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Dissertations, Theses, and Masters Projects Theses, Dissertations, & Master Projects

2002

Molecular and morphological evolution of the amphipod radiation of Lake Baikal

Kenneth S. Macdonald III College of William and Mary - Virginia Institute of Marine Science

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Recommended Citation Macdonald, Kenneth S. III, "Molecular and morphological evolution of the amphipod radiation of Lake Baikal" (2002). Dissertations, Theses, and Masters Projects. Paper 1539616759. https://dx.doi.org/doi:10.25773/v5-axk5-fs83

This Dissertation is brought to you for free and open access by the Theses, Dissertations, & Master Projects at W&M ScholarWorks. It has been accepted for inclusion in Dissertations, Theses, and Masters Projects by an authorized administrator of W&M ScholarWorks. For more information, please contact [email protected]. Reproduced with with permission permission of the of copyright the copyright owner. owner.Further reproduction Further reproduction prohibited without prohibited permission. without permission. Molecular and Morphological Evolution

of the Amphipod Radiation

of Lake Baikal

A Dissertation

Presented to

The Faculty of the School of Marine Science

The College of William and Mary

In Partial Fulfillment

Of the Requirements for the Degree of Doctor of Philosophy

by

Kenneth S. Macdonald III 2002

Reproduced with permission of the copyright owner. Further reproduction prohibited without permission. Approval Sheet

This dissertation is submitted in partial fulfillment of

the requirements for the degree of

Doctor of Philosophy

Kenneth Macdonald III

Approved, September 2002

f j J. Emmett Duffy, Ph.D. Committee Chairman/Advisor

John Graves

Kuehl

John Holsinger Dept, of Biological Sciences

Old Dominion University

CftfF Cunningham Department of Biology Duke University

ii

Reproduced with permission of the copyright owner. Further reproduction prohibited without permission. Table of Contents

Acknowledgments ...... v

List of Tables...... vii

List of Figures...... viii

Abstract...... x

Introduction...... 2

Literature Cited ...... 12

Chapter 1: A molecular phylogeny of the amphipods of Lake Baikal using 16S rDNA

Abstract...... 18

Introduction ...... 19

Materials and Methods ...... 24

Results...... 28

Discussion ...... 31

Literature Cited ...... 41

Chapter 2: A Combined Molecular and Morphological Phylogenetic Analysis of the

Amphipods of Lake Baikal, Russia

Abstract...... 65

Introduction ...... 66

Materials and Methods ...... 69

Results...... 74

iii

Reproduced with permission of the copyright owner. Further reproduction prohibited without permission. Discussion. 76

Literature Cited ...... 83

Chapter 3: Morphological Character Evolution of the Amphipods of Lake Baikal

Abstract...... 100

Introduction ...... 101

Materials and Methods ...... 104

Results...... 105

Discussion ...... 107

Literature Cited ...... 116

General Conclusions...... 141

Literature Cited ...... 145

Appendices...... 147

Vita...... 161

iv

Reproduced with permission of the copyright owner. Further reproduction prohibited without permission. Acknowledgments

I would first and most importantly thank my major advisor. Dr. Emmett Duffy. Emmett

not only took me. an aspiring "fish biologist”, under his wing and opened my eyes to the

wonders of the invertebrate world, he was also very generous with his time and support. He

also allowed me to not only achieve my goals, but also to have fun along the way. I also want

to thank Dr. John Graves, who was a second major advisor in almost every way but name, for

his support and for generously allowing almost unfettered use of his laboratory. I want to thank

the rest of my committee: Dr. Cliff Cunningham, for his enthusiastic support and his analytical

prowess; Dr. John Holsinger. for his amphipod expertise; and Dr. Steve Kuehl, for his different

(i.e. non-biological) viewpoint and questions.

I would also like to thank my two Russian colleagues: Dr. Nikolai Muguc provided

numerous samples, and Dr. Lev Yampolsky not only supplied me with specimens, he also

guided me to Lake Baikal, and allowed me to experience this wondrous place for myself.

Thanks to all my lab mates, both in the Fisheries Genetics Lab and in the Evolutionary

Ecology Lab (Go Team MOBEE!) for unending support, numerous lab lunches, beautiful days

on the Ferry Pier, and all the juicy gossip I could bear. Also thanks to Dr. Dave Carlini, who

helped me create a sturdy foundation of phylogenetic knowledge that has been steadily built

upon during my years at VIMS, and Jan McDowell, who taught me most of the lab techniques

I’ve been botching (through no fault of her own) for the last several years.

I also want to thank my family, who, along with all the snide comments, also gave me

v

Reproduced with permission of the copyright owner. Further reproduction prohibited without permission. their undying love and support through many, many years of schooling. I want to thank my

many wonderful friends I've collected over my seven years at VIMS, especially Sara, who has

helped me deal with both the good and bad for over half of those years. When you spend

seven years in once place, you tend to accumulate debts to practically everyone, so I finally

want to thank the VIMS community in general, for making my tenure here an enjoyable one.

This dissertation was financially supported by an NSF grant (DEB 9S-157S5). by part

of a NOAA NMFS CMER award (NA17FE1497). and by numerous VIMS Minor Research

Grants. VIMS GSA Minigrants, and William and Mary Minor Research Grants.

Reproduced with permission of the copyright owner. Further reproduction prohibited without permission. List of Tables

Chapter 1

1. Species Sampled ...... 47

2. 16S Pairvvise Distances ...... 48

Chapter 2

1. Species Sampled ...... 87

2. Results of Phylogenetic Analyses ...... 88

C hapter 3

1. Species Sampled ...... 120

vii

Reproduced with permission of the copyright owner. Further reproduction prohibited without permission. List of Figures

Chapter 1

1. Baikal’s amphipods ...... 51

2. Tree from parsimony anaiysis of 16S data ...... 53

3. Tree from 1 ikel ihood analysis o f 16S data ...... 55

4. Tree from Bayesian analysis of 16S data ...... 57

5. Saturation plots of numbers of substitutions vs. distance ...... 59

6. Plot ofbootstrap support value versus branch length ...... 61

7. Acanthogammarid distance frequency histogram ...... 63

Chapter 2

1. Saturation plots of numbers of substitutions vs. distance ...... 90

2. Trees from parsimony analyses ofindividual datasets ...... 92

3. Tree from parsimony analysis of combined molecular data ...... 94

4. Trees from likelihood and Bayesian analyses of combined molecular data ...... 96

5. Trees from parsimony analyses of combined molecular/morphological data ...... 98

Chapter 3

1. Baikal’s amphipods ...... 122

2. Trees from separate parsimony analyses of 16S and morphological data...... 124

3. Plot ofmorphological patristic distance versus 16S pairwise distance ...... 126

4. Rescaled Consistency Index (RC) plots ...... 128

viii

Reproduced with permission of the copyright owner. Further reproduction prohibited without permission. 5. Body armour and process characters traced