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The Biodiversity and Systematic Relationships of the 'Labeoin' Group

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The Biodiversity and Systematic Relationships of the 'Labeoin' Group THE BIODIVERSITY AND SYSTEMATIC RELATIONSHIPS OF THE LABEOIN GROUP OF FISHES WITHIN THE SUB-FAMILY CYPRINIDAE IN PENINSULAR MALAYSIA EMI SHERIZAN BINTI AB RAHIM UNIVERSITI SAINS MALAYSIA 2007 THE BIODIVERSITY AND SYSTEMATIC RELATIONSHIPS OF THE LABEOIN GROUP OF FISHES WITHIN THE SUB-FAMILY CYPRINIDAE IN PENINSULAR MALAYSIA by EMI SHERIZAN BINTI AB. RAHIM Thesis submitted in fulfillment of the requirements for the degree of Master of Science January 2007 ACKNOWLEDGEMENTS To begin with, I would like to express my sincere thanks and appreciation to both my supervisors, Assoc. Prof. Siti Azizah Mohd Nor and Assoc. Prof. Khoo Khay Huat who has always been a source of support, advices and encouragements on all the aspects of this study, throughout my candidature. Thanks to Universiti Sains Malaysia for providing funding through the Fundamental Research Grant Scheme (FRGS); School of Biological Sciences, The Cambodian Mekong Fish Conservation Project, Inland Fisheries Research and Development Institute (IFReDI) for such a fruitful collaboration. Next, a special thanks goes to all colleagues; Ruzainah, Fatimah, Ain, Mila, Darlina, Ghows, Jamsari, Aje and Zul (Lab 308), Zarul, Kok Yeng and En. Amir Shah Rudin (Lab 237), Fini, Che Pah, Khalidah, Kar Loon and Kwan Shern (Lab 307), Azlin (Lab 208), Lai, Ana, Beng Keok, Sarifuddin, Mazlan and Mac (ASO’s Laboratory), Sabrina (Lab 406), Sairatul and Annette (Lab 407), Izzi and Irwan (Metrolab) for their support and assistance especially during the sampling trip. Hope we can go to catch fish together again and I enjoy every moment we spent together especially the day we accidentally trapped a big freshwater snake. Thank you guys! Last but not least, a deepest gratitude to my parents, Tn. Hj. Ab. Rahim Bin Ab. Kadir and Pn. Hjh. Norlin Othman; my fantastic four brothers Mohd Ezuan, Mohd Efham, Mohd Ezat Amir and Mohd Eqbal for their never-ending support and sacrifices during the completion of my studies. Let’s pizza! Above all, thanks to ALLAH ALLMIGHTY. Without HIS consent none of this is possible. ii TABLE OF CONTENTS Page Acknowledgements ii Table of Contents iii List of Tables vii List of Figures x List of Plates xii Abstrak xiv Abstract xvi CHAPTER 1 - INTRODUCTION 1 CHAPTER 2 - LITERATURE REVIEW 5 2.1 Genus Garra 14 2.1.1 Garra taeniata (Smith, 1931) 14 2.2 Genus Labeo 16 2.2.1 Labeo chrysophekadion (Bleeker, 1850) 16 2.3 Genus Labiobarbus 17 2.3.1 Labiobarbus festivus (Heckel, 1843) 17 2.3.2 Labiobarbus leptocheilus (Valenciennes, 1842) 18 2.3.3 Labiobarbus ocellatus (Heckel, 1843) 18 2.3.4 Labiobarbus siamensis (Sauvage, 1881) 18 2.4 Genus Osteocheilus 19 2.4.1 Osteocheilus hasselti (Valenciennes, 1842) 19 2.4.2 Osteocheilus melanopleura (Bleeker, 1852) 19 2.4.3 Osteocheilus spilurus (Bleeker, 1851) 21 2.4.4 Osteocheilus vittatus (Valenciennes, 1842) 21 iii 2.4.5 Osteocheilus waandersii (Bleeker, 1852) 21 2.5 Genus Tylognathus 22 2.5.1 Tylognathus caudimaculatus (Fowler, 1934) 22 2.6 Genus Botia 22 2.6.1 Botia modesta (Bleeker, 1864) 23 2.7 Meristic and Morphometric 23 2.8 Genetics tools for phylogenetic analysis 25 2.9 Mitochondrial DNA 25 CHAPTER 3 - MATERIALS & METHODS 29 3.1 Specimen Collection, Sampling Technique and Identification 29 3.2 General Methods for Meristic and Morphometric 33 3.3 Sample Sizes in Meristic and Morphometric Study 35 3.4 Quantification Morphological 35 a) Meristic Technique 35 b) Classical Morphometric 38 c) Truss Network Morphometric 38 3.5 Data Analysis 42 3.6 General Procedure in Phylogenetic Analysis of the Labeoin 44 Fishes Using 16S rRNA mtDNA Gene 3.7 Sample Preparation and Preservation 44 3.8 DNA Extraction 47 3.9 Spectrophotometric Procedure 48 3.10 DNA Amplification of partial 16S rRNA Gene 49 3.11 DNA Optimisation 51 3.12 Agarose gel preparation 51 iv 3.13 PCR Products Analysis 51 3.14 PCR Product Purification 52 3.15 Sequencing 53 3.16 Sequence Analysis 53 CHAPTER 4 - RESULTS 55 4.1 Quantitative Morphological Analysis 55 4.2 Meristic Technique 55 a) Descriptive and One-way ANOVA 55 b) Principal Component Analysis, PCA 60 c) Discriminant Function Analysis, DFA 64 4.3 Classical Morphometric Technique 70 a) Descriptive and One-way ANOVA 70 b) Principal Component Analysis, PCA 74 c) Discriminant Function Analysis, DFA 76 4.4 Truss Network Morphometric 81 a) Descriptive and One Way ANOVA 81 b) Principal Component Analysis 88 c) Discriminant Function Analysis 91 4.5 Revealing Phylogenetic Status of the Labeoin Fishes 97 Using partial 16S rRNA mtDNA Gene 4.6 DNA Extraction 97 4.7 DNA Optimisation 97 4.8 PCR Amplification of the 16S rRNA mtDNA Gene 97 4.9 PCR Product Sequencing and Sequence Description 100 v 4.10 Phylogenetic Analyses 101 a) Maximum Parsimony Analysis 101 b) Neighbour-Joining 107 CHAPTER 5 - DISCUSSION 112 5.1 Merging Qualitative and Quantitative Techniques to Improve 112 Labeoin Species Identification 5.1.1 Comparison of Discrimination Efficiency Offered by Meristic 117 and Morphometric Techniques 5.2 Phylogenetic Relationships and Systematics Within the Labeoin 121 Group Based On Partial rRNA gene CHAPTER 6 - CONCLUSION 128 References 130 Appendix A 142 Appendix B 150 Appendix C 158 Appendix D 165 Appendix E 168 Appendix F 170 Appendix G 175 Appendix H 177 Appendix I 189 Appendix J 192 List of Publications 193 vi LIST OF TABLES Tables Page 3.1 Species, number of individuals analysed for the various 32 quantitative techniques, locality and coordinates. 