Genomic insights into the formation of human populations in East Asia

Abstract

The deep population history of East Asia remains poorly understood due to a lack of ancient DNA data and sparse sampling of present-day people 1 , 2 . We report genome-wide data from 166 East Asians dating to 6000 BCE – 1000 CE and 46 present-day groups. Hunter-gatherers from Japan, the Amur River Basin, and people of Neolithic and Iron Age Taiwan and the Tibetan plateau are linked by a deeply-splitting lineage likely reflecting a Late Pleistocene coastal migration. We follow Holocene expansions from four regions. First, hunter-gatherers of Mongolia and the Amur River Basin have ancestry shared by Mongolic and Tungusic language speakers but do not carry West Liao River farmer ancestry contradicting theories that their expansion spread these proto-languages. Second, Yellow River Basin farmers at ~3000 BCE likely spread Sino-Tibetan languages as their ancestry dispersed both to Tibet where it forms up ~84% to some groups and to the Central Plain where it contributed ~59–84% to Han Chinese. Third, people from Taiwan ~1300 BCE to 800 CE derived ~75% ancestry from a lineage also common in modern Austronesian, Tai-Kadai and Austroasiatic speakers likely deriving from Yangtze River Valley farmers; ancient Taiwan people also derived ~25% ancestry from a northern lineage related to but different from Yellow River farmers implying an additional north-to-south expansion. Fourth, Yamnaya Steppe pastoralist ancestry arrived in western Mongolia after ~3000 BCE but was displaced by previously established lineages even while it persisted in western China as expected if it spread the ancestor of Tocharian Indo-European languages. Two later gene flows affected western Mongolia: after ~2000 BCE migrants with Yamnaya and European farmer ancestry, and episodic impacts of later groups with ancestry from Turan.

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

“…S9 D, E, and J)). This is consistent with the recent analysis of ancient individuals from East Asia, which revealed gene flow between populations across various points of time (18)(19)(20) and showed that there is some genetic affiliation between nEAs and southern East Asians, including Liangdao individuals (19).…”

“…We find no genetic evidence for an association between currently established dates for the arrival and expansion of paddy field rice agriculture (∼2 to 3 kya) (31,32) and the demographic movement of people from the South China-Taiwan greater area into the Philippines. Given the genetic makeup of the Liangdao-2 woman and other ancient Taiwanese and southern East Asian individuals (18) who all present some nEA ancestry, the most parsimonious explanation is that Cordillerans entered the Philippines prior to the nEA gene flow. This observation sets a boundary for the date of arrival of Cordillerans in the Philippines, at least ∼7 to 8 kya or earlier, indicating that early Cordillerans in the Philippines were mobile hunter-gatherers.…”

Significant East Asian Affinity of the Sichuan Hui Genomic Structure Suggests the Predominance of the Cultural Diffusion Model in the Genetic Formation Process

“…They also revealed significant population stratification among East Asians according to language categories. Next, we focused on the population differentiation between Huis and East Asians (Wang et al, 2021). As shown in Supplementary Table 15, most statistically positive f 4 values observed among modern Eastern panels based on the merged 1,240 K dataset demonstrated that the Boshu Huis harbored more East Asian-derived ancestry than their respective predefined comparative populations, which is consistent with the genetic affinity identified via the outgroup f 3 statistics and pairwise f 4 analysis based on the Human Origin 16).…”

Modern Japanese ancestry-derived variants revealed the formation process of the current Japanese regional gradations

“…A previous study of modern and ancient East Asians including the seven Jomon individuals suggest that the Jomon people have two ancestry components from ancient East Asians, i.e. the Interior South ancestry and the Coastal ancestry 33 . Considering the results of this study and previous studies, at least the ancestral population of Jomon people seem to have migrated to the Japanese archipelago from the south of East Eurasia (southern parts of the Himalayas) via the southern of China, although it cannot be concluded whether they passed through coastal or inland areas.…”