Ancient genomes from northern China suggest links between subsistence changes and human migration

Abstract

Northern China harbored the world's earliest complex societies based on millet farming, in two major centers in the Yellow (YR) and West Liao (WLR) River basins. Until now, their genetic histories have remained largely unknown. Here we present 55 ancient genomes dating to 7500-1700 BP from the YR, WLR, and Amur River (AR) regions. Contrary to the genetic stability in the AR, the YR and WLR genetic profiles substantially changed over time. The YR populations show a monotonic increase over time in their genetic affinity with present-day southern Chinese and Southeast Asians. In the WLR, intensification of farming in the Late Neolithic is correlated with increased YR affinity while the inclusion of a pastoral economy in the Bronze Age was correlated with increased AR affinity. Our results suggest a link between changes in subsistence strategy and human migration, and fuel the debate about archaeolinguistic signatures of past human migration.

Peopling of Tibet Plateau and multiple waves of admixture of Tibetans inferred from both modern and ancient genome-wide data

“…We also identified the subtle genetic differences of these Neolithic to Iron Age individuals from northern (Ning, et al 2020). Here, we observed the late Neolithic populations in the southern cluster was localized between Patterns of genetic relationship revealed from the top two components (extracting 43% variation: PC1: 31.04% and PC2: 11.86%) revealed a genomic affinity between modern Tibetans, ancient Nepal populations, and modern/ancient East Asians and Siberians.…”

“…More and more ancient DNA studies from the surrounding of East Asia have been conducted and reported the population dynamics in Southeast Asia (Lipson, Cheronet, et al 2018;McColl, et al 2018) and South Siberia or Eurasia's Eastern Steppe (Lazaridis, et al 2014;Raghavan, et al 2014;Mathieson, et al 2015;Damgaard, et al 2018;Sikora, et al 2019), but lack in China. Fortunately, six ancient DNA studies from China (Yang, et al 2017;Ning, et al 2019;Ning, et al 2020;Wang, Yeh, et al 2020; have been recently published to elucidate the prehistory of East Asian independently with 161 Paleolithic to historic (ranging from 40,000 ybp to 300 ybp). Yang et al sequenced 40,000-year-old Tianyuan people from Beijing and found the early Asian population structures existed before the divergence between East Asian and Native American and the peopling of America by anatomically modern human populations (Yang, et al 2017).…”

“…Besides, they also identified southward migration from Shandong Houli populations and northward migration from Fujian Tanshishan populations, as well as a Neolithic coastal connection from southeastern Vietnam to Russia Far East, and a Pro-Austronesian connection between southern East Asians and southeast Pacific Vanuatu islanders. Besides, Ning et al reported the population history of North China with fifteen ancient genomes from the Yellow River, West Liao River and Amur River, and discovered the subsistence strategy changes were associated with the population movements and admixtures (Ning, et al 2020). Ning and Wang et.al.…”

“…To explore the genomic history of modern Tibetans and elucidate the peopling of Qinghai-Tibet Plateau, we used the genome-wide data from 98 modern Tibetans ( Figure 1A) collecting from eleven geographically different regions and cultural backgrounds from Tibet Autonomous Region (five), Qinghai (two), Gansu (one), Sichuan (two) and Yunnan (One), which were used to reconstruct the genetic background of modern East Asians in our recent ancient genome research of the deep genomic history of East Asia (Wang, Yeh, et al 2020). Besides, we merged our data with other modern and ancient East Asians (Patterson, et al 2012;Lipson, Cheronet, et al 2018;Jeong, et al 2019;, in which modern samples from Altai-speaking (also referred as Mongolic, Tungusic, and Turkic language families by other scholars), Sino-Tibetan (Sinitic and Tibeto-Burman), Hmong-Mien, Austronesian, Austroasiatic, and Tai-Kadai language families, and ancient populations included eight individuals from Nepal (Jeong, et al 2016) (Chokhopani, Samdzong, and Mebrak cultures), eighty-four samples from Yellow River (Ning, et al 2020;Wang, Yeh, et al 2020;, Amur River and West Liao River in the coastal and inland northern East Asia (including Houli, Yangshao, Longshan, Qijia, Hongshan, Yumin, and other cultures), fifty-eight individuals (Ning, et al 2020;Wang, Yeh, et al 2020; belonged to Tanshishan and other cultures in the coastal southeast China, islands of Taiwan strait and Taiwan. We also included the Neolithic to Bronze Age or Iron Age populations from Southwest Asia (Lipson, Cheronet, et al 2018;McColl, et al 2018) and Siberia (Allentoft, et al 2015;Mathieson, et al 2015;Damgaard, et al 2018;de Barros Damgaard, et al 2018;Sikora, et al 2019) in some of the following comprehensive population genetic analyses.…”

“…Genomic evidence supported that multiple variants may jointly deliver the fitness of the modern Tibetans on the TP, and Denisovan introgression into modern Tibetans and surrounding populations including positively selected haplotypes of HIF-1α prolyl hydroxylase1 (EGLN1) and Endothelial PAS domain protein 1 (EPAS1) is significantly associated with the high-altitude adaptation to hypoxia (Simonson, et al 2010;Xu, et al 2011;Huerta-Sanchez, et al 2014;Gnecchi-Ruscone, et al 2018;Chen, Welker, et al 2019;Deng, et al 2019). Compared to other parts of East Asia (Reich 2018;Ning, et al 2019;Jeong, et al 2020;Ning, et al 2020;Wang, Yeh, et al 2020;, the greatest problem facing researchers is the lack of excavated archaeological sites on the TP, which means that certain types of critical data, such as zooarchaeological and archaeobotanical data for reconstructing the subsistence strategy, ancient DNA (aDNA) for dissecting the genomic correlation between ancient individuals and modern Tibetan-like Highlanders, are in short supply.…”