Ancient Genetic Signatures of Orang Asli Revealed by Killer Immunoglobulin-Like Receptor Gene Polymorphisms

Abstract

The aboriginal populations of Peninsular Malaysia, also known as Orang Asli (OA), comprise three major groups; Semang, Senoi and Proto-Malays. Here, we analyzed for the first time KIR gene polymorphisms for 167 OA individuals, including those from four smallest OA subgroups (Che Wong, Orang Kanaq, Lanoh and Kensiu) using polymerase chain reaction-sequence specific primer (PCR-SSP) analyses. The observed distribution of KIR profiles of OA is heterogenous; Haplotype B is the most frequent in the Semang subgroups (especially Batek) while Haplotype A is the most common type in the Senoi. The Semang subgroups were clustered together with the Africans, Indians, Papuans and Australian Aborigines in a principal component analysis (PCA) plot and shared many common genotypes (AB6, BB71, BB73 and BB159) observed in these other populations. Given that these populations also display high frequencies of Haplotype B, it is interesting to speculate that Haplotype B may be generally more frequent in ancient populations. In contrast, the two Senoi subgroups, Che Wong and Semai are displaced toward Southeast Asian and African populations in the PCA scatter plot, respectively. Orang Kanaq, the smallest and the most endangered of all OA subgroups, has lost some degree of genetic variation, as shown by their relatively high frequency of the AB2 genotype (0.73) and a total absence of KIR2DL2 and KIR2DS2 genes. Orang Kanaq tradition that strictly prohibits intermarriage with outsiders seems to have posed a serious threat to their survival. This present survey is a demonstration of the value of KIR polymorphisms in elucidating genetic relationships among human populations.

Killer cell immunoglobulin-like receptors (KIR) and human leukocyte antigen-C (HLA-C) allorecognition patterns in women with endometriosis

“…Previous studies have shown that KIR2DL2 is in the linkage disequilibrium with KIR2DS2, which caused the relative activation of KIR receptor, which is responsible for the loss of recognition of HLA-C [60][61][62] . The different ethnic populations showed different values of KIR polymorphisms in elucidating genetic relationships among human populations 63 . Moreover, HLA genotyping is traditionally performed using a serological method.…”

Detection of CYP2C19 Genetic Variants in Malaysian Orang Asli from Massively Parallel Sequencing Data

“…The Orang Asli are the indigenous people of Peninsular Malaysia and the estimated population size is only ~180,000 people [31]. The Senoi tribe, which consists of six sub-tribes (Che Wong, Jahut, Mah Meri, Semoq Beri, Semai and Temiar) formed the largest group of Orang Asli with ~ 98,000 people followed by the Proto-Malays with ~75,000 people from 6 sub-tribes (Kanaq, Kuala, Seletar, Jakun, Semelai and Temuan) and the smallest group are those that expressed the negrito phenotypes (Bateq, Jahai, Kensiu, Kintaq, Mendriq and Lanoh) with an estimated number of only 5,000 people [32]. Their settlements are scattered across the Peninsular Malaysia whereby the Negritos and Senoi are generally localized in the northern and central regions while Proto-Malays settlements are found in the central and southern regions [33].…”

The combinatorial diversity of KIR and HLA class I allotypes in Peninsular Malaysia

“…The Malay group represents Deutero‐Malays, whose ancestors settled in Malaysia 3–5000 years ago 32 and subsequently admixed with immigrants from multiple origins including Arabs, Chinese and Indians. Previous studies of KIR diversity in Malaysians were limited to low‐resolution analyses 33–35 . In the current study, we characterized the KIR and HLA genes of 92 Malay and 75 Malaysian Chinese individuals at high resolution using targeted high‐throughput sequencing technology, and then compared them with available data from other populations.…”