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Lim Hong Chiun GENETIC DIVERSITY AND PHYLOGEOGRAPHY OF THE FRESHWATER HALFBEAK, GENUS Hemirhamphodon (TELEOSTEI: HEMIRAMPHIDAE: ZENARCHOPTERINEA) IN SUNDALAND RIVER BASINS LIM HONG CHIUN UNIVERSITI SAINS MALAYSIA 2017 GENETIC DIVERSITY AND PHYLOGEOGRAPHY OF THE FRESHWATER HALFBEAK, GENUS Hemirhamphodon (TELEOSTEI: HEMIRAMPHIDAE: ZENARCHOPTERINEA) IN SUNDALAND RIVER BASINS by LIM HONG CHIUN Thesis submitted in fulfillment of the requirements for the degree of Doctor of Philosophy August 2017 ACKNOWLEDGEMENT My most sincere gratitude and appreciation to my great supervisor Prof. Siti Azizah Mohd Nor who was always behind me in giving endless support, guidance, patience, encouragement throughout my research and believing in me for the ‘flexi working time’. Without her big helping hand, I think I would not get this far. Thanks again to Mummy Sazzy. Besides, I would like to say thank you to Prof. Geoffrey Chambers and Dr. Eleanor for sharing their knowledge and expertise during their visit in USM. My appreciation also goes to Dr. Mark de Bruyn for providing very helpful ideal, information and technique to make this research better. Special thanks to Pisceslim (Lim Teow Yeong) for unconditional assistance in field works and the knowledge shared with me. Not forgetting also thanks to Mr. Michael Lo and the late Mr. Heng Wei Ann for great assistance during field work in Sarawak, Prof. Muchlisin from Syiah Kuala Universiti, Aceh and Prof. Chaidir from Riau University in spending their precious time and helping hand during field work in Sumatra. My gratitude also goes to members and friends of Lab 308, Kak Adel, Jamsari, Danial, Adib, Lia, Nurul, Wani, Fong, Nazia, Min Pau as well as the new lab members and everyone that might have cross my path. Thank you for helping me in lab work, accompanying me for lunches, trips (field and holiday) and sometimes need to bear with me (nagging). ii My profound gratitude to my parents who is loving and supporting me all the time in my life. To my dear beloved wife, ‘Missi’, a simple word of ‘Thank you’ is not enough for your patience in waiting me to complete this ‘slow moving’ PhD journey, your sacrifice in building our lovely little family and your greatest love. All of these will be in my heart for ever and I love you. Last but not least, my appreciations to Ministry of Higher Education for financial support through MyBrian15 Scholarship and Universiti Sains Malaysia for funding my research under iReC Project. iii TABLE OF CONTENTS ACKNOWLEDGEMENT ii TABLE OF CONTENTS iv LIST OF TABLES ix LIST OF FIGURES xiv LIST OF PLATES xxiv LIST OF ABBREVIATIONS xxv ABSTRAK xxvi ABTRACT xxviii CHAPTER ONE: GENERAL INTRODUCTION 1.1 Introduction 1 1.2 Problem statement 6 1.3 Objectives 8 CHAPTER TWO: LITERATURE REVIEW 2.1 Sundaland 10 2.2 Palaeogeography of Southeast Asia focusing on Sundaland 12 2.3 The cyclical glaciations and the impact on SE Asian biota 18 2.4 Biodiversity and biogeography of Southeast Asia (Sundaland) 21 2.5 Phylogeography 24 2.6 The genus Hemirhamphodon 27 2.7 Molecular markers in phylogenetics and phylogeographic studies 32 2.8 Mitochondrial DNA markers- DNA Barcoding and cytochrome b 33 iv 2.9 Nuclear DNA markers 38 2.10 Biodiversity and conservation in Southeast Asia focusing on Sundaland 40 CHAPTER THREE: SPECIES DIVERSITY ASSESSMENT OF THE GENUS Hemirhamphodon THROUGH DNA BARCODING 3.1 Introduction 43 3.1.1 Current status/ problems 45 3.2 Objectives 46 3.3 Materials and methods 47 3.3.1 Sample collection, preservation and DNA extraction 47 3.3.2 Gene amplification and sequencing 52 3.3.3 Data Analysis 52 3.4 Results 56 3.4.1 Genetic diversity, intraspecific and interspecific divergences 56 3.4.2 Gene tree and OTU counts based on DNA Barcoding 58 3.4.3 Genetic divergence based on the newly assigned groups 64 3.5 Discussion 68 3.5.1 High levels of intraspecific divergences 68 3.5.2 Influence of Paleo-drainage systems 69 3.5.3 Evidence of cryptic species 70 3.5.4 Conservation and management 73 3.6 Conclusions 74 v CHAPTER FOUR: POPULATION STUDY AND PHYLOGEOGRAPHY OF Hemirhamphodon pogonognathus IN SUNDALAND RIVER BASINS 4.1 Introduction 75 4.2 Objectives 81 4.3 Materials and methods 82 4.3.1 Sample collection, preservation and DNA extraction 82 4.3.2 Gene amplification and sequencing 82 4.3.3 Data sorting and haplotype generation 85 4.3.3(a) Mitochondrial DNA analysis 85 4.3.3(b) Nuclear DNA analysis 85 4.3.3(c) Genetic diversity 86 4.3.3(d) Gene tree construction 87 4.3.3(e) Haplotype network 88 4.3.3(f) Population structure 88 4.3.3(g) Historical demographic analysis 90 4.4 Results 93 4.4.1 Mitochondrial DNA Analysis 93 4.4.1(a) Nucleotide composition and genetic diversity 93 4.4.1(b) Haplotype distribution 95 4.4.1(c) Phylogeography and evolutionary