Multi-layered population structure in Island Southeast Asians

Abstract

The history of human settlement in Southeast Asia has been complex and involved several distinct dispersal events. Here, we report the analyses of 1825 individuals from Southeast Asia including new genome-wide genotype data for 146 individuals from three Mainland Southeast Asian (Burmese, Malay and Vietnamese) and four Island Southeast Asian (Dusun, Filipino, Kankanaey and Murut) populations. While confirming the presence of previously recognised major ancestry components in the Southeast Asian population structure, we highlight the Kankanaey Igorots from the highlands of the Philippine Mountain Province as likely the closest living representatives of the source population that may have given rise to the Austronesian expansion. This conclusion rests on independent evidence from various analyses of autosomal data and uniparental markers. Given the extensive presence of trade goods, cultural and linguistic evidence of Indian influence in Southeast Asia starting from 2.5 kya, we also detect traces of a South Asian signature in different populations in the region dating to the last couple of thousand years.

The Early Peopling of the Philippines based on mtDNA

“…An especially interesting example is the Philippine archipelago. There is a clear evidence of an early settlement of the Philippines 6,8,10,11 , however little is known about the population genetics, migration routes and migration patterns that occurred in this settlement. Concerning its geography, the Philippines is a particularly relevant region to test the influence of the geography on human migration and to understand the causes of the currently observed population structure and genetic diversity.…”

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

“…In contrast, a similar genetic component with similar proportions was not found in Dusun and Murut from Brunei. Their genetic structure resembled to Lebbo (Kalimantan) and Malay (Peninsular Malaysia) instead (Mӧrseburg et al., ). This merits further analyses in the future.…”

“…The northern region of Borneo, historically known as North Borneo, is currently home to the state of Sabah, Malaysia. Northern Borneo is located nearest to the South Philippine Islands and might have served as a viaduct for human migration event(s) such as ‘’Out of Taiwan” toward the archipelago of Southeast Asia (i.e., the Philippines, Borneo, Indonesia, and Papua New Guinea) (Jinam et al., ; Lipson et al., ; Mӧrseburg et al., ; Tabbada et al., ). This north‐to‐south direction of migration has been questioned, and a south‐to‐north migration from the islands of Southeast Asia toward mainland Southeast Asia (e.g., Thailand and Cambodia) and southern China has been proposed (The HUGO Pan‐Asian SNP Consortium, ).…”

“…Analyses of the genetic structure of the Dusun and Murut from Brunei were previously reported by Mӧrseburg et al. (). This study aimed to characterize the genetic structure among the indigenous ethnic groups of northern Borneo and to infer their genetic relatedness to other neighboring populations from islands in Southeast Asia, mainland Southeast Asia, and southern China.…”