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

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 genomewide 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. 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.The Southeast Asian region represents an intriguing avenue into the study of human population genetics, given the rich ethnic diversity of the region. The general consensus from various population genetic studies are the African origin of modern human populations based on mitochondrial, Y-chromosomal, and autosomal DNA markers (e.g., Underhill 2003;Li et al. 2008;Stoneking and Delfin 2010). With

Unravelling the Genetic History of Negritos and Indigenous Populations of Southeast Asia

“…This suggests more recent gene flow between them and their neighboring populations, most likely Malays. A similar observation was reported in Jehai, a Negrito subgroup using a less SNP ( Jinam et al 2013 ).…”

Discerning the Origins of the Negritos, First Sundaland People: Deep Divergence and Archaic Admixture

“…Subsequent studies reported various demographic and evolutionary factors that affected their genetic diversity. These included admixture ( Jinam et al 2013 ), long term isolation and bottlenecks ( Deng et al 2014 ; Aghakhanian et al 2015 ), and adaptation to malaria ( Liu et al 2015 ). However, compared with Malaysian Negritos, genome-wide studies involving the Philippine Negritos are relatively limited.…”

Exploring models of human migration to the Japanese archipelago using genome-wide genetic data

“…Among descendants of the migrants, Papuans, aboriginal Australians, and Philippine Negritos show a larger amount of introgression of genomic fragments with Denisovan ancestry than the other East Asians, including Andamanese (Onge) and Malaysian Negritos (Jehai). This suggests that archaic humans related to the Denisovan lived somewhere in (or nearby) Southeast Asia (Reich et al, 2011;Jinam et al, 2013Jinam et al, , 2017. When East Asian populations are clustered as a tree with no assumption of migration between populations, most East and Northeast Asian populations form a single cluster, with Papuans, Australians, and Onge people at root positions, suggesting that the Southern route predominantly shaped the genetic features of present-day East and Northeast Asian populations (HUGO Pan-Asian SNP Consortium, 2009;Mallick et al, 2016;Lipson and Reich, 2017;).…”