Copyright 2012, Christopher A. Cheek

Spatial and Temporal Variation in Fish Assemblage of the Lower Pecos River, Texas

by

Christopher A. Cheek, B.S.

A Thesis

In

Wildlife, Aquatic, and Wildlands Science and Management

Submitted to the Graduate Faculty

of Texas Tech University in

Partial Fulfillment of

the Requirements for

the Degree of

Master of Sciences

Approved

Dr. David Rogowski

Chair of Committee

Dr. Christopher M. Taylor

Dr. Gene R. Wilde

Dr. Peggy Gordon Miller

Dean of the Graduate School

August, 2012

Copyright 2012, Christopher A. Cheek

Texas Tech University, Christopher Cheek, August 2012 Texas Tech University, Christopher Cheek, August 2012

ii

Acknowledgements

Many people contributed to the success of this project. First, I would like to thank

my committee for the countless hours of work that they have contributed to this project. I

would especially like to thank my thesis advisor, Dr. Christopher Taylor for making this

project possible. I am eternally grateful for Dr. Taylor’s advice and guidance through this

process. I am also thankful to Dr. David Rogowski for his time and effort. Dr. Gene

Wilde provided me with valuable editing and commentary that was very helpful. I would

also like to thank my undergraduate advisor, Dr. Tim Patton, for his contribution as a

collaborator and mentor. This project was made possible through funding from Texas

Parks and Wildlife. I would also like to thank Mark McKinstry and the Bureau of

Reclamation for providing funding to sample the lower Canyons sites. I would like to

thank Gordon Linam and Leroy Kleinsasser for their assistance and providing data to

make this project possible. Thank you to Jason Wrinkle and Corbin Neil from The Nature

Conservancy for allowing access to Independence Creek Preserve. I am also thankful to

the International Boundary Waters Commission for allowing access to their property.

Thank you to Kyle Davis and Mayme and Odell Brotherton for graciously allowing me to

sample on their property. I would also like to thank Seiji Miyazono, Cameron Gallegos,

Logan Cross, Marshall Bailey, Jennifer Zavaleta, and Matt VanLandeghem who

volunteered their time to assist with field collections. Last, but certainly not least I would

like to thank Jennifer Zavaleta and my family for much needed moral support.


iii

Table of Contents

Acknowledgements ................................................................................................. ii

Abstract ...................................................................................................................v

List of Tables ......................................................................................................... vi

List of Figures ....................................................................................................... vii

I. Introduction ..........................................................................................................1

Study Area .........................................................................................................2

Previous Study ...................................................................................................6

II. Materials and Methods ........................................................................................9

Fish Collection ................................................................................................9

Physical Parameters ......................................................................................10

Analysis.........................................................................................................11

Species Richness Comparisons ...............................................................11

Temporal Fish Assemblage Comparisons ..............................................12

Fish assemblages and Environmental Correlations ................................13

III. Results ..............................................................................................................14

Species Richness Comparisons .....................................................................14

Fish Assemblage Comparisons .....................................................................22

Salinity ..........................................................................................................25

Habitat ...........................................................................................................26

Fish assemblage and Environmental Correlations ........................................27

IV. Discussion ........................................................................................................31

Temporal Variation in Fish Assemblages .....................................................31


iv

Spatial Variation Fish Assemblages .............................................................36

Literature Cited ......................................................................................................40


v

Abstract

Most river systems have been heavily impacted by human alterations that have

long-term ecological consequences. The lower Pecos River in the Trans-Pecos region of

Texas has undergone anthropogenic changes that include decreased flow, elevated

salinity, species loss, and species invasion. Comparative studies are important to

determine the long-term effects of these changes on fish assemblages. I compared

historical and contemporary fish assemblages from the Pecos River at local (site-specific)

and regional (Trans-Pecos region) scales across 24 years. Fish assemblage data were

collected during two time periods, October 1987 and 2011, by seining at 15 sites

spanning 430 km of the river in Texas. Additionally, I examined contemporary

environmental conditions to determine species-environment relationships. I found that

fish assemblages were significantly different between time periods, likely due to

increased salinization caused by irrigation and oil field pollution. Decreased species

richness, species replacement, and increases in tolerant species were documented in the

upstream sites. Freshwater springs lower the salinity in the downstream reach which

allows for higher species diversity. Better management of regional aquifers, changes to

irrigation practices, mitigation of petroleum waste water, and proper flow regulation are

necessary for protecting biodiversity in the lower Pecos River.


vi

List of Tables

1. Comparisons of local species richness for 15 (14 sites for abundance level

of 128) sites on the lower Pecos River in 1987 and 2011. P-values

correspond to paired t-tests of local species richness between the two time

periods. Differences were assessed for all sites, upstream sites, and

downstream sites. Differences were also tested using rarefied species

richness at two abundance levels (All species: 113 and 128; Native

species: 57 and 112). P-values ≤ 0.05 indicate a significant difference in

species richness between time periods. Degrees of freedom are listed in

parentheses for each test. Direction of change in species richness from

1987 to 2011 is indicated by (+) or (-). ..........................................................21

2. Pearson correlations for fish species with NMS axes for fish assemblages

in the lower Pecos River (Figures 4 & 5).Fish were collected in October

1987 and Summer and October 2011. Comparisons were made between

October 1987 and Oct 2011, and between summer and October 2011.

Strong correlations (r≥0.50) are indicated by bold ........................................23

3. Pearson correlations of measured environmental variables with NMS axes

1 and 2 for fish assemblages of the lower Pecos River in summer and

October 2011.Pearson correlations (r≥0.60, bold) indicate strong

assemblage-environment relationships ..........................................................30


vii

List of Figures

1. Figure 1. Map of study area. Sites are represented by numbered squares.

Site numbers correspond to site names in Figure 4 .............................................8

2. The 95% confidence intervals for regional rarefaction curves based on15

sites on the lower Pecos River in 1987 (solid line) and 2011 (dashed line).

