RELATIONSHIPS BETWEEN SMALL BODIED FISHES AND …ufdcimages.uflib.ufl.edu/UF/E0/04/13/92/00001/camp_e.pdf · relationships between small bodied fishes and crustaceans and submersed

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RELATIONSHIPS BETWEEN SMALL BODIED FISHES AND CRUSTACEANS AND SUBMERSED AQUATIC VEGETATION: IMPLICATIONS OF HABITAT CHANGE

By

EDWARD VINCENT CAMP

A THESIS PRESENTED TO THE GRADUATE SCHOOL OF THE UNIVERSITY OF FLORIDA IN PARTIAL FULFILLMENT

OF THE REQUIREMENTS FOR THE DEGREE OF MASTER OF SCIENCE

UNIVERSITY OF FLORIDA

2010

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© 2010 Edward Vincent Camp

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To my parents, Peter and Marcia, whose unwavering support has enabled me to enjoy

pursuing my passions

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ACKNOWLEDGMENTS

I would like to thank all the members of my supervisory committee for their support

and guidance throughout this project. Dr. Bill Pine provided assistance with the study

design, and Dr. Tom Frazer was tremendously influential by mentoring my development

as an ecologist and a professional. Dr. Christie Staudhammer has been hugely helpful

and patient in fostering my understanding of the data analysis components of this

project. I would also like to thank the Florida Fish and Wildlife Conservation

Commission State Wildlife Initiative Grant Program for funding that made this project

possible.

I am also grateful to my fellow students and co-workers. Many people in the FAS

program worked in difficult conditions to help collect and process data for this project,

including Drew Dutterer, Morgan Edwards, Brandon Baker, and Jared Flowers. I am

especially grateful to Jake Tetzlaff who has given me advice and assistance throughout

all aspects of this project. Additionally I would like to acknowledge the impact that Dr.

Dorothy Boorse, Warren Colyer, and Jason Robinson have had on the development of

my scientific understanding and research interests. Finally, I would like to thank my

family and friends and especially Genevieve for understanding and supporting me over

the last several years.

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TABLE OF CONTENTS page

ACKNOWLEDGMENTS .................................................................................................. 4

LIST OF TABLES ............................................................................................................ 6

LIST OF FIGURES .......................................................................................................... 8

ABSTRACT ................................................................................................................... 11

CHAPTER

1 GENERAL INTRODUCTION .................................................................................. 13

Submersed Aquatic Vegetation .............................................................................. 14 Small bodied fish and Macroinvertebrates .............................................................. 15

Research needs and study Objectives ................................................................... 15

2 EXAMINING RELATIONSHIPS BETWEEN SMALL BODIED FISH AND MACROINVERTEBRATES AND SPECIFIC SAV HABITAT TYPE ........................ 17

Introduction ............................................................................................................. 17 Methods .................................................................................................................. 18

Study Location .................................................................................................. 18 Study Species and Sampling Gear ................................................................... 19

Sampling Design and Methods ......................................................................... 19 Analyses ........................................................................................................... 22

Comparisons of overall SFI Density and Diversity among SAV Habitats ... 22

Comparisons of Densities of specific SFI size Classes and Taxa among SAV Habitats .......................................................................................... 23

Comparisons of specific SFI Taxa Densities between Systems................. 23 Results .................................................................................................................... 24

Sampling and Catch Estimation ....................................................................... 24

Comparisons of overall SFI Density and Diversity among Habitats .................. 25 Comparisons of Densities of SFI size Classes and Taxa among Habitats ....... 26

Comparisons of SFI taxa Densities between Systems ..................................... 27 Discussion .............................................................................................................. 27

3 SUMMARY AND CONCLUSIONS .......................................................................... 70

REFERENCES .............................................................................................................. 74

BIOGRAPHICAL SKETCH ............................................................................................ 79

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LIST OF TABLES

Table page 2-1 Specific response variables compared either among SAV habitats, between

rivers, or both. ..................................................................................................... 33

2-2 Proportional species composition of the Chassahowitzka River June 2008 – May 2009 ............................................................................................................ 33

2-3 Proportional species composition of the Homosassa River November 2008 – May 2009 ............................................................................................................ 34

2-4 Repeated measures analysis of variance results for overall SFI density per

m 2 in the Chassahowitzka river, from June 2008-May 2009 ............................... 34

2-5 Repeated measures analysis of variance results for overall SFI diversity in the Chassahowitzka river, from June 2008-May 2009 ........................................ 34

2-6 Repeated measures analysis of variance results for ln-transformed small

sized SFI densities per m 2 in the Chassahowitzka River, from June 2008-May 2009 ............................................................................................................ 34

2-7 Repeated measures analysis of variance results for ln-transformed medium


2-8 Repeated measures analysis of variance results for ln-transformed large


2-9 Repeated measures analysis of variance results for ln-transformed L. parva

densities per m 2 in the Chassahowitzka River, from June 2008-May 2009 ....... 35

2-10 Repeated measures analysis of variance results for ln-transformed

Palaemonetes spp. densities per m 2 in the Chassahowitzka River, from June 2008-May 2009 ................................................................................................... 35

2-11 Repeated measures analysis of variance results for ln-transformed Gobiidae

densities per m 2 in the Chassahowitzka River, from June 2008-May 2009 ....... 36

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2-12 Repeated measures analysis of variance results for ln-transformed L.

punctatus densities per m 2 in the Chassahowitzka River, from June 2008-May 2009 ............................................................................................................ 36

2-13 Results from comparisons between mean densities per m 2 in the Chassahowitzka and Homosassa rivers using Welch’s two sample T test, p = 0.05 .................................................................................................................... 36

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LIST OF FIGURES

Figure page 2-1 Mapping and sample selection are illustrated. .................................................... 37

2-2 Recovery probabilities for small fish and macroinvertebrates in 5 specific habitat types. ...................................................................................................... 38

2-3 Pearson’s residuals for the ln-transformed overall SFI density repeated measures model for Chassahowitzka River ....................................................... 39

2-4 Pearson’s residuals for overall SFI diversity repeated measures model for Chassahowitzka River ........................................................................................ 40

2-5 Pearson’s residuals for ln-transformed L. parva repeated measures model, Chassahowitzka River ........................................................................................ 41

2-6 Pearson’s residuals for ln-transformed Palaemonetes spp. repeated measures model, Chassahowitzka River ............................................................ 42

2-7 Pearson’s residuals for the ln-transformed L. punctatus repeated measure’s model, Chassahowitzka River ............................................................................ 43

2-8 Pearson’s residuals for the ln-transformed Gobiidae repeated measures model Chassahowitzka River ............................................................................. 44

2-9 Pearson’s residuals of ln-transformed small SFI repeated measures model Chassahowitzka River ........................................................................................ 45

2-10 Pearson’s residuals for ln-transformed medium SFI repeated measure’s model, Chassahowitzka River. ........................................................................... 46

2-11 Pearson’s residuals from large SFI group (not ln transformed) mixed (not repeated measures) model, for the Chassahowitzka River. ............................... 47

2-12 Overall SFI density per m 2 by habitat type and months at the Chassahowitzka River, June 2008 – May 2009. ................................................. 48

2-13 Pairwise comparisons of overall SFI densities per m 2 between SAV habitat types at the Chassahowitzka River, June 2008-May 2009. Mean and 95% confidence intervals around data are shown. ..................................................... 49

2-14 Mean overall SFI diversity per m 2 and one standard deviation are shown by habitat type and months at the Chassahowitzka River, June 2008 – May 2009. .................................................................................................................. 50

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2-15 Pairwise comparisons of overall SFI diversity per m 2 between SAV habitat types at the Chassahowitzka River, June 2008-May 2009. Mean and 95% confidence intervals around data are shown. ..................................................... 51

2-16 Mean small SFI density per m 2 and one standard deviation are by habitat type and months at the Chassahowitzka River, June 2008 – May 2009. ........... 52

2-17 Pairwise comparisons of small SFI density per m 2 between SAV habitat types at the Chassahowitzka River, June 2008-May 2009. ................................ 53

