzed. Community structure varied 

significantly among RTA (R = 0.83; P < 0.001) 

and years (R = 0.226; P = 0.001), but the 

relatively small R associated with years suggests 

that most of the dissimilarity among our data 

was associated with differences among river 

reaches. Nonmetric multidimensional scaling 

revealed little overlap between upper and lower 

Figure 2. Nonmetric multidimensional scaling ordination of fish community 

composition data (presence/absence) for the Upper Mississippi River System 

collected by the Long Term Resource Monitoring Program, 1994–2002. Data were 

from a combination of day electrofishing, large and small hoop nets, fyke nets, and 

mini-fyke nets. Each point represents community composition for a single year 

within the designated regional trend area. Ecological similarity was measured 

using the Euclidean Distance metric. The upper resource trend areas (Pools 4, 

8, and 13) are represented by open symbols whereas the lower resource trend 

areas (Pool 26, La Grange Pool, and Open River Reach) are represented by shaded 

symbols. 4 = Pool 4, 8 = Pool 8, 13 = Pool 13, 26 = Pool 26, LG = La Grange Pool, and 

OR = Open River Reach.

Table 2. Common and scientific names for 19 fishes found 

only in the lower regional trend areas (Pool 26, La Grange 

Pool, and Open River Reach).

Common name Scientific name

Bighead carp Hypopthalmichthys nobilis

Blue catfish Ictalurus furcatus

Blacktail shiner Cyprinella venusta

Blackstripe topminnow Fundulus notatus

Freckled madtom Noturus nocturnus

Goldfish Carassius auratus

Grass carp Ctenopharyngodon idella

Inland silverside Menidia beryllina

Longear sunfish Lepomis megalotis

Western mosquitofish Gambusia affinis

Red shiner Cyprinella lutrensis

Redear sunfish Lepomis microlophus

Silverband shiner Notropis shumardi

Striped bass Morone saxatilis

Skipjack herring Alosa chrysochloris

Spotted bass Micropterus punctulatus

Silver carp Hypothalmichthys molitrix

Threadfin shad Dorosoma petenense

White perch Morone americana
7

RTA (Figure 5). Furthermore, four groups were 

apparent: A, Pool 8; B, Pools 4 and 13; C, 

Pool 26 and La Grange Pool; and D, the Open 

River Reach. The similarity breakdown revealed 

that 13 species accounted for more than 90% of 

dissimilarity between upper and lower groups. 

Emerald shiner, bluegill, largemouth bass, spotfin 

shiner, bullhead minnow, shorthead redhorse, 

and silver redhorse (Moxostoma anisurum) 

were more abundant in the upper river reaches, 

whereas gizzard shad, common carp, channel 

catfish (Ictalurus punctatus), smallmouth buffalo, 

white bass, and freshwater drum were more 

abundant in the lower river reaches. Fourteen 

species accounted for more than 90% of 

dissimilarity among groups (Table 4). Group A 

had the greatest abundance of bluegill, spotfin 

shiner, largemouth bass, bullhead minnow, 

shorthead redhorse, silver redhorse, 

and black crappie. Group B had 

the greatest abundance of emerald 

shiner, and group C had the greatest 

abundance of gizzard shad, common 

carp, freshwater drum, white bass, 

smallmouth and bigmouth buffalo 

(Ictiobus cyprinellus).

Analysis of community structure 

using the multigear index revealed 

more defined differences among 

the six RTA and greater temporal 

variation. Community composition 

varied significantly among RTA 

(R = 0.793; P < 0.001) and years 

(R = 0.324; P < 0.001). As with our 

analyses of day electrofishing data 

alone, NMDS revealed little overlap 

of upper and lower river reaches 

and each of the six RTA were fairly 

distinct (Figure 6). When data were 

averaged by year across the six 

RTA, 1994 was disassociated from 

all other years (Figure 7), and a 

group of seven species—common 

carp, black crappie, channel catfish, 

bluegill, emerald shiner, gizzard 

shad, and smallmouth buffalo—

were associated strongly with 

variation among years (Figure 8). 

Some of these species decreased

 after 1994, whereas others increased

 after 1994 (Figure 9).