Curves were constructed with 25 species and 8310 individuals in 1987 and

25 species and 15699 individuals in 2011. ..........................................................15

3. Rarefaction curves and 95% confidence intervals of native regional

species richness across 15 sites on the lower Pecos River. Sites were

sampled in 1987 (solid line) and 2011 (dashed line). Curves were

constructed with 7441 individuals and 21 native species in 1987 and

11132 individuals and 21 native species in 2011.................................................17

4. Rarefaction curves and 95% confidence intervals of combined species

richness from 9 upstream sites on the lower Pecos River. Sites were

sampled in 1987 (solid line) and 2011 (dashed line). Curves were

constructed with 5150 individuals and 14 native species in 1987 and 7467

individuals and 10 native species in 2011............................................................18

5. Rarefied species richness at an abundance level of 113 individuals for 15

sites on the lower Pecos River. Sample site names and site numbers are

listed on the X-axis. Samples were collected in October of 1987 (black

bars) and 2011 (grey bars). Sites are ordered longitudinally from upstream

to downstream. .....................................................................................................20

6. Nonmetric Multidimensional Scaling analysis of 1987 (open symbols) and

2011 (closed symbols) fish samples from the lower Pecos River. NMS

axes 1, 2 and 3 account for 18.9%, 10.2% and 60.3% of the variation,

respectively. Upstream sites show greatest differences between time

periods. Circles indicate upstream sites and triangles represent

downstream sites. Site numbers correspond to site names in Figure 3. ...............24

7. Specific conductance for 15 sites on the Pecos River. Measurements were

collected in October of 1987 (black bars) and 2011 (grey bars). .........................26

8. Nonmetric Multidimensional Scaling analysis of 2011 fish samples from

the 15 sites on the lower Pecos River. Summer samples are represented by

open symbols and fall samples are designated by closed symbols.

Upstream sites are represented by squares and downstream sites are

represented by triangles. Site numbers correspond to sites names in Figure

3............................................................................................................................28


1

Chapter I

Introduction

Rivers and streams, particularly in arid regions, have been severely altered by

humans. Rivers primarily have been affected by impoundments, water quality

degradation, water diversion, and extensive introduction of invasive species (Miller and

Chernoff 1979; Williams1985; Hubbs 1990; Propst and Stefferud 1994; Rinne 1995).

These alterations have caused decreases in aquatic biodiversity around the world (Dirzo

and Raven 2003). Texas also has experienced a major loss of native species. Within

Texas, 44% of native fishes are considered to be extinct, extirpated, or imperiled (Hubbs

2008).

The Pecos River has been impacted by several anthropogenic alterations such as

fragmentation, altered flow regime, pollution, and channelization; this has led to

increasing salinization. Salinity along with habitat availability greatly influences

community structure of fishes in the lower Pecos River. Therefore, changes to salinity

and habitat quality could have a profound impact on fish community structure.

In order to document the magnitude and extent of anthropogenic impacts, it is

necessary to examine ecosystems over long temporal scales. Comparisons of historical

and contemporary assemblages provide a way to detect assemblage shifts and individual

species declines. Temporal comparisons also allow for examination of environmental

factors that contribute to the loss of biodiversity. Understanding the processes and

mechanisms of assemblage change can aid in the development of management practices

that best preserve biodiversity.


2

In this study I examined changes in biota and environmental conditions over a 24-

year period in the lower Pecos River. The specific objectives for this study were to

compare historical and contemporary fish assemblages from the Pecos River at local

(site-specific) and regional (Trans-Pecos region) scales and to examine contemporary

associations between environmental factors and fish assemblages.

Study Area

The Pecos River begins in the Sangre de Cristo Mountains in north-central New

Mexico and flows south-southeast to Texas. The river concludes at the confluence with

the Rio Grande just upstream of Amistad Reservoir. The lower Pecos River begins near

Carlsbad, New Mexico and flows 770 kilometers to the Rio Grande River (Hoagstrom

2001). This study focuses on the Texas portion of the river from Red Bluff Reservoir to

the Rio Grande confluence (Figure 1).

Along its course, the lower Pecos River flows through two major geomorphic

divisions. The river flows through the Permian Basin beginning near Artesia, NM and

enters the Edwards Plateau near Iraan, TX. In the Permian Basin, the river is wide and

low gradient, and becomes incised in limestone canyons after it enters the Edwards

Plateau. Upstream flow and irrigation returns provide the greatest contribution to flow in

the Permian Basin because there is little perennial surface water in the region (Hoagstrom

2009). In the Edwards Plateau freshwater springs greatly increase discharge especially

during drought conditions. Live Oak Creek, Independence Creek, and Howard Creek are

spring-fed tributaries in this region. Salinity is greatest in the reach between Red Bluff

Reservoir and Iraan, TX (Linam and Kliensasser 1996; Hoagstrom 2001; Hoagstrom


3

2009). Past studies indicate that salinity increases from the headwaters to Iraan and then

decreases downstream (Linam and Kleinsasser 1996; Davis 1987; Hoagstrom 2009).

Decreases in salinity associated with freshwater springs occur in a fairly short distance

between Sheffield and Independence Creek.

Natural sources of salinity and anthropogenic land use in the region contribute to

high contemporary salinity levels. Historical accounts indicate that the water had a

“salty” taste but settlers used it as a source for drinking (Lingle and Linford 1961).

Natural sources of salinity often are associated with the brine aquifer near Malaga, NM

(Havens and Wilkins 1979). Hoagstrom et al. (2009) concluded that salinity levels have

increased since major water development began.

Irrigation has directly contributed to salinization through the concentration of salts

in return channels and field runoff (Pillsbury 1981; Williams 1987). Crop production in

this arid region heavily relies on irrigation since rainfall only amounts to 30-40 cm

annually (Davis 1987). Agricultural areas in the Pecos River area are associated with

alluvial valleys in the Fort Sumner, Roswell, Carlsbad, and Toyah Basins (Ashworth

1990). Overdraft of water from local aquifers is also associated with decreases in river

flow and increases in salinity. Groundwater levels in the region have fallen as much as

150m since water resource development began around the turn of the century (Brune

2002). Freshwater springs throughout the Permian Basin now have decreased flows or no

longer contribute freshwater to the river. In some cases, springs that once supplied fresh

water now discharge saline water from depleted aquifers (Hoagstrom 2009). Increased


4

evaporation associated with reservoirs also contributes to water loss and increased

salinity (Hoagstrom 2009).

Oil and gas production in the Pecos drainage may also be linked to increased

salinity levels. Saline water is a major byproduct of petroleum production in this area.

Waste water is disposed of by two methods, injection into saline aquifers or pumping into

evaporation or storage ponds. This water has been documented to contain varying

amounts of sodium, calcium, magnesium chloride, sulfate, and several trace metals

(Baker and Brendecke 1983). Several studies have observed contamination of

groundwater and surface water has as a result of local petroleum production (Chipman

1959; Pettyjohn 1971; Baker and Brendecke 1983; Shipley 1991). Waste water can reach

aquifers and surface flows through seepage from holding ponds, subsurface flows, and

accidental releases (Baker and Brendecke 1983). Reduced water quality resulting from

waste water pollution has been documented to reduce species richness and diversity in

bivalve and fish communities (Pettyjohn 1971; Fuller 1974; Shipley 1991). Major oil and

gas production is active in every county that borders the Pecos River in Texas, and likely

contributes to salinization (Campbell 1959; Gregory and Hatler 2008).