2-18 Mean medium SFI density per m 2 and one standard deviation shown by habitat type and months in the Chassahowitzka River, June 2008 – May 2009. .................................................................................................................. 54

2-19 Pairwise comparisons of medium SFI density per m 2 between SAV habitat types at the Chassahowitzka River, June 2008-May 2009. ................................ 55

2-20 Mean large SFI density per m 2 and one standard deviation are shown by habitat type and months in the Chassahowitzka River, June 2008 – May 2009. .................................................................................................................. 56

2-21 Pairwise comparisons of large SFI density per m 2 between SAV habitat types at the Chassahowitzka River, June 2008-May 2009. ................................ 57

2-22 Mean L. parva density per m 2 with one standard deviation are shown by habitat type and month at the Chassahowitzka River, June 2008 – May 2009. . 58

2-23 Pairwise comparisons of L. parva density per m 2 between SAV habitat types at the Chassahowitzka River, June 2008-May 2009. .......................................... 59

2-24 Mean Palaemonetes spp. density per m 2 and one standard deviation are shown by habitat type and months in the Chassahowitzka River, June 2008 – May 2009. ........................................................................................................... 60

2-25 Pairwise comparisons of Palaemonetes spp. density per m 2 between SAV habitat types at the Chassahowitzka River, June 2008-May 2009. .................... 61

2-26 Mean Gobiidae density per m 2 and one standard deviation are shown by habitat type and month in the Chassahowitzka River, June 2008 – May 2009. .. 62

2-27 Pairwise comparisons of Gobiidae density per m 2 between SAV habitat types at the Chassahowitzka River, June 2008-May 2009. ................................ 63

2-28 Mean L. punctatus density per m 2 with one standard deviation shown by habitat type and month in the Chassahowitzka River, June 2008 – May 2009. .. 64

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2-29 Pairwise comparisons of L. punctatus density per m 2 between SAV habitat types at the Chassahowitzka River, June 2008-May 2009. ................................ 65

2-30 Comparisons of L. parva. mean density per m 2 with one standard deviation between the Chassahowitzka and Homosassa rivers cumulative over the months November 2008 – May 2009. ................................................................. 66

2-31 Comparisons of Palaemonetes spp. mean density per m 2 with one standard deviation between the Chassahowitzka and Homosassa rivers cumulative over the months November 2008 – May 2009 .................................................... 67

2-32 Comparisons of Gobiidae mean density per m 2 with one standard deviation between the Chassahowitzka and Homosassa rivers cumulative over the months November 2008 – May 2009 .................................................................. 68

2-33 Comparisons of L. punctatus mean density per m 2 with one standard deviation between the Chassahowitzka and Homosassa rivers cumulative over the months November 2008 – May 2009. ................................................... 69

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Abstract of Thesis Presented to the Graduate School of the University of Florida in Partial Fulfillment of the Requirements for the Degree of Master of Science

RELATIONSHIPS BETWEEN SMALL BODIED FISHES AND CRUSTACEANS

AND SUBMERSED AQUATIC VEGETATION: IMPLICATIONS OF HABITAT CHANGE

By

Edward Vincent Camp

May 2010

Chair: William Pine Cochair: Thomas Frazer Major: Fisheries and Aquatic Sciences

Alterations of aquatic habitats can have profound consequences on the

abundances and distributional patterns of associated faunal organisms. Recognition of

this fact has motivated multiple state and federal agency initiatives related to habitat

management, and encouraged a mechanistic understanding of plant-animal

relationships vital for assessing ecological change. I investigated relationships between

specific aquatic habitat types (submerged aquatic vegetation, SAV) and small bodied

fish and macroinvertebrates (SFI) in the Chassahowitzka and Homosassa rivers; spring-

fed rivers along the west coast of peninsular Florida. A decade of research in these

rivers indicates a shift in the SAV communities within each of these systems, with

decreases in rooted macrophytes (e.g., Vallisneria americana and Sagittaria kurziana)

and concomitant increases in the relative abundance of nuisance filamentous

macroalgae. To assess how these shifts in SAV might affect the SFI community I: (1)

determined if SFI assemblages differed between specific types of SAV, (2) analyzed a

suite of response variables to investigate how SFI size groups and species used SAV

habitat types, and (3) made comparisons of SFI abundances between similar systems

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characterized by dissimilar SAV habitat to infer habitat requirements. I sampled SFI

associated with five SAV habitat types. My results suggest that both SFI density and

species composition were significantly related to SAV habitat type. Contrary to common

perception, overall SFI densities were generally highest in filamentous macroalgae.

However, SFI species diversity was lower in filamentous macroalgae in comparison to

rooted macrophytes. Additionally, I found the densities of specific size classes and taxa

of SFI to differ significantly between SAV habitat types, with larger individuals

associated with rooted macrophytes. These findings, in combination with the available

longer-term monitoring data, provide insight into how continued shifts in SAV may affect

the structure and function of Florida’s spring-fed rivers and other aquatic ecosystems.

This information is essential for understanding how habitat-animal relationships impact

the ecology of an ecosystem undergoing broad-scale habitat change, and may be

useful to managers as a decision support tool.

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CHAPTER 1 GENERAL INTRODUCTION

A key goal in the study and management of natural environments is to understand

the ecological consequences of habitat alterations (Rosenfeld and Hatfield 2006). To

understand these consequences it is useful to characterize the relationships between

animals and their habitats, and specifically to assess which habitats are required to

maintain animal populations (Rosenfeld 2003). Required habitats have been defined as

those habitats that are necessary for growth and survival of individuals and the

persistence of species (Rosenfeld 2003), but in practice required habitats have been

often designated as those that animals use or occupy in greater density than other

habitats (Rosenfeld and Boss 2001). While patterns of habitat use are likely to provide

some insight into particular species’ habitat requirements, such patterns alone are

insufficient to reliably indicate required habitat (Van Horne 1983). Designating habitat

requirements from patterns of use alone presumes that animal species could not persist

in habitats other than those they currently use. This presumption has rarely been

validated in aquatic ecosystems (Rosenfeld 2003). Directly assessing animals’

response to a change in habitat is preferable for determining habitat requirements, and

may validate inferences drawn from habitat use (Van Horne 1983; Rosenfeld 2003).

Correspondingly, there is a recognized need for studies combining patterns of habitat

use with such direct assessments, such as controlled manipulative or natural

experiments, to provide stronger insight into how animals’ populations and ecosystem

structure may be impacted by changes in habitat (Hobbs and Hanley 1990; Rosenfeld

and Hatfield 2006).

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Submersed Aquatic Vegetation

Submersed aquatic vegetation (SAV) is a structural habitat found in aquatic

ecosystems that is considered important to many animals (Orth et al. 1984; Heck et al.

1989), and is also perceived to be undergoing widespread changes. A pattern of SAV

change observed globally is the decline in abundance of rooted macrophytes,

particularly of grass-like species (Hauxwell et al. 2003), and concomitant increases in

abundance of filamentous macroalgae (Duarte 1995). These two SAV habitat types

exhibit very dissimilar structural composition and life histories (Hughes et al. 2002).

Rooted macrophytes are relatively slow-growing, long-lived species whose varied

densities and morphological stem and leaf arrangements generally create

heterogeneously structured habitat characterized by larger, differently sized interstitial

spaces (Duffy and Baltz 1998). In contrast, many filamentous macroalgae have a short

life cycle, rapid turnover, and are characterized by dense, fine, similar sized filaments

that provide a more homogenously structured habitat characterized by uniformly small

interstitial spaces (Dodds and Gudder 1994). Rooted macrophytes are also more

resistant to infrequent disturbances, e.g., high flow events, than are filamentous

macroalgae, which may be removed by such disturbances (Duarte 1995). In contrast,

filamentous macroalgae are considered more resilient than rooted macrophytes to

anthropogenic-related frequent or chronic disturbance, e.g., increased nutrient delivery

and decreased water levels. As such disturbances are ongoing, shifts between rooted

macrophytes and filamentous macroalgae are likely to continue. The continuation of

these shifts, combined with differences in the structural composition of these two SAV

habitat types has led to researchers’ and managers’ concern that a shift from rooted

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macrophytes to filamentous macroalgae will have profound and likely adverse

consequences on associated animal communities (Pihl et al. 1995; Wyda et al. 2002).

