Multiple migrations to the Philippines during the last 50,000 years

Abstract

Island Southeast Asia has recently produced several surprises regarding human history, but the region’s complex demography remains poorly understood. Here, we report ∼2.3 million genotypes from 1,028 individuals representing 115 indigenous Philippine populations and genome-sequence data from two ∼8,000-y-old individuals from Liangdao in the Taiwan Strait. We show that the Philippine islands were populated by at least five waves of human migration: initially by Northern and Southern Negritos (distantly related to Australian and Papuan groups), followed by Manobo, Sama, Papuan, and Cordilleran-related populations. The ancestors of Cordillerans diverged from indigenous peoples of Taiwan at least ∼8,000 y ago, prior to the arrival of paddy field rice agriculture in the Philippines ∼2,500 y ago, where some of their descendants remain to be the least admixed East Asian groups carrying an ancestry shared by all Austronesian-speaking populations. These observations contradict an exclusive “out-of-Taiwan” model of farming–language–people dispersal within the last four millennia for the Philippines and Island Southeast Asia. Sama-related ethnic groups of southwestern Philippines additionally experienced some minimal South Asian gene flow starting ∼1,000 y ago. Lastly, only a few lowlanders, accounting for <1% of all individuals, presented a low level of West Eurasian admixture, indicating a limited genetic legacy of Spanish colonization in the Philippines. Altogether, our findings reveal a multilayered history of the Philippines, which served as a crucial gateway for the movement of people that ultimately changed the genetic landscape of the Asia-Pacific region.

Genomic insights into population history and biological adaptation in Oceania

“…Assuming isolation with migration, we estimated that Taiwanese Indigenous peoples and Malayo-Polynesian speakers (Philippine Kankanaey and Polynesian individuals from the Solomon Islands) diverged around 7.3 ka (95% confidence interval, 6.4-11 ka) (Extended Data Fig. 2c), in agreement with a recent genetic study of Philippine populations 25 . Similar estimates were obtained when modelling other Austronesian-speaking groups (>8 ka) (Supplementary Table 6).…”

Mitogenomes Reveal Two Major Influxes of Papuan Ancestry across Wallacea Following the Last Glacial Maximum and Austronesian Contact

“…These patterns suggest that the majority of Wallacean mitogenomes were derived versions of Papuan lineages, which were likely introduced into Wallacea in the period following the LGM. Notably, a recent genomic study of population genetic history of the Philippines detected the introgression of Papuan genetic lineages into southeastern Philippine populations from 15 ka [ 60 ], and our mtDNA data also support the movement of mainland Papuan Q1 haplogroup into Island Melanesia around this time (i.e., clade 12 in Figure 3 and Table S5, Supplementary Materials ). These results suggest that the internal population expansions occurring in mainland New Guinea around the end of the LGM also coincided with the movement of Papuan genetic lineages into neighbouring islands that might have also included the Southeastern Philippines.…”

Insights on the historical biogeography of Philippine native pigs and its relationship with Continental domestic and wild boars

“…The distribution of the haplotype frequencies indicated no equilibrium thus, the geographically distributed haplotypes suggested that the present-day Philippine native pigs have multiple ancestral origins spread across the Eurasian Continent. The close genetic connection between the continental wild boars and domestic pigs from the MSEA and NEA present in the Philippine pig genetic pool corroborates our hypothesis of a genetic signal that could potentially be associated with the recently reported multiple waves of human migrations to the Philippines during the last 50,000 years [49]. During the glacial periods, extensive gene flow has suggested to occurred among the Sus species [50] and was considered as an important driving factor that has established the present-day geographic distribution of Sus populations throughout the world [51].…”