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When Does Gene Flow Stop? a Mechanistic Approach to the Formation of Phylogeographic Breaks in Nature

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When Does Gene Flow Stop? a Mechanistic Approach to the Formation of Phylogeographic Breaks in Nature When Does Gene Flow Stop? A Mechanistic Approach to the Formation of Phylogeographic Breaks in Nature by Iris Holmes A dissertation submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy Ecology and Evolutionary Biology in the University of Michigan 2020 Doctoral Committee: Assistant Professor Alison Davis Rabosky, Chair Research Professor Liliana Cortés Ortiz Professor Patrick Schloss Associate Professor Stephen Smith Iris A. Holmes [email protected] ORCID iD: 0000-0001-6150-6150 © Iris A. Holmes 2020 Dedication I dedicate this thesis to Michael Grundler, who is always there. ii Acknowledgements The research in this dissertation was supported by funding from the University of Michigan, including the Department of Ecology and Evolutionary Biology, the Museum of Zoology, and the Rackham Graduate School. It was also supported by grants from the Bureau of Land Management, and the STEPS Institute for Innovation in Environmental Research at the University of California. The research in my dissertation was greatly facilitated by the National Science Foundation Graduate Research Fellowship, the Rackham Predoctoral Fellowship, and the Rackham Graduate School Anna Olcott Smith Women in Science Award. I would like to thank my adviser, Alison Davis Rabosky, for her care and attention in developing both my strengths and weaknesses as a scientist. I would also like to thank the rest of my committee, Patrick Schloss, Stephen Smith, and Liliana Cortez Ortiz, for their help and support in completing my dissertation. In addition, I have had the privilege to work with excellent coauthors on the manuscripts in this dissertation, including Maggie Grundler, William Mautz, Ivan Monagan Jr, and Mike Westphal. I would like to thank the communities in the University of Michigan Museum of Zoology, and the UMMZ Department of Herpetology and Genomic Diversity Laboratory in particular, as well as the University of Michigan Department of Ecology and Evolutionary Biology. I am particularly indebted to the Davis Rabosky and Rabosky labs for their help and support of all kinds. iii Table of Contents Dedication .....................................................................................................................................................ii Acknowledgements .................................................................................................................................... iii List of Tables ................................................................................................................................................ x List of Figures ............................................................................................................................................. xi Abstract ......................................................................................................................................................xii Chapter 1 Introduction ............................................................................................................................... 1 Chapter 2 Historical Environment is Reflected in Modern Population Genetics and Biogeography of an Island Endemic Lizard (Xantusia riversiana reticulata) ................................................................. 6 2.1 Abstract .............................................................................................................................................. 6 2.2 Introduction ....................................................................................................................................... 7 2.2.1 San Clemente Island biogeography.............................................................................................. 8 2.2.2 Xantusia riversiana and its phylogenetic relationships ............................................................... 8 2.2.3 Human impacts on San Clemente Island ................................................................................... 10 2.3 Methods ............................................................................................................................................ 10 2.3.1 Ethics Statement ......................................................................................................................... 10 2.3.2 Tissue collection and site descriptions ....................................................................................... 11 iv 2.3.3 Primer design and locus amplification ....................................................................................... 12 2.3.4 Next generation sequencing ....................................................................................................... 13 2.3.5 Locus linkage and disequilibrium .............................................................................................. 13 2.3.6 Genetic diversity, gene flow, and population structure ............................................................. 14 2.3.7 Effective population size ............................................................................................................ 15 2.3.8 Population bottlenecks ............................................................................................................... 16 2.3.9 Spatial genetic structure ............................................................................................................. 16 2.4 Results............................................................................................................................................... 18 2.4.1 Locus behavior, genetic diversity, and population structure ..................................................... 18 2.4.2 Effective population size and genetic bottlenecks ..................................................................... 19 2.4.3 Spatial genetic structure ............................................................................................................. 20 2.5 Discussion ......................................................................................................................................... 21 2.5.1 Genetic diversity of Xantusia riversiana ................................................................................... 21 2.5.2 Effects of previous conservation action: goat removal .............................................................. 23 2.5.3 Future conservation focus .......................................................................................................... 23 2.6 Data Archiving .............................................................................................................................. 24 2.7 Acknowledgments ......................................................................................................................... 24 2.8 Funding ......................................................................................................................................... 25 Chapter 3 Parsing Variance by Marker Type: Testing Biogeographic Hypotheses and Differential Contribution of Historical Processes to Population Structure in a Desert Lizard .............................. 43 3.1 Abstract ............................................................................................................................................ 43 3.2 Introduction ..................................................................................................................................... 44 v 3.2.1 Biogeographic hypotheses ......................................................................................................... 46 3.2.2 Predictions of marker variance .................................................................................................. 47 3.3 Methods ............................................................................................................................................ 49 3.3.1 Field collection and tissue acquisition ....................................................................................... 49 3.3.2 Habitat classifications ................................................................................................................ 49 3.3.3 DNA extraction and Microsatellite Genotyping ........................................................................ 50 3.3.4 Next-Generation Sequencing and Data Processing ................................................................... 50 3.3.5 Locus diversity and characteristics ............................................................................................ 51 3.3.6 Phylogeography ......................................................................................................................... 51 3.3.7 Historical movement corridors................................................................................................... 52 3.4 Results............................................................................................................................................... 54 3.4.1 Locus characteristics, diversity, and private alleles ................................................................... 54 3.4.2 Phylogeography ......................................................................................................................... 54 3.4.3 Historical movement corridors................................................................................................... 55 3.4.4 Locus comparison .....................................................................................................................
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