Small bodied fish and Macroinvertebrates

Shifts in SAV from rooted macrophytes to filamentous macroalgae would likely

affect epibenthic small bodied fish and macroinvertebrates (hereafter SFI) (Deegan et

al. 2002). In most freshwater systems, the SFI community is generally composed of

small (<60 mm) individuals and plays a key role in food web dynamics. While the SFI

community is often abundant in many SAV habitats, it has been found to differ between

species of SAV. For example, Troutman et al. (2007) found that densities of small

bodied fish differed between three SAV types (Hydrilla verticillata, Sagittaria lancifolia,

and Eichhornia crassipes) within the Atchafalaya basin, Louisiana. Similarly, Chick and

McIvor (1997) found SFI use to differ between three SAV types (H. verticillata,

Potamogeton illinoensis, and Panicum hemitomon) in Lake Okeechobee, Florida.

Additionally, SFI communities may differ between differently structured SAV habitats.

Numerous studies have shown SAV structural characteristics, specifically size of

interstitial spaces, to impact SFI foraging success, predation risks, and abundance

(Chick and McIvor 1994; Bartholomew et al. 2000; Warfe and Barmuta 2004). The

relationships between SAV and SFI and the differences between rooted macrophytes

and filamentous macroalgae imply that a shift between these habitats will likely impact

the SFI community, an impact which may alter food web dynamics.

Research needs and study Objectives

Despite the potential ecological implications associated with such widely observed

changes in SAV, few investigations, particularly in freshwater ecosystems, have

examined how the SFI communities may change following the shift from rooted

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macrophytes to filamentous macroalgae (but see Pihl et al. 1995, Deegan et al. 2002).

Such shifts in SAV have been documented over the last several decades in a number of

Florida’s spring fed rivers, including the Chassahowitzka and the Homosassa rivers

(Frazer et al. 2006; Heffernan et al. in press). These river systems historically

supported similar, extensive, rooted macrophyte beds (primarily Vallisneria americana

and Sagittaria kurziana) and fish communities (Odum 1957a, b). Currently, these rivers

are characterized by having very dissimilar SAV habitat (Notestein et al. 2003; Frazer et

al. 2006). Ongoing monitoring efforts in both rivers document that the Chassahowitzka

River currently contains declining rooted macrophytes, and increasing filamentous

macroalgae and unvegetated substrate, whereas the Homosassa River is comprised

almost exclusively of filamentous macroalgae and unvegetated substrate (Frazer et al.

2006). My objective is to understand how this continued shift from rooted macrophytes

to filamentous macroalgae may affect SFI in coastal freshwater rivers by characterizing

which SAV habitats are required by the SFI community. To accomplish this, I combine

inferences drawn from SFI use of specific SAV habitats in the Chassahowitzka River

with inferences drawn from comparisons of habitat specific SFI use between the

Chassahowitzka (intact vegetation) and Homosassa (degraded vegetation) rivers.

Specifically, I ask:

1. Does the overall density and diversity of the SFI community differ between SAV habitat types, specifically between rooted macrophytes (notably V. americana, filamentous macroalgae, and bare substrate?

2. Do the densities of specific size classes and taxa differ between these SAV habitats?

3. Do the densities of key SFI taxa differ among similar habitat types between rivers that differ in respect to SAV?

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CHAPTER 2 EXAMINING RELATIONSHIPS BETWEEN SMALL BODIED FISH AND

MACROINVERTEBRATES AND SPECIFIC SAV HABITAT TYPE

Introduction

Submersed aquatic vegetation (SAV) is a structural habitat found in aquatic

ecosystems that is considered important to many animals (e.g, SFI) (Orth et al. 1984;

Heck et al. 1989), and is also perceived to be undergoing widespread changes. A

pattern of SAV change observed globally is the decline in abundance of rooted

macrophytes, particularly of grass-like species (Hauxwell et al. 2003), and concomitant

increases in abundance of filamentous macroalgae (Duarte 1995). These two SAV

habitat types exhibit very dissimilar structural composition and life histories (Hughes et

al. 2002), and are perceived to be used differently by SFI (Heffernan et al. in press).

Shifts in SAV from rooted macrophytes to filamentous macroalgae would likely

affect SFI (Deegan et al. 2002). The SFI community has been found to differ between

species of SAV (Chick and McIvor 1997; Troutman et al. 2007). Additionally, SFI

communities may differ between differently structured SAV habitats (Chick and McIvor

1994; Bartholomew et al. 2000; Warfe and Barmuta 2004). The relationships between

SAV and SFI and the differences between rooted macrophytes and filamentous

macroalgae imply that a shift between these habitats will likely impact the SFI

community.

Few investigations have examined how SFI communities may change following a

shift from rooted macrophytes to filamentous macroalgae (but see Pihl et al. 1995;

Deegan et al. 2002). Such shifts in SAV have been documented in the Chassahowitzka

and the Homosassa rivers (Frazer et al. 2006; Heffernan et al. in press). The

Chassahowitzka River currently contains declining rooted macrophytes, and increasing

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filamentous macroalgae and bare substrate, whereas the Homosassa River is

comprised almost exclusively of filamentous macroalgae and unvegetated substrate

(Frazer et al. 2006). These shifts are discussed in more detail in Chapter 1.

In Chapter 2, my objective is to understand how this continued shift from rooted

macrophytes to filamentous macroalgae may affect SFI in coastal freshwater rivers by

characterizing which SAV habitats are required by the SFI community. I examine if the

overall density and diversity of the SFI community differs between specific SAV habitat

types, specifically between rooted macrophytes (notably V. americana), filamentous

macroalgae, and bare substrate. I then determine if the densities of specific size

classes and associated taxa differ between these SAV habitats. Finally I assess

whether the densities of key SFI taxa differ among similar habitat types between rivers

that differ in respect to SAV.

Methods

Study Location

The Chassahowitzka and Homosassa rivers are short (8 and 12 km, respectively),

low gradient spring fed rivers on the Gulf coast of peninsular Florida. I conducted my

research in the freshwater portions of both rivers, which are similar with respect to their

physical (temperature, depth, substrate) and chemical (nutrients, salinity)

characteristics, but characterized by markedly different SAV communities (Hoyer et al.

2004; Frazer et al. 2006). Designated as critical habitat areas by the state of Florida,

these spring-fed coastal rivers support freshwater, oligohaline and marine faunal

communities and associated recreational and commercial activities. Natural resource

management agencies and the general public are concerned that the documented shifts

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in SAV habitat may degrade the valuable function of these systems (Hefferenan et al. in

press).

Study Species and Sampling Gear

Small fishes and crustaceans were sampled with a 1 x 1 x 0.75-m throw trap. This

gear type was selected due to its proficiency at capturing small bodied (less than 60

mm) fish and invertebrates in both densely vegetated and unvegetated shallow areas

(Jordan et al. 1997; Rozas and Minello 1997). To sample sites where water depth

exceeded 0.75 m, I created an extension to the trap by attaching a 0.75-m tall, 3-mm

mesh net with floats to the top of the throw trap. I removed SFI from the trap using a

modified 3-mm mesh bar seine with dimensions matching those of the interior of the

throw trap. Because throw traps very rarely captured larger fish occupying higher

trophic levels (Chick and McIvor 1997), all fish captured were included in analyses.

However, my samples commonly captured much smaller macroinvertebrates (e.g.,

amphipods and isopods) that likely occupied lower trophic levels. Such smaller

macroinvertebrates were not collected or included in these analyses. Commonly

captured species collected and analyzed as SFI included rainwater killifish (Lucania

parva), bluefin killifish (Lucania goodei) spotted sunfish (Lepomis punctatus), Gobiidae

species, grass shrimp (Palaemonetes spp.), blue crab (Callinectes sapidus), and

crayfish (Procambarus spp.).