Community Structure—Environmental 

Relationships

Similarity among RTA and years in community 

structure was significantly correlated with 

environmental variables (Mantel R = 0.60; 

P < 0.001). Canonical Mantel correlations 

showed the greatest correlation (R = 0.76) with a 

combination of Secchi disk transparency, water 

temperature, current velocity, and vegetation 

abundance. Upper RTA had greater abundance 

of aquatic vegetation and deeper Secchi depths. 

Lower RTA had faster current velocity and higher 

temperature (Figure 10).

Table 3. Presence/absence data for 31 fishes contributing to compositional 

differences among the three lower regional trend areas (26 = Pool 26, 

LG = La Grange Pool, and OR = Open River Reach).

Common name Scientific name

Pools

collected in

Trout perch Percopsis omiscomaycus OR

River redhorse Moxostoma carinatum OR

Pugnose minnow Opsopoeodus emiliae OR

Bluntnose darter Etheostoma chlorosoma OR

Mimic shiner Notropis volucellus OR

Inland silverside Menidia beryllina OR

Blacktail shiner Cyprinella venusta OR

Spotted bass Micropterus punctulatus OR

Silver lamprey Ichthyomyzon unicuspis 26

Rock bass Ambloplites rupestris LG

Yellow perch Perca flavescens LG

Northern hog sucker Hypentelium nigricans LG

Pumpkinseed Lepomis gibbosus LG

Highfin carpsucker Carpiodes velifer LG

Silver redhorse Moxostoma anisurum LG

White perch Morone americana LG

Shovelnose sturgeon Scaphirhynchus platorynchus 26, OR

Speckled chub Macrhybopsis aestivalis 26, OR

River darter Percina shumardi 26, OR

Mississippi slivery minnow Hybognathus nuchalis 26, OR

Spotfin shiner Cyprinella spiloptera 26, OR

Channel shiner Notropis wickliffi 26, OR

Grass pickerel Esox americanus vermiculatus 26, LG

Northern pike E. lucius 26, LG

Brown bullhead Ameiurus nebulosus 26, LG

Striped bass Morone saxatilis LG, OR

White sucker Catostomus commersoni LG, OR

Longear sunfish Lepomis megalotis LG, OR

Johnny darter Etheostoma nigrum LG, OR

Fathead minnow Pimephales promelas LG, OR

Pirate perch Aphredoderus sayanus LG, OR
8

Discussion

Community structure 

and composition of 

UMRS fishes varied 

more in space than 

in time. Our analyses 

suggest a hierarchy 

of spatial variation. 

Observations first 

grouped according 

to large-scale 

differences between 

upper and lower river 

reaches, then grouped 

at smaller scales 

including individual 

RTA or groups of 

RTA, and finally 

grouped according to 

habitat stratum. For 

these data, temporal 

patterns were largely 

limited to variation 

among observations 

within spatial 

groupings. If systemic 

temporal trends of 

a magnitude greater 

than the observed 

spatial variation had 

been prevalent, our 

observations would 

have grouped first 

by year and then by 

spatial groupings. 

Our observations 

that spatial variation 

of UMRS fish 

communities were 

predominate over 

temporal variation may 

appear trivial, but have 

important implications 

for understanding 

the ecology of this 

system and for the 

design of research and 

monitoring programs. 

Figure 4. Nonmetric multidimensional scaling ordination of fish community structure 

data (square root catch/15 min of day electrofishing) for the Upper Mississippi River 

System collected by the Long Term Resource Monitoring Program, 1994–2002. Each 

point represents fish community structure for a combination of year and habitat strata 

within the designated regional trend area. Ecological similarity was measured using the 

Bray-Curtis Similarity metric. The ordination is identical to Figure 3 (year × habitat strata 

× resource trend area) but with points coded by habitat strata (B = backwaters, M = main 

channel, and S = side channel) rather than resource trend area. 

Figure 3. Nonmetric multidimensional scaling ordination of fish community structure data 

(square root catch/15 min of day electrofishing) for the Upper Mississippi River System 

collected by the Long Term Resource Monitoring Program, 1994–2002. Each point represents 

fish community structure for a combination of year and habitat strata within the designated 

regional trend area. Ecological similarity was measured using the Bray-Curtis Similarity 

metric. The upper resource trend areas (Pools 4, 8, and 13) are represented by open 

symbols whereas the lower resource trend areas (Pool 26, La Grange Pool, and Open River 

Reach) are represented by shaded symbols. 4 = Pool 4, 8 = Pool 8, 13 = Pool 13, 26 = Pool 26, 

LG = La Grange Pool, and OR = Open River Reach.
9

For example, the stratified random design used 

in the LTRMP stratifies by habitat, whereas our 

analyses demonstrated that fish communities 

varied more across larger spatial scales (e.g., 

RTA and upper and lower reaches).