relationships 102 among haplotypes 4.4.1(d) Population genetic divergence and population 107 structure 4.4.1(e) Population history and demographic changes 112 4.4.2 Nuclear DNA (SCNP: Hp5 and Hp54) analysis 118 vi 4.4.2(a) Nucleotide composition and genetic diversity 118 4.4.2(b) Haplotype distribution 121 4.4.2(c) Phylogeography and evolutionary relationships 132 among haplotypes 4.4.2(d) Population structure 141 4.4.2(e) Population history and demographic changes 150 4.5 Discussion 159 4.5.1 Genetic Diversity and haplotype distribution 159 4.5.2 Population structure and phylogeography 164 4.5.3 Historical demography 167 4.5.4 Evidence for Cryptic Species 169 4.5.5 Conservation 171 4.6 Conclusion 173 CHAPTER FIVE: GENETIC DIVERSITY AND PHYLOGEOGRAPHY OF H. byssus AND H. kuekenthali IN SARAWAK RIVER BASINS (NORTHWESTBORNEO) 5.1 Introduction 174 5.2 Objectives 182 5.3 Materials and methods 183 5.3.1 Sample collection, preservation and DNA extraction 183 5.3.2 Gene amplification and sequencing 184 5.3.3 Data analyses 185 5.3.3(a) Data sorting and haplotype generation 185 5.3.3(b) Genetic diversity 186 5.3.3(c) Gene tree and haplotype network construction 186 vii 5.3.3(d) Population structure 187 5.3.3(e) Historical demographic analysis 188 5.4 Results 190 5.4.1 Nucleotide composition and genetic diversity 190 5.4.2 Haplotype distribution 196 5.4.3 Phylogeography and evolutionary relationships among haplotypes 204 5.4.4 Population structure 216 5.4.5 Population Genetic divergence 229 5.4.6 Population history and demographic changes 236 5.5 Discussion 249 5.5.1 Genetic Diversity 249 5.5.2 Population structure and phylogeography 250 5.5.3 Historical demography 256 5.5.4 Taxonomic implications 257 5.5.5 Conservation 260 5.6 Conclusion 260 CHAPTER SIX: GENERAL DISCUSSION AND CONCLUSIONS 262 REFERENCES 267 APPENDICES LIST OF PUBLICATIONS /CONFERENCE PRESENTATIONS viii LIST OF TABLES Page Table 3.1 Species name, locations, sample size (n) code, regional 48 locations within Peninsular Malaysia, Sarawak (Borneo), and Sumatra; and the newly assigned groups of Hemirhamphodon species (based on the constructed Neighbour-Joining COI gene tree). Table 3.2 A total of 112 COI gene sequences of Hemirhamphondon 53 species obtained from GenBank and the sampling locations. Table 3.3 Sample size (n), mean values, ranges of genetic 57 divergences based on K2P across taxonomic levels from 311 sequences of the genus Hemirhamphod on. Table 3.4 Pairwise comparisons of the COI gene based on K2P 57 distance among six presumed (morphologically identified) Hemirhamphodon species. Table 3.5 Pairwise comparison of the COI gene based on K2P 65 distance among newly assigned Hemirhamphodon groupings. Table 4.1 Sampling locations, sample size (n), code, the hypothetical 84 Paleo-drainages in Sundaland where the sampling locations are situated, and regional locations within Peninsular Malaysia and Sumatra. Ma = Malacca, Si = Siam, nS = North Sunda Table 4.2 Sample location in abbreviation, no. of sequences (n), no. 94 of haplotype (hp), no. of polymorphic sites (#V), nucleotide diversity (π), haplotype diversity (h) and expected heterozygosity per site based on number of segregating sites (ϴs) of cyt b for H. pogonognathus populations. Table 4.3 The 39 haplotypes with 209 variable sites within a 883 bp 96 segment of cyt b for H. pogonognathus populations. Table 4.4 Haplotype distribution of cyt b across 25 H. pogonognathus 100 populations in Sundaland. ix Table 4.5 Best model across partitions after PartitionFinder analysis 105 for cyt b of H. pogonognathus. Table 4.6 Pairwise genetic distances with TN93+G model of cyt b 108 between H. pogonognathus populations. Table 4.7 Pairwise ФST values of cyt b (below diagonal) between H. 110 pogonognathus populations. Geographical distances (above diagonal in italics) between populations based on the shortest path following the Paleo-drainages systems (km). Table 4.8 AMOVA result for hierarchical genetic subdivision for 111 percentage of variation and fixation indices (ФST, ФSC and ФCT) of cyt b of H. pogonognathus populations. Bold values indicate significant value (p < 0.05). Table 4.9 Summary of population neutrality tests and demographic 113 analyses based on Tajima’s D, Fu’s Fs, Rasmos-Onsins & Rozas (R2) and Harpending’s raggedness index (Hri) for H. pogonognathus populations based on cyt b gene. Table 4.10 Sample location in abbreviation, no of sequences (n), no. 119 of haplotype (hp), no. of polymorphic sites (#V), nucleotide diversity (π), haplotype diversity (h) and expected heterozygosity per site based on number of segregating sites (ϴs) of Hp5 and Hp54 for H. pogonognathus populations. Table 4.11 The 71 haplotypes with 79 variable sites generated from 123 264 nucleotide bases of Hp5 in H.
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