Genetic relatedness of indigenous ethnic groups in northern Borneo to neighboring populations from Southeast Asia, as inferred from genome‐wide SNP data

Abstract

The region of northern Borneo is home to the current state of Sabah, Malaysia. It is located closest to the southern Philippine islands and may have served as a viaduct for ancient human migration onto or off of Borneo Island. In this study, five indigenous ethnic groups from Sabah were subjected to genome-wide SNP genotyping. These individuals represent the "North Borneo"-speaking group of the great Austronesian family. They have traditionally resided in the inland region of Sabah. The dataset was merged with public datasets, and the genetic relatedness of these groups to neighboring populations from the islands of Southeast Asia, mainland Southeast Asia and southern China was inferred. Genetic structure analysis revealed that these groups formed a genetic cluster that was independent of the clusters of neighboring populations. Additionally, these groups exhibited near-absolute proportions of a genetic component that is also common among Austronesians from Taiwan and the Philippines. They showed no genetic admixture with Austro-Melanesian populations. Furthermore, phylogenetic analysis showed that they are closely related to non-Austro-Melansian Filipinos as well as to Taiwan natives but are distantly related to populations from mainland Southeast Asia. Relatively lower heterozygosity and higher pairwise genetic differentiation index (F ) values than those of nearby populations indicate that these groups might have experienced genetic drift in the past, resulting in their differentiation from other Austronesians. Subsequent formal testing suggested that these populations have received no gene flow from neighboring populations. Taken together, these results imply that the indigenous ethnic groups of northern Borneo shared a common ancestor with Taiwan natives and non-Austro-Melanesian Filipinos and then isolated themselves on the inland of Sabah. This isolation presumably led to no admixture with other populations, and these individuals therefore underwent strong genetic differentiation. This report contributes to addressing the paucity of genetic data on representatives from this strategic region of ancient human migration event(s).

Analysis of five deep-sequenced trio-genomes of the Peninsular Malaysia Orang Asli and North Borneo populations

“…Second, the estimated mutation rate and accurate phasing of the trio haplotypes could potentially be used as a reference to genomic studies of similar populations. Third, the differentiation of OA and NB genomes imply discrepant demographic history of these two populations, in accordance with previous studies [20]. Last, the inherited novel insertions with shared with archaic hominids identified in our samples may imply unique population history of the native inhabitants in Malaysia.…”

The Early Peopling of the Philippines based on mtDNA

“…Considering the geography of the Philippines, its neighboring regions and suggestions from previous studies 14,32,33 , we designed a total of 7 scenarios based on migration patterns and migration routes to the archipelago: (i) migration presenting LDD events (LDD, as suggested for Eurasia 15 ; details about the LDD model are shown in the Supplementary Material) and, 6 scenarios of migration through different routes and without LDD proposed in the "Beyer's Wave Migration Theory" 32 and other studies 14,33 : (ii) a north route and three south routes (AllCorr), (iii) only a north route (North), (iv) only the three south routes (AllSouth), (v) only the southwest route (SW), (vi) only the south-central route (SC) and, (vii) only the southeast route (SE) (Figs. 1 and S2).…”

“…Another finding is the presence in the archipelago of Negritos groups related to the first migrations of Homo sapiens outside Africa 4,8,9 . Indeed, several genetic studies detected an archaic substrate in current populations of the Philippines 4,5,[10][11][12][13][14] . Hence, the human presence in the Philippines during the first stages of expansion of anatomically modern Homo sapiens is very likely.…”

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]. …”