The most consistent pattern observed in 

our analyses of community composition and 

structure was a clear separation of the upper three 

RTA from the lower RTA. Similar results were 

found in a 1-year study 

that extended LTRMP 

day electrofishing to 

river reaches upstream 

and downstream of three 

RTA (Chick and Pegg 

2004). Two previous 

studies also found 

distinct differences 

between upper and lower 

UMRS reaches based on 

habitat variables (U.S. 

Geological Survey 1999; 

Koel 2001). Similar 

spatial patterns of fish 

community structure 

have also been observed 

in the Missouri and 

Illinois Rivers (Pegg 

and Pierce 2002; Pegg 

and McClellend 2004). 

Geographic range 

limitations of fishes 

probably influenced 

our community composition results, as several 

species reach the northern or southern limits of 

their range in the lower or upper portion of the 

UMRS. Additionally, habitat factors and possibly 

contemporary and/or historical barriers to 

migration probably influenced differences in fish 

composition and community structure between 

upper and lower reaches. Upper river reaches had 

deeper Secchi depths and greater abundance of 

Figure 5. Nonmetric multidimensional scaling ordination of fish community structure 

data (square root catch/15 min of day electrofishing) for the Upper Mississippi River 

System collected by the Long Term Resource Monitoring Program, 1994–2002. Each point 

represents community structure (based on poolwide means) for a single year within the 

designated regional trend area. Ecological similarity was measured using the Bray-Curtis 

Similarity metric. The upper resource trend areas (Pools 4, 8, and 13) are represented by 

open symbols whereas the lower resource trend areas (Pool 26, La Grange Pool, and Open 

River Reach) are represented by shaded symbols. 4 = Pool 4, 8 = Pool 8, 13 = Pool 13, 26 = 

Pool 26, LG = La Grange Pool and OR = Open River Reach.

Table 4. Mean catch-per-unit-effort (square root catch/15 min) of 14 species of fish accounting for more than 

90% of the dissimilarity among the groups (A = Pool 8; B = Pools 4 and 13; C = Pool 26 and La Grange Pool; and 

D = Open River Reach).

Group

Species Scientific name A B C D

Gizzard shad Dorosoma petenense 1.72 3.51 7.13 5.83

Bluegill Lepomis macrochirus 5.21 3.04 1.43 0.22

Spotfin shiner Cyprinella spiloptera 2.99 0.84 0.18 0.01

Bullhead minnow Pimephales vigilax 2.58 0.71 0.21 0.06

Largemouth bass Micropterus salmoides 2.94 2.06 0.83 0.03

Emerald shiner Notropis atherinoides 2.46 2.62 1.31 1.49

Common carp Cyprinus carpio 1.43 2.22 3.11 1.55

Shorthead redhorse Moxostoma macrolepidotum 1.3 0.77 0.14 0.01

Freshwater drum Aplodinotus grunniens 0.41 0.98 1.61 1.11

Silver redhorse Moxostoma anisurum 0.99 0.48 0 0

Smallmouth buffalo Ictiobus bubalus 0.09 0.38 1.4 0.45

White bass Morone chrysops 0.49 0.84 1.64 0.95

Bigmouth buffalo Ictiobus cyprinellus 0.05 0.15 0.68 0.15

Black crappie Pomoxis nigromaculatus 0.8 0.76 0.52 0.04
10

aquatic vegetation compared to lower river 

reaches, whereas lower river reaches had faster 

current velocity and higher water temperature.

In addition to 

differences between 

upper and lower river 

reaches, there were 

differences in fish 

communities among 

RTA and stratum. 

Differences among RTA 

were significant in every 

analysis conducted. 

Community composition 

was more variable among 

the three lower RTA than 

among the three upper 

RTA. In our analyses 

of day electrofishing 

data, some overlap in 

community structure was 

apparent for Pools 4 and 

13, as well as for Pool 26 

and La Grange Pool. We 

used fairly conservative 

criteria for the inclusion 

of species in this analysis. 

