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

NurWaliyuddin HZ, Norazmi MN, Edinur HA, Chambers GK, Panneerchelvam S, Zafarina Z - PLoS ONE (2015)

Bottom Line: 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 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.

View Article: PubMed Central - PubMed

Affiliation: Human Identification/DNA Unit, School of Health Sciences, Universiti Sains Malaysia, Health Campus, Kelantan, Malaysia.

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.

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Related in: MedlinePlus

The KIR genotype profiles of six OA subgroups in Peninsular Malaysia.ID is the genotype number assigned by Allele Frequency Net Database [15]. Numbers in brackets represent the ‘unrelated sample’ of OA subgroups.
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pone.0141536.g001: The KIR genotype profiles of six OA subgroups in Peninsular Malaysia.ID is the genotype number assigned by Allele Frequency Net Database [15]. Numbers in brackets represent the ‘unrelated sample’ of OA subgroups.

Mentions: All of the 16 KIR genes presently known were detected in all of the OA subgroups, except for KIR2DL2 and KIR2DS2 genes which are completely absent in Orang Kanaq (Table 1). There were also relatively low frequencies of KIR2DS3 (0.05) in Orang Kanaq and KIR2DS1, KIR2DS5 and KIR3DS1 genes (0.04 each) in Semai. There were high frequencies of KIR inhibitory genes (0.32–1.00) in Lanoh, Kensiu and Che Wong. On the contrary, Batek and Orang Kanaq have a balance distribution of both functional types of KIR genes. We have also examined the frequencies of KIR genes in the ‘unrelated’ OA subgroups, but only minor differences were observed when compared with the corresponding total OA subgroups (Table 1 and S1 Table). The framework genes; KIR2DL4, KIR3DL2, KIR3DL3 and KIR3DP1 together with one pseudogene KIR2DP1 were present in all individuals. Fifteen individuals were observed to have all 16 KIR genes; 9 Kensiu, 3 Batek, 2 Lanoh and 1 individual from Semai (Fig 1).


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

NurWaliyuddin HZ, Norazmi MN, Edinur HA, Chambers GK, Panneerchelvam S, Zafarina Z - PLoS ONE (2015)

The KIR genotype profiles of six OA subgroups in Peninsular Malaysia.ID is the genotype number assigned by Allele Frequency Net Database [15]. Numbers in brackets represent the ‘unrelated sample’ of OA subgroups.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4643969&req=5

pone.0141536.g001: The KIR genotype profiles of six OA subgroups in Peninsular Malaysia.ID is the genotype number assigned by Allele Frequency Net Database [15]. Numbers in brackets represent the ‘unrelated sample’ of OA subgroups.
Mentions: All of the 16 KIR genes presently known were detected in all of the OA subgroups, except for KIR2DL2 and KIR2DS2 genes which are completely absent in Orang Kanaq (Table 1). There were also relatively low frequencies of KIR2DS3 (0.05) in Orang Kanaq and KIR2DS1, KIR2DS5 and KIR3DS1 genes (0.04 each) in Semai. There were high frequencies of KIR inhibitory genes (0.32–1.00) in Lanoh, Kensiu and Che Wong. On the contrary, Batek and Orang Kanaq have a balance distribution of both functional types of KIR genes. We have also examined the frequencies of KIR genes in the ‘unrelated’ OA subgroups, but only minor differences were observed when compared with the corresponding total OA subgroups (Table 1 and S1 Table). The framework genes; KIR2DL4, KIR3DL2, KIR3DL3 and KIR3DP1 together with one pseudogene KIR2DP1 were present in all individuals. Fifteen individuals were observed to have all 16 KIR genes; 9 Kensiu, 3 Batek, 2 Lanoh and 1 individual from Semai (Fig 1).

Bottom Line: 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 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.

View Article: PubMed Central - PubMed

Affiliation: Human Identification/DNA Unit, School of Health Sciences, Universiti Sains Malaysia, Health Campus, Kelantan, Malaysia.

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.

Show MeSH
Related in: MedlinePlus