Old Dominion University ODU Digital Commons Biological Sciences Theses & Dissertations Biological Sciences Fall 2017 Tracing the Genetic Footprints of the Redbelly Yellowtail Fusilier, Caesio Cuning, Across Multiple Spatial and Evolutionary Scales Amanda Susanne Ackiss Old Dominion University Follow this and additional works at: https://digitalcommons.odu.edu/biology_etds Part of the Biology Commons, Ecology and Evolutionary Biology Commons, and the Genetics Commons Recommended Citation Ackiss, Amanda S.. "Tracing the Genetic Footprints of the Redbelly Yellowtail Fusilier, Caesio Cuning, Across Multiple Spatial and Evolutionary Scales" (2017). Doctor of Philosophy (PhD), dissertation, Biological Sciences, Old Dominion University, DOI: 10.25777/t8md-tf35 https://digitalcommons.odu.edu/biology_etds/20 This Dissertation is brought to you for free and open access by the Biological Sciences at ODU Digital Commons. It has been accepted for inclusion in Biological Sciences Theses & Dissertations by an authorized administrator of ODU Digital Commons. For more information, please contact [email protected]. TRACING THE GENETIC FOOTPRINTS OF THE REDBELLY YELLOWTAIL FUSILIER, CAESIO CUNING, ACROSS MULTIPLE SPATIAL AND EVOLUTIONARY SCALES by Amanda Susanne Ackiss B.A. May 2002, University of Virginia A Dissertation Submitted to the Faculty of Old Dominion University in Partial Fulfillment of the Requirements for the Degree of DOCTOR OF PHILOSOPHY ECOLOGICAL SCIENCES OLD DOMINION UNIVERSITY December 2017 Approved by: Kent E. Carpenter (Director) Daniel Barshis (Member) David Gauthier (Member) Christopher Bird (Member) ABSTRACT TRACING THE GENETIC FOOTPRINTS OF THE REDBELLY YELLOWTAIL FUSILIER, CAESIO CUNING, ACROSS MULTIPLE SPATIAL AND EVOLUTIONARY SCALES Amanda Susanne Ackiss Old Dominion University, 2017 Director: Dr. Kent E. Carpenter Overfishing is one of the most pervasive threats to coral reef ecosystems, and management of these multi-species resources is hampered by limited species-specific population level information. The reefs in the western tropical Pacific Ocean, including the Coral Triangle, are the most bio-diverse in the world. Home to more than 400 million people, this region contains some of the most threatened coral reef ecosystems. Presented here is the first comprehensive analysis of the genetic structure of Caesio cuning, planktivorous fish inhabiting reefs in the Coral Triangle and western Pacific Ocean. Data from both classical Sanger and next- generation sequencing were analyzed across multiple spatial scales to test hypotheses regarding the biogeography, ecology, and population connectivity of this important food fish. Across the Coral Triangle, mitochondrial DNA sequencing was used to examine broad- scale genetic patterns from 33 locations. Results show the presence of two clades found on either side of the Sunda Shelf, a biogeographic pattern attributed to vicariant isolation during low sea level stands during the Pleistocene Epoch. No evidence for isolation-by-distance across the sampling region was found, however, within the clade associated with the Pacific Ocean, AMOVA and BARRIER analyses indicate significant genetic differences between central Indonesia and the Philippines relative to eastern Indonesia. Restriction site-associated DNA (RAD) sequencing data from five sites along the Kuroshio Current were used to examine fine-scale gene flow from the core to the northern limit of the species range. Results indicate that C. cuning in this region conform to the predictions of the central-peripheral population model described by Mayr (1963). Edge effects were found in peripheral populations including decreasing effective sample size, increased relatedness, and disjunct peripheral populations. Finally, since management of reef fish resources occurs at the country-level, RAD sequencing data from seven sites were used to examine fine-scale patterns of population structure within the Philippines. Results suggest that C. cuning from Palawan are genetically distinct from all other sites in the north, central, and eastern Philippines. Excluding Palawan, no isolation-by-distance was found despite significant genetic structure between many sites, indicating that gene flow within the Philippines is largely impacted by regional oceanographic features. iv Copyright, 2017, by Amanda Susanne Ackiss and Kent E. Carpenter, All Rights Reserved. v This thesis is dedicated to my family, who has whole-heartedly supported me as I traveled the long and winding road to my PhD. vi ACKNOWLEDGMENTS There are many people who have been essential to the successful completion of this dissertation. Foremost, I would like to thank my advisor, Dr. Kent Carpenter, for taking a chance on a graduate student with a Bachelor of Arts in