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In particular, the lack of whole-genome sequencing data on the Yao population has prevented a full investigation of the origins and evolutionary history of HM speakers. As such, their origins are debatable.<\/jats:p><\/jats:sec><jats:sec><jats:title>Results<\/jats:title><jats:p>Here, we made a deep sequencing effort of 80 Yao genomes, and our analysis together with 28 East Asian populations and\u00a0968 ancient Asian genomes suggested that there is a strong genetic basis for the formation of the HM language family. We estimated that the most recent common ancestor dates to 5800\u00a0years ago, while the genetic divergence between the HM and Tai\u2013Kadai speakers was estimated to be 8200\u00a0years ago. We proposed that HM speakers originated from the Yangtze River Basin and spread with agricultural civilization. We identified highly differentiated variants between HM and Han Chinese, in particular, a deafness-related missense variant (rs72474224) in the<jats:italic>GJB2<\/jats:italic>gene is in a higher frequency in HM speakers than in others.<\/jats:p><\/jats:sec><jats:sec><jats:title>Conclusions<\/jats:title><jats:p>Our results indicated complex gene flow and medically relevant variants involved in the HM speakers\u2019 evolution history.<\/jats:p><\/jats:sec>","DOI":"10.1186\/s12915-024-01838-9","type":"journal-article","created":{"date-parts":[[2024,3,13]],"date-time":"2024-03-13T02:10:01Z","timestamp":1710295801000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":13,"title":["Reconstructing the ancestral gene pool to uncover the origins and genetic links of Hmong\u2013Mien speakers"],"prefix":"10.1186","volume":"22","author":[{"given":"Yang","family":"Gao","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Xiaoxi","family":"Zhang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Hao","family":"Chen","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yan","family":"Lu","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sen","family":"Ma","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yajun","family":"Yang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Menghan","family":"Zhang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1975-1002","authenticated-orcid":false,"given":"Shuhua","family":"Xu","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2024,3,13]]},"reference":[{"issue":"3","key":"1838_CR1","doi-asserted-by":"publisher","first-page":"385","DOI":"10.1075\/dia.29.3.06han","volume":"29","author":"Z Handel","year":"2012","unstructured":"Handel Z. 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