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Levi Otwoma-Thesis2012.Pdf Genetic population structure of the coral reef starfish Linckia laevigata in the Indo-West Pacific By Levy Michael Otwoma “Thesis submitted for the degree of Master of Biology – specialisation Human Ecology of the Vrije Universiteit Brussel” Msc thesis Supervisor: Professor Dr. Marc Kochzius September 2012 1 ACKNOWLEDGEMENT I am grateful to my Supervisor Professor Dr. Marc Kochzius for giving me an opportunity to work in the field of molecular ecology and for his scientific guidance from laboratory work to thesis preparation. Special thanks also go to the Flemish Inter-university council (VLIR) and Free University of Brussels (VUB) for the scholarship award that facilitated this Msc study. Many thanks, to the management of Kenya Marine and Fisheries Research Institute (KMFRI) for granting me permission to attend this master program. Much gratitude goes to Tim Seriens for his far-reaching assistance during the entire laboratory work. Specials thanks to the entire human ecology team Professor Ludwig Triest, Iris Stiers, Petra, and fellow classmates. Much gratitudes go to my family and friends for love and support, and for all the joy it brings to life. i ABSTRACT The blue starfish Linckia laevigata is common on shallow water coral reefs of the Indo-West Pacific. Since L. laevigata is sedentary, long distance dispersal is only possible by their planktonic larval stage. This long larval dispersal mechanism can allow interconnection of populations that are separated by several hundred kilometers. However, a growing number of studies report genetic breaks in populations of L. laevigata across the Indo-Malay Archipelago and between the Indian and Pacific Oceans. Only limited information on the genetic connectivity of this species is available for the Indian Ocean, showing genetic structuring between samples collected in SouthAfrica and Thailand. The study investigates the genetic population structure and connectivity of L. laevigata in the Western Indian Ocean and compares it to previous studies in the Indo-Malay Archipelago by mitochondrial cytochrome oxidase I gene. A total of 138 samples were collected from nine locations in the WIO coastline, from Kenya to Madagascar. AMOVA revealed a low but significant ΦST value of 0.024 in the WIO population, which indicated reduced gene flow. The genetic structure was stronger (ΦST = 0.13) in the comparative analysis of WIO and Indo-Malay Archipelago population. Five clades were detected from the haplotype network analysis which corresponded to different geographical locations that might have been separated during the glacial sea level low stands in the Pleistocene. The strong genetic differentiation suggests that the population of Linckia laevigata can be classified in the following groups: (1) Western Indian Ocean (2) Eastern Indian Ocean (3) Central Indo-Malay Archipelago and (4) Western Pacific. Keywords: Linckia laevigata, mtDNA, WIO, Indo-Malay Archipelago, Genetic break, ii TABLE OF CONTENTS ACKNOWLEDGEMENT ............................................................................................................... i ABSTRACT .................................................................................................................................... ii LIST OF FIGURES ........................................................................................................................ v LIST OF TABLES ......................................................................................................................... vi LIST OF ABBREVIATIONS ....................................................................................................... vii CHAPTER 1: General Introduction ................................................................................................ 1 1.1 Introduction ...................................................................................................................... 1 1.2 Linckia laevigata .............................................................................................................. 2 1.3 Genetic diversity and gene flow ....................................................................................... 4 1.4 Connectivity and its implication to management ............................................................. 6 1.5 Status of genetic population structure in the Western Indian Ocean ............................... 9 1.6 Status of genetic structure in the Indo-Malay Archipelago ............................................ 10 1.7 Factors affecting larval dispersal .................................................................................... 12 1.8 Oceanographic conditions in the Western Indian Ocean region .................................... 13 1.9 Oceanographic condition in the Indo-Malay Archipelago ............................................. 14 1.10 Assessment of genetic structure ..................................................................................... 15 1.11 Choice of marker and Mitochondria DNA ..................................................................... 16 1.12 Polymerase chain reaction .............................................................................................. 17 1.13 DNA Sequencing............................................................................................................ 18 1.14 Problem statement .......................................................................................................... 20 1.15 Objective of the study .................................................................................................... 21 CHAPTER 2: Materials and methods ........................................................................................... 22 2.1 Study site and sample collections................................................................................... 22 2.2 DNA extraction .............................................................................................................. 22 2.3 Gel electrophoresis ......................................................................................................... 23 2.4 Preparation of the Gel .................................................................................................... 23 2.5 Running the Gel ............................................................................................................. 23 2.6 Amplification and sequencing ........................................................................................ 25 2.7 Genetic diversity ............................................................................................................ 25 2.8 Historical demography ................................................................................................... 26 iii 2.9 Genetic population structure and connectivity ............................................................... 26 CHAPTER 3: Results ................................................................................................................... 27 3.1 Genetic diversity ............................................................................................................ 27 3.2 Historical demography ................................................................................................... 27 3.3 Genetic population structure and connectivity ............................................................... 28 3.3.1 Western Indian Ocean .................................................................................................. 28 3.3.2 Indo-West Pacific ......................................................................................................... 29 CHAPTER4: Discussion ............................................................................................................... 32 4.1 Genetic diversity ............................................................................................................ 32 4.2 Historical demography ................................................................................................... 32 4.3 Genetic population structure and connectivity ............................................................... 33 4.3.1 Western Indian Ocean ............................................................................................. 33 4.3.2 Indo-West Pacific.................................................................................................... 34 CHAPTER 5: Conclusion and implications for management ...................................................... 38 REFERENCES ............................................................................................................................. 40 APPENDICES .............................................................................................................................. 51 iv LIST OF FIGURES Figure. 1 A schematic representation of ocean currents in the Indian Ocean. ............................. 14 Figure. 2. Map of WIO and Indo-Malay Archipelago sample sites. ............................................. 24 Figure. 3. Mismatch distribution graph of pooled WIO population ............................................. 28 Figure. 4. Plot of pairwise ΦST values against geographic distance (Km) .................................... 31 v LIST OF TABLES Table 1. Genetic diversity, neutrality tests and mismatch distribution. ........................................ 27 Table.2. Pairwise ΦST values among populations of Linckia laevigata in the WIO. .................. 29 Table 3. Hierarchical AMOVA based
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