Media Studies, for introducing me to the spectacular marine ecosystems of the Coral Triangle, and for providing me with the incredible opportunity to live and work there. I would like to thank my committee members, Dr. David Gauthier, Dr. Daniel Barshis, and Dr. Christopher Bird, for generously making their labs available to me through months (years) of library prep and for their support through many unforeseen obstacles. I would also like to thank Dr. Annette Meñez, Dr. Menchie Ablan- Lagman, Dr. Ngurah Mahardika, and Dr. Hilconida Calumpang for welcoming me into their labs while I was in the Philippines and Indonesia. I am so thankful for the many years of shared field work, workshops, videoke, oyster roasts, crab feasts, pig roasts, bonfires, and trivia nights with my academic family, the current and past members of the Carpenter lab: Milli and Jonell Sanciangco, Eric Crandall, Adam Hanson, Jeremy Raynal, Mia Comoros-Raynal, Brian Stockwell, Demian Willette, Ellen Biesack, Jack Buchanan, Christi Linardich, Mike Harvey, Gina Ralph, Andy Hines, and Emilie Stump. Our assorted shenanigans got me through many difficult challenges. Tagay! I am grateful for the financial support of the Department of Biological Sciences through graduate teaching assistantships and the Dominion Scholar Award and of my advisor through graduate research assistantships. This dissertation would not have been possible without funding support to Kent Carpenter from the National Science Foundation grants OISE-0730256 and DEB-1257632. vii TABLE OF CONTENTS Page LIST OF TABLES ............................................................................................................. ix LIST OF FIGURES ............................................................................................................ x LIST OF GRAPHS ............................................................................................................ xi INTRODUCTION .............................................................................................................. 1 RESEARCH OBJECTIVES ................................................................................... 8 PROUNOUNCED GENETIC STRUCTURE IN A HIGHLY MOBILE CORAL REEF FISH, CAESIO CUNING, IN THE CORAL TRIANGLE ..................................... 17 INTRODUCTION ................................................................................................ 17 METHODS ........................................................................................................... 20 RESULTS ............................................................................................................. 25 DISCUSSION ....................................................................................................... 32 ACKNOWLEDGEMENTS .................................................................................. 39 TESTING THE CENTRAL-PERIPHERAL POPULATION MODEL ALONG THE KUROSHIO CURRENT. ........................................................................................ 40 INTRODUCTION ................................................................................................ 40 METHODS ........................................................................................................... 44 RESULTS ............................................................................................................. 52 DISCUSSION ....................................................................................................... 60 RAD SEQUENCING ILLUMINATES THE POPULATION DYNAMICS OF A CORAL REEF FISHERY ACROSS THE PHILIPPINE ARCHIPELAGO .................... 66 INTRODUCTION ................................................................................................ 66 METHODS ........................................................................................................... 70 RESULTS ............................................................................................................. 76 DISCUSSION ....................................................................................................... 87 DISCUSSION ................................................................................................................... 93 CONCLUSIONS AND FUTURE DIRECTIONS ................................................ 99 LITERATURE CITED ................................................................................................... 101 APPENDICES A. CORRECTED AND UNCORRECTED PAIRWISE ΦST VALUES ............ 124 B. RELATEDNESS AND ALIGNMENT SUMMARY TABLES .................... 128 C. RELATEDNESS AND MIGRATION TABLES .......................................... 130 D. TABLES OF IACUC PROTOCOL APPROVAL NUMBERS .................... 133 viii E. PERMISSION FOR REPRINTING