Northern gene flow into southeastern East Asians inferred from genome‐wide array genotyping

Abstract

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.

Multiple founding paternal lineages inferred from the newly-developed SNPSeqTyper 639 Y-SNP panel suggested the complex admixture and migration history of Chinese people

“…Han Chinese is the largest ethnic group in the world and has a significant influence on the formation of the gene pool of Chinese populations [37, 38, 55-57]. To further explore phylogenetic topology among Han Chinese and illuminate the genetic relationship between Han Chinese and aforesaid minorities, we collected and genotyped 711 individuals via Affymetrix array, which included 690 Han Chinese from 25 geographically different populations.…”

“…However, Chinese populations possessed complex cultural, geographical, ethnic and genetic diversity patterns, these dedicated Y-SNP genotyping tools could not cover the dominant paternal lineages of Chinese populations and meet the requirement of high-resolution paternal lineage classification. Whole-genome sequencing-based genetic studies have illuminated Chinese population structures strongly correlated with the geographical regions or language families [37, 38]. Ancient DNA of East Eurasians further identified the westward steppe pastoralist ancestry, north-to-south di-directional population movements along the Yangtze River and Yellow River basins, peopling of the Tibetan Plateau and extensive interaction with ancient Siberians [39-43].…”

Differentiated genomic footprints and connections inferred from 440 Hmong-Mien genomes suggest their isolation and long-distance migration

“…Ancient population substructures in East Asia were also observed in modern East Asians. Our previous genetic studies identified genetic substructures in the Amur River, Tibetan Plateau, and inland and coastal South China associated with geographic locations and linguistic affiliations [13,[19][20][21]. However, these efforts have been made primary foundational work to dissect the mystery of Chinese populations' evolutionary and adaptive history.…”

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

“…Altaic-speaking populations in North China showed predominant ancestry related to ancient Mongolian ancestry and western Eurasian ancestry [14,15]. Other populations from Sino-Tibetan language families in central and southern East Asia harboured more primary ancestry related to ancient Yellow River Basin and Yangtze River Basin ancestry [9,10,16]. These population stratifications provided a new opportunity for the development and validation of new forensic kits focused on the fine-scale genetic background of East Asians with different genetic markers and higher resolution.…”