Admixture Patterns and Genetic Differentiation in Negrito Groups from West Malaysia Estimated from Genome-wide SNP Data

Document Type

Open Access Article

Authors

Timothy A. Jinam, Department of Genetics, School of Life Science, Graduate University for Advanced Studies (SOKENDAI), Mishima, Japan
Maude E. Phipps, School of Medicine and Health Sciences, Monash University (Sunway Campus), Selangor, Malaysia
Naruya Saitou, Division of Population Genetics, National Institute of Genetics, Mishima, JapanFollow
The Hugo Pan-Asian SNP Consortium

Abstract

Southeast Asia houses various culturally and linguistically diverse ethnic groups. In Malaysia, where the Malay, Chinese, and Indian ethnic groups form the majority, there exist minority groups such as the "negritos" who are believed to be descendants of the earliest settlers of Southeast Asia. Here we report patterns of genetic substructure and admixture in two Malaysian negrito populations (Jehai and Kensiu), using ~50,000 genome-wide single-nucleotide polymorphism (SNP) data. We found traces of recent admixture in both the negrito populations, particularly in the Jehai, with the Malay through principal component analysis and STRUCTURE analysis software, which suggested that the admixture was as recent as one generation ago. We also identified significantly differentiated nonsynonymous SNPs and haplotype blocks related to intracellular transport, metabolic processes, and detection of stimulus. These results highlight the different levels of admixture experienced by the two Malaysian negritos. Delineating admixture and differentiated genomic regions should be of importance in designing and interpretation of molecular anthropology and disease association studies.

Recommended Citation

Jinam, Timothy A.; Phipps, Maude E.; Saitou, Naruya; and The Hugo Pan-Asian SNP Consortium (2013) "Admixture Patterns and Genetic Differentiation in Negrito Groups from West Malaysia Estimated from Genome-wide SNP Data," Human Biology: Vol. 85: Iss. 1, Article 8.
Available at: https://digitalcommons.wayne.edu/humbiol/vol85/iss1/8