Not surprisingly, salinity and water quality have influenced the species

distribution in the Pecos River (Hoagstrom 2001). The stretch of river between Red Bluff

Dam and Iraan, the most saline area, is dominated by seven euryhaline fish species

(Hoagstrom 2009). The earliest fish assessments in this section do not predate the

development of water resources in the region, but loss of noneuyhaline species has been

documented in this highly saline reach (Hoagstrom 2001).


5

Species composition has also been impacted by the introduction of non-native,

invasive species. Vectors of introduction include intentional stocking of game fish as well

as bait bucket releases (Hoagstrom 2003). Native fish populations have suffered as a

result of non-native introductions due to hybridization and competition. For example, the

introduction of Cyprinodon variegatus has led to genetic introgression with the native

Cyprinodon pecosensis (Echelle and Connor 1989). A hybrid swarm is now prevalent in

the main stem of the river, with pure populations only persisting in wetlands and a single

tributary. Hybognathus amarus is another species that has been negatively impacted by

invasion and flow regime shifts. Hybognathus amurus has been replaced by the

Hybognathus placitus in New Mexico (Hoagstrom et al. 2010). Hybognathus placitus is

not native to the Pecos River but is more naturally tolerant of reduced base flows than H.

amurus (Hoagstrom et al. 2010). Other introduced species, including Fundulus grandis,

Cyprinus carpio, Cyprinella venusta, and Lepomis auritus also occur in the Pecos River

and have unknown effects on local fish assemblages (Smith and Miller 1986).

The widespread establishment of non-native salt cedar has altered the banks of the

Pecos River (Davis 1980; Hubbs 1990). Salt cedar is an aggressive riparian invader that

can develop dense monotypic stands along rivers and streams. Salt cedar can deplete

water levels, alter native bank vegetation, increase soil salinity, and change channel

morphology (Shafroth et al. 2005). Removal of salt cedar occurred in the Pecos River

drainage in Texas from 1999-2003 with the goal of decreasing salinity and increasing

flow although success was minimal (Hart et al. 2005).


6

Another stressor that impacts fish assemblages in the lower Pecos is golden algae,

Prymnesium parvum. This introduced algal species can produce toxins that are fatal to

freshwater fish. For example, In November 1986 a toxic algae bloom resulted in a 99%

kill of fish in the Pecos River between Iraan and Amistad Reservoir (Rhodes and Hubbs

1992). The bloom originated near Iraan and the toxic “wedge” reached Amistad reservoir.

These toxins caused major fish kills in 1985, 1986, and 1988 (Rhodes and Hubbs 1992).

Earlier fish kills in the 1960 were likely due to golden algae but were not confirmed.

More recently toxic algae blooms have occurred in the Pecos River in 1993, 1995, and

2005-2007 (Southard et al. 2010).

Previous Study

Linam and Kliensasser (1996) published a report by Texas Parks and Wildlife

Department examining the relationship between water quality and fish communities in

the Pecos River. Fish and water quality were sampled at 16 sites in October of 1987.

They reported that the distribution and abundance of fish species appeared to be strongly

related to salinity. Salt tolerant species such as pupfish, rainwater killifish (Lucania

parva), red shiner (Cyprinella lutrensis), inland silverside (Menidia beryllina) and

western mosquitofish (Gambusia affinis) were found to comprise the greatest portion of

the fish community in areas with high conductivity. Dominance of these euryhaline

species decreased with in areas with lower conductance.

Linam and Kliensasser (1996) also noted significant declines of roundnose

minnow (Dionda episcopa) and gray redhorse (Moxostoma congestum) from historical

studies. Declines in spring flow and surface water depletion are suggested reasons for


7

declines. Increased dominance of red shiners was noted from previous collections. Linam

and Kliensasser’s report (1996) was chosen as for comparison purposes because of the

large area sampled as well as the environmental data available.


8

Figure 1. Map of study area. Sites are represented by numbered squares. Site numbers

correspond to site names in Figure 4.


9

Chapter II

Materials and Methods

I followed methods outlined by Linam and Kleinsasser (1996) in order to assess

change in fish assemblages across a 24-year time span. For comparison I collected fish

and environmental data at corresponding locations in May-July and October, 2011. I

sampled 15 main-stem sites and 2 tributary sites at Independence Creek and Salt Creek.

One site was not sampled in 2011 due to access issues. I consulted with Gordon Linam so

that localities and sampling techniques were matched as closely as possible. Salt Creek

was sampled only in October 2011 and the Harkell Canyon site was not sampled in 2011.

October samples were used for comparison and sample dates were matched as closely as

possible to minimize natural, seasonal differences.

Fish Collection

Fish were collected using a 1.8 m by 6.1 m, 4.8 mm braided cotton mesh seine.

Seining was performed in a downstream pattern with pulls ranging from 1-5m. All habitat

types were sampled at each site. For example, all riffles, runs, and pools present within a

sample reach were seined. Sampling effort depended on habitat complexity and ranged

between 45 and 50 minutes per site. All fish less than 25 cm in length were preserved in

a 10% formalin solution, except at sites on Independence Creek Preserve. At

Independence Creek rare and threatened species were enumerated and returned to the

water. All preserved fish were identified in the laboratory. Fish greater than 25 cm were

identified in the field and returned to the water. All specimens were cataloged and

deposited at the University of Texas Museum.


10

Physical Parameters

Water temperature, pH, dissolved oxygen, specific conductance, total dissolved

solids, and salinity were measured in the field using a multi-probe Hanna water quality

meter. Turbidity and chlorophyll-a were measured using a fluorometer (Turner Designs,

AuqaFluor®). Turbidity and chlorophyll-a were averaged from three samples at each site

to account for sample variability. Water quality data was collected below the surface of

the water usually in areas with some flow near the center of the sample reach.

A minimum of six transects were designated at each sample site prior to sampling

for fish. The number of transects reflected the site length and habitat complexity. For

example, a seventh transect would be added if a unique habitat did not fall within the first

six transects. Transects spanned the width of the river and were evenly spaced throughout

the area sampled. Dominate substrate type was recorded at three points along each

transect. Depth also was measured at each substrate sample point. Percentage of each

substrate type was calculated from at least18 point classifications sampled on the

transects. Substrate measurements were classified using a modified Wentworth scale

(Cummins 1962). Substrate was classified as boulder, cobble, gravel, sand, or mud.

Measurements for each substrate class are provided in Cummins (1962). Stream width,

average depth, and maximum velocity were measured at each site. Maximum velocity

(m/s) was measured by floating a neutrally buoyant object over two meters.

The presence of algae, aquatic macrophytes, woody debris, and over stream

herbaceous vegetation was visually ranked by percent coverage. Percent coverage

estimates of each habitat variable were assessed in the area between each transect (20-


11

30m), always looking upstream. The area between each transect was also classified as

riffle, run, or pool. This allowed for percentage calculation of riffle, run, and pool habitat

present at a site. Rank values were averaged to allow for ranking of the site as a whole.

