Skin Color Variation in Orang Asli Tribes of Peninsular Malaysia

Abstract

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.

Loci associated with skin pigmentation identified in African populations

“…This raises the possibility that other phenotypes shared between Africans and some South Asian and Australo-Melanesian populations may also be due to genetic variants identical by descent from African populations rather than convergent evolution (65). This observation is consistent with a proposed southern migration route out of Africa ~80 kya (66).…”

Differential positive selection of malaria resistance genes in three indigenous populations of Peninsular Malaysia

“…The Senoi people arrived around 10,000 years ago, are of Austroasiatic origin and reside mostly in the central part of Peninsular Malaysia. They have a wide range of skin color, wavy hair and are generally taller than the Negrito (Ang et al 2012). Due to the habitats and hunter-gatherer lifestyle, all three Orang Asli groups are routinely exposed to medical stresses including malnutrition and persistent exposure to communicable diseases such as leptospirosis, smallpox, and of notably, malaria (Baer et al 1976;Eng et al 1973;Wee et al 2008;Bellwood 2007, page 256).…”

Why Have the Peninsular “Negritos” Remained Distinct?

“…2 Ang et al (2012) found that several gene loci are involved in the variable skin color of at least two of the Peninsular negrito populations. Despite having darker skin on average, the "Negrito" range nevertheless overlapped considerably with the range exhibited by the other Orang Asli populations in the study, the "Senois" and the "Proto-Malays" (Ang et al 2012: 4, Figure 2).…”

“…Consequently, the same on-the-ground ethnolinguistic population may appear differently classified in different publications. Ang et al (2012) appear to have taken the "official" classification of the Malaysian Department of Orang Asli Development without further discussion. In at least some respects, this has a bearing on their conclusions.…”