Sequence analyses of Malaysian Indigenous communities reveal historical admixture between Hoabinhian hunter-gatherers and Neolithic farmers

Abstract

Southeast Asia comprises 11 countries that span mainland Asia across to numerous islands that stretch from the Andaman Sea to the South China Sea and Indian Ocean. This region harbors an impressive diversity of history, culture, religion and biology. Indigenous people of Malaysia display substantial phenotypic, linguistic, and anthropological diversity. Despite this remarkable diversity which has been documented for centuries, the genetic history and structure of indigenous Malaysians remain under-studied. To have a better understanding about the genetic history of these people, especially Malaysian Negritos, we sequenced whole genomes of 15 individuals belonging to five indigenous groups from Peninsular Malaysia and one from North Borneo to high coverage (30X). Our results demonstrate that indigenous populations of Malaysia are genetically close to East Asian populations. We show that present-day Malaysian Negritos can be modeled as an admixture of ancient Hoabinhian hunter-gatherers and Neolithic farmers. We observe gene flow from South Asian populations into the Malaysian indigenous groups, but not into Dusun of North Borneo. Our study proposes that Malaysian indigenous people originated from at least three distinct ancestral populations related to the Hoabinhian hunter-gatherers, Neolithic farmers and Austronesian speakers.

Figure 1

PCA and ADMIXTURE analysis. (A) ADMIXTURE analysis results at K = 5 of indigenous Malaysians, Andamanese, Malay, and selected HGDP-CEPH population samplesshowes that the ancestral component related to Southeast Asia (blue) is the most pronounced in OAs while ancestral components related to East Asia (yellow) and South Asia (green) are also present in most of OA groups. (B) Global PCA with indigenous Malaysian populations, Andamanese, Malay and selected HGDP-CEPH samples showes that OAs are in general genetically closer to East Asians while Malaysian Negritos have tendency towards Andaman islanders. (C) PCA representing ancient Southeast Asian with indigenous Malaysian, Andamanese, Malay and HGDP-CEPH populations from East Asia (EA), Central South Asia (CSA) and Oceania (OCE). Most of OAs positioned between Hoabinhian hunter-gatheres and ancient farmers. Plots are generated using ggplot2 version 3.3.3 package (https://ggplot2.tidyverse.org/) in R version 4.0.4 (https://www.R-project.org/).

Figure 2

Inference of effective population size (Ne) and population divergence using MSMC2. (a) Inference of Ne in Jehai, Seletar and selected HGDP populations using eight haplotypes per population. Pattern of Ne through time in Jehai and Seletar is consistent with Out-of-Africa human migration, however both tribes retained a low Ne after the bottleneck 70–50 KYBP. (b) Estimation of divergence time between indigenous Malaysian and Han using four randomly selected haplotypes per population (in case of Mah Meri and Jakun limited to two haplotypes). A relative cross coalescence rate (CCR) around 0.5 heurostically can be used as a split time between the two populations. Plots are generated using ggplot2 version 3.3.3 package (https://ggplot2.tidyverse.org/) in R version 4.0.4 (https://www.R-project.org/).

Figure 3

TreeMix maximum likelihood tree with five migration events of indigenous Malaysian and Hobinhian culture and Neolithic farmer ancient Southeast Asia samples. Malaysian Negritos and Jakun make a separate clade while the rest of OAs clustered with East Asians. Results show gene flow events from Malysian Hoabinhian hunther-gatheres (Ma911) and Malaysian Neolithic farmers (Ma912) into modern-day Malaysian Negritos.

Figure 4

Allele sharing estimation using Outgroup-f3 statistics between Orang Asli and Gua Cha samples. The results indicate that Ma911 (Hoabinhian hunther-gatherer) share more drift with Malaysian Negritos (Jehai and Mendriq), while Ma912 (Neolithic farmer) share more drift with Senois (MahMeri). Plot is generated using ggplot2 version 3.3.3 package (https://ggplot2.tidyverse.org/) in R version 4.0.4 (https://www.R-project.org/).