The Ami and Yami aborigines of Taiwan and their genetic relationship to East Asian and Pacific populations

Abstract

This article reports on the genetic characteristics of the Ami and Yami, two aboriginal populations of Taiwan. Y-SNP and mtDNA markers as well as autosomal SNPs were utilized to investigate the phylogenetic relationships to groups from MSEA (mainland Southeast Asia), ISEA (island Southeast Asia), and Oceania. Both the Ami and Yami have limited genetic diversity, with the Yami having even less diversity than the Ami. The partitioning of populations within the PCA plots based on autosomal SNPs, the profile constitution observed in the structure analyses demonstrating similar composition among specific populations, the average IBD (identical by descent) tract length gradients, the average total length of genome share among the populations, and the outgroup f3 results all indicate genetic affinities among populations that trace a geographical arc from Taiwan south into the Philippine Archipelago, Borneo, Indonesia, and Melanesia. Conversely, a more distant kinship between the Ami/Yami and MSEA based on all the markers examined, the total mtDNA sequences as well as the admixture f3 and f4 analyses argue against strong genetic contribution from MSEA to the Austronesian dispersal. The sharing of long IBD tracts, total genome length, and the large number of segments in common between the Ami/Yami and the Society Archipelago populations East Polynesia standout considering they are located about 10,700 km apart.

Genetic characterization of populations in the Marquesas Archipelago in the context of the Austronesian expansion

“…Immediately following this threesome cluster there are the populations from the Philippines, MSEA and Indonesia, in that order. This partitioning of populations mirrors the putative relationship and migration route of Austronesians during their expansion into Oceania starting in the island of Taiwan 10 . Except for one individual from Bora Bora that segregates with the Bajo of Indonesia, most of the samples from the Marquesas and Society Islands plot into a distinctly separate and tight cluster with a number of them radiating out towards a Indonesian-Filipino conglomerate.…”

“…Unlike many areas of anthropological research the general model of the peopling of the Pacific by Austronesians generated from archaeological and linguistic data is generally corroborated by genetic findings. The putative migration arc that traces a dispersal of Asian people from the island of Taiwan into Oceania by way of the Philippine Archipelago, Indonesia and Melanesia that culminated in the settlement of what is known today as Polynesia is for the most part congruent with genetic data 10 . High resolution genomic DNA, blood proteins, globin genes, uniparental DNA markers, commensal animal models and gut bacteria all support the standard model of human dispersal of the Pacific 11 .…”

“…Using genome-wide SNP diversity previous research show that the Ami population of Taiwan shares strong genetic affinities with the Islands of Bora Bora and Rai’atea suggesting recent long distance dispersal from Island South East Asia (ISEA) 10 . Although structure analysis based on genome-wide SNP markers fails to identify the genetic components responsible for the IBD (identical by descend) signals from Taiwan in East Polynesia, clear contribution from Tonga and Samoa in West Polynesia is observed 4 .…”

The genomic diversity of Taiwanese Austronesian groups: implications for the ‘Into and Out of Taiwan’ models

“…Furthermore, genome-wide studies, which can provide much more detailed insights into population histories, are very limited. To our knowledge, genome-wide data have only been generated for the Atayal, Amis, Paiwan, and Tao (Yami) (Patterson, et al 2012; Mallick, et al 2016; Choin, et al 2021; Tatte, et al 2021), and a systematic genomic assessment of the diversity and relationships among Taiwan groups, and how these relate to the “Into Taiwan” and “Out-of-Taiwan” migrations, is still lacking.…”

Preceramic riverside hunter-gatherers and the arrival of Neolithic farmers in northern Luzon

“…Taiwan was also the most likely immediate archaeological source for the Neolithic settlement of the northern Philippines more than 4000 years ago (Hung 2005, 2008; Bellwood et al 2011; Bellwood 2017; Carson & Hung 2018). Recent research on ancient DNA from northern Luzon, the Mariana Islands and the south-western Pacific suggests that the modern Austronesian-speaking populations of Island Southeast Asia and Oceania (beyond New Guinea and Island Melanesia) acquired much of their genetic heritage through ancient migration from southern China, via Taiwan, and through the Philippines (Skoglund et al 2016; McColl et al 2018; Pugach et al 2021; Wang et al 2021; for support from living DNA relationships, see Choin et al 2021; Tätte et al 2021; for a recent, thoughtful review, see Chambers & Edinur 2021).…”