Sampling Design and Methods

I sampled the SFI community monthly in the Chassahowitzka River from June

2008-May 2009, and in the Homosassa River from November 2008-May 2009. During

these months, SFI were sampled in five specific SAV habitat types: (1) V. americana,

(2) Potamogeton spp., (3) filamentous macroalgae (multiple species), (4) mix of

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filamentous macroalgae and V. americana, and (5) unvegetated substrate. To locate

and sample these SAV habitats, I mapped available habitat types within two study

reaches of each river. Within each reach, I selected two transects perpendicular to river

flow and subdivided each transect at 5-m intervals to create sub-transects extending 5-

m upstream and 5-m downstream (parallel to river flow) from the transect (generally 5 to

17 sub-transects per transect, depending on river width). Along each sub-transect,

snorkeling gear was used to map and characterize 1-m 2 ―cells‖ of SAV habitat at 1-m

intervals (Figure 2-1). To assign sampling sites within study reaches each month, I

randomly selected three replicate ―cells‖ per habitat type. If less than three cells were

available to sample in each reach, each month, I searched for the remaining sample

sites in an additional 5-m upstream and downstream from the mapped areas, and

selected the first appropriate sample sites encountered.

To sample each of the selected SAV habitat cells, I deployed the throw trap and

removed and weighed to the nearest 0.1-kg all above ground SAV material from within

the throw trap. Five passes with a bar seine were then made to remove SFI from within

the trap. The SFI captured in each of the five successive bar seine passes were

removed, placed in a bag, and stored on wet ice. If the first three consecutive passes

were completed without recovering a single SFI, the throw trap was considered

depleted (Glancy et al. 2003) and no further passes were made. All SFI samples were

transported to a laboratory in ice slurry and frozen within 24 hours of being collected.

All individuals were subsequently identified to the lowest taxonomic level possible and

measured to the nearest millimeter of total length for fish taxa and carapace length for

crustaceans. Thirty individuals of each taxa from each sample were randomly selected

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and wet weighed to the nearest 0.0001 gram. Samples were then refrozen for future

analysis.

Because of uncertainty over whether the 5 bar seine passes captured all SFI from

each throw trap sample, I compared counts of total SFI, to estimated abundances of SFI

from each depletion pass using a multinomial depletion approach (Pollock and Gould

1997) as follows:

]})1([ln{

)]}1(ln{[)1(

)]1(ln[{)ln()()1ln(

)]1(ln[)]1([ln)]1(ln[

)|,(

1

1

1

1 1

1 1

x

j

j

j

x

j

j

j

x

j

x

j

jj

x

j

x

j

jj

C

CQ

ppCQCNQC

CNCNN

CpNLL (eq. 1)

where LL = log likelihood ln = natural log N = abundance of SFI p = probability of capture, j = pass number, x = total number of passes, Ci = in pass j, Г(x) = Gamma function which is used to scale factorials of large numbers, Q = 1-Σj=1 to x[p(1-p)j-1].

If estimated catch exceeded the observed catch, confidence intervals around the

catch estimate were calculated. If the upper confidence intervals of the estimate

exceeded observed catch by >5% (indicative of the total catch not representing all SFI,

5%), the estimated catch was used for further analysis. The multinomial depletion

estimates were also used to estimate and compare capture probability between specific

SAV habitats.

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Analyses

Comparisons of overall SFI Density and Diversity among SAV Habitats

To assess if the SFI community differed between SAV habitat types within a

system, I examined two SFI response metrics--overall density and species diversity.

Overall density was measured as the total number of SFI individuals per m 2 .

Shannon’s index was used to measure species diversity, as follows:

s

i

ii ppH1

))(ln( (2)

where H’=Index of species diversity, s= Number of species pi= Proportion of total sample belonging to ith species

Shannon’s index was chosen over other diversity indices due to its sensitivity to

rare species (Peet 1974; Kwak and Peterson 2007). I analyzed differences in SFI

density and diversity using repeated measures analysis of variance (ANOVA) with the

SAS procedure PROC GLIMMIX (SAS, version 9.2). The ANOVA assumptions of

homoscedastic variance and normally distributed residuals were assessed with plots of

residual versus predicted values. When assumptions were not met, I transformed the

response variable by taking the natural log (ln) of each. For each SFI response metric

ANOVA, fixed effects were SAV habitat type, month, and reach, and all interactions

between these terms. To properly account for autocorrelation between monthly

measures of SFI per SAV habitat type, a random effect was included to group

measurements in each reach by transect combination. If the SAV habitat type effect

was significant (p 0.05) in the repeated measures ANOVA, I used Tukey HSD

(honestly significant differences) tests to determine differences in the mean SFI

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response metric between pre-planned comparisons of the SAV habitat types V.

americana, filamentous macroalgae, and bare substrate. Vallisneria americana was

chosen to represent the rooted macrophytes due to its availability at study reaches

throughout the study period. I assessed statistical significance using p 0.05, but also

considered statistically insignificant differences for ecological importance.

Comparisons of Densities of specific SFI size Classes and Taxa among SAV Habitats

To determine how SFI size and species might differ between SAV habitat types, I

investigated the density of specific SFI size classes and taxa as seven additional

response variables (Table 2-1). I analyzed densities of small (0-25 mm), medium (26-

50 mm) and large (>50 mm) size classes of SFI, inclusive of all taxa. I also analyzed

the densities of L. parva, Palaemonetes spp., Gobiidae, and L. punctatus, regardless of

size. These species were chosen to represent different guilds of the SFI community—L.

parva was the most ubiquitous, small fish species, Palaemonetes spp. were the most

abundant crustacean species, L. punctatus was the most common larger SFI species,

and Gobiidae species (multiple genera) were used as characteristic of benthic oriented

SFI. Repeated measures ANOVAs and Tukey HSD tests were used as previously

described to determine differences in response between SAV habitat types for each of

these response metrics, except for density of large sized SFI. A paucity of non-zero

data for the density of large SFI prevented the random effect from being included in the

ANOVA.

Comparisons of specific SFI Taxa Densities between Systems

Historically, the Chassahowitzka and Homosassa rivers were thought to support

similar SAV, and likely SFI communities (Odum 1957a, b). However, in recent years,

24

the Homosassa River has undergone significant declines in SAV while the

Chassahowitzka River has maintained a more intact SAV community (Frazer et al.

2006). Differences in the SAV community and in their associated faunal organisms

(Table 2-1) were used to directly assess how SFI are likely to be impacted by

subsequent loss of rooted macrophytes in the Homosassa River. While such a scenario

does not constitute a true manipulative experiment, strong inferences can still be drawn

from comparisons of the SFI community between these dissimilarly vegetated systems

(Rosenfeld 2001). I compared mean densities of L. parva, Palaemonetes spp.,

Gobiidae, and L. punctatus associated with filamentous macroalgae and bare substrate

between the Chassahowitzka and Homosassa rivers over the months November 2008

through May 2009. I also examined differences in system wide densities, by comparing

the mean densities of each species from all available SAV habitat types between each

river. I tested for differences in densities between river systems using a two sample t

test.

Results

Sampling and Catch Estimation

Vallisneria americana, Potamogeton spp., mixed V. americana and filamentous

macroalgae, filamentous macroalgae and unvegetated (bare) substrate were sampled

in the Chassahowitzka River most months (Potamogeton spp. was not present in

November 2008 and April 2009). In the Homosassa River, only filamentous macroalgae

and unvegetated substrate were available for sampling. I collected a total of 314 throw-

trap samples containing 32 species (30,410 individuals) from the aforementioned

habitats within the Chassahowitzka River monthly between June 2008-May 2009. From

monthly sampling of habitats in the Homosassa River, I collected 40 samples

25

comprising 17 species (1,769 individuals) monthly November 2008-May 2009. I report

proportional abundance of the ten most abundant species of each river (Tables 2-2 and

2-3), which comprised 97% and 99% of all organisms observed for the Chassahowitzka

and Homosassa rivers, respectively. For all habitat types, multinomial depletion

estimates of catch were identical to observed catch in nearly every sample, and capture

probability was nearly identical between habitat types (Figures 2-2). Therefore I used

observed catch for all analyses.

