CALIFORNIA STATE UNIVERSITY, NORTHRIDGE GENETIC DIVERSITY, POPULATION STRUCTURE AND CONNECTIVITY OF MILLEPORA ALCICORNIS (HYDROZOA: ANTHOMEDUSAE: MILLEPORIDAE) IN THE FLORIDA REEF TRACT A thesis submitted in partial fulfillment of the requirements For the degree of Master of Science in Biology by Diana M. Jacinto August 2014 i The thesis of Diana M. Jacinto is approved: Peter J. Edmunds, Ph.D. Date Jeanne Robertson, Ph.D. Date Elizabeth Torres, Ph.D. Date Steve Dudgeon, Ph.D., Chair Date California State University, Northridge ii DEDICATION This thesis is dedicated to my parents for providing me with the constant love and encouragement to achieve academic success. To my mom, thank you for always supporting and encouraging me throughout my life. To my dad, you have always nurtured my inquisitive mind and for that I am forever grateful. Thank you for being not only the best father but also a best friend. iii ACKNOWLEDGMENTS I would like to thank my committee members who supported and encouraged my efforts in completing this thesis. To my advisor Dr. Steve Dudgeon, you have impacted my growth as a scientist and my perspective on the world around me, for that I am grateful. To Dr. Jeanne Robertson, thank you for the time you invested in guiding this project and the positivity you provided me with throughout my academic journey. To Dr. Peter Edmunds, thank you for input and guidance in writing my thesis. To Dr. Elizabeth Torres, thank you for providing me with the scientific foundation and support that has led to the completion of this thesis. I would especially like to thank the individuals who helped with the collection of the samples used in this study, Sylvia Zamudio and William Precht. I would also like to thank the various individuals who have provided input and advice that led to the completion of this thesis. I am also grateful for my labmate Lareen Smith, who has been supportive and positive throughout my time at CSUN. I am grateful for the invaluable friendships I have formed with my fellow graduate students and wish them nothing but success. I would also like to thank my friends and Daniel Gray Longino, who have been supportive and understanding throughout my academic journey. This research was supported by funding from the National Science Foundation California State University Louis Stokes Alliance for Minority Participation Bridge to the Doctorate (CSU-LSAMP BD) Award (HRD-1139803), CSUN-Graduate Equity Fellowship, CSUN Thesis Support, and CSU California Pre-Doctoral honorable mention fund. iv TABLE OF CONTENTS Signature Page ii Dedication iii Acknowledgments iv Abstract v INTRODUCTION 1 Millepora 4 Southern Florida ocean current patterns 8 Genetic diversity, population structure and connectivity of M. alcicornis in the FRT 11 Hypotheses 12 METHODOLOGY 15 Sample collection 15 DNA extraction, microsatellite amplification and genotyping 16 Microsatellite quality analysis 18 Statistical analyses 19 Clustering analysis 20 Clonal analysis 21 RESULTS 23 Microsatellite loci, HWE, null alleles, and linkage disequilibria 23 Genetic diversity and differentiation 23 Clustering analysis 25 Clonal analysis 26 DISCUSSION 27 Differentiation and connectivity of M. alcicornis 27 Genetic diversity 30 Genotypic diversity 31 Conclusion 32 TABLES AND FIGURES 35 REFERENCES 48 APPENDIX A: Multilocus genotypes in data set 57 APPENDIX B: Psex values 62 v ABSTRACT GENETIC DIVERSITY, POPULATION STRUCTURE AND CONNECTIVITY OF MILLEPORA ALCICORNIS (HYDROZOA: ANTHOMEDUSAE: MILLEPORIDAE) IN THE FLORIDA REEF TRACT by Diana M. Jacinto Master of Science in Biology Coral reefs are experiencing global declines due to changing environmental conditions triggered by climate change and anthropogenic effects impacting important reef-building organisms and their inhabitants. Millepores are calcareous hydrocorals found on shallow reefs worldwide, however little information is known about their genetic diversity and population biology. The present study sought to determine the population structure and genetic diversity of Millepora alcicornis, a branching fire coral, in reefs found in the Florida Reef Tract (FRT) and population connectivity was inferred. Five microsatellite markers were used to detect genetic differentiation between 12 sampling sites from reefs from the middle Keys and Miami within the FRT. A single panmictic population of M. alcicornis in the FRT (K=1; FST=0.001) was found with moderate levels of genetic diversity (Ho=0.426, SE=0.023; Na=6.0, SE=0.763) inferring high connectivity and gene flow among reefs in the FRT. High connectivity of M. alcicornis in the FRT along with moderate levels of genetic diversity is a hopeful indication that M. alcicornis will be better able to acclimate to changing environmental conditions. vi