The genome landscape of Tibetan sheep reveals adaptive introgression from argali and the history of early human settlements on the Qinghai-Tibetan Plateau

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cg.authorship.typesCGIAR and developing country instituteen
cg.contributor.affiliationChinese Academy of Sciencesen
cg.contributor.affiliationUniversity of Chinese Academy of Sciencesen
cg.contributor.affiliationXinjiang Academy of Animal Scienceen
cg.contributor.affiliationKashgar Universityen
cg.contributor.affiliationInner Mongolia Agricultural Universityen
cg.contributor.affiliationYunnan Agricultural Universityen
cg.contributor.affiliationShandong Binzhou Academy of Animal Science and Veterinary Medicineen
cg.contributor.affiliationNanjing Agricultural Universityen
cg.contributor.affiliationNingxia Academy of Agriculture and Forestry Sciences, Chinaen
cg.contributor.affiliationChinese Academy of Agricultural Sciencesen
cg.contributor.affiliationInternational Livestock Research Instituteen
cg.contributor.crpLivestock
cg.contributor.donorNational Natural Science Foundation of Chinaen
cg.contributor.donorChinese Academy of Sciencesen
cg.coverage.countryChina
cg.coverage.iso3166-alpha2CN
cg.coverage.regionAsia
cg.coverage.regionEastern Asia
cg.howPublishedFormally Publisheden
cg.identifier.doihttps://doi.org/10.1093/molbev/msy208en
cg.isijournalISI Journalen
cg.issn1537-1719en
cg.issue2en
cg.journalMolecular Biology and Evolutionen
cg.reviewStatusPeer Reviewen
cg.subject.ilriANIMAL BREEDINGen
cg.subject.ilriBREEDSen
cg.subject.ilriGENETICSen
cg.subject.ilriINDIGENOUS BREEDSen
cg.subject.ilriLIVESTOCKen
cg.subject.ilriSHEEPen
cg.subject.ilriSMALL RUMINANTSen
cg.volume36en
dc.contributor.authorXiao-Ju Huen
dc.contributor.authorJi Yangen
dc.contributor.authorXing-Long Xieen
dc.contributor.authorFeng-Hua Lven
dc.contributor.authorYin-Hong Caoen
dc.contributor.authorWen-Rong Lien
dc.contributor.authorMing-Jun Liuen
dc.contributor.authorYu-Tao Wangen
dc.contributor.authorJin-Quan Lien
dc.contributor.authorYong-Gang Liuen
dc.contributor.authorYan-Lin Renen
dc.contributor.authorZhi-Qiang Shenen
dc.contributor.authorHan Jianlinen
dc.contributor.authorMeng-Hua Lien
dc.date.accessioned2019-01-02T13:07:55Zen
dc.date.available2019-01-02T13:07:55Zen
dc.identifier.urihttps://hdl.handle.net/10568/98927
dc.titleThe genome landscape of Tibetan sheep reveals adaptive introgression from argali and the history of early human settlements on the Qinghai-Tibetan Plateauen
dcterms.abstractTibetan sheep are the most common and widespread domesticated animals on the Qinghai–Tibetan Plateau (QTP) and have played an essential role in the permanent human occupation of this high-altitude region. However, the precise timing, route, and process of sheep pastoralism in the QTP region remain poorly established, and little is known about the underlying genomic changes that occurred during the process. Here, we investigate the genomic variation in Tibetan sheep using whole-genome sequences, single nucleotide polymorphism arrays, mitochondrial DNA, and Y-chromosomal variants in 986 samples throughout their distribution range. We detect strong signatures of selection in genes involved in the hypoxia and ultraviolet signaling pathways (e.g., HIF-1 pathway and HBB and MITF genes) and in genes associated with morphological traits such as horn size and shape (e.g., RXFP2). We identify clear signals of argali (Ovis ammon) introgression into sympatric Tibetan sheep, covering 5.23–5.79% of their genomes. The introgressed genomic regions are enriched in genes related to oxygen transportation system, sensory perception, and morphological phenotypes, in particular the genes HBB and RXFP2 with strong signs of adaptive introgression. The spatial distribution of genomic diversity and demographic reconstruction of the history of Tibetan sheep show a stepwise pattern of colonization with their initial spread onto the QTP from its northeastern part ∼3,100 years ago, followed by further southwest expansion to the central QTP ∼1,300 years ago. Together with archeological evidence, the date and route reveal the history of human expansions on the QTP by the Tang–Bo Ancient Road during the late Holocene. Our findings contribute to a depth understanding of early pastoralism and the local adaptation of Tibetan sheep as well as the late-Holocene human occupation of the QTP.en
dcterms.accessRightsOpen Access
dcterms.audienceScientistsen
dcterms.available2018-11-16
dcterms.bibliographicCitationXiao-Ju Hu, Ji Yang, Xing-Long Xie, Feng-Hua Lv, Yin-Hong Cao, Wen-Rong Li, Ming-Jun Liu, Yu-Tao Wang, Jin-Quan Li, Yong-Gang Liu, Yan-Lin Ren, Zhi-Qiang Shen, Feng Wang, Eer Hehua, Han Jianlin and Meng-Hua Li. 2019. The genome landscape of Tibetan sheep reveals adaptive introgression from argali and the history of early human settlements on the Qinghai-Tibetan Plateau. Molecular Biology and Evolution 36(2):283–303.en
dcterms.extentp. 283-303en
dcterms.issued2019-02-01
dcterms.languageen
dcterms.licenseCC-BY-NC-4.0
dcterms.publisherOxford University Pressen
dcterms.subjectanimal breedingen
dcterms.subjectsheepen
dcterms.subjectsmall ruminantsen
dcterms.subjectgeneticsen
dcterms.subjectgenomesen
dcterms.subjectmolecular biologyen
dcterms.typeJournal Article

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