Comparisons of overall SFI Density and Diversity among Habitats

Natural log-transformation of overall SFI density resulted in meeting the

assumptions of homoscedasticity (Figures 2-3 – 2-11). The repeated measures

ANOVA for ln-transformed overall SFI density showed the SAV*month interaction was

significant (Table 2-4; p 0.05), indicating differences of SFI densities between SAV

habitats should be investigated on a month to month basis. Similarly, the analysis for

SFI species diversity indicated the SAV*month*reach interaction was significant for SFI

diversity (Table 2-5; p 0.05). However, because the SFI mean diversity differed

between reaches only by magnitude—i.e. patterns between SAV habitat types were

consistent across sites—I focused on differences in SFI diversity between SAV habitats

by month.

Both density and diversity of the SFI community differed between SAV habitats.

Overall density was greater in all vegetated habitats (V. americana and filamentous

macroalgae) than in bare substrate for most months (Figures 2-12 and 2-13). Densities

of SFI in filamentous macroalgae were greater than V. Americana, when differences

occurred between vegetated habitats, (Figures 2-12 and 2-13). Diversity of SFI was

greater in vegetated habitats than bare habitat for all months (Figures 2-14 and 2-15),

26

with SFI diversity higher in V. americana than filamentous macroalgae for most months

when vegetation types differed (Figures 2-14 and 2-15).

Comparisons of Densities of SFI size Classes and Taxa among Habitats

Natural log-transforming each of the specific SFI size classes and taxa response

metrics (Table 2-1) met model assumptions of homoscedasticity in most cases, as

assessed with plots of residuals (Figures 2-5 – 2-11). For each of these transformed

response metrics, the SAV*month interaction term was a significant effect (Tables 2-6 –

2-12). While the SAV*reach*month interaction was significant for Palaemonetes

spp.(Table 2-10), and the SAV*reach interaction was also significant for Gobiidae

(Table 2-11), pairwise examinations revealed differences between reach were in

magnitude only, and patterns in density by SAV habitat were similar between reaches.

Therefore, I focused on differences in the SFI size group and species mean densities

between SAV habitat types on a month to month basis.

Densities of small SFI, medium SFI, large SFI, L. parva, Palaemonetes spp. and L.

punctatus were higher in vegetated habitats than bare substrate for most months

(Figures 3-6,8). Only Gobiidae had consistently similar densities between bare and

vegetated habitats (Figures 2-26 and 2-27). When densities differed between V.

americana and filamentous macroalgae, densities of small SFI and L. parva were

greater in filamentous macroalgae, whereas densities of larger SFI and L. punctatus

were greater in V. americana (Figures 2-16 – 2-17, 2-20 – 2-23, 2-28 – 2-29). Densities

of Palaemonetes spp, Gobiidae, and medium sized SFI rarely differed between

vegetated habitat types (Figures 2-18 – 2-19, 2-24 – 2-27).

27

Comparisons of SFI taxa Densities between Systems

Differences in SFI densities between the Homosassa and Chassahowitzka rivers

varied among key taxa. Densities of both L. parva and Palaemonetes spp. in

filamentous macroalgae, bare substrate, and pooled from all available SAV habitats

were statistically similar between the two rivers (Table 13, Figures 2-30 – 2-31).

However, densities of Palaemonetes spp. were greater in the Chassahowitzka River

across all habitat types. Gobiidae densities in filamentous macroalgae were also similar

between rivers, but Gobiidae densities associated with bare habitats were significantly

greater in the Homosassa River (Table 2-13, Figure 2-32). Cumulative Gobiidae

densities from all habitats available were also greater in the Homosassa River (Table 2-

13). Densities of L. punctatus associated with filamentous macroalgae were

significantly lower in the Homosassa River compared to the Chassahowitzka River,

while densities associated with bare habitat were similar between rivers (Table 2-13,

Figure 2-33).

Discussion

My results suggest strong associations between SFI taxa and SAV habitats in the

Chassahowitzka and Homosassa rivers, and that a shift from rooted macrophytes to

filamentous macroalgae will elicit changes in the SFI community. Larger SFI taxa will

likely decline following the loss of rooted macrophytes, while some smaller SFI species

may flourish in filamentous macroalgae. This use of filamentous macroalgae is

surprising. Dominance of filamentous macroalgae, however, may precipitate a

subsequent shift to bare substrate and elicit additional declines in SFI. Regardless of a

subsequent SAV shift, the decline of larger SFI associated with the loss of rooted

macrophytes may impact higher trophic levels. Overall, inferences of SAV-SFI

28

relationships provided from this study may be useful for identifying broad patterns of

changes occurring in these systems.

My results provide two lines of inference regarding the impacts of a shift from

rooted macrophytes to filamentous macroalgae on SFI communities. Comparisons of

SFI communities among SAV habitats in the Chassahowitzka River provided weak

inference that overall SFI density, and densities of smaller SFI species, like L. parva

and Palaemonetes spp. would not significantly decline following a loss of rooted

macrophytes, while overall diversity and density of larger SFI, like L. punctatus would.

These comparisons suggest that all SFI, with the exception of Gobiidae, would be

negatively affected by a loss of all vegetated habitat (rooted macrophytes and

filamentous macroalgae). Similarly, comparisons of key species densities between the

Chassahowitzka and Homosassa rivers, provided stronger inferences that following the

loss of rooted macrophytes, L. parva, Gobiidae, and Palaemonetes spp. could maintain

their populations (with Palaemonetes spp. perhaps suffering slight declines), but that L.

punctatus populations would decline to very low abundances. The consistency of the

weaker and stronger inferences drawn from my results provides confidence that larger

SFI may require rooted macrophytes, smaller SFI may not, but almost all SFI require

some vegetated habitat.

The SFI communities’ use of filamentous macroalgae contradicted common

perceptions of the ecological values of this habitat type (Deegan et al. 2002, Hughes et

al. 2002), providing new insight and understanding. Concern over increasing

occurrence of filamentous macroalgae in lotic ecosystems is due, in large part, to the

perception that filamentous macroalgae is poor quality habitat for most fish and

29

invertebrates compared to rooted macrophytes (Paerl 1988). My findings of higher SFI

densities in filamentous macroalgae compared to the native rooted macrophyte V.

americana are novel, and may be explained by the relationships between interstitial

space size and size of the SFI in my study. The size of interstitial spaces may affect

SFI predation risk (Warfe and Barmuta 2006) and foraging opportunities (Grenouillet

and Pont 2001), and small fish have been shown to use habitats proportional to their

body size (Bartholomew et al. 2000). Accordingly, the small size of L. parva and

Palaemonetes spp. may allow them to forage and take refuge in the small interstitial

spaces typical of filamentous macroalgae. These smaller sized SFI’s use of filamentous

macroalgae suggests that this habitat is not ―poor‖ habitat for these species’, despite

constituting less complex physical structure.

Shifts in SAV from rooted macrophytes to filamentous macroalgae may precipitate

further complex habitat changes with additional impacts to the SFI community. The life

history characteristics of filamentous macroalgae (self-shading, short life cycle, and low

resilience to stochastic environmental disturbances) predispose this type of SAV to

subsequent temporary or permanent shifts to bare substrate (Dodds and Gudder 1994;

Duarte 1995; Pihl et al. 1994; Valiela et al. 1997). A shift to bare substrate would be

expected to elicit wide-scale declines in abundance of the SFI community, as shown by

this and previous studies comparing SFI abundance and vital rates between vegetated

to unvegetated habitats (Killgore et al. 1989; Pihl et al. 1995; Jordan 2002). Such a

decline in most SFI species could also affect higher trophic levels (Rozas and Odum

1987) and possibly lead to cascading responses within these ecosystems (Carpenter

and Kitchell 1993).