Habitat variables were visually classified on a scale of zero to three (Taylor et al. 2003),

with zero indicating absence and 3 indicating ubiquity. Salt cedar bank coverage also was

ranked on this scale at each transect. The same observer ranked the coverage of each

variable at all sites to minimize observer variability.

Analysis

Species Richness Comparisons

Rarefaction was used to compare local and regional species richness between time

periods (Taylor et al. 2008). Rarefaction allows for comparisons of species richness

between samples with differing levels of abundance (Sanders 1968; Taylor et al. 2008)

and was implemented using EcoSim700 software (Gotelli and Entsminger 2001).

Random subsamples drawn from the observed data were used to create species richness

distributions at each abundance level using a Monte Carlo procedure (Gotelli and Graves

1996). All estimates of species richness were sampled with 5000 iterations.

To compare regional diversity between 1987 and 2011, I constructed rarefaction

curves and visually compared the 95% confidence intervals of those curves. For this

analysis, species abundance was combined for 15 sites (excluding Harkell Canyon and

Salt Creek) in 1987 and 2011. Linam and Kleinsasser (1996) in October 1987, collected

25 species and 8310 individuals. In October 2011, 25 species and 15699 individuals were

collected. Regional species richness was compared for the two time periods by visually


12

assessing overlap of the confidence intervals. If the curves diverged then a significant

difference in species richness was present between time periods.

To compare mean species richness between the two time periods, I rarefied

species richness values to the lowest abundance collected at a single site in each time

period. Species richness values were rarefied to abundance levels of 113 and 128 for

comparison using all species, and 57 and 112 for native species. Designation of native

species followed Smith and Miller (1986) and Hoagstrom (2001). I then used a two-tailed

paired t-test to examine differences in species richness between time periods and within

upstream and downstream sites between time periods. Upstream sites were defined as the

nine sites from Orla to Sheffield. Downstream sites were defined as the six sites from

above Independence Creek to Shumla (Fig. 1). Paired t-tests were implemented using

SYSTAT 13. Statistical significance was defined at an alpha level of 0.05.

Temporal Fish Assemblage Comparisons

To compare assemblages between samples collected in 1987 to 2011, I used

Nonmetric Multidimensional Scaling (NMS) (Taylor et al. 2008; Gauch 1982). NMS is

used to summarize complex community data and is well suited to for non-normal data or

data measured on discontinuous or questionable scales (Guach 1982, McCune and Grace

2002). NMS analysis was conducted using PC-ORD 5 software. Ordinations of sites were

based on site-specific species abundance data and the Sorensen distance metric. Square-

root transformations were used to decrease the influence of highly abundant species.

Pearson correlations of fish species with NMS axes were calculated to determine which

species were driving the ordination.


13

A Multiresponse Permutation Procedure (MRPP) was used to test the hypothesis

of no difference in fish assemblages between October 1987 and October 2011. This

procedure is similar to a multivariate analysis of variance (MANOVA), but MRPP does

not make distributional assumptions (McCune and Grace 2002). This makes MRPP well

suited to handle the skewed distributions often associated with community data (Grace

and McCune, 2002). Species abundance values were square-root transformed and the

Sorenson distance metric was used. A-values in MRPP analysis indicate the effect size of

the difference in fish assemblages between groups. An effect size of A=0 means that the

heterogeneity between groups is equal. In ecological communities A<0.1 is common, but

if A<0.01 ecological significance should be questioned (Grace and McCune 2002).

MRPP was also used to determine differences in fish assemblages between upstream and

downstream sites within each time period and between summer and October samples in

2011.

Fish assemblages and Environmental Correlations

Nonmetric multidimensional scaling was also used to ordinate contemporary

samples to identify environmental correlates of fish assemblages. Pearson correlations

were calculated between the measured environmental variables and the NMS axes. Some

variables were discarded due to equipment failure and natural diel variation. For the final

analysis 22 variables were assessed for environmental-assemblage relationships (Table

3). Continuous variables were log10 transformed and included width, depth, specific

conductance, turbidity, chlorophyll a, and max velocity. Substrate and riffle/pool


14

(percentages) values were arcsine square root transformed. Rank variables were not

transformed for this analysis.

Chapter III

Results

Species Richness Comparisons

No difference in regional species richness was observed between 1987 and 2011

(Figure 2.) based on comparisons of the rarefaction curves. While sample size was

approximately twice as large in 2011 as in 1987, there was complete overlap of the

rarefaction curves for both time periods (Figure 2). Twenty-five fish species were

collected in both 1987 and 2011. Linam and Kleinsasser observed 26 fish species, but for

this study Gambusia affinis and Gambusia geiseri were treated as one species due to

difficulty of identification and hybridization (Bonner et al. 2005). G. affinis and G.

geiseri were also combined for the 1987 data. Macrhybopsis aestivalis and Notropis

jemezanus was collected in 1987 but was not found in 2011. Pylodictis olivaris and

Lepomis auritus were collected in 2011 but not in 1987.

When confining the analysis to native species only, regional species richness was

found to be greater in 1987 than in 2011. Observed regional species richness in 1987 was

22 at an abundance level of 7441. In 2011 11,132 individuals were collected with a

species richness of 21. The difference in native species richness is significant because the

observed species richness in 1987 was outside of the 95% confidence interval for the

2011 rarefaction curve.


15

Figure 2. The 95% confidence intervals for regional rarefaction curves based on15 sites

on the lower Pecos River in 1987 (solid line) and 2011 (dashed line). Curves were

constructed with 25 species and 8310 individuals in 1987 and 25 species and 15699

individuals in 2011.


16

The observed difference was only one, but the samples sizes were considerably

higher in 2011 (Figure 3). In 1987, a total of 8310 individuals were collected, and 15,699

were collected in 2011. Macrhybopsis aestivalis and N. jemezanus, both native species,

were found in 1987 but not in 2011. M. aestivalis was listed as a species of special

concern by Hubbs et al. 2008. Neither species is listed as threatened or endangered by

Texas Parks and Wildlife, US Fish and Wildlife Service, or the IUCN Red List. Hubbs et

al. (1991) listed N. jemezanus as threatened in Texas, and was supported by the findings

of Edwards et al. (2002). P. olivaris was the only native species that was found in 2011

that was not observed in 1987.

Rarefaction curves were constructed to determine differences in observed species

richness for the nine upstream sites in 1987 and 2011 (Figure 4). Curves were constructed

with 5150 individuals and 14 native species in 1987 and 7467 individuals and 10 native

species in 2011. The observed species richness in 1987 did not overlap with the

confidence interval for 2011 indicating that species richness was significantly different

between time periods. Cyprinella proserpina, Notropis braytoni, Pimephales vigilax, and

Fundulus zebrinis were collected in the upstream sites in 1987, but were not collected in

2011. To compare mean local species richness, I eliminated Harkell Canyon (Site 15,

sampled only in 1987) and used the15 sites sampled during October in both time periods.

