Genomic structure of the native inhabitants of Peninsular Malaysia and North Borneo suggests complex human population history in Southeast Asia

Abstract

Southeast Asia (SEA) is enriched with a complex history of peopling. Malaysia, which is located at the crossroads of SEA, has been recognized as one of the hubs for early human migration. To unravel the genomic complexity of the native inhabitants of Malaysia, we sequenced 12 samples from 3 indigenous populations from Peninsular Malaysia and 4 native populations from North Borneo to a high coverage of 28-37×. We showed that the Negritos from Peninsular Malaysia shared a common ancestor with the East Asians, but exhibited some level of gene flow from South Asia, while the North Borneo populations exhibited closer genetic affinity towards East Asians than the Malays. The analysis of time of divergence suggested that ancestors of Negrito were the earliest settlers in the Malay Peninsula, whom first separated from the Papuans ~ 50-33 thousand years ago (kya), followed by East Asian (~ 40-15 kya), while the divergence time frame between North Borneo and East Asia populations predates the Austronesian expansion period implies a possible pre-Neolithic colonization. Substantial Neanderthal ancestry was confirmed in our genomes, as was observed in other East Asians. However, no significant difference was observed, in terms of the proportion of Denisovan gene flow into these native inhabitants from Malaysia. Judging from the similar amount of introgression in the Southeast Asians and East Asians, our findings suggest that the Denisovan gene flow may have occurred before the divergence of these populations and that the shared similarities are likely an ancestral component.

Genetic Diversity of Five Native Populations (Dusun, Rungus, Sonsogon, Murut and Sungai-Lingkabau Paitan) of North Borneo, East Malaysia based on 17 Y-chromosomal Short-Tandem Repeats Polymorphism

“…The number of alleles ranged between 2 to 10 ( Table-2 distinct separation from the other members of the family probably due to their long history of isolation [21]. We see a similar differentiation of the populations using whole genome genotyping (with Single Nucleotide Polymorphisms) and whole genome sequencing data [21,22]. …”

Inference of past demography, dormancy and self-fertilization rates from whole genome sequence data

“…Recent advances in sequencing technologies enable us to obtain whole genome data for many individuals across several populations, even for non-model species [2][3][4][5]. In particular, inferring demography is of interest in its own right as it allow us to understand the history of existing and/or extinct species (population expansion, colonization of new habitats, past bottlenecks) [5][6][7]. Inferring demography is also necessary to generate null models for outlier scans, e.g.…”

Inference of past demography, dormancy and self-fertilization rates from whole genome sequence data

“…Recent advances in sequencing technologies enable us to obtain whole genome data for many individuals across several populations even for non-model species [49, 50, 25, 36]. In particular, inferring demography is of interest in its own right so as to understand the history of existing and/or extinct species (population expansion, colonization of new habitats, past bottlenecks) [58, 28, 36]. Inferring demography is also necessary to generate null models for outlier scans, e.g.…”