30

The decline in larger SFI concurrent with the observed shift from rooted

macrophytes to filamentous macroalgae is a key result from this study. By providing

recreational fishing opportunities (Dequine 1950), larger SFI such as L. punctatus are

important in and of themselves to these systems. Additionally, these taxa of SFI

provide critical larger sized forage for predators, such as largemouth bass, Micropterus

salmoides (Tetzlaff 2008). Micropterus salmoides and similar predators may require

larger food items to maintain optimal growth rates (Dunlop 2005). Therefore, the

decline of larger SFI associated with a loss of rooted macrophytes may negatively

impact M. salmoides growth rates. This is supported by results from Tetzlaff (2008) that

showed higher adult M. salmoides growth rates in the Chassahowitzka River compared

to the Homosassa River. Taken in concert with my results, these findings suggest a

trophic cascade linkage (Carpenter and Kitchell 1993) between SAV habitat and M.

salmoides growth, and illustrate that the shift from rooted macrophytes to filamentous

macroalgae may have impacts throughout these ecosystems.

The shifts in SFI and SAV observed in this study may be part of a broader pattern

of declining heterogeneously structured aquatic habitat associated with a shift towards

animal communities characterized by lower abundance, less diversity, and/or smaller

dominant species. Such changes have been described as a progression towards biotic

homogeneity (Airoldi et al. 2008). Biotic homogeneity is defined by McKinney and

Lockwood (1999) as ―… a reduction in overall structural complexity, native biota,

functional traits and the expansion of few widespread and less complex broadly tolerant

biota‖. Shifts in aquatic ecosystems to more homogenous habitat types and declines in

species diversity have been documented in a wide variety of ecosystems such as

31

seagrass beds (Hughes et al. 2002), live bottom communities (Thrush and Dayton

2002; Coleman and Williams 2002), and nearshore oyster reefs (Coen et al. 1999,

Eggleston 1999).

The shifts in habitat and associated SFI observed in the Chassahowitzka and

Homosassa rivers may represent a similar example of increasing biotic homogeneity.

Rooted macrophytes feature greater interstitial and patch scale heterogeneity than

filamentous macroalgae, which provides more structural heterogeneity than bare

substrate. Therefore, shifts in habitat from rooted macrophytes to filamentous

macroalgae to bare substrate constitute increasing structural homogeneity. My study

indicates such a shift would likely cause a decline in SFI abundance, species diversity

and abundance of larger species like L. punctatus, and the dominance of a few smaller

species like L. parva or Gobiidae. The findings reported here represent one of the first

reports of a progression to biotic homogeneity in freshwater systems, and may be useful

as a model for describing similar changes in other systems.

Alternative interpretations of my study results and inferences are possible and

should be noted. I relied on observations of the historic similarity and subsequent

changes in SAV habitat in the Chassahowitzka and Homosassa rivers to make

inferences about SFI habitat requirements. However, other factors unrelated to SAV

habitat may have differed between these two rivers, and caused the observed

differences in the SFI community. Additional studies will be useful to validate the

assumptions of this study and strengthen inferences. Manipulative experiments to

assess habitat specific SFI survival and growth would provide a mechanistic

understanding of why certain SFI species change in response to SAV habitat

32

alterations. Additionally, a mechanistic understanding would further strengthen

inferences of how SFI and their predators may be affected by changes in SAV habitat.

Finally, meta-analyses assessing how other changes in habitat structure have affected

associated animals communities in these and other ecosystems may help determine if

patterns of biotic homogeneity are occurring in freshwater lotic ecosystems.

33

Table 2-1. Specific response variables compared either among SAV habitats, between

rivers, or both.

Response Variable Assessed

Density of SFI size classes and taxa among

Chassahowitzka SAV habitats

Comparisons of certain SFI taxa densities within

SAV habitats types between Chassahowitzka

and Homosassa rivers

Density of rainwater killifish (Lucania parva)

Yes

Yes

Density of grass shrimp (Palaemonetes spp.)

Yes Yes

Density of species of the family Gobiidae

Yes Yes

Density of species of spotted sunfish (Lepomis punctatus)

Yes Yes

Density of small sized SFI (individuals < 25-mm)

Yes No

Density of medium sized SFI (individuals 26-50-mm)

Yes No

Density of large sized SFI (individuals >50-mm

Yes No

Table 2-2. Proportional species composition of the Chassahowitzka River June 2008 –

May 2009 Chassahowitzka River

Rank Species Proportion

1 Lucania parva 0.560

2 Palaemonetes spp. 0.196

3 Lepomis punctatus 0.054

4 Lucania goodei 0.047

5 Procambarus spp 0.035

6 Menedia beryllina 0.031

7 Syngnathus scovelli 0.021

8 Grapsidae 0.010

9 Gobiidae 0.008

10 Notropis petersoni 0.008

34

Table 2-3. Proportional species composition of the Homosassa River November 2008 – May 2009

Homosassa River

Rank Species Proportion

1 Lucania parva 0.343

2 Grapsidae family 0.178

3 Gobiidae family 0.152

4 Anchoa mitchilli 0.115

5 Palaemonetes spp 0.101

6 Eucinostomus argenteus 0.051

7 Menedia beryllina 0.032

8 Calinectes sapidus 0.008

9 Gambusia holbrookii 0.006

10 Syngnathus scovelli 0.005

Table 2-4. Repeated measures analysis of variance results for overall ln-transformed

SFI density per m 2 in the Chassahowitzka River, from June 2008-May 2009 Effect Num DF Den DF F Value Pr > F

Reach 1 10 0.52 0.5207 SAV 4 10 50.73 <.0001

Reach*SAV 4 10 1.17 0.3919 Month 11 34 9.46 <.0001

Reach * Month 11 34 1.36 0.2412 SAV * Month 42 34 1.82 0.0344

SAV * Reach *Month 30 34 0.97 0.4594

Table 2-5. Repeated measures analysis of variance results for overall SFI diversity in

the Chassahowitzka River, from June 2008-May 2009 Effect Num DF Den DF F Value Pr > F

Reach 1 10 2.95 0.1166 SAV 4 10 27.01 <.0001

Reach*SAV 4 10 0.99 0.4582 Month 11 34 1.13 0.3681


SAV * Reach *Month 30 34 2.17 0.0152

Table 2-6. Repeated measures analysis of variance results for ln-transformed small

sized SFI densities per m 2 in the Chassahowitzka River, from June 2008-May 2009

Effect Num DF Den DF F Value Pr > F

Reach 1 10 2.31 0.1597 SAV 4 10 42.01 <.0001

Reach*SAV 4 10 0.94 0.4796 Month 11 34 7.43 <.0001


SAV * Reach *Month 30 34 1.25 0.2609

35

Table 2-7. Repeated measures analysis of variance results for ln-transformed medium

sized SFI densities per m 2 in the Chassahowitzka River, from June 2008-May 2009


Reach 1 10 0.60 0.4572 SAV 4 10 35.57 <.0001

Reach*SAV 4 10 0.65 0.6378 Month 11 34 15.58 <.0001


SAV * Reach *Month 30 34 1.13 0.3676

Table 2-8. Repeated measures analysis of variance results for large sized SFI densities

per m 2 in the Chassahowitzka River, from June 2008-May 2009 Effect Num DF Den DF F Value Pr > F

Reach 1 10 0.00 0.9853 SAV 4 10 0.00 1.000

Reach*SAV 4 10 0.02 0.9988 Month 11 34 0.62 0.8122

Reach * Month 11 34 0.33 0.9791 SAV * Month 42 34 75.55 <.0001

SAV * Reach *Month 30 34 1.07 0.2876

Table 2-9. Repeated measures analysis of variance results for ln-transformed L. parva

densities per m 2 in the Chassahowitzka River, from June 2008-May 2009 Effect Num DF Den DF F Value Pr > F

Reach 1 10 0.20 0.6667 SAV 4 10 52.73 <.0001

Reach*SAV 4 10 1.47 0.2822 Month 11 34 11.42 <.0001


SAV * Reach *Month 30 34 1.12 0.3709

Table 2-10. Repeated measures analysis of variance results for ln-transformed

Palaemonetes spp. densities per m 2 in the Chassahowitzka River, from June 2008-May 2009


