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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