INTRODUCTION Coral reefs are not only a great source of biodiversity in marine habitats, but a great source of biodiversity on the planet (Knowlton 2001a). Coral reef-building organisms create habitats for thousands of species, with diversity estimates of marine inhabitants ranging from 600,000 to more than 9 million (Knowlton 2001b; Reaka-Kudla 1997; Knowlton et al. 2010). Globally, reefs have experienced declines in cover (the percentage of hard substrate covered by living coral tissue; Selig and Bruno 2010) due to climate change and human impacts such as coral bleaching, habitat destruction, overfishing and pollution from agriculture and land development (Hughes et al. 2003; Hughes et al. 2010). The decline in coral cover is in large part due to the loss of important reef-framework builders, scleractinians in addition to reef-building octocorals and hydrocorals (Carpenter et al. 2008). Understanding the genetic population structure, the partitioning of putative populations based on allele frequencies (Freeland et al. 2011), and connectivity, the genetic exchange of individuals among geographically separated populations (Cowen et al. 2007), of reef-building species is crucial to develop and implement appropriate management strategies that could prevent further decline of coral cover in reef ecosystems. Marine Protected Areas (MPAs) are currently the best management tool for conserving these threatened reef systems (Hughes et al. 2003). Exploring the extent of genetic connectivity within and among coral reefs provides MPA managers with the correct information to determine the spatial management and appropriate placement of MPAs in coral reef habitats (Palumbi 2003; McCook et al. 2009; Cvitanovic et al. 2013). High levels of gene flow or connectivity promotes high genetic diversity (the amount of 1 genetic variation contained within population; Freeland et al. 2011) and genotypic diversity (the number of unique multilocus genotypes present in a population; Baums et al. 2006a) within a species, which results in an increased potential ability to adapt to and recover from environmental changes (Markert et al. 2010; Hughes et al. 2003). Exploring the degree of connectivity among reefs can determine how broad (regional; i.e., involving two or more countries) or localized (only encompassing certain areas over a short distance) MPAs should be, based on conserving reef-building organisms with high genotypic diversity (Hughes et al. 2003). MPAs are unlikely to prevent mortality of corals due to bleaching because MPAs cannot control rising water temperatures (Hughes et al. 2003); however, MPAs will facilitate a partial recovery of reefs that are populated by different reef-building organisms with diverse genotypes (Hughes et al. 2003). High genotypic diversity suggests high rates of gene flow in which various alleles into are introduced into a population creating new gene combinations on which selection can potentially act (van Oppen and Gates 2006). Investigating population connectivity in a marine environment remains a challenge due to the technical limitations of tracking large numbers of small propagules (i.e., larvae) from an organism in a vast fluid environment (larval dispersal; Selkoe and Toonen 2011; van Oppen and Gates 2006). Connectivity among marine populations can be inferred by estimation of genetic differentiation, the magnitude of genetic divergence among and within putative populations (Bird et al. 2011), through the use of molecular markers. Molecular markers, such as microsatellites (short tandem repeats of DNA motifs; Freeland et al. 2011), not only provide estimates of genetic diversity but also allow for the identification of clones caused by asexual reproduction or unique genotypes 2 produced by sexual reproduction. Determining levels of connectivity among coral reefs can help to determine how populations will respond to natural and anthropogenic disturbances. Low levels of genetic differentiation would infer gene flow (high connectivity) between reefs causing a population to be more likely replenished by migrating individuals between reefs after a disturbance (Jones et al. 2009). Contrary, high levels of genetic differentiation and low levels of connectivity can lead to habitat loss of a reef after a disturbance, since it is unlikely that there would be population replenishment from migrating individuals (Jones et al. 2009). Studies of genetic population structure and connectivity of reef-building organisms have focused on scleractinians (i.e., stony corals, Class: Anthozoa; Baums et al. 2005; Baums et al. 2006a; Baums et al. 2010; Goffredo et al. 2004; Hemond and Vollmer 2010; Ayre and Hughes 2004; Nakajima et al. 2010; Mackenzie et al. 2004) and little attention has been given to sympatric hydrocorals