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The population history of Southeast (SE) China remains poorly understood due to the sparse sampling of present‐day populations and limited modeling with ancient genomic data. We report genome‐wide genotyping data from 207 present‐day Han Chinese and Hmong‐Mien (HM)‐speaking She people from Fujian and Taiwan Island, SE China. We coanalyzed 66 Early Neolithic to Iron Age ancient Fujian and Taiwan Island individuals obtained from previously published works to explore the genetic continuity and admixture based on patterns of genetic variations of the high‐resolution time transect. We found the genetic differentiation between northern and southern East Asians was defined by a north–south East Asian genetic cline and our studied southern East Asians were clustered in the southern end of this cline. The southeastern coastal modern East Asians are genetically similar to other southern indigenous groups as well as geographically close to Neolithic‐to‐Iron Age populations, but they also shared excess alleles with post‐Neolithic Yellow River ancients, which suggested a southward gene flow on the modern southern coastal gene pool. In addition, we identified one new HM genetic cline in East Asia with the coastal Fujian HM‐speaking She localizing at the intersection between HM and Han clines. She people show stronger genetic affinity with southern East Asian indigenous populations, with the main ancestry deriving from groups related to southeastern ancient indigenous rice farmers. The southeastern Han Chinese could be modeled with the primary ancestry deriving from the group related to the Yellow River Basin millet farmers and the remaining from groups related to rice farmers, which was consistent with the northern China origin of modern southeastern Han Chinese and in line with the historically and archaeologically attested southward migrations of Han people and their ancestors. Our estimated north–south admixture time ranges based on the decay of the linkage disequilibrium spanned from the Bronze Age to historic periods, suggesting the recent large‐scale population migrations and subsequent admixture participated in the formation of modern Han in SE Asia. [ABSTRACT FROM AUTHOR]

Archaeological, genetic, and linguistic evidence has supported the idea that northern China is the original center of modern Sino‐Tibetan‐speaking populations. However, the demographic history of subsequent southward migration and genetic admixture of Han Chinese with surrounding indigenous populations remain uncharacterized, and the language shifts and assimilations accompanied by movement of people, or just an adaptation of cultural ideas among populations in central China is still unclear, especially for Tibeto‐Burman‐speaking Tujia and central Han Chinese populations. To resolve this, we genotyped over 60K genome‐wide markers in 505 unrelated individuals from 63 indigenous populations. Our results showed both studied Han and Tujia were at the intermediate position in the modern East Asian North–South genetic cline and there was a correlation between the genetic composition and the latitude. We observed the strong genetic assimilation between Tujia people and central Han Chinese, which suggested massive population movements and genetic admixture under language borrowing. Tujia and central Han Chinese could be modeled as a two‐way admixture deriving primary ancestry from a northern ancestral population closely related to the ancient DevilsCave and present‐day Tibetans and a southern ancestral population closely related to the present‐day Tai‐Kadai and Austronesian‐speaking groups. The ancestral northern population we suspect to be related to the Neolithic millet farming groups in the Yellow River Basin or central China. We showed that the newly genotyped populations in Hubei Province had a higher proportion of DevilsCave or modern Tungusic/Mongolic‐related northern ancestries, while the Hunan populations harbored a higher proportion of Austronesian/Tai‐Kadai‐related southern ancestries. [ABSTRACT FROM AUTHOR]