The analysis of human mitochondrial DNA in peninsular Malaysia
Mitochondrial DNA analysis was undertaken on samples collected from two populations in Peninsular Malaysia, the Modern Malay (102 samples) and Orang Asli (59 samples from Jahai and Kinsiu sub-groups). The hypervariable region 1 (HV1) of the mtDNA control region was amplified and sequenced. Polymorphisms were reported by aligning each sequence to the Cambridge Reference Sequence (CRS). A total of 94 polymorphisms were observed in the Modern Malay samples, which formed 75 different haplotypes. The Orang Asli showed notably lower number of the HV1 region variations, with only 28 polymorphisms and 13 haplotypes observed. Genetic diversity calculated for the Modern Malays and Orang Asli were 0.989 and 0.818, respectively. Probability of random match calculated was 0.0202 for the Modern Malays and 0.1962 for the Orang Asli. The mtDNA coding region variations was examined using RFLP analysis. Combination of both RFLP and HV1 sequence data had placed the Modern Malays into three major Southeast Asian haplogroups, M, B and F. These findings had initially suggested that the Modern Malays shared a common lineage with other populations within this region. Two novel sub-clusters, M21a and R21 were found at a high frequency within the Orang Asli samples. These sub-clusters, which have also been found in other Semang sub-groups appear to be indigenous Semang haplogroups. The limited number of mtDNA haplotypes shared between the Modern Malays and Orang Asli suggested discontinuity of mtDNA between these populations. Even though both populations were believed to be among the earliest populations of Peninsular Malaysia, this result indicates that the Modern Malays were not direct descendants of the Orang Asli. Minisequencing analysis was carried for further interrogation of the mtDNA coding region polymorphisms. Besides mtDNA analysis, the autosomal STR markers were also examined using PowerPlex® 16 system for both populations. These data could provide more information when added to the available STR database for Malaysian populations.