Reach 1 10 5.11 0.0474 SAV 4 10 37.04 <.0001

Reach*SAV 4 10 2.81 0.0846 Month 11 34 15.45 <.0001


SAV * Reach *Month 30 34 1.96 0.0295

36

Table 2-11. Repeated measures analysis of variance results for ln-transformed

Gobiidae densities per m 2 in the Chassahowitzka River, from June 2008-May 2009


Reach 1 10 38.25 0.001 SAV 4 10 3.92 0.0363

Reach*SAV 4 10 3.18 0.0628 Month 11 34 7.02 <.0001


SAV * Reach *Month 30 34 2.88 0.0017

Table 2-12. Repeated measures analysis of variance results for ln-transformed L.

punctatus densities per m 2 in the Chassahowitzka River, from June 2008-May 2009


Reach 1 10 3.09 0.1094 SAV 4 10 7.14 0.0055

Reach*SAV 4 10 0.19 0.9368 Month 11 34 2.97 0.0072


SAV * Reach *Month 30 34 1.26 0.2558

Table 2-13. Results from comparisons between mean densities per m 2 in the Chassahowitzka and Homosassa rivers using Welch’s two sample T test, p = 0.05

Comparison Mean CHA

Mean HOM

t DF p-value

L. parva, macroalgae 46.078 42.500 0.318 21 0.753 L. parva, bare substrate 0.564 3.344 -1.697 33 0.099

L. parva, all habitats 20.288 14.805 1.208 63 0.231 Palaemonetes spp.,

macroalgae 22.89 10.83 1.513 44 0.137

Palaemonetes spp., bare substrate

0 1.690 -1.067 28 0.295

Palaemonetes spp., all habitats

11.298 4.366 1.787 109 0.077

Gobiidae, macroalgae 1.079 8.08 -1.972 11 0.074 Gobiidae, bare substrate 0.256 5.897 -3.199 28 0.003

Gobiidae, all habitats 0.711 6.536 -3.628 40 0.001 L. punctatus, macroalgae 0.474 0.083 2.2793 48 0.027

L. punctatus, bare substrate

0.026 0.000 1 38 0.324

L. punctatus, all habitats 2.209 0.024 5.9972 177 1.097e-08

37

Figure 2-1. Mapping and sample selection are illustrated. The white rectangle shows

sampling universe per transect. The yellow line shows the transect, the short, red lines are sub-transects, shaded polygon represents an example habitat type, such as V. americana. Small squares represent actual throw trap samples.

38

Figure 2-2. Recovery probabilities for small fish and macroinvertebrates in 5 specific

habitat types. Recovery probabilities are given on the x-axis and the probability density function is given on the y-axis.

39

Pearson Residual

-3

-2

-1

0

1

2

3

4

Linear Predictor

-1 0 1 2 3 4 5 6 7

Figure 2-3. Pearson’s residuals for the ln-transformed overall SFI density repeated

measures model for Chassahowitzka River

40

Pearson Residual

-3

-2

-1

0

1

2

3

Linear Predictor

-1 0 1 2

Figure 2-4. Pearson’s residuals for overall SFI diversity repeated measures model for Chassahowitzka River

41

Pearson Residual

-3

-2

-1

0

1

2

3

Linear Predictor

-1 0 1 2 3 4 5 6 7

Figure 2-5. Pearson’s residuals for ln-transformed L. parva repeated measures model, Chassahowitzka River

42

Pearson Residual

-4

-3

-2

-1

0

1

2

3

4

5

Linear Predictor

-1 0 1 2 3

Figure 2-6. Pearson’s residuals for ln-transformed Palaemonetes spp. repeated measures model, Chassahowitzka River

43

Pearson Residual

-3

-2

-1

0

1

2

3

Linear Predictor

-1 0 1 2 3 4

Figure 2-7. Pearson’s residuals for the ln-transformed L. punctatus repeated measure’s model, Chassahowitzka River

44

Pearson Residual

-3

-2

-1

0

1

2

3

4

Linear Predictor

-1 0 1 2 3

Figure 2-8. Pearson’s residuals for the ln-transformed Gobiidae repeated measures

model Chassahowitzka River

45

Pearson Residual

-4

-3

-2

-1

0

1

2

3

4

Linear Predictor

-1 0 1 2 3 4 5 6 7

Figure 2-9. Pearson’s residuals of ln-transformed small SFI repeated measures model

Chassahowitzka River

46

Pearson Residual

-3

-2

-1

0

1

2

3

4

Linear Predictor

-1 0 1 2 3 4 5

Figure 2-10. Pearson’s residuals for ln-transformed medium SFI repeated measure’s

model, Chassahowitzka River.

47

Pearson Residual (Mu scale)

-4

-3

-2

-1

0

1

2

3

4

5

6

7

Mu

0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15

Figure 2-11. Pearson’s residuals from large SFI group (not ln transformed) mixed (not

repeated measures) model, for the Chassahowitzka River.

48

Figure 2-12. Overall SFI density per m 2 by habitat type and months at the Chassahowitzka River, June 2008 – May 2009. Shown with one standard deviation (for clarity). Different letters indicate statistically significant differences (p≤0.05), and asterisks (*) indicate a habitat was not available for sampling.

49

Figure 2-13. Pairwise comparisons of overall SFI densities per m 2 between SAV habitat types at the Chassahowitzka

River, June 2008-May 2009. Mean and 95% confidence intervals around data are shown.

50

Figure 2-14. Mean overall SFI diversity per m 2 and one standard deviation are shown by habitat type and months at the

Chassahowitzka River, June 2008 – May 2009. Different letters indicate statistically significant differences (p≤0.05), and asterisks (*) indicate a habitat was not available for sampling.

51

Figure 2-15. Pairwise comparisons of overall SFI diversity per m 2 between SAV habitat types at the Chassahowitzka


52

Figure 2-16. Mean small SFI density per m 2 and one standard deviation are by habitat type and months at the


53

Figure 2-17. Pairwise comparisons of small SFI density per m 2 between SAV habitat types at the Chassahowitzka River,

June 2008-May 2009. Mean and 95% confidence intervals around data are shown.

54

Figure 2-18. Mean medium SFI density per m 2 and one standard deviation shown by habitat type and months in the


55

Figure 2-19. Pairwise comparisons of medium SFI density per m 2 between SAV habitat types at the Chassahowitzka


56

Figure 2-20. Mean large SFI density per m 2 and one standard deviation are shown by habitat type and months in the


57

Figure 2-21. Pairwise comparisons of large SFI density per m 2 between SAV habitat types at the Chassahowitzka River,


58

Figure 2-22. Mean L. parva density per m 2 with one standard deviation are shown by habitat type and month at the


59

Figure 2-23. Pairwise comparisons of L. parva density per m 2 between SAV habitat types at the Chassahowitzka River,


60

Figure 2-24. Mean Palaemonetes spp. density per m 2 and one standard deviation are shown by habitat type and months

in the Chassahowitzka River, June 2008 – May 2009. Different letters indicate statistically significant differences (p≤0.05), and asterisks (*) indicate a habitat was not available for sampling.

61

Figure 2-25. Pairwise comparisons of Palaemonetes spp. density per m 2 between SAV habitat types at the

Chassahowitzka River, June 2008-May 2009. Mean and 95% confidence intervals around data are shown.

62

Figure 2-26. Mean Gobiidae density per m 2 and one standard deviation are shown by habitat type and month in the


63

Figure 2-27. Pairwise comparisons of Gobiidae density per m 2 between SAV habitat types at the Chassahowitzka River, June 2008-May 2009. Mean and 95% confidence intervals around data are shown.

64

Figure 2-28. Mean L. punctatus density per m 2 with one standard deviation shown by habitat type and month in the


65

Figure 2-29. Pairwise comparisons of L. punctatus density per m 2 between SAV habitat types at the Chassahowitzka

River, June 2008-May 2009. Mean and 95% confidence intervals around data are shown

66

Figure 2-30. Comparisons of L. parva. mean density per m 2 with one standard

deviation between the Chassahowitzka and Homosassa rivers cumulative over the months November 2008 – May 2009. Asterisks (*) indicate habitat types were not available for sampling. Minus signs (-) and equal signs (=) represent densities in the Homosassa River were lower than or equal to, respectively, that of the Chassahowitzka River.