Observed and rarefied mean local species richness was compared between time periods

using a paired t-test. Species richness values were rarefied to an abundance level of 113

(Figure 5, 15 sites) and 128 (14 sites) corresponding to the lowest two abundance levels


17

of fish collected at a single site. Orla (Site 1) was excluded from the analysis at an

abundance level of 128 because less than 128 fish were captured at that site in 2011.

Figure 3. Rarefaction curves and 95% confidence intervals of native regional species

richness across 15 sites on the lower Pecos River. Sites were sampled in 1987 (solid

line) and 2011 (dashed line). Curves were constructed with 7441 individuals and 22

native species in 1987 and 11132 individuals and 21 native species in 2011.


18

Figure 4. Rarefaction curves and 95% confidence intervals of combined species richness

from 9 upstream sites on the lower Pecos River. Sites were sampled in 1987 (solid

line) and 2011 (dashed line). Curves were constructed with 5150 individuals and 14

native species in 1987 and 7467 individuals and 10 native species in 2011.


19

No difference was found between observed mean local species richness in 1987

and 2011 samples (T14= -0.467, p=0.338; Table 1). There was also no difference for

rarefied mean local species richness between time periods for either abundance level

(113: T14=-0.166, p=0.435; 128: T13=0.285, p=0.390). Significant differences in fish

assemblage between upstream and downstream sites within each time period (1987: T=-

4.11, A= 0.077, p=0.001; 2011: T=-6.82, A=0.18, p=0.0002). Thus, I proceeded with

comparisons of species richness in 1987 and 2011 within the upstream and downstream

reach.

Within the upstream sites, observed mean local species richness was greater in

1987 than in 2011 (T8=3.19, p=0.006). Local mean rarefied species richness was also

greater in 1987 than in 2011 (113: T8=5.51, p=0.0002, 128: T7=5.31, p=0.0004). Species

richness within the lower sites was significantly different between time periods for both

observed and rarefied values (Obs: T5=-2.95 p=0.01; 113: T5=-3.06, p=0.01; 128: T4=-

2.36, p=0.04), but species richness was greater in 2011 than in 1987. Greater species

richness in 2011 for the downstream sites indicates that different processes may be

limiting species presence in the upstream and downstream reach.


20

Figure 5. Rarefied species richness at an abundance level of 113 individuals for 15 sites

on the Pecos River. Sample site names and site numbers are listed on the X-axis. Samples

were collected in October of 1987 (black bars) and 2011 (grey bars). Sites are ordered

longitudinally from upstream to downstream.


21

Table 1. Comparisons of local species richness for sites on the lower Pecos River in 1987

and 2011. P-values correspond to paired t-tests of local species richness between the two

time periods. Differences were assessed for all sites, upstream sites, and downstream

sites. Differences were also tested using rarefied species richness at two abundance levels

(All species: 113 and 128; Native species: 57 and 112). P-values ≤ 0.05 indicate a

significant difference in species richness between time periods. Degrees of freedom are

listed in parentheses for each test. Direction of change in species richness from 1987 to

2011 is indicated by (+) or (-).

p-values

Abundance

Level

All Sites Upper Sites Lower Sites

All Species Observed 0.338 (14) 0.006 (8) - 0.01 (5)+

15 sites 113 0.435 (14) 0.0002 (8) - 0.01 (5)+

14 sites 128 0.390 (13) 0.0004 (8) - 0.03 (4)+

Native Species Observed 0.414 (14) 0.002 (8) - 0.010 (5) +

15 sites 57 0.479 (14) 0.0004 (8) - 0.016 (5) +

15 sites 112 0.488 (13) 0.002 (7)- 0.020 (5)+


22

Fish Assemblage Comparisons

Nonmetric multidimensional scaling was used to examine differences in fish

assemblage between October 1987 and 2011 (Figure 6). The first (18.9 %) and third

(60.3%) NMS Axes accounted for 79.2% of the variance between distances in ordination

space and original space. Axis 2 accounted for 10.2% of the variance. Because a three

dimensional solution was suggested, I also plotted the second and third NMS axes

(Figure 6). The final stress for a three dimensional solution was 9.633. Clarke (1993)

stated that stress scores between 5 and 10 indicate a good ordination with no real risk of

drawing false inferences. The final stability criterion was 0.00001.

Fish assemblages in 1987 and 2011 were found to be significantly different (T=-

6.83, A=0.07, p=0.000064). Differences in the location of upstream sites (Orla to

Sheffield) in the NMS figure revealed grouping between time periods. This was primarily

due to increases in species that were negatively correlated with Axes 1 and 3. NMS axis 1

was negatively correlated (r>0.5) with Lucania parva and Cyprinodon spp. (Table 2).

Axis 3 was negatively correlated with Menidia beryllina, F. grandis, and Cyprinodon

spp. These species are known to be tolerant of elevated salinity when compared with

other freshwater species (Griffith 1974; Pillard et al. 1999). Increases in salinity tolerant

species could indicate that change in salinity of the upstream sites is driving the shifts in

fish assemblage. Axis 2 was negatively correlated with species that are intolerant of the

high salinity and were found in the downstream sites. This includes Cyprinella lutrensis,

C. proserpina, Astyanax mexicanus, N. braytoni, P. vigilax, Lepomis megalotis, and

Cichlasoma cyanoguttatum (Table 2). When Axis 2 and 3 are compared (Figure 6), it is


23

obvious that the downstream sites were associated with the abundance of these intolerant

species.

Table 2. Pearson correlations for fish species with NMS axes for fish assemblages in the

lower Pecos River (Figures 4 & 5). Comparisons were made between years (October

1987 and Oct 2011), and between seasons (summer and October 2011). Strong

correlations (r≥0.50) are indicated by bold.

