Ancient Genomes Reveal Yamnaya-Related Ancestry and a Potential Source of Indo-European Speakers in Iron Age Tianshan

Ning, Chao; Wang, Chuan‐Chao; Gao, Shizhu; Yang, Yang; Zhang, Xue; Wu, Xutong; Zhang, Fan; Nie, Zhongzhi; Tang, Yunpeng; Robbeets, Martine; Ma, Jian; Krause, Johannes; Cui, Yinqiu

doi:10.1016/j.cub.2019.06.044

Cited by 75 publications

(74 citation statements)

References 59 publications

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“…While the Afanasievo-derived lineages are consistent with having largely disappeared in Mongolia by the Late Bronze Age when our data showed that later groups with Steppe pastoralist ancestry made an impact, we confirm and strengthen previous ancient DNA analysis suggesting that the legacy of this expansion persisted in western China into the Iron Age Shirenzigou culture (410-190 BCE) 27 . The only parsimonious model for this group that fits according to our criteria is a 3-way mixture of groups related to Mongolia_N_East, Russia_Afanasievo, WSHG.…”

supporting

confidence: 87%

“…Repeating the modeling using other ancient Nepalese with very similar genetic ancestry to that in Mebrak results in uniformly poor fits (Online Table 5). Thus, ancestry typical of the Afanasievo culture and Mongolian Neolithic contributed to the Shirenzigou individuals, supporting the theory that the Tocharian languages of the Tarim Basin—from the second-oldest-known branch of the Indo-European language family—spread eastward through the migration of Yamnaya steppe pastoralists to the Altai Mountains and Mongolia in the guise of the Afansievo culture, from where they spread further to Xinjiang 5,7,8,27,29,30 . These results are significant for theories of Indo-European language diversification, as they increase the evidence in favor of the hypothesis the branch time of the second-oldest branch in the Indo-European language tree occurred at the end of the fourth millennium BCE 27,29,30 .…”

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confidence: 55%

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The Genomic Formation of Human Populations in East Asia

Wang

Yeh

Popov

et al. 2020

Preprint

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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. We report genome-wide data from 191 individuals from Mongolia, northern China, Taiwan, the Amur River Basin and Japan dating to 6000 BCE – 1000 CE, many from contexts never previously analyzed with ancient DNA. We also report 383 present-day individuals from 46 groups mostly from the Tibetan Plateau and southern China. We document how 6000-3600 BCE people of Mongolia and the Amur River Basin were from populations that expanded over Northeast Asia, likely dispersing the ancestors of Mongolic and Tungusic languages. In a time transect of 89 Mongolians, we reveal how Yamnaya steppe pastoralist spread from the west by 3300-2900 BCE in association with the Afanasievo culture, although we also document a boy buried in an Afanasievo barrow with ancestry entirely from local Mongolian hunter-gatherers, representing a unique case of someone of entirely non-Yamnaya ancestry interred in this way. The second spread of Yamnaya-derived ancestry came via groups that harbored about a third of their ancestry from European farmers, which nearly completely displaced unmixed Yamnaya-related lineages in Mongolia in the second millennium BCE, but did not replace Afanasievo lineages in western China where Afanasievo ancestry persisted, plausibly acting as the source of the early-splitting Tocharian branch of Indo-European languages. Analyzing 20 Yellow River Basin farmers dating to ∼3000 BCE, we document a population that was a plausible vector for the spread of Sino-Tibetan languages both to the Tibetan Plateau and to the central plain where they mixed with southern agriculturalists to form the ancestors of Han Chinese. We show that the individuals in a time transect of 52 ancient Taiwan individuals spanning at least 1400 BCE to 600 CE were consistent with being nearly direct descendants of Yangtze Valley first farmers who likely spread Austronesian, Tai-Kadai and Austroasiatic languages across Southeast and South Asia and mixing with the people they encountered, contributing to a four-fold reduction of genetic differentiation during the emergence of complex societies. We finally report data from Jomon hunter-gatherers from Japan who harbored one of the earliest splitting branches of East Eurasian variation, and show an affinity among Jomon, Amur River Basin, ancient Taiwan, and Austronesian-speakers, as expected for ancestry if they all had contributions from a Late Pleistocene coastal route migration to East Asia.