67

Figure 2-31. Comparisons of Palaemonetes spp. mean density per m 2 with one

standard deviation between the Chassahowitzka and Homosassa rivers cumulative over the months November 2008 – May 2009. Asterisks (*) indicate habitat types were not available for sampling. Minus signs (-) and equal signs (=) represent densities in the Homosassa were lower than or equal to, respectively, that of the Chassahowitzka.

68

Figure 2-32. Comparisons of Gobiidae mean density per m 2 with one standard

deviation between the Chassahowitzka and Homosassa rivers cumulative over the months November 2008 – May 2009. Asterisks (*) indicate habitat types were not available for sampling. Minus signs (-) and equal signs (=) represent densities in the Homosassa were lower than or equal to, respectively, that of the Chassahowitzka.

69

Figure 2-33. Comparisons of L. punctatus mean density per m 2 with one standard

deviation between the Chassahowitzka and Homosassa rivers cumulative over the months November 2008 – May 2009. Asterisks (*) indicate habitat types were not available for sampling. Minus signs (-) and equal signs (=) represent densities in the Homosassa were lower than or equal to, respectively, that of the Chassahowitzka.

70

CHAPTER 3 SUMMARY AND CONCLUSIONS

I found SFI taxa were strongly related to SAV habitats in the Chassahowitzka and

Homosassa rivers, such that a shift from rooted macrophytes to filamentous macroalgae

would likely elicit changes in the SFI community. Larger SFI taxa will likely decline

following the loss of rooted macrophytes, while some smaller SFI species may flourish

in filamentous macroalgae. Dominance of filamentous macroalgale, however, may

precipitate a subsequent shift to bare substrate and elicit additional declines in SFI.

Regardless of a subsequent SAV shift, the decline of larger SFI associated with the loss

of rooted macrophytes may impact higher trophic levels in these ecosystems. Overall,

inferences of SFI/SAV relationships provided from this study may be useful for

identifying broad patterns of changes occurring in these systems.

Both lines of inference (described in detail in Chapter 2) showed consistent

impacts of a shift from rooted macrophytes to filamentous macroalgae on SFI

communities. First, comparisons of SFI communities among SAV habitats in the

Chassahowitzka River provided weak inference that overall SFI density, and densities

of smaller SFI species, like L. parva and Palaemonetes spp. would not significantly

decline following a loss of rooted macrophytes, while overall diversity and density of

larger SFI, like L. punctatus would. Second, comparisons of key species densities

between the Chassahowitzka and Homosassa rivers, provided stronger inferences that

following the loss of rooted macrophytes, L. parva, Gobiidae, and Palaemonetes spp.

could maintain their populations (with Palaemonetes spp. perhaps suffering slight

declines), but that L. punctatus populations would decline to very low abundances. The

consistency of the weaker and stronger inferences drawn from my results provides

71

confidence that larger SFI may require rooted macrophytes, smaller SFI may not, but

almost all SFI require some vegetated habitat.

My findings that SFI communities’ use of filamentous macroalgae in greater

densities than rooted macrophytes are novel and contradicted the common perception

that filamentous macroalgae is of little ecological value (Paerl 1988; Deegan et al. 2002;

Hughes et al. 2002). These unexpected results may be explained by the relationships

between interstitial space size of the SAV habitat types and size of the SFI in my study.

Smaller SFI may use habitat with proportionally smaller interstitial spaces to decrease

predation risk and increase foraging opportunities (Bartholomew et al. 2000; Grenouillet

and Pont 2001; Warfe and Barmuta 2006). Accordingly, the small size of L. parva and

Palaemonetes spp. may allow them to forage and take refuge in the small interstitial

spaces typical of filamentous macroalgae.

The shift in SAV from rooted macrophytes to filamentous macroalgae may

precipitate further complex habitat changes with additional impacts to the SFI

community. The life history characteristics of filamentous macroalgae predispose this

type of SAV to subsequent temporary or permanent shifts to bare substrate (Dodds and

Gudder 1994; Pihl et al. 1994; Duarte 1995; Valiela et al. 1997). A shift to bare

substrate would be expected to elicit wide-scale declines in abundance of the SFI

community, which could also affect higher trophic levels. Such a cascading effect

(Carpenter and Kitchell 1993) is described in greater detail in Chapter 2.

A key result from this study is that the observed shift from rooted macrophytes to

filamentous macroalgae was associated with a decline in larger SFI. Larger SFI such

as L. punctatus are important in and of themselves to these systems (Dequine 1950),

72

and provide critical larger sized forage for predators, such as Micropterus salmoides

(Tetzlaff 2008). Because M. salmoides and similar predators may require larger food

items to maintain optimal growth rates (Dunlop 2005), the decline of larger SFI may

negatively impact M. salmoides growth rates. This is supported by results from Tetzlaff

(2008) that showed higher adult M. salmoides growth rates in the Chassahowitzka River

compared to the Homosassa River. Taken in concert with my results, these findings

suggest a trophic cascade linkage (Carpenter and Kitchell 1993) between SAV habitat

and M. salmoides growth, and illustrate that the shift from rooted macrophytes to

filamentous macroalgae may have impacts throughout these ecosystems.

The shifts in SFI and SAV observed in this study may be part of a broader pattern

of increasing biotic homogeneity. Increasing biotic homogeneity is described as the

decline of the structural complexity of habitat, associated with the decline of more

specialized native taxa and functional groups and the increase of more tolerant fauna

(McKinney and Lockwood 1999). Biotic homogeneity is described in greater detail in

Chapter 2. In these systems, habitat has shifted from rooted macrophyte (more

complex) to filamentous macroalgae (less complex), and may shift further to bare

substrate (least complex). My study indicates these shifts will be associated a decline

in SFI abundance, species diversity and abundance of larger species like L. punctatus,

and the dominance of a few smaller species like L. parva or Gobiidae. These findings

represent one of the first reports of a progression to biotic homogeneity in freshwater

systems, and may be useful as a model for describing similar changes in other systems.

Alternative interpretations of my study results and inferences are possible and

should be noted. I relied on observations of the historic similarity and subsequent

73

changes in SAV habitat in the Chassahowitzka and Homosassa rivers to make

inferences about SFI habitat requirements. However, other factors unrelated to SAV

habitat may have differed between these two rivers, and caused the observed

differences in the SFI community. Additional studies will be useful to validate the

assumptions of this study and strengthen inferences. Manipulative experiments to

assessing habitat specific SFI survival and growth would provide a mechanistic

understanding of why certain SFI species change in response to SAV habitat

alterations. Additionally, a mechanistic understanding would further strengthen

inferences of how SFI and their predators may be affected by changes in SAV habitat.

Finally, meta-analyses assessing how other changes in habitat structure have affected

associated animals communities in these and other ecosystem may help determine the

if patterns of biotic homogeneity are occurring in freshwater lotic ecosystems.

74

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BIOGRAPHICAL SKETCH

Edward Camp was born in 1983 in Malden, Massachusetts. He was

homeschooled by his parents throughout grade school and was encouraged to explore

and study the natural world. In 2001, he graduated from Whitinsville Christian High

School and entered Gordon College in Wenham, Massachusetts. At Gordon College

Edward pursued an interdisciplinary academic track by studying communications,

ecology, economics, sociology and political sciences, and studied abroad in New

Zealand, Western Samoa, as well as Washington, USA. In May 2005 Edward

graduated with a degree in environmental studies.

In May 2005, Edward moved to Logan, Utah to begin work as a research assistant

studying Bonneville Cutthroat trout. Over the next several years Edward worked as a

research assistant in Utah, Wyoming, Colorado, New York and Florida and gained

experience studying fish and fisheries. Over these years Edward hiked, ran, skied and

fished some of the most amazing parts of this country.

Upon the completion of his master’s degree, Edward plans to continue his

education by pursuing a Doctor of Philosophy in the study of fisheries. Ultimately,

Edward is interested in coupling an understanding of fish ecology with social and

economic realities to better sustain both the beauty and utility of aquatic ecosystems.

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