Between years Between seasons

Species Axis: 1 2 3 Axis: 1 2

D. cepedianum 0.114 -0.107 -0.103 0.014 -0.377

A. mexicanus 0.018 -0.520 0.479 -0.506 -0.349

C. lutrensis 0.374 -0.653 0.006 -0.321 -0.673

C. proserpina -0.098 -0.649 0.375 -0.579 -0.528

C. venusta -0.052 -0.186 0.679 -0.722 -0.405

C. carpio 0.355 0.240 -0.134 0.291 0.18

D. episcopa -0.210 -0.366 0.358 -0.479 -0.226

M. aestivalis 0.181 -0.382 0.023

N. amabilis -0.125 -0.471 0.614 -0.818 -0.362

N. braytoni 0.106 -0.543 0.297 -0.406 -0.518

N. jemezanus -0.093 -0.233 0.049

P. vigilax -0.087 -0.591 0.127 -0.306 -0.602

P. promelas -0.050 -0.146

M. congestum 0.152 -0.261 -0.008 -0.282 -0.36

P. olivaris 0.000 -0.295 0.194 -0.329 -0.557

I. punctatus -0.206 -0.138 0.373 -0.316 -0.041

Cyprinodon sp -0.563 -0.031 -0.555 0.206 0.467

F. grandis -0.510 0.230 -0.593 0.716 0.530

F. zebrinis 0.030 0.006 -0.014 -0.23 0.010

L. parva -0.576 0.109 -0.281 0.191 0.326

Gambusia sp -0.319 0.058 0.364 -0.484 -0.361

M. beryllina -0.358 -0.183 -0.645 0.293 -0.339

L. macrochirus -0.070 -0.192 0.599 -0.632 -0.328

L. megalotis 0.065 -0.552 0.323 -0.695 -0.502

L. auritus -0.041 -0.368 0.406 -0.605 -0.541

M. salmoides -0.052 -0.389 0.293 -0.582 -0.498

E. grahami -0.122 -0.405 0.613 -0.805 -0.534

C. cyanoguttatum -0.003 -0.563 0.105 -0.377 -0.646

O. aureus -0.233 -0.063

Texas Tech University, Christopher Cheek, August 2012


24

Figure 6. Nonmetric multidimensional scaling analysis of 1987 (open symbols) and 2011 (closed symbols) fish samples from the

lower Pecos River. NMS axes 1, 2 and 3 account for 18.9%, 10.2% and 60.3% of the variation, respectively. Circles indicate

upstream sites and triangles represent downstream sites. Site numbers correspond to site names in Figure 3.


25

Axis 2 also shows that assemblages in the upstream reach have become more

homogenous between time periods. Upstream sites in 1987 were widely distributed

across axis 2, whereas in 2011 sites were more tightly grouped. The proliferation of

tolerant species has lead to homogenization of fish assemblages in the region

The downstream sites were not differentiated between time periods. Fish

assemblage at some sites substantially changed between time periods, but as a group,

sites did not exhibit an overall pattern of change. Axis 3 was positively correlated with C.

venusta, Notropis amabilis, and Etheostoma grahami. These species are intolerant of the

high salinity levels that influence fish communities in the upstream sites.

Salinity

Specific conductance was higher in the upstream sites in 2011 than in 1987

(Figure 7). The downstream sites show a different pattern with conductance being greater

in 1987 than in 2011. In both time periods conductance increased in a downstream

pattern from Red Bluff Reservoir to Iraan, TX. The greatest specific conductance (27,600

umhos/cm) was measured at Iraan (site 7) in October of 2011. High salinity

(conductivity) likely contributed to the high abundance of salinity tolerant species and

absence of intolerant species at upstream sites. Conductance was lower in the

downstream sites than the upstream sites in both time periods but differences between

reaches were greater in 2011.


26

Figure 7. Specific conductance for 15 sites on the Pecos River. Measurements were

collected in October of 1987 (black bars) and 2011 (grey bars).

Habitat

Habitat data was not collected by Linam and Kliensasser in 1987 so no temporal

habitat comparisons could be made in this study. However, contemporary habitat

measurements showed differences between the upstream and downstream reaches. One

major difference between sites in the upstream and downstream reach was substrate

composition. Substrate in the upstream sites was mostly composed of mud (Average:


27

64.4%) and gravel (16.1%). Sand (6.1%), cobble (8.9%), boulder (4.5%), and bedrock

(0.0%) we rare or absent in the upstream reach. Substrate diversity was greater in the

downstream reach with higher percentages of larger substrate such as cobble (27.7%),

boulder (19.8%), and bedrock (21.6%). Gravel (21.0%) was also abundant at many of the

downstream sites, whereas sand (1.9%) and mud (8.0%) were rare.

Sites in the upstream reach consisted of mostly run (57.5%) and pool (34.2%)

habitats with few riffles (8.3%) Downstream sites had more pools (43.8%) and riffles

(31.9%) and less runs (24.3%) than the upstream sites. This reflects the amount of

channelization that has occurred in the upstream sites. Downstream sites (depth: 0.51 m;

width: 36.0 m) had a greater depth and width than did the upstream sites (depth: 0.39 m;

width: 12.5 m. Salt cedar and woody debris were more abundant in the upstream reach

than in the downstream. Differences in habitat and water quality likely account for

differences in fish assemblage between upstream and downstream reach.

Fish assemblage and Environmental Correlations

NMS was used to ordinate the species abundance data from October and summer

of 2011. Combining data from two sample periods inherently adds some variation due to

seasonal differences in fish community. No difference in fish assemblage was found

between the October and summer collection events (A=0.011, p= 0.171).

The combined NMS with species abundance data from October and summer of

2011 accounted for a total of 85.8% of the variation between distances in ordination

space and original space.. NMS Axes 1 and 2 accounted for 70.2% and 15.6% of the

variation, respectively (Figure 8). The number of iterations used for the final solution was


28

70 and the stability criterion was 0.00001. A two dimensional solution had the least

amount of stress with a final stress of 11.366. Stress values between 10 and 20 are

common for ecological data. Values at the lower end of this spectrum represent a good

and useable picture for drawing inferences (Clarke 1993).

Figure 8. Nonmetric multidimensional scaling analysis of 2011 fish samples from the 15

sites on the lower Pecos River. NMS axis 1 represents 72.0% of the variation and axis 2

accounts for 13.9% of the variation. Summer samples are represented by open symbols

and fall samples are designated by closed symbols. Upstream sites are represented by

squares and downstream sites are represented by triangles. Site numbers correspond to

sites names in Figure 3.


29

The ordination had a distinct split between sites located in the upstream and

downstream reach (Figure 8). Both axes were positively correlated with F. grandis (Table

2). Notropis amabilis and Etheostoma grahami were strongly negatively correlated with

axis 1. C. proserpina, C. venusta, A. mexicanus, L. macrochirus, L. megalotis, and L.

auritus were also positively correlated with axis 1. Axis 1 represents differences in fish

communities between the upstream and downstream sites. Downstream sites were

characterized by species that were intolerant of high salinity, whereas the upstream sites

were dominated by tolerant species. Axis 2 was also negatively correlated with minnow

species, Lepomis species, E. grahami, and C. cyanoguttatum.

Both NMS axes 1 and 2 were positively correlated with specific conductance

(Table 3). Conductivity was highest in the upstream sites and greatly contributed to

assemblage structure in this reach. The downstream sites had much lower conductivity

due to large amounts of freshwater input from springs. Axis 1 was also negatively

correlated with larger substrate types such as cobble, boulder, and bedrock, and positively

correlated with fine muddy substrates. This substrate gradient represents the shifts in

substrate composition between the upstream and downstream reach. Axis 1 is also

positively correlated with salt cedar and abundance of woody debris.


