Abstract
The Tibetan Plateau (TP) is considered to be one of the last terrestrial environments conquered by the anatomically modern human. Understanding of the genetic background of highland Tibetans plays a pivotal role in archeology, anthropology, genetics, and forensic investigations. Here, we genotyped 22 forensic genetic markers in 1,089 Tibetans residing in Nagqu Prefecture and collected 1,233,013 single nucleotide polymorphisms (SNPs) in the highland East Asians (Sherpa and Tibetan) from the Simons Genome Diversity Project and ancient Tibetans from Nepal and Neolithic farmers from northeastern Qinghai-Tibetan Plateau from public databases. We subsequently merged our two datasets with other worldwide reference populations or eastern ancient Eurasians to gain new insights into the genetic diversity, population movements, and admixtures of high-altitude East Asians via comprehensive population genetic statistical tools [principal component analysis (PCA), multidimensional scaling plot (MDS), STRUCTURE/ADMIXTURE, f3, f4, qpWave/qpAdm, and qpGraph]. Besides, we also explored their forensic characteristics and extended the Chinese National Database based on STR data. We identified 231 alleles with the corresponding allele frequencies spanning from 0.0005 to 0.5624 in the forensic low-density dataset, in which the combined powers of discrimination and the probability of exclusion were 1–1.22E-24 and 0.999999998, respectively. Additionally, comprehensive population comparisons in our low-density data among 57 worldwide populations via the Nei’s genetic distance, PCA, MDS, NJ tree, and STRUCTURE analysis indicated that the highland Tibeto-Burman speakers kept the close genetic relationship with ethnically close populations. Findings from the 1240K high-density dataset not only confirmed the close genetic connection between modern Highlanders, Nepal ancients (Samdzong, Mebrak, and Chokhopani), and the upper Yellow River Qijia people, suggesting the northeastern edge of the TP served as a geographical corridor for ancient population migrations and interactions between highland and lowland regions, but also evidenced that late Neolithic farmers permanently colonized into the TP by adopting cold-tolerant barley agriculture that was mediated via the acculturation of idea via the millet farmer and not via the movement of barley agriculturalist as no obvious western Eurasian admixture signals were identified in our analyzed modern and ancient populations. Besides, results from the qpAdm-based admixture proportion estimation and qpGraph-based phylogenetic relationship reconstruction consistently demonstrated that all ancient and modern highland East Asians harbored and shared the deeply diverged Onge/Hoabinhian-related eastern Eurasian lineage, suggesting a common Paleolithic genetic legacy existed in high-altitude East Asians as the first layer of their gene pool.
Highlights
East Asia, one of the oldest centers of plant and animal domestication, is home to almost one-quarter of the world’s population and encompasses substantial genetic, cultural, linguistic, and physical diversity
We first used forensic short tandem repeat markers with high polymorphic and informative features to explore the genetic relationships between highland Tibetan and worldwide reference populations based on the allele frequency spectrum and found that East Asian Highlanders had a close genetic relationship with modern Tibeto-Burmanspeaking populations and northern Han Chinese
Different from subpopulation structures observed in Highland East Asians (Zhang et al, 2017), our present study identified a genetic similarity between Sherpa and Tibetan, which may be caused by the small sample size and low density of genetic sampling
Summary
East Asia, one of the oldest centers of plant and animal domestication, is home to almost one-quarter of the world’s population and encompasses substantial genetic, cultural, linguistic, and physical diversity. Ning et al reported 55 ancient genomes dating to 7,500–1,700 years ago from the Yellow River (Henan Yangshao, Longshan, and Shangzhou cultures and Qinghai Qijia culture), West Liao River (Hongshan and Xiajiadian cultures), and Amur River (Haminmangha culture) basins and illustrated a link between changes in subsistence strategy and human activities (migration and admixture; Ning et al, 2020) These ancient genomes from the lowland East Asians showed a finer-scale landscape of population origin, diversification, and admixture in the lowland regions, and the population genetic admixture history of the highland region kept underrepresented and unclear due to the sparse genetic sampling of modern and ancient populations from the Qinghai-Tibet Plateau, which impedes our ability to connect temporally and geographically dispersed ancient East Asians and modern Tibetans
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