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.

Keywords: Austronesian; ISEA; Negrito; Philippines; human population genetics.

Fig. 1.

Overview of Philippine population structure. (A) Location of indigenous cultural communities included in the study. The populations are color-coded to represent ethnic group clusters. (B) PCA with worldwide populations, with sample size matched for each regional group. (C) PCA restricted to Philippine ethnic groups. (D) Clustering of Asia-Pacific populations (315,692 SNPs) with an Inset Graph showing clustering of 115 Philippine populations (2.3 million SNPs), assuming K number of genetic ancestry components.

Fig. 2.

Inferred admixture graph models for Australasians and East Asians. Inferred admixture graph models based on a combination of qpGraph and f statistical analyses presented in SI Appendix, Figs. S4–S8. (A) Topology of Australasian cluster indicating pulses of Denisovan introgression events, and estimation of divergence time between Philippine Negritos and AustraloPapuans. (B) Topology of the East Asian cluster showing relationships between Cordillerans, Manobo, Sama, and mainland Asian ethnic groups with inferred admixture events and divergence dates. See main text for divergence time confidence intervals.

Fig. 3.

Model for Philippine demographic history. Suggested models for the five major migration events into the Philippines, (A) starting with entry of Northern Negritos and Southern Negritos into the Philippines from Sundaland, (B and C) followed by south-to-north movement of Manobo-related and Sama-related populations during the end of Last Glacial Period, and (D) culminating with the Holocene expansion of Cordilleran-related populations.