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, 7 (8), e42752

Skin Color Variation in Orang Asli Tribes of Peninsular Malaysia


Skin Color Variation in Orang Asli Tribes of Peninsular Malaysia

Khai C Ang et al. PLoS One.

Erratum in

  • PLoS One. 2012;7(9). doi:10.1371/annotation/dfb89198-58fe-49e5-be23-325be58fedd0


Pigmentation is a readily scorable and quantitative human phenotype, making it an excellent model for studying multifactorial traits and diseases. Convergent human evolution from the ancestral state, darker skin, towards lighter skin colors involved divergent genetic mechanisms in people of European vs. East Asian ancestry. It is striking that the European mechanisms result in a 10-20-fold increase in skin cancer susceptibility while the East Asian mechanisms do not. Towards the mapping of genes that contribute to East Asian pigmentation there is need for one or more populations that are admixed for ancestral and East Asian ancestry, but with minimal European contribution. This requirement is fulfilled by the Senoi, one of three indigenous tribes of Peninsular Malaysia collectively known as the Orang Asli. The Senoi are thought to be an admixture of the Negrito, an ancestral dark-skinned population representing the second of three Orang Asli tribes, and regional Mongoloid populations of Indo-China such as the Proto-Malay, the third Orang Asli tribe. We have calculated skin reflectance-based melanin indices in 492 Orang Asli, which ranged from 28 (lightest) to 75 (darkest); both extremes were represented in the Senoi. Population averages were 56 for Negrito, 42 for Proto-Malay, and 46 for Senoi. The derived allele frequencies for SLC24A5 and SLC45A2 in the Senoi were 0.04 and 0.02, respectively, consistent with greater South Asian than European admixture. Females and individuals with the A111T mutation had significantly lighter skin (p = 0.001 and 0.0039, respectively). Individuals with these derived alleles were found across the spectrum of skin color, indicating an overriding effect of strong skin lightening alleles of East Asian origin. These results suggest that the Senoi are suitable for mapping East Asian skin color genes.

Conflict of interest statement

Competing Interests: The authors have declared that no competing interests exist.


Figure 1
Figure 1. Map of Peninsular Malaysia indicating sampling sites.
For Orang Asli tribes and their corresponding village locations, see Table S1.
Figure 2
Figure 2. M-indices of Orang Asli who are homozygous ancestral for SLC24A5 & SLC45A2.
Notably, the Negrito show the highest average M-index and the Proto Malay the lowest, while the Senoi have the broadest distribution of skin color. 40 Orang Asli samples containing either SLC24A5A111T or SLC45A2L374F alleles have been excluded from this plot. For plots including all individuals, see Figure S1.
Figure 3
Figure 3. Distribution of M-indices of Senoi with and without derived alleles for SLC24A5 and SLC45A2.
(A) Senoi samples with SLC24A5 and SLC45A2 ancestral alleles. (B) Senoi with derived alleles for either SLC24A5 or SLC45A2, or a combination of both. (C) Senoi with the derived allele of SLC24A5. (D) Senoi with the derived allele of SLC45A2.
Figure 4
Figure 4. Beeswarm dotplot showing the effect of SLC24A5A111T and SLC45A2L374F on the Orang Asli skin color.
A) SLC24A5A111T showed a statistically significant effect on skin color (p = 0.0013) B) SLC45A2L374F does not reach significance effect for the Orang Asli skin color (p = 0.37). The black line indicates the average M-index of samples with homozygous ancestral alleles, and the red line indicates the average M-index of samples with heterozygous derived alleles.

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