Genomic history and forensic characteristics of Sherpa highlanders on the Tibetan Plateau inferred from high-resolution InDel panel and genome-wide SNPs

Wang, Mengge; Du, Weian; Tang, Renkuan; Liu, Yan; Zou, Xing; Yuan, Dejian; Wang, Zheng; Liu, Jing; Guo, Jianxin; Yang, Xiaomin; Chen, Jing; Yang, Meiqing; Zhang, Xianpeng; Wei, Lan‐Hai; Yuan, Haibing; Yeh, Hui‐Yuan; Wang, Chuan‐Chao; Liu, Chao; He, Guanglin

doi:10.1016/j.fsigen.2021.102633

Cited by 17 publications

(21 citation statements)

References 67 publications

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“…Previous genetic analysis has mainly focused on the fine-scale population genetic structure of Han Chinese and Tibetan people using genome-wide SNP data, however, this important Qiang population in this language family keeps uncharacterized until now [11,34]. There is limited knowledge of the genetic diversity and fine-scale admixture structure of Qiang people and their genetic origin and detailed evolutionary history reconstructed based on the genome-wide SNP data also remains uncharacterized.…”

Section: Introductionmentioning

confidence: 99%

Genetic admixture history and forensic characteristics of Tibeto-Burman-speaking Qiang people explored via the newly developed Y-STR panel and genome-wide SNP data

Adnan

Wang

et al. 2022

Preprint

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Fine-scale patterns of population genetic structure and diversity of ethnolinguistically diverse populations are important for biogeographical ancestry inference, kinship testing and also for the development and validation of new kits focused on forensic personal identification. Analyses focused on forensic markers and genome-wide SNP data can provide new insights into the origin, admixture processes and forensic characteristics of targeted populations. Qiang people with a large sample size among Tibeto-Burman-speaking populations widely reside in the middle latitude of the Tibetan Plateau. However, their genetic structure and forensic features have remained uncharacterized due to the paucity of comprehensive genetic analyses. Here, we first developed and validated the AGCU-Y30 Y-STR panel, which contains slowly and moderately mutating Y-STRs, and then we conducted comprehensive population genetic analyses based on Y-STRs and genome-wide SNPs to explore the admixture history of Qiang people and their neighbours. The validated results of this panel showed that the new Y-STR kit was sensitive and robust enough for forensic applications. Haplotype diversity (HD) ranging from 0.9932 to 0.9996 and allelic frequencies ranging from 0.001946 to 0.8326 in 514 Qiang people demonstrated that all included markers were highly polymorphic in Tibeto-Burman people. Population genetic analyses based on Y-STRs (RST, FST, MDS, NJ, PCA and MJNs) revealed that the Qiang people harboured a paternally close relationship with lowland Tibetan-Yi corridor populations. Furthermore, we made a comprehensive population admixture analysis among Eurasian modern and ancient populations based on the shared alleles. We determined that the Qiang people were a genetically admixed population and showed the closest relationship with Tibetan and Neolithic Yellow River farmers. Admixture modelling showed that Qiang people shared the primary ancestry with Tibetan and was derived from North China, supporting the hypothesis of common origin between Tibetan and Qiang people.

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Section: Introductionmentioning

confidence: 99%

Genetic admixture history and forensic characteristics of Tibeto-Burman-speaking Qiang people explored via the newly developed Y-STR panel and genome-wide SNP data

Adnan

Wang

et al. 2022

Preprint

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“…So far, only two ancient nuclear DNA-based paleogenomics studies have been reported. All ∼3.4-1.4 ka culture-diverse ancients from the Nepalese side of the Himalayas derived the predominant ancestry from lowland Neolithic Qijia culture-related upper Yellow River (YR) farmers and the rest from an uncertain deeply diverged East Eurasian-related ancestry, suggesting the massive migrations of lowlanders to TP might be more likely to occur before the advent of barley agriculture in TP (∼3.6 ka) (Jeong et al, 2016;Liu et al, 2022). Denser ancient nuclear DNA sampling from archeological sites in TP will lead to a more detailed human Abbreviations: TP, Tibetan Plateau; SNP, single-nucleotide polymorphism; HO, Human Origin; N, Neolithic; EN, Early Neolithic; MN, Middle Neolithic; LN, Late Neolithic; BA, Bronze Age; IA, Iron Age; H, Historical; SEA, Southeast Asian; EA, East Asian; WE, Western Eurasian; SA, South Asian; ST, Sino-Tibetan; TB, Tibeto-Burman; TK, Tai-Kadai; AN, Austronesian; AA, Austroasiatic; HM, Hmong-Mien; YR, Yellow River; HG, hunter-gatherer; Ne, effective population size; ka, thousand years ago.…”

