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Molecular Systematics of Subterranean MOLECULAR SYSTEMATICS OF SUBTERRANEAN TERMITES COPTOTERMES SPP., MICROSATELLITE DEVELOPMENT AND POPULATION GENETICS OF Coptotermes gestroi (WASMANN) (BLATTODEA: RHINOTERMITIDAE) YEAP BENG KEOK UNIVERSITI SAINS MALAYSIA 2010 MOLECULAR SYSTEMATICS OF SUBTERRANEAN TERMITES COPTOTERMES SPP., MICROSATELLITE DEVELOPMENT AND POPULATION GENETICS OF Coptotermes gestroi (WASMANN) (BLATTODEA: RHINOTERMITIDAE) BY YEAP BENG KEOK Thesis submitted in fulfillment of the requirements for the degree of Doctor of Philosophy March 2010 ACKNOWLEDGEMENTS This work would not have been completed without the generosity, support, and encouragement of many people. Utmost thanks must extend to my mentors, Professor Dr. Lee Chow Yang and Associate Professor Dr. Ahmad Sofiman Othman. Prof. Lee, my main supervisor, constantly guided and lifted me with his wisdom. He introduced me to termites and gave me a lot of encouragement by providing me many opportunities to attend seminars and conferences throughout Asia countries. He has continued to support and promote my work tirelessly and widen my vision in this ground. Dr. Sofiman, my co-supervisor, gave me a very friendly and valuable advices and guidance, supported me to many useful workshops, and provided a well-equipped laboratory for my molecular study. I extend my sincerest gratitude to Professor Abu Hassan, for being the ever helpful and generous Dean of School of Biological Sciences. To Dr. Zairi Jaal, thank you for being the very supportive, cheerful and bighearted coordinator of Vector Control Research Unit. To Dr. Siti Azizah, for her support and always put a lot of effort organizing very informative workshops. To all staff of School of Biological Sciences and VCRU who have help me in one way and another, thank you for your assistance throughout my research. Not forgetting Jing Wen, Lay Tyng, and Pooi Yen who never fail to offer their hands and brains to help me in solving my problems. Thanks for their caring, bringing the joyousness into my days. Say Piau, who always with serious face, always stands by my side and help in editing my writing. To the rest of the past and present members of Urban Entomology Laboratory, Annie, Boon Hoi, Edwin, Fong Kuan, Hui Siang, Jia i Wei, Kean Teik, Kim Fung, Kok Boon, Nadiah, Nellie, Ru Yuan, Sam, Su Yee, Sui Yaw, Tomoki, Veera, Yee Fatt etc., thank you for whatever big or little things that you have done that made my research life a different. I also would like to record my gratefulness to Charunee Vongkaluang (Royal Forest Department, Bangkok, Thailand); Carlos Garcia (Forest Product Department, Laguna, the Philippines); Julian Yates, III (University of Hawaii, Honolulu, HI); Tsuyoshi Yoshimura (Kyoto University, Kyoto, Japan); Lim Kay Min and Tee Pui Lai (NLC General Pest Control, Penang, Malaysia); Kean-Teik Koay (Ridpest Shah Alam, Selangor, Malaysia), Sulaeman Yusuf (LIPI, Bogor, Indonesia), Theo Evans (Commonwealth Scientific and Industrial Research Organization Entomology, Canberra, Australia); John Ho and Tan Eng Kooi (Singapore Pest Management Association, Singapore); Chun-Chun Tsai (Aletheia University, Tainan, Taiwan); Nancy Lee (ChungHsi Chemical Co., Taipei, Taiwan); Xie (Jia Fei Jie Pest Control Co., Tainan, Taiwan); and Junhong Zhong (Guangdong Entomological Institute, Guangzhou, China) who helped with the collection of the termite specimens used in this study. Special thanks to Ed Vargo (North Carolina State University, US); M. E. Scharf (University of Florida, Gainesville, FL); Michael Lenz (Commonwealth Scientific and Industrial Research Organization Entomology, Canberra, Australia) for constructive criticism and comments on my manuscripts. My candidature as Ph.D. student in USM was supported by a scholarship from Ministry of Science, Technology and Innovation, Malaysia. and a Research University (RU) grant from Universiti Sains Malaysia. ii Last but not least, I express my sincere thanks from the bottom of my heart to my family members for their endless love, understanding, support, and encouragement Thanks for always been there, cheering me on to greater achievements and success. iii TABLE OF CONTENTS Page ACKNOWLEDGEMENTS i TABLE OF CONTENTS iv LIST OF TABLES viii LIST OF FIGURES x LIST OF ABBREVIATION xiii ABSTRAK xiv ABSTRACT xvii CHAPTER ONE: GENERAL INTRODUCTION 1 CHAPTER TWO: LITERATURE REVIEW 2.1 Significance of termites in the ecosystem 4 2.2 Subterranean termites: Coptotermes spp. 6 2.2.1 Colony structure 9 2.2.2 Species identification and distribution of C. gestroi 13 2.2.3 Economic important of C. gestroi in Southeast Asia 17 2.3 Advances in molecular genetic techniques 18 2.3.1 Genetic markers 19 2.3.2 Application of mitochondrial DNA for studying termite genetic 21 2.3.3 Application of DNA microsatellites for studying termite population genetic 24 CHAPTER THREE: MOPHOLOGICAL COMPARISONS AND GENETIC RELATIONSHIP BETWEEN Coptotermes gestroi AND Coptotermes vastator (BLATTODEA: RHINOTERMITIDAE) 3.1 Introduction 27 3.2 Materials and methods 