30

Table 3. Pearson correlations of measured environmental variables with NMS axes 1 and

2 for fish assemblages of the lower Pecos River in summer and October 2011. Pearson

correlations (r≥0.60, Bold) indicate strong assemblage-environment relationships.

r

Environmental

Variable Axis 1 Axis 2

Width -0.519 -0.686

Depth -0.0110 -0.445

Conductivity 0.732 0.617

pH 0.216 0.295

Chlorophyll-a 0.660 0.232

Turbidity 0.490 -0.00700

Maximum velocity 0.353 0.358

% Mud 0.746 0.506

% Sand 0.277 0.0200

% Gravel -0.0700 -0.133

% Cobble -0.534 -0.228

% Boulder -0.630 -0.526

% Bedrock -0.702 -0.445

% Riffle -0.538 -0.364

% Run 0.432 0.488

% Pool -0.167 -0.365

Algae -0.296 -0.128

Woody debris 0.614 0.103

Undercut -0.158 -0.387

Terrestrial vegetation 0.140 -0.095

Salt cedar 0.659 0.470

Macrophytes 0.408 0.369


31

Chapter IV

Discussion

Temporal Variation in Fish Assemblages

Fish assemblages in the lower Pecos River have changed markedly over a 24 year

time-span. Species replacement and distributional changes between time periods for

several species may be associated with increased salinity. For example, in 1987 F.

grandis was collected in low abundance (≤26 specimens) at five sites, four of which were

the most downstream. In 2011, this species was found to be highly abundant (up to 562

specimens) and sometimes dominant at upstream sites. F. grandis is tolerant to high

salinity levels that naturally exist in coastal waters of the Gulf of Mexico (Griffith 1974).

Natural tolerance to saline environments has allowed this non-native species to

proliferate in the upstream sites. Several other species also experienced changes in

abundance between the two time periods including Cyprinidon hybrids, M. beryllina, and

L. parva. Their ability to tolerate the high salinity levels and lack of competition from

stenohaline species has likely contributed to increased abundance of these species.

The inability of some species to tolerate high levels of salinity likely caused shifts

in spatial distribution. For example, the distribution of C. lutrensis largely decreased

between time periods. In 1987, C. lutrensis was the most abundant fish species and was

collected at every site except the most downstream location (Shumla). In 2011, C.

lutrensis was only collected at sites downstream of Sheffield. C. lutrensis is relatively

tolerant of salinity but the critical threshold of salinity tolerance was exceeded at five of

the nine upstream sites in 2011 (Mathews and Hill 1977). For this species, salinity may

have been a leading cause in distribution and abundance declines. Other species that


32

experienced decreases in distribution included, the stenohaline, A. mexicanus and C.

proserpina. Both were found in the upstream sites in 1987, but were only found in the

downstream sites in 2011.

Increased salinity may have also affected the distribution and abundance of the

euryhaline F. zebrinus, which was once abundant in the upstream reach of the Pecos

River, but has experienced recent and sugnificant declines (Hubbs 1957; Rhodes and

Hubbs 1992; Linam and Kleinsasser 1996). In 1987, F. zebrinus was collected at seven

sites in 1987, but it was only found in Independence Creek in 2011. Salinity levels are not

likely to limit the distribution of F. zebrinus in this system because their tolerance

exceeds the maximum salinity measured in the field (Ostrand and Wilde 2001). It is

plausible that the establishment of F. grandis, and subsequent interspecific competition

has led to a reduction in F. zebrinus abundance, rather than abiotic regulation. F. grandis

matures at a much greater size than F. zebrinis which may allow for competitive

advantages (Sublette et al. 1990). Previous studies also have suggested that F. zebrinus is

most successful in communities with few fish species (Echelle et al. 1972). Fish

communities in the upstream sites were comprised of only a few euryhaline species, but

those species were highly successful. Through competition, the high abundance of

tolerant species may play a role in declines of F. zebrinus.

Fundulus zebrinus is considered native to the Pecos River, and introduced into

Rio Grande tributaries in the Big Bend Region (Hubbs 1957; Kreiser et al. 2010). These

contrasting designations are surprising, because the regions are inherently linked by the

Rio Grande. If F. zebrinus is truly native to the Pecos River, natural dispersal could


33

account for the presence in Rio Grande tributaries. The introduced/native status of F.

zebrinus should be investigated further in this region.

Increased salinity levels between time periods may be perpetuated by oil and gas

production in the Pecos River Drainage. The results of this study resemble other studies

that examined the effects of waste water pollution from petroleum production. For

example, Shipley (1991) showed decreases in species richness from 20 to 4 species below

a waste water discharge in Texas. Chipman (1959) documented the persistence of tolerant

fish during fish kills in a freshwater pond polluted by oil waste. Other pollutants from oil

field waste such as trace metals and sulfate may also influence community structure, but

were not measured in this study. Sources of contemporary salinity should be investigated

to determine if oil and gas production is contributing to the increasing salinity.

Several studies have examined the effects of salinity on stream ecosystems. In

Great Plains streams, studies have indicated that salinity can play a large role in

structuring fish assemblages (Taylor et al. 1993; Higgins and Wilde 2005). Higgins and

Wilde (2005) also noted that salinity tolerance of some species may be associated with

species persistence in tributaries to the Red River, TX. In this case, species that had high

salinity tolerances were more likely to persist over time than intolerant species. Salinity

tolerant species are often adapted to high levels of disturbance, which allows for greater

survival (Higgins and Wilde 2005). The dominance of tolerant species in the upstream

reach may be explained by their natural adaptation to high levels of disturbance.

Decreases in biodiversity of flowing waters due to salinization have been well

documented. Much like the Pecos River, streams in Western Australia have been

negatively impacted by salinization due to agricultural irrigation and natural salinity


34

sources (Williams 2001). Decreases in diversity and increasing dominance of salt

tolerant species have been observed in Australia for several taxa including fishes,

macroinvertebrates, and aquatic plants (Bunn and Davies 1990; Williams 2001; James et

al. 2003).

Along with salinization, anthropogenic land use in the upstream reach may be

impacting fish assemblages. Many of the upstream sites have been affected by

channelization and increases in fine sediments. Association between channelization and

degradation of stream habitat has been well documented. Channelization causes

decreased riffle/pool habitat, riparian vegetation, and stream sinuosity (Emerson 1971;

Shields et al. 1998) as well as, channel erosion and decreased habitat heterogeneity

(Sullivan et al. 2004). Decreases in fish diversity and community quality have been

attributed to this type of habitat alteration (Etnier 1972; Gorman and Karr 1978). Along

with increases in salinity, this shallow monotypic habitat may be contributing to

decreases in fish diversity in the upstream reach (Hoagstrom 2009).