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confidence: 87%

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confidence: 55%

The Genomic Formation of Human Populations in East Asia

Wang

Yeh

Popov

et al. 2020

Preprint

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“…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).…”

Section: Discussionmentioning

confidence: 99%

“…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.…”

Section: Introductionmentioning

confidence: 99%

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

Wang

Zou

et al. 2020

Preprint

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AbstractArcheologically attested human occupation on the Tibet Plateau (TP) can be traced back to 160 thousand years ago (kya, Xiahe) via archaic people and 30~40 kya via anatomically modern human in Nwya Devu. However, the past human movements and peopling of the TP keep in its infancy in the modern/ancient DNA studies. Here, we performed the first modern/ancient genomic meta-analysis among 3,017 Paleolithic to present-day eastern Eurasian genomes (2,444 modern individuals from 183 populations (including 98 Ü-Tsang/Ando/Kham Tibetans) and 573 ancients (including 161 Chinese ancients first meta-analyzed here)). Closer genetic connection between ancient-modern highland Tibetans and lowland island/coastal Neolithic northern East Asians was identified, reflecting the main ancestry of high-altitude Tibeto-Burman speakers originated from the ancestors of Houli/Yangshao/Longshan ancients in the middle and lower Yellow River basin, consistent with the common North-China origin of Sino-Tibetan language and dispersal pattern of millet farmers. Although the shared common northern East Asian lineage between Tibetans and lowland East Asians, we still identified genetic differentiation between Highlanders and lowland northern East Asians, the former harboring more deeply diverged Hoabinhian/Onge ancestry and the latter possessing more modern Neolithic southern East Asian and Siberian ancestry, which suggested the co-existence of Paleolithic and Neolithic ancestries in modern and Neolithic East Asian Highlanders. Tibetans from Ü-Tsang/Ando/Kham Tibetan regions showed strong population stratifications consistent with their cultural backgrounds and geographic terrains (showed as barriers for human movements): stronger Chokhopani affinity in Ü-Tsang Tibetans, more western Eurasian ancestry in Ando and greater Neolithic southern East Asian ancestry in Kham Tibetan. Modern combined ancient genomes documented multiple waves of human migrations in TP past: the first layer of local Hunter-Gatherer mixed with Qijia Farmer arose the Chokhopani-associated Proto-Tibetan-Burman, admixture with the additional genetic materials from the western Eurasian steppe, Yellow River and Yangtze River respectively gave rise to modern Ando, Ü-Tsang and Kham Tibetans.

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“…In recent times, NGS has opened up possibilities not just for recovering DNA data from extant species, but also from historical samples and even extinct species. Collectively, this has shed light on human adaptation [4], relationships among humans and other hominids [5][6][7], and the place of extinct species, such as moa and mammoth, in evolutionary history [8,9].…”

Section: Introductionmentioning

confidence: 99%

Effects of sample age on data quality from targeted sequencing of museum specimens: what are we capturing in time?

McGaughran

2020

BMC Genomics

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Background: Next generation sequencing (NGS) can recover DNA data from valuable extant and extinct museum specimens. However, archived or preserved DNA is difficult to sequence because of its fragmented, damaged nature, such that the most successful NGS methods for preserved specimens remain sub-optimal. Improving wetlab protocols and comprehensively determining the effects of sample age on NGS library quality are therefore of vital importance. Here, I examine the relationship between sample age and several indicators of library quality following targeted NGS sequencing of~1300 loci using 271 samples of pinned moth specimens (Helicoverpa armigera) ranging in age from 5 to 117 years.Results: I find that older samples have lower DNA concentrations following extraction and thus require a higher number of indexing PCR cycles during library preparation. When sequenced reads are aligned to a reference genome or to only the targeted region, older samples have a lower number of sequenced and mapped reads, lower mean coverage, and lower estimated library sizes, while the percentage of adapters in sequenced reads increases significantly as samples become older. Older samples also show the poorest capture success, with lower enrichment and a higher improved coverage anticipated from further sequencing. Conclusions: Sample age has significant, measurable impacts on the quality of NGS data following targeted enrichment. However, incorporating a uracil-removing enzyme into the blunt end-repair step during library preparation could help to repair DNA damage, and using a method that prevents adapter-dimer formation may result in improved data yields.

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Ancient Genomes Reveal Yamnaya-Related Ancestry and a Potential Source of Indo-European Speakers in Iron Age Tianshan

Cited by 75 publications

References 59 publications

The Genomic Formation of Human Populations in East Asia

The Genomic Formation of Human Populations in East Asia

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

Effects of sample age on data quality from targeted sequencing of museum specimens: what are we capturing in time?

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