3.2.1 Termite samples 29 iv 3.2.2 DNA extraction 31 3.2.3 Data collection 31 3.2.4 Nucleotide data analysis 32 3.3 Results and discussion 3.3.1 Morphological characteristics 33 3.3.2 Nucleotide analyses 37 3.3.3 Phylogenetic relationships inferred from 12S, 16S, and COII genes 37 3.3.4 Implication of finding to pest management industry 43 CHAPTER FOUR: MOLECULAR SYSTEMATICS OF COPTOTERMES (BLATTODEA: RHINOTERMITIDAE) FROM EAST ASIA AND AUSTRALIA 4.1 Introduction 45 4.2 Materials and methods 4.2.1 Sample collection 47 4.2.2 DNA extraction 52 4.2.3 Polymerase chain reaction (PCR) amplification and DNA sequencing 52 4.2.4 Phylogenetic analysis 54 4.3 Results and discussion 4.3.1 Morphology 55 4.3.2 DNA sequence results 59 4.3.3 Phylogenetic analysis 59 4.3.4 Australian Coptotermes 65 4.3.5 Southeast Asian Coptotermes 66 4.3.6 Coptotermes gestroi 67 4.3.7 Chinese Coptotermes 69 v CHAPTER FIVE: GENETIC RELATIONSHIP BETWEEN Coptotermes heimi AND Coptotermes gestroi (BLATTODEA: RHINOTERMITIDAE) 5.1 Introduction 74 5.2 Materials and methods 5.2.1 Termite samples 75 5.2.2 Morphological measurements 78 5.2.3 DNA extraction, amplification, and sequencing 81 5.2.4 Phylogenetic analysis 82 5.3 Results and discussion 5.3.1 Morphological characteristics 83 5.3.2 Genetic analysis 89 5.3.3 Phylogenetic relationship inferred from 12S, 16S, COII, and combined gene analysis 90 CHAPTER SIX: IDENTIFICATION OF POLYMORPHIC MICROSATELLITE MARKERS FOR THE ASIAN SUBTERRANEAN TERMITE Coptotermes gestroi (WASMANN) (BLATODEA: RHINOTERMITIDAE) 6.1 Introduction 98 6.2 Materials and methods 99 6.3 Results and discussion 100 CHAPTER SEVEN: GENETIC ANALYSIS OF COLONY AND POPULATION STRUCTRUTURE OF THE ASIAN SUBTERRANEAN TERMITE, Coptotermes gestroi, IN NATIVE AND INTRODUCED POPULATIONS 7.1 Introduction 104 7.2 Materials and methods 7.2.1 Site and sample collection 105 7.2.2 Genotype analysis and markers evaluation 105 vi 7.2.3 Population genetic structure 110 7.2.4 Colony breeding structure 112 7.3 Results 7.3.1 Basic genetic data 113 7.3.2 Breeding system and simulations of population structure 114 7.3.3 Genetic differentiation within and among populations 119 7.4 Discussion 7.4.1 Breeding system and population structure 123 7.4.2 Gene flow 125 CHAPTER EIGHT: SUMMARY AND CONCLUSION 128 BIBLIOGRAPHY 131 VITAE 153 vii LIST OF TABLES Page Table 2.1. Methods available for genetically characterizing individuals 20 and populations and their applicability to each issue. Techniques with + can be used for the purpose specified, and several +s indicate that the technique has high utility; ? indicates that the technique is useful in only some cases; and – indicates that the technique is not useful in this context (Adapted from Frankham et al. 2002) Table 3.1 Termite specimens and Genbank published sequences used in 30 this study Table 3.2 Measurements (in mm) of termite soldiers of three Coptotermes 35 spp. Table 4.1 Information on the termite specimens collected and used in 48 this study Table 4.2 Published GenBank sequences used in this study 50 Table 4.3 Primers used for PCR and sequencing 53 Table 4.4 Measurement (in millimeters) of the soldier termite specimens 57 used in this study and those from Chapter Three Table 4.5 Nucleotide and haplotype variations for 12S gene among 71 C. formosanus, C. dimorphus and C. cochlearus Table 4.6 Nucleotide and haplotype variations for 16S gene among 72 C. formosanus, C. dimorphus, and C. cochlearus Table 5.1 Information on termite samples used in this study 76 Table 5.2 Morphometric data (in millimeters) of the soldier termite 79 specimens of C. heimi and C. gestroi Table 5.3 Eigenvector elements and percentage of total variance of 85 principle components of morphometic data from C. gestroi and C. heimi soldiers Table 5.4 Within-group correlation of variables to the canonical variates 86 Table 6.1 Characterization of 11 microsatellite loci of C. gestroi. 102 viii Number of individuals examined (n) (only one individual per colony was genotyped), sequenced allele (*), annealing temperature (Ta), number of alleles (Na), observed heterozygosity (HO), expected heterozygosity (HE), and probability by HW exact test (P) are listed for each locus Table 7.1 Population, location, number of colony (N), and number of 107 Coptotermes gestroi workers that were analyzed (n) Table 7.2 Number of alleles and frequency of most common allele at 109 ten microsatellite loci for the three populations with the highest number of alleles and sum of the 12 putative populations Table 7.3 Empirical measures of F-statistics and worker relatedness 115 coefficients for total colonies, simple and extended families of Coptotermes gestroi in 12 population groups and computer simulations data for several possible breeding systems of subterranean termites derived from Thorne et al. (1999), Bulmer et al. (2001), and Vargo (2003) ix LIST OF FIGURES Page Figure 2.1 Phylogenetic scheme of termite evolution showing the 6 presumed relationships of the seven termite families (adapted from Higashi and Abe 1997).
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