Interpretation of assemblage shifts between time periods was complicated by fish

kills that occurred in 1986. In this study I documented increases in species richness

between time periods in the downstream sites. This pattern is opposite of what I found in

the upstream reach. Species richness in 1987 was likely reduced by a massive fish kill

that occurred in the previous year (Rhodes and Hubbs 1992). Golden algae blooms

occurred near Iraan, TX and extended downstream to Amistad Reservoir, affecting three

upstream sites and all downstream sites, except Independence Creek. Recolonization of

fishes after the fish kill was likely still occurring during the October 1987 collections.

This may have resulted in the absence of some species in the 1987 collections. Upstream


35

sites were likely colonized more rapidly by salinity tolerant species that were still

abundant upstream of the algae bloom. Some salinity tolerant species were not

significantly affected by the golden algae toxic blooms including Cyprinodon hybrids and

G. affinis (Rhodes and Hubbs 1992). This allowed for rapid recolonization of upstream

reach. Fishes in the downstream reach were confined by high salinity upstream and

Amistad Reservoir downstream. Therefore, the mainstem of the river was likely

recolonized by populations in spring fed tributaries. Tributaries such as Independence

Creek, likely acted as refugia for colonizing populations in the downstream reach

(Rhodes and Hubbs 1992).

Recent observations in the downstream reach suggest that many fish species have

recolonized since the 1987 collections, although at least two species never recovered.

Notropis jemezanus and M. aestivalis were common before the fish kill, but abundances

were significantly reduced in subsequent samples (Hubbs 1990). In October 1987, N.

jemezanus was represented by only one specimen and M. aestivalis was represented by

16 specimens at a single site. Both species were absent from recent collections indicating

that they may have never recovered from the fish kill or that other factors affected their

contemporary abundance.

Overall, our results show that the downstream sites have a relatively intact fish

fauna when compared to recent historical accounts. The presence of fish species that are

more sensitive to anthropogenic disturbance in the downstream sites may indicate that

these areas are isolated from the salinization and hydraulic alteration that affects the

upstream reach. The presence of spring flow is likely associated with the persistence of

species that are intolerant of anthropogenic impacts in the lower reach.


36

Spatial Variation of Fish Assemblages

Changes in species assemblages along a longitudinal gradient have widely been

attributed to two processes, biotic zonation and continual addition of species. Biotic

zonation refers distinct community composition that results from discontinuities in the

geomorphic or abiotic conditions along a longitudinal gradient (Schlosser 1982; Rahel

and Hubert 1991; Oberdorff et al.1993; Belliard et al.1997). Species addition is most

often observed where environmental gradients exhibit smooth transitions (Sheldon 1968;

Rahel and Hubert 1991). In this case, accumulation of species is often attributed to

increases in habitat size, habitat diversity, and environmental stability in a downstream

pattern (Winemiller 1983; Angermeier and Schlosser 1989; Winemiller and Leslie 1992;

Matthews and Styron 1981; Grossman et al. 1982).

The results of this study show a pattern of zonation with two major zones of fish

assemblages, upstream and downstream. These zones are primarily determined by two

factors, salinity and habitat heterogeneity. Disparity in these factors between reaches is

associated with the level of anthropogenic disturbance as well as natural geologic

formations.

Water quality differences appear to contribute to the division of distinct fish

assemblages in the upstream and downstream reach. In the upstream reach fish

assemblages are controlled primarily by high salinity. The downstream reach has lower

salinity levels due to freshwater spring inflows. Several studies have indicated that

competitive advantages of fish can shift based on abiotic factors such as salinity or


37

temperature (Baltz et al. 1982; Dunson and Travis 1991). Species intolerant of the high

salinity levels likely out compete tolerant species in the lower salinity waters, leading to

assemblage differences. Springs also increase the total discharge and supply constant

flow downstream which increases habitat size and stability. Tributaries fed by spring

flow are also important for reproduction of some species, such as Dionda episcopa

(Hubbs 1957). Therefore, spring flows that separate the upstream and downstream reach

alter fish assemblages along a longitudinal gradient.

Differences in fish assemblage between the upstream and downstream reach is

likely related to differences in habitat, particularly substrate heterogeneity. Changes in

substrate composition downstream are attributable to natural characteristics of the

Permian Basin and Edwards Plateau. Land use practices also may affect each region,

individually. In the Permian Basin (upstream sites), mud was the dominant substrate type,

with little large substrate present in the river. The upstream reach mostly consisted of run

habitat with few riffles and pools. Habitat heterogeneity in this reach is influenced by the

lack of historical flow regimes that would naturally transport fine sediments. Monotypic

habitat features along with salinity may have led to decreased fish diversity and increased

dominance of tolerant species. Alternatively, the Edwards plateau reach (downstream

reach) is dominated by large substrate such as cobble, boulder, and bedrock. Riffles are

also more prominent with increased gradient and substrate size in the downstream reach.

The presence of species adapted to riffle habitat, such as E. grahami, may partially

explain increases in diversity. Substrate heterogeneity may also be important for species

that require multiple substrate types for reproduction or recruitment. The downstream

reach has been less impacted by human alteration, and likely retains habitat heterogeneity


38

similar to historical standards. In the Pecos River this may partly explains the increase in

diversity between upstream and downstream reach.

Historical records indicate that this zonation pattern was likely present but not as

pronounced as was found in this study. In an analysis of historical and recent fish

collections, Hoagstrom (2001) found that there were once 27 species of fish that had

distributions that spanned the entire lower Pecos River. In recent collections only 9

species were found in every segment. Increases in salinity and anthropogenic disturbance

likely lead to altered distributions of fishes in the lower Pecos River and enhanced the

effects of natural zonation.

This study illustrates the importance of the downstream reach of the Pecos River

for preserving the system’s biodiversity. Because the upstream reach has unsuitable water

quality for many species, the protection of this region is vital. To prevent the degradation

of water quality and habitat it is important to preserve the many springs that reduce

salinity and provide downstream flow. This includes the protection of aquifers and

spring-fed tributaries that feed the downstream reach. The Nature Conservancy has taken

the initiative to protect Independence Creek, but other sources of freshwater and the

surrounding watershed should also be protected.

Upstream sources of anthropogenic alteration must also be managed to preserve

diversity in the downstream reach. Regulation and mitigation of saline waste water

disposal could prevent further pollution. Preventing the salinization of surface and ground

water is both economically and ecological beneficial. Aquatic communities will benefit

from the reduced salinity, but crop producers and municipalities would also benefit by

preventing further salinization of aquifers used for drinking and irrigation water. Better


39

management of regional aquifers, changes to irrigation practices, mitigation of petroleum

waste water, and proper flow regulation could reduce salinity levels and restore habitat in

this region.


40

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