Our multigear analyses, 

which included a total 

of 81 species, showed 

more distinct groupings 

of observations for each 

of the RTA. As expected, 

fish community structure 

differed among strata, 

but this variation was less 

important than variation 

between upper and 

lower river reaches, and 

variation among RTA.

Classification systems 

recognizing major habitat 

types, such as main 

channel borders, side 

channels, and backwaters, 

are fundamental to the 

study of large rivers 

(Welcomme 1979, 1985). 

As a result, monitoring 

programs and ecological studies conducted on 

large river systems (including the LTRMP) often 

explicitly incorporate these habitat types into 

Figure 7. Nonmetric multidimensional scaling ordination of fish community 

structure data, indexed by multiple gears, and averaged by year across all 

resource trend areas for the Upper Mississippi River System collected by the 

Long Term Resource Monitoring Program, 1994–2002. Ecological similarity was 

measured using the Bray-Curtis Similarity metric. Labels reflect the averaged 

community structure for each year.

Figure 6. Nonmetric multidimensional scaling ordination of fish community structure data 

and indexed by multiple gears for the Upper Mississippi River System collected by the 

Long Term Resource Monitoring Program, 1994–2002. Each point represents community 

structure for a single year within the designated resource trend area. Ecological 

similarity was measured using the Bray-Curtis Similarity metric. The upper resource 

trend areas (Pools 4, 8, and 13) are represented by open symbols whereas the lower 

resource trend areas (Pool 26, La Grange Pool, and Open River Reach) are represented 

by shaded symbols. 4 = Pool 4, 8 = Pool 8, 13 = Pool 13, 26 = Pool 26, LG = La Grange Pool, 

and OR = Open River Reach.
11

their experimental design. Variation of fish 

communities at larger spatial scales is less 

understood. Much of the variance in UMRS 

fish communities was associated with large 

spatial scales, suggesting that our understanding 

of the dynamics of fish communities in the 

UMRS and other large river systems probably 

would benefit from focused investigations 

into the factors contributing to these patterns. 

What environmental or biological variables are 

influencing this variation? How can we separate 

the influence of environmental variables on 

these spatial patterns from demographic factors 

such as immigration/emigration, propagule/

offspring dispersal, zoogeography, etc.? If fish 

communities vary at large spatial scales as much 

or more than they do among major habitat types, 

how should monitoring and research studies 

incorporate this scale of variation into their 

experimental design?

Temporal patterns of fish community variation 

may reflect an effect of the 1993 Flood. The year 

1994 was distinct from all other years within 

our time series, and the multigear index was 

especially useful for identifying this pattern. 

Observations made during the 1993 Flood 

suggest that several fishes took advantage of 

increased access to floodplain habitats for 

feeding and reproduction, and many appeared 

to produce exceptional year classes (National 

Biological Service et al. 1994). In the time 

series we examined (1994 to 2002), common 

carp, freshwater drum, and black crappie had 

their peak abundance in 1994, possibly as a 

result of successful reproduction in 1993. Other 

species had their lowest abundance in 1994, 

Figure 8. Nonmetric multidimensional scaling ordination of fish community structure data, indexed by multiple 

gears, and averaged by year across all resource trend areas for the Upper Mississippi River System collected by 

the Long Term Resource Monitoring Program, 1994–2002. Ecological similarity was measured using the Bray-Curtis 

Similarity metric. Each point represents one species, with information averaged across regional trend areas. 

Species grouping closely together varied similarly through time. Labels reflect the four-digit letter codes used to 

identify species by the Long Term Resource Monitoring Program (Gutreuter et al. 1995). The circle encloses seven 

fish species (BKCP = black crappie [Pomoxis nigromaculatus], BLGL = bluegill [Lepomis macrochirus], CARP = 

common carp , [Cyprinus carpio] CNCF = channel catfish [Ictalurus punctatus], ERSN = emerald shiner [Notropis 

atherinoides], GZSD = gizzard shad [Dorosoma cepedianum]) that are grouping disjunctively from all other species, 

suggesting stronger variation through time for these species.
12

��

��

Figure 9. Nonmetric multidimensional scaling ordination of fish community structure data, indexed by multiple gears, and averaged by year across all resource trend areas for the Upper Mississippi River System collected by the Long Term Resource Monitoring Program, 1994–2002. Ecological similarity was measured using the Bray-Curtis Similarity metric. The ordination is identical to Figure 7, but overlaid with the relative abundance of seven fish species (A = common carp [Cyprinus carpio]; B = black crappie [Pomoxis nigromaculatus]; C = channel catfish [Ictalurus punctatus]; D = bluegill [Lepomis macrochirus]; E = emerald shiner [Notropis atherinoides]; F = gizzard shad [Dorosoma cepedianum]; and G = smallmouth buffalo [Ictiobus bubalus]) associated strongly with variation among years. Size of the circles is directly proportional to the abundance of each species for the specified year.
13

