TEMPORAL AND SPATIAL VARIATION IN POPULATION STRUCTURE AND DISTRIBUTION OF A DIRECT-DEVELOPING CRYPTIC SPECIES COMPLEX, LEP TASTERIAS A s A thesis submitted to the faculty of San Francisco State University In partial fulfillment of the requirements for 6 /0 L the Degree ■ M $ Master of Science In Biological Sciences: Ecology, Evolution and Conservation by Laura Michelle Melroy San Francisco, California January 2015 Copyright by Laura Michelle Melroy 2015 CERTIFICATION OF APPROVAL I certify that I have read TEMPORAL AND SPATIAL VARIATION IN POPULATION STRUCTURE AND DISTRIBUTION OF A DIRECT-DEVELOPING CRYPTIC SPECIES COMPLEX, LEPTASTERIAS by Laura Michelle Melroy, and that in my opinion this work meets the criteria for approving a thesis submitted in partial fulfillment of the requirement for the degree Master of Science in Biology: Ecology, Evolution and Conservation Biology at San Francisco State University. C. Sarah Cohen, Ph.D. Professor, Biology Professor, Biology TEMPORAL AND SPATIAL VARIATION IN POPULATION STRUCTURE AND DISTRIBUTION OF A DIRECT-DEVELOPING CRYPTIC SPECIES COMPLEX, LEPTASTERIAS SPP. Laura Michelle Melroy San Francisco, California 2015 Temporal genetic studies of direct developing organisms are rare. Marine invertebrates lacking a planktonic larval stage are expected to have lower dispersal, low gene flow, and a higher potential for local adaptation than organisms with planktonic dispersal. Leptasterias is a genus of brooding sea stars that contains several cryptic species complexes. Population genetic methods were used to resolve patterns of fine-scale population structure in central California Leptasterias using three loci from nuclear and mitochondrial genomes. Historic samples were compared to contemporary samples to delineate changes in species distributions in space and time. Contemporary sampling confirmed a pattern of shared haplotypes at both mitochondrial and nuclear loci around the mouth of San Francisco Bay with distinct, shared haplotypes bracketing populations north and south of the bay. Phylogenetic analysis confirmed the presence of a bay- localized clade and revealed the presence of an additional bay-localized and previously undescribed clade of Leptasterias. Analysis of contemporary and historic samples indicated these two clades may be experiencing a constriction in their southern range limit and suggest a decrease in abundance at sites at which they were once prevalent. Historic sampling revealed a different distribution of diversity along the California coastline compared to contemporary sampling and illustrates the importance of temporal genetic sampling in phylogeographic studies. I certify that the Abstract is a correct representation of the content of this thesis. Date ACKNOWLEDGEMENTS I would like to thank members of the Cohen Lab, Jason Helvey and Shana Gallagher for help with sample collections and bench work. I would also like to thank John Largier, Eric Routman and Greg Spicer for helpful discussion. We would like to thank the California Academy of Science Invertebrate Zoology Collection for allowing me to sample their collections of Leptasterias, specifically the help of Kelly Markello and Chrissy Piotrowski. I would like to thank David Foltz for providing samples and for helpful discussion. I would like to thank Mamie Chapman, Sara Caldwell, and Sherry Tamone for assistance with sample collection in Alaska. Thanks for Renate Eberl for comments on the manuscript. Funding was provided to LM by SFSU Graduate Student Council, SFSU Instructional Research Award, and RTC. The Romberg Tiburon Center, SFSU gene lab use was made possible by National Science Foundation FSML Grant 0435033 (CSC) and donations from Biolink CCSF, SFSU COSE, and the Koret Foundation. v TABLE OF CONTENTS List of Tables........................................................................................... vii List of Figures........................................................................................................................viii List of Appendices...................................................................................................................ix Introduction................................................................................................................................ 1 Methods......................................................................................................................................4 Sample Collection and Extraction.................................. 4 PCR Amplification...................................................................................................... 5 Sequencing Reactions.................................................................................................. 7 Phylogenetic Analysis.................................................................................................. 7 Population Analysis..................................................................................................... 9 Results.............................................................................. 11 Phylogenetic Analysis of Contemporary and Historical Samples..........................12 Population Genetic Analysis.....................................................................................14 Historical Analysis......................................................................................................17 Discussion................................................................................................................................18 Divergence Times and Phylogenetics....................................................................... 18 Patterns of Population Structure........................ 20 Population Expansion and Evidence for Range Shifts........................................... 25 References................................................................................................................................28 Appendices...............................................................................................................................44 vii LIST OF TABLES Table Page 1. Sample Collection Data.....................................................................................35 2. Genetic distances............................................................................................... 36 3. Molecular Diversity Statistics............................................................................36 LIST OF FIGURES Figures Page 1. Leptasterias mtDNA Phylogeny............................................... 37 2. Time Since Divergence Tree..............................................................................38 3. Haplotype Maps.................................................................................................. 39 4. Clade Maps.......................................................................................................... 40 5. Haplotype Network..............................................................................................41 6. Mismatch Distributions........................... 42 7. Change in Clade Frequency Map ............................................................... 43 ixx \ LIST OF APPENDICES Appendix Page 1. Reference Sequences.............................................................................................. 44 2. Population pairwise differences........................................................................ 44-45 3. AMOVA.................... 45 4. Mismatch Statistics................................. 46 5. Intron Phylogeny......................................................................................................47 6. Minimum Spanning Tree Excluding Indels...........................................................48 x 1 Introduction The marine environment is heterogeneous with many instances of speciation and genetic differentiation due to adaptive and neutral processes of divergence. Geographic patterns of genetic variation in the marine environment are shaped by life history, oceanographic and transport processes, sea level and land changes, and selection. These processes influence the population structure of marine invertebrates on both temporal and spatial levels. Temporal studies of genetic structure are rare, and even more so are temporal genetic studies of direct developing organisms (Lee and Boulding 2009). Marine organisms with direct development tend to have lower vagility than organisms with planktonic larvae, low levels of gene flow and high genetic structure between populations, a higher potential for local adaptation, and more frequent speciation and extinction events (Strathmann and Strathmann 1982; Jablonski 1986; Levin 2006; Kelly and Palumbi 2010). Direct developers are also expected to show higher temporal genetic stability than planktonic dispersers (Lee and Boulding 2009). However, predictions of genetic structure based on development mode are not always consistent (Sotka 2004; Becker et al. 2007; Bradbury et al. 2008). These inconsistencies have been explained by intrinsic and extrinsic factors influencing dispersal on temporal and spatial scales such as larval behavior, currents and circulation, habitat discontinuity, and geographic features (Avise 1992; Billot et al. 2003; Selkoe et al. 2010; Winston 2012; Kamel et al. 2014). Connectivity influences the evolutionary trajectory of populations and properly quantifying gene flow between populations depends on accurate taxonomic groupings 2 (Pante et al. 2015). Successful management of marine