The Pennsylvania State University The Graduate School Department of Biology THE ORIGIN, MEANING, AND DETECTION OF CLUSTERS IN POPULATION GENETIC DATA A Dissertation in Biology by Francis Condon Wham Jr. Submitted in Partial Fulfillment of the Requirements for the Degree of Doctor of Philosophy May 2016 The dissertation of Francis Condon Wham Jr. was reviewed and approved* by the following: Todd C. LaJeunesse Associate Professor of Biology The Pennsylvania State University Dissertation Advisor Stephen W. Schaeffer Professor of Biology Assistant Department Head for Graduate Education The Pennsylvania State University Chair of Committee Iliana B. Baums Associate Professor of Biology The Pennsylvania State University George Perry Assistant Professor of Anthropology and Biology The Pennsylvania State University Tracy Langkilde Head of the Department of Biology The Pennsylvania State University *Signatures are on file in the Graduate School iii ABSTRACT In light of modern genetic techniques, there is growing awareness that taxonomic designations of do not reflect biological reality. When hidden species boundaries go undetected they cause spurious conclusions about biology. Here I discuss several new analytical approaches useful for finding and making inferences from clusters in genetic data. I then apply these techniques to the results of several recent studies and highlight how critical errors in interpretation might have been avoided by first resolving species boundaries. I then show that these approaches are an important first step in connectivity studies. Finally, I highlight the critical role they have played in justifying the taxonomic status of several new species of Symbiodinium. iv TABLE OF CONTENTS LIST OF FIGURES .................................................................................................................. vi! LIST OF TABLES ................................................................................................................... x! ACKNOWLEDGEMENTS ..................................................................................................... xi Chapter 1: ON THE ORIGIN OF CLUSTERS IN POPULATION GENETIC DATA…............1 References ................................................................................................................................ 21 Chapter 2: EVALUATING THE SPECIES HYPOTHESIS WITH A BAYESIAN SYMPATRIC STRUCTURE TEST IN ZOANTHUS SANSIBARICUS AND ITS SYMBIONTS…………........…….........................................................................................................23 Abstract ................................................................................................................................... 23! Introduction .............................................................................................................................. 23! Methods .................................................................................................................................... 26 Results .................................................................................................................................... 32! Discussion ................................................................................................................................ 36 Conclusion ................................................................................................................................ 44 References ................................................................................................................................ 48 Chapter 3: SYMBIODINIUM POPULATION GENETICS: TESTING FOR SPECIES BOUNDARIES AND ANALYZING SAMPLES WITH MIXED GENOTYPES ……………….54 Abstract ................................................................................................................................... 54! Introduction .............................................................................................................................. 55! Methods .................................................................................................................................... 58 Results .................................................................................................................................... 66! Discussion ................................................................................................................................ 75 Conclusion ................................................................................................................................ 85 References ................................................................................................................................ 87 Chapter 4: THE COALESCENT THEORY OF CLONAL ORGANISMS …………………….96 Abstract ................................................................................................................................... 96! Introduction .............................................................................................................................. 97! Methods .................................................................................................................................... 98 Results .................................................................................................................................... 113! Discussion ................................................................................................................................ 122 Conclusion ................................................................................................................................ 133 References ................................................................................................................................ 135 Chapter 5: MICROSATELLITE LOCI FOR THE HOST-GENERALIST ‘‘ZOOXANTHELLA’’ SYMBIODINIUM TRENCHI AND OTHER CLADE D SYMBIODINIUM……….…………………………………………………………………….........140 Abstract ................................................................................................................................... 140 References ................................................................................................................................ 146 Chapter 6: MICROSATELLITE LOCI FOR SYMBIODINIUM GOREAUI AND OTHER CLADE C SYMBIODINIUM....................................................................................……….……………….151 Abstract ................................................................................................................................... 151 Introduction .............................................................................................................................. 153! Methods .................................................................................................................................... 155 v Conclusion ................................................................................................................................ 156 References ................................................................................................................................ 157 Chapter 7: EIGHT POLYMORPHIC MICROSATELLITE LOCI FOR THE INDO-PACIFIC- WIDE ZOANTHID, ZOANTHUS SANSIBARICUS…………………………….……………….162 Abstract ................................................................................................................................... 162 References ................................................................................................................................ 166 vi LIST OF FIGURES Figure 1-1: Figure 1-1) Pairwise genetic distance and Pairwise genetic difference of Symbiodinium genotypes. a) Pairwise genetic distance of Symbiodinium genotypes previously published in Wirshing et al. (2013), arrows point to clonal individuals on the left and unique individuals on the right b) ) Pairwise genetic difference of Symbiodinium trenchii genotypes previously published in Pettay et al. (2015) ), arrows point to clonal individuals on the left and unique individuals on the right……………………………8 Figure 1-2: Expected results of flipping a fair coin n-times modeled with a continuous beta distribution. ................................................................................. 14 Figure 1-3: Expected frequency of pairwise relationships modeled with the dirichlet distribution .............................................................................................. 16 Figure 1-4: Pairwise relationship between individuals in a forward time simulation modeling divergence, sex, clonality and mutation. Histogram colored by the relationship between pairwise comparisons, members of different species shown in red, members of the same species in green, identical individual in the same clone family in blue and members of the same clone family with a single mutation event between them colored in orange. .................................................................................................................. 18 Figure 2-1: Simplified depiction of experimental design, where the effect of geographic distance is compared to the effect of putative reproductive barriers to assess the species hypothesis ............................................................... 29 Figure 2-2: Bayesian sympatric structure test approach to use a region of population equivalence to accept or reject the hypothesis of species ................... 30 Figure 2-3: Results of STRUCTURE analysis on multi-locus genotypes of Z. sansibaricus and their associated clade C symbiodinum.