Figure 10. Nonmetric multidimensional scaling ordination of fish community structure data (square root catch/15 min of day electrofishing) for the Upper Mississippi River System collected by the Long Term Resource Monitoring Program, 1994–2002. Ecological similarity was measured using the Bray-Curtis Similarity metric. The ordination is identical to Figure 5 but with environmental conditions overlaid on the ordination to demonstrate associations across resource trend areas and years. Size of each circle reflects the mean value of each habitat factor (A = Secchi disk transparency, B = temperature, C = current velocity, and D = vegetation abundance) for each regional trend area (4 = Pool 4, 8 = Pool 8, 13 = Pool 13, 26 = Pool 26, LG = La Grange Pool, and OR = Open River Reach) and year. 

������������������������ �����������

�������������������� ����������������
14

possibly as a result of dramatic changes to habitat 

associated with the flood such as reductions 

in aquatic vegetation (Spink and Rogers 1996) 

and sedimentation effects (National Biological 

Service et al. 1994). Given the magnitude of the 

1993 Flood, the relatively modest amount of 

temporal variation of UMRS fish communities 

further emphasizes the importance of the spatial 

variation observed.

Our use of a multigear index of fish community 

structure was novel and should be further 

examined as a potential useful method for 

examining community dynamics. Because 

several questions regarding the efficacy of this 

approach need to be addressed, we limited our 

use of this index to a secondary and supportive 

role to the more conservative analysis conducted 

with day electrofishing data alone. The results 

from the multigear analyses were, in general, 

corroborative of those from day electrofishing. 

Therefore, we believe further investigation into 

this analysis technique is warranted.

Implications for LTRMP

Our study demonstrated that LTRMP fish data 

can be used to detect variation in community 

composition and structure through space and 

time. We were able to detect temporal variation 

that was consistent across all RTA, while 

simultaneously detecting large-scale spatial 

variation. Additionally, we were able to correlate 

large-scale spatial patterns with environmental 

variables measured locally within each river 

reach. This last result points to the importance of 

the habitat data collected during fish monitoring, 

including observational data (i.e., vegetation 

cover and density). Finally, our analyses suggest 

that further examination of spatial variability of 

fish communities and habitat in the UMRS may 

yield important insights into ecological dynamics 

and function within this river-floodplain 

ecosystem. 

Acknowledgments

This study was funded by the U.S. Army 

Corps of Engineers and administered by the 

U.S. Geological Survey, Upper Midwest 

Environmental Sciences Center. Further support 

was provided by the Minnesota Department 

of Natural Resources, Wisconsin Department 

of Natural Resources, Iowa Department of 

Natural Resources, Missouri Department of 

Natural Resources, and Illinois Natural History 

Survey. We thank all of the field crews, team 

leaders, and component specialists associated 

with the LTRMP who were responsible for data 

collection and management. Barry Johnson and 

three anonymous reviewers provided valuable 

comments on an earlier version of this report.

References

Carlson, B. D., D. B. Propst, D. J. Synes, and 

R. S. Jackson. 1995. Economic impact of 

recreation on the Upper Mississippi River 

System. Prepared for the U.S. Army Corps 

of Engineers Waterways Experiment Station, 

Vicksburg, Mississippi. Technical Report EL95-16. 

Chick, J. H., and M. A. Pegg. 2004. Long 

Term Resource Monitoring Program outpool 

fisheries analysis: Final report. U.S. Geological 

Survey, Upper Midwest Environmental 

Sciences Center, La Crosse, Wisconsin, 

March 2004. LTRMP 2004-T001. 21 pp.

Clarke, K. R., and R. M. Warwick. 1994. Change 

in marine communities: an approach to 

statistical analysis and interpretation. Plymouth 

Marine Laboratories, Plymouth, United 

Kingdom.