Section: Introductionmentioning

confidence: 99%

“…Recent genomic studies, focusing on genome-wide SNP data and lower resolution forensic genetic markers (e.g., Indels, STRs) in systematic sampling of present-day Tibetans and Sherpa highlanders (Yao et al, 2017;Zhang et al, 2017;He et al, 2019He et al, , 2021Liu et al, 2021;Wang et al, 2021Wang et al, , 2022, repeatedly characterized (1) the genetic connection between TP highlanders and lowland Han Chinese/Neolithic upper YR millet farmers (Yao et al, 2017;He et al, 2021;Liu et al, 2021;Wang et al, 2021Wang et al, , 2022 that was in line with the linguistic phylogenetic evidence for the Northern China origin of Sino-Tibetan language (Zhang et al, 2019); (2) the genetic continuity in Himalayan region within at least 3,400 years (Liu et al, 2022);…”

Section: Introductionmentioning

confidence: 99%

“…(3) the patterns of co-existence of both Paleolithic and Neolithic ancestries in present-day Tibetan highlanders' gene pool from both uniparental and autosomal genetic markers perspectives, providing clues of the Upper Paleolithic colonization and Neolithic expansion of anatomically modern humans in TP (Shi et al, 2008;Lu et al, 2016;He et al, 2021;Liu et al, 2021Liu et al, , 2022Wang et al, 2021Wang et al, , 2022; and (4) the population genetic structure strongly correlated to the culturally defined regions of historical Tibet (Zhang et al, 2017;He et al, 2021;Wang et al, 2021): Amdo Tibetan groups from northeast TP (Qinghai and Gansu) and Kham Tibetan groups from Tibetan-Yi corridor possessed amounts of Ü-Tsang Tibetanrelated ancestry (denoted as core Tibetan-related ancestry in Wang et al, 2021) from central and western region of the Tibet Autonomous Region. Moreover, Amdo Tibetans and Kham Tibetans received additional gene flow from Western Eurasian Steppe Herder-related and lowland southeast Asianrelated ancestry, respectively.…”

Section: Introductionmentioning

confidence: 99%

“…Multiple variants have been identified as targets of positive selection based on SNP array genotyping and exome or whole-genome sequencing data (Beall et al, 2010;Simonson et al, 2010Simonson et al, , 2012Xu et al, 2011;Yang et al, 2017;Deng et al, 2019). EPAS1 and EGLN1 genes, the two well-established candidates with strong selection signals, contributed functionally to the high-altitude adaptive phenotype of present-day ethnic groups and prehistorical ancients in the Himalayan valley (Jeong et al, 2016;Liu et al, 2022). The adaptive introgression of Denisovan-like archaic humans also accelerated the adaptative process of present-day highlanders in the Himalayas (Huerta-Sánchez et al, 2014;Hackinger et al, 2016).…”

Section: Introductionmentioning

confidence: 99%

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Genomic insight into the population history and biological adaptations of high-altitude Tibetan highlanders in Nagqu

Wang²,

Feng³

et al. 2022

Front. Ecol. Evol.

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Tibetan, one of the largest indigenous populations living in the high-altitude region of the Tibetan Plateau (TP), has developed a suite of physiological adaptation strategies to cope with the extreme highland environment in TP. Here, we reported genome-wide SNP data from 48 Kham-speaking Nagqu Tibetans and analyzed it with published data from 1,067 individuals in 167 modern and ancient populations to characterize the detailed Tibetan subgroup history and population substructure. Overall, the patterns of allele sharing and haplotype sharing suggested (1) the relatively genetic homogeny between the studied Nagqu Tibetans and ancient Nepalese as well as present-day core Tibetans from Lhasa, Nagqu, and Shigatse; and (2) the close relationship between our studied Kham-speaking Nagqu Tibetans and Kham-speaking Chamdo Tibetans. The fitted qpAdm models showed that the studied Nagqu Tibetans could be fitted as having the main ancestry from late Neolithic upper Yellow River millet farmers and deeply diverged lineages from Southern East Asians (represented by Upper Paleolithic Guangxi_Longlin and Laos_Hoabinhian), and a non-neglectable western Steppe herder-related ancestry (∼3%). We further scanned the candidate genomic regions of natural selection for our newly generated Nagqu Tibetans and the published core Tibetans via FST, iHS, and XP-EHH tests. The genes overlapping with these regions were associated with essential human biological functions such as immune response, enzyme activity, signal transduction, skin development, and energy metabolism. Together, our results shed light on the admixture and evolutionary history of Nagqu Tibetan populations.

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Genetic history of esophageal cancer group in southwestern China revealed by Y‐chromosome STRs and genomic evolutionary connection analysis

Jia,

Wang,

Duan

et al. 2024

Heliyon

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Genomic history and forensic characteristics of Sherpa highlanders on the Tibetan Plateau inferred from high-resolution InDel panel and genome-wide SNPs

Cited by 17 publications

References 67 publications

Genetic admixture history and forensic characteristics of Tibeto-Burman-speaking Qiang people explored via the newly developed Y-STR panel and genome-wide SNP data

Genetic admixture history and forensic characteristics of Tibeto-Burman-speaking Qiang people explored via the newly developed Y-STR panel and genome-wide SNP data

Genomic insight into the population history and biological adaptations of high-altitude Tibetan highlanders in Nagqu

Genetic history of esophageal cancer group in southwestern China revealed by Y‐chromosome STRs and genomic evolutionary connection analysis

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