Thesis (M.Sc.)--Chulalongkorn University, 2008

Short mackerel Rastrelliger brachysoma is an economical pelagic fish commonly found widely distributed along the coast of the Gulf of Thailand and Andaman Sea. The present study is to use Inter-simple sequence repeat (ISSR) and mitochondrial DNA sequencing methods to investigate genetic diversity, population genetic structure and phylogeographic relationships of R. brachysoma in Thai waters. ISSR method was used to investigate genetic diversity and population genetic structure of R. brachysoma. Forty-nine primers were screened, five reliable and polymorphic primers (HB13, HB15, UBC811, UBC840 and UBC841) were obtained and used. After the investigation on genetic diversity of two hundred and seventy-six R. brachysoma samples from eight sites (Chanthaburi, Rayong, Samut Songkhram, Prachuap Khiri Khan, Surat Thani, Songkhla, Satun and Krabi), fifty-two DNA bands can be scored, of which forty-two were polymorphic (80.77%). High genetic diversity at species level was found (PPB: 80.77%, H: 0.1485, I: 0.2373). The highest and lowest genetic diversity within population were detected in Satun (PPB: 46.15%, H: 0.1336, I: 0.2064) and Surat Thani (PPB: 28.85%, H: 0.0887, I: 0.1356) respectively. Pairwise genetic distances among populations ranged from 0.0061 to 0.1226. UPGMA dendrogram based on Nei’s genetic distances divided the populations of R. brachysoma into three groups, the upper area of Gulf of Thailand (Chanthaburi, Rayong, Samut Songkhram, Prachuap Khiri Khan, and Surat Thani), the southern area of the Gulf of Thailand (Songkhla) and Andaman Sea (Satun and Krabi). The hierarchical analysis of molecular variance tested by AMOVA showed highly significant genetic differences among populations (P<0.001). When the populations divided into two regions (the Gulf of Thailand and Andaman Sea), which showed significant genetic differentiation among the regions (Fct: 0.1984, P=0.0342), among populations within regions (Fsc: 0.2223, P<0.001) and within populations (Fst: 0.3766, P<0.001). Mantel test showed correlation between genetic distances and geographic distances (r = 0.6925, P<0.0003). The partial mtDNA control region and cytochrome b gene sequencing method was used to investigate phylogeographic relationships of 40 R. brachysoma samples in Thai waters. The sequences of partial mtDNA control region (549 base pairs) and the mitochondrial DNA cytochrome b gene (627 base pairs) were obtained. The variable sites of the two sequences were low. The 7 variable sites and 10 haplotypes of partial mtDNA control region sequences were identified and no distinct haplotype between the Gulf of Thailand and Andaman Sea. The 17 variable sites and 6 haplotypes of cytochrome b gene sequences and the 24 variable sites and 16 haplotypes of the combined sequence of the two regions showed unique haplotype for the Gulf of Thailand and Andaman Sea. Phylogeographic relationships were established using neighbor-joining and maximum parsimony methods. The partial mtDNA control region sequences did not showed population genetic structure between the Gulf of Thailand and Andaman Sea. Cytochrome b gene and the combined sequence of the two regions showed population genetic structure between the Gulf of Thailand and Andaman Sea. However, Songkhla population is likely to be separated from other populations of the Gulf of Thailand. The information obtained from this study will be useful for stock management and conservation plans of R. brachysoma in Thailand