Gammon, J. R., and T. P. Simon. 2000. Variation 

in a great river index of biotic integrity over a 

20-year period. Hydrobiologia 422/423:291–

304.

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

1995. Long Term Resource Monitoring 

Program procedures: Fish monitoring. 

National Biological Service, Environmental 

Management Technical Center, Onalaska, 

Wisconsin. LTRMP 95-P002-1. 

42 pp. + Appendixes A–J.

Ickes, B. S., and R. W. Burkhardt. 2002. 

Evaluation and proposed refinement of the 
15

sampling design for the Long Term Resource 

Monitoring Program’s fish component. 

U.S. Geological Survey, Upper Midwest 

Environmental Sciences Center, La Crosse, 

Wisconsin, October 2002. LTRMP 2002-T001. 

17 pp. + Appendixes A–E. CD-ROM included. 

(NTIS # PB2003-500042)

Koel, T. M. 2001. Classification of Upper 

Mississippi River pools based on contiguous 

aquatic/geomorphic habitats. Journal of 

Freshwater Ecology 16:159–170.

Lubinski, K, R. Burkhardt, J. Sauer, D. Soballe, 

and Y. Yin. 2001. Initial analyses of change 

detection capabilities and data redundancies in 

the Long Term Resource Monitoring Program. 

U.S. Geological Survey, Upper Midwest 

Environmental Sciences Center, La Crosse, 

Wisconsin, September 2001. LTRMP 2001-

T001. 23 pp. + Appendixes A–E (NTIS # 

PB2002-100123).

National Biological Service, Illinois Natural 

History Survey, Iowa Department of Natural 

Resources, and Wisconsin Department of 

Natural Resources. 1994. Long Term Resource 

Monitoring Program 1993 Flood observations. 

National Biological Service, Environmental 

Management Technical Center, Onalaska, 

Wisconsin, December 1994. LTRMP 94-S011. 

190 pp. (NTIS #PB95-181582).

Primer-E Ltd. 2001. Primer for Windows 

Version 5.2.4. Plymouth, United Kingdom.

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

community structure in the Missouri and 

Lower Yellowstone rivers in relation to flow 

characteristics. Hydrobiologia 479:155–167.

Pegg, M. A., and M. A. McClelland. 2004. 

Assessment of spatial and temporal fish 

community patterns in the Illinois River. 

Ecology of Freshwater Fish 13:125–135.

Schiemer, F. 2000. Fish as indicators for the 

assessment of ecological integrity of large 

rivers. Hydrobiologia 422/423:271–278.

Schmutz, S., M. Kaufmann, B. Vogel, M. 

Jungwirth, and S. Muhar. 2000. A multilevel concept for fish-based, river-typespecific assessment of ecological integrity. 

Hydrobiologia 422/423:279–289.

Sparks, R. E., J. C. Nelson, and Y. Yin. 1998. 

Naturalization of the flood regime in regulated 

rivers: the case of the upper Mississippi River. 

Bioscience 48:706–720.

Spink, A., and S. Rogers. 1996. The effects of 

a record flood on the aquatic vegetation of 

the Upper Mississippi River System: some 

preliminary findings. Hydrobiologia 340:51–

57.

U.S. Army Corps of Engineers. 1997. Report 

to Congress, An evaluation of the Upper 

Mississippi River System Environmental 

Management Program, December 1997. 

Chapters 1–8 + Appendixes A-B.

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

Plan for the Upper Mississippi River System 

Long Term Resource Monitoring Program. 

Environmental Management Technical Center, 

Onalaska, Wisconsin, Revised September 

1993. EMTC 91-P002R. 179 pp. (NTIS 

#PB94-160199)

U.S. Geological Survey. 1999. Ecological 

status and trends of the Upper Mississippi 

River System 1998: a report of the Long 

Term Resource Monitoring Program. 

U.S. Geological Survey, Upper Midwest 

Environmental Sciences Center, La Crosse, 

Wisconsin, April 1999. LTRMP 99-T001. 

236 pp.

Welcomme, R. L. 1979. Fisheries ecology of 

floodplain rivers. Longman Group Limited. 

London. 317 pp.