3.2 Description of meristic variables. 36 3.3 Description of classical morphometric variables. 39 3.4 Description of truss network morphometric variables. 41 3.5 Samples for phylogenetic analysis among Labeoin species 46 based on partial 16S rRNA gene. 3.6 PCR profile used to amplify 16S rRNA mtDNA gene. 50 4.1 Mean, standard deviation and range (minimum and 56 maximum) for Labeoin species analysed based on meristic characters. Lowest and highest values of mean and standard deviation are highlighted in bold. 4.2 Results of one way ANOVA for each of fifteen meristic 59 characters among eleven species of Labeoin fishes. 4.3 Eigenvalue, variance and principal component loadings 61 (varimax rotation) explained by each component of the 15 meristic characters for Labeoin group. 4.4 Pooled within-group correlation matrix for 15 meristic 65 characters in Labeoin fish. 4.5 Summary of stepwise discriminant analysis and contribution 66 of the 15 meristic characters to the discriminant functions. 4.6 Classification results of the individuals from each species 69 according to the affinities revealed by the discriminant functions for meristic characters. 4.7 Mean, std. deviation and range (minimum and maximum) 71 for Labeoin species analysed based on classical morphometric characters. Lowest and highest values of mean and std. deviation are highlighted in bold. 4.8 Results of one way ANOVA for each of the ten classical 73 morphometric characters among eleven species of Labeoin fishes. vii 4.9 Eigenvalue, variance and principal component loadings 75 (varimax rotation) explained by each component of the classical morphometric characters for Labeoin group. 4.10 Pooled within-group correlation matrix of classical 77 morphometric variables. 4.11 Summary of stepwise discriminant analysis and contribution 77 of the classical morphometric characters to the discriminant functions. Only functions with eigenvalue of more than 1 are presented. 4.12 Classification results of the individuals from each species 80 according to the affinities revealed by the discriminant functions for classical morphometric characters. 4.13 Mean, standard deviation and range (minimum and 82 maximum) for Labeoin species analysed based on truss network morphometric characters. Lowest and highest values of mean are highlighted in bold. 4.14 Results of one way ANOVA for each of truss network 86 morphometric characters among eleven species of Labeoin fishes. 4.15 Eigenvalue, variance and principal component loadings 89 (varimax rotation) explained by each component of the truss network morphometric characters for Labeoin group. 4.16 Pooled within-group correlation matrix of truss network 92 morphometric variables. 4.17 Summary of stepwise discriminant analysis and contribution 93 of the truss network morphometric characters to the discriminant functions. 4.18 Classification results of the individuals from each species 96 according to the affinities revealed by the discriminant functions for truss network morphometric characters. 4.19 Phylogenetic tree description. 103 4.20 Summary of character-status for MP analysis of partial 16S 103 rRNA gene. 4.21 Average interspecies distance. 108 4.22 Intraspecies genetic distance. 110 viii 5.1 Morphological characters to the Sub-families and genera of 113 Garra, Labeo, Labiobarbus, Osteocheilus and Tylognathus (modified from Lim, 1975). ix LIST OF FIGURES Figures Page 2.1 Side view of the upper lip structure (a) and ventral view of 15 modified sucker lip (b) in Garra species. 2.2 Lips of the genus Osteocheilus species. 20 3.1 Location of sampling sites in Peninsular Malaysia. 30 3.2 Location of the Tonle Sap is indicated by arrow. Tonle 31 Sap is the deepest Southeast Asia’s freshwater lake located in Cambodia. 3.3 Framework in generating output to species identification 34 via meristic and morphometric methods. 3.4 Diagram of meristic variables. 37 3.5 Diagram of classical morphometric variables. 39 3.6 Diagram of truss network morphometric variables. 40 3.7 Flow-chart of DNA analysis. 45 4.1 All group scatterplot of PC 2 vs. PC 1 generated via 63 Principal Component Analysis in Labeoin fishes for meristic characters. *For species name, refer to Table 4.1. 4.2 All group scatterplot of canonical discriminant function 2 68 versus function 1 in Labeoin fishes according to meristic characters. *For species name, refer to Table 4.1.
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