Welcomme, R. L. 1985. River fisheries. Food 

and Agriculture Organization, United Nations, 

Rome. FAO Fisheries Technical Paper 262.
REPORT DOCUMENTATION PAGE Form approved

OMB No. 0704-0188

2. REPORT DATE 3. REPORT TYPE AND DATES COVERED

5. FUNDING NUMBERS

8. PERFORMING ORGANIZATION

REPORT NUMBER

10. SPONSORING, MONITORING

AGENCY REPORT NUMBER

12b. DISTRIBUTION CODE

15. NUMBER OF PAGES

16. PRICE CODE

20. LIMITATION OF ABSTRACT

Public reporting burden for this collection is estimated to average 1 hour per response, including time for reviewing instructions, searching existing data sources,

gathering and maintaining the data needed, and completing and reviewing the collection of information. Send comments regarding this burden estimate or any other

aspect of this collection of information, including suggestions for reducing this burden, to Washington Headquarters Services, Directorate for Information Operations and

Reports, 1215 Jefferson Davis Highway, Suite 1204, Arlington, VA 22202-4302, and to the Office of Management and Budget, Paperwork Reduction Project (0704-0188)

Washington, DC 20503.

1. AGENCY USE ONLY (Leave

Blank)

4. TITLE AND SUBTITLE

6. AUTHOR(S)

7. PERFORMING ORGANIZATION NAME(S) AND ADDRESSES

9. SPONSORING/MONITORING AGENCY NAME(S) AND ADDRESSES

11. SUPPLEMENTARY NOTES

12a. DISTRIBUTION/AVAILABILITY STATEMENT

13. ABSTRACT (Maximum 200 words)

14. SUBJECT TERMS (Keywords)

17. SECURITY CLASSIFICATION

OF REPORT

18. SECURITY CLASSIFICATION OF

THIS PAGE

19. SECURITY CLASSIFICATION OF

ABSTRACT

Standard Form 298 (rev. 2-89)

Prescribed by ANSI Std. Z39-18

298-102

NSN 7540-01-280-5500

Variation in community composition (presence/absence data) and structure (relative abundance) of Upper Mississippi River fishes was 

assessed using data from the Long Term Resource Monitoring Program collected from 1994 to 2002. Community composition of fishes 

varied more in space than through time. We found substantial variation in community composition across two spatial scales: large-scale 

differences between upper and lower river reaches and small-scale differences among individual regional trend areas (RTA). Community 

structure (relative abundance data) of fishes also varied more through space than through time. We found substantial variation in fish 

community structure at three spatial scales: (1) large-scale differences between upper and lower river reaches, (2) differences among 

individual RTA, and (3) differences among habitat strata, with backwaters having a distinct community structure relative to the main 

channel and side channels. When averaged across all RTA, fish community structure in 1994 and 1995 was distinct from all other years, 

possibly as a result of the 1993 Flood. Fish community structure observations for each RTA and year correlated with the environmental 

variables measured at each sample site. A canonical approach revealed that the combination of Secchi depth, water temperature, current 

velocity, and vegetation abundance had the greatest correlation with community structure.

 fish communities, LTRMP, ordination, spatial scale, Upper Mississippi River System

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

Springfield, VA 22161 (1-800-553-6847 or 703-487-4650. Available to registered users from the 

Defense Technical Information Center, Attn: Help Desk, 8725 Kingman Road, Suite 0944, Fort 

Belvoir, VA 22060-6218 (1-800-225-3842 or 703-767-9050).

Unclassified Unclassified Unclassified

John H. Chick1, Brian S. Ickes2, Mark A. Pegg3, Valerie A. Barko4, Robert A. Hrabik4, 

and David P. Herzog4

1

Illinois Natural History Survey, Great Rivers Field Station, 8450 Montclair Avenue, Brighton, Illinois 62012; 

2

U.S. Geological Survey, Upper Midwest Environmental Sciences Center, 2630 Fanta Reed Road, La Crosse, 

Wisconsin 54603; 3Illinois Natural History Survey, Illinois River Biological Station, 704 North Schrader, 

Havana, Illinois 62644; 4Missouri Department of Conservation, Open River and Wetlands Field Station, 3815 E. 

Jackson Blvd., Jackson, Missouri 63755

U.S. Geological Survey

Upper Midwest Environmental Sciences Center

2630 Fanta Reed Road

La Crosse, Wisconsin 54603

15 pp.

2005-T004

Spatial Structure and Temporal Variation of Fish Communities in the Upper Mississippi River System

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

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

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

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

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

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

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