Genomic insights into the population history and biological adaptation of Southwestern Chinese Hmong-Mien people

Abstract

Hmong-Mien-speaking (HM) populations, widely distributed in South China, North of Thailand, Laos and Vietnam, have experienced different settlement environments, dietary habits and pathogen exposure. However, their specific biological adaptation also remained largely uncharacterized, which is important in the population evolutionary genetics and Trans-Omics for regional Precision Medicine. Besides, the origin and genetic diversity of HM people and their phylogenetic relationship with surrounding modern and ancient populations are unknown. Here, we reported genome-wide SNPs in 52 representative Miao people and combined them with 144 HM people from 13 geographically representative populations to characterize the full genetic admixture and adaptive landscape of HM speakers. We found that obvious genetic substructures existed in geographically different HM populations and also identified one new ancestral lineage specifically exited in HM people, which spatially distributed from Sichuan and Guizhou in the North to Thailand in the South and temporally dated to at least 500 years. The sharing patterns of the newly-identified homogeneous ancestry component combined the estimated admixture times via the decay of Linkage Disequilibrium and haplotype sharing in GLOBETROTTER suggested that the modern HM-speaking populations originated from Southwest China and migrated southward recently, which is consistent with the reconstructed phenomena of linguistic and archeological documents. Additionally, we identified specific adaptive signatures associated with several important human nervous system biological functions. Our pilot work emphasized the importance of anthropologically-informed sampling and deeply genetic structure reconstruction via whole-genome sequencing in the next step in the deep Chinese population genomic diversity project (CPGDP), especially in the ethnolinguistic regions.

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

“…More than 10 different language families/groups widely existed here, including Uralic, Altai/trans‐Eurasian (Turkic, Mongolic, Tungusic, Koreanic, and Japonic) in Siberia and northern China and Sinitic (SN), Tibeto‐Burman (TB), Austronesian (AN), Austroasiatic (AA), Hmong‐Mien (HM), and Tai‐Kadai (TK) in East Asia and Southeast (SE) Asia. Recent genetic studies based on the modern and/or ancient genomes of East Asians have subsequently elucidated the strong association between the genetic structure, linguistic categories, and geographical divisions, which was consistent with the proposed hypothesis of the language‐farming codispersal model (He et al, 2020c; Ning et al, 2020; Yang et al, 2020; Zhang & Fu, 2020; Wang et al, 2021a; Yan et al, 2021). Modern and ancient genetic studies based on the genetic variations of modern Sino‐Tibetan and Neolithic Yellow River farmers have elucidated that the northern millet farmer expansion from northern China dispersed the Sino‐Tibetan language (Wang et al, 2021a; He et al, 2021b), which was consistent with the common northern China origin of Sino‐Tibetan languages based on the linguistic phylogeny (Sagart et al, 2019; Zhang et al, 2019).…”

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

“…Wang et al recently also identified the extensive population admixture between HM people and Chongqing Han [37]. Interestingly, a similar pattern of the unique and differentiated genetic structure of Sichuan Miao (SCM) has been reported by Liu et al [38]. They identified the close genetic relationship between SCM and Vietnam HM people.…”

“…Large-scale population genetic analyses focused on the Chinese populations, included in the 10K_CPGDP or beyond East Asia in the HUGO Pan-Asian SNP project, showed that fine-scale population substructure in the eastern Eurasian strongly associated with the cultural boundaries of geography or language [12, 13, 52], which was also confirmed in our genetic admixture pattern reconstruction among eastern Eurasians. Our previous genetic study focused on the single HM population has identified the previously unidentified genetic cline in Southeast China, which widely existed in the mountainous region of the Yungui Plateau [37, 38]. Liu et al generated the genome-wide data from Vietnam Hmong, Dao, and PaThen and found that Vietnam HM people received genetic influence from southern East Asians [40].…”

“…To analyze the complete admixture and interaction landscape between HM people and other ancestral source groups, we merged our dataset with ancient eastern Eurasians included in the 1240K dataset. The Illumina reference populations included two AA Blang and Wa, nine Mongolic-speaking Baoan, Dongxiang, Mongolian, and Yugur, Sinitic-speaking Han and Hui populations from Shaanxi, Sichuan, Gansu, Guizhou, and Fujian provinces, six TB-speaking Pumi, Bai, Hani, Tibetan and Tujia, one Tungusic Manchu, and two Turkicspeaking Kazakh and Salar (Figure 1d) [13,20,21,37,38,[63][64][65][66][67][68][69] Mongolic people from 18 populations, 62 Tungusic people from 62 populations [18,40,41]. Ancient eastern Eurasians were included in both the HO dataset and the 1240K dataset, which included 48 ancient Yellow River Basin farmers from 20 populations in Shandong, Henan, Shaanxi, and Gansu [15,18,70]; 30 ancient people from 13 populations in Amur River Basin or West Liao River Basin [2,70]; 23 ancient people from 9 population in Guangxi province [3]; 54 ancient people from 9 populations in Fujian province and Taiwan island [15]; 26 ancient people from 10 populations in Japan and Korea Peninsula [17]; 33 ancient people from 7 populations in Nepal in the Tibetan Plateau [54,71]; 54 ancient people from 9 populations southern Russia around Baikal lake regions [1,16,72]; 243 ancient people from 20 populations in the Mongolia Plateau [1]; 18 ancient people from 4 populations in Xinjiang [73].…”

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

“…Tibeto-Burman groups from Tibetan Plateau had the highest proportion of ancestry related to core Tibet Tibetan and Nepal Chokhopani, Mebrak, and Samdzong people[69, 70]. The primary ancestral component of Hmong-Mien people from southwestern China was maximized in ancestry related to Miao and Yao people [71], and Austronesian-speaking people from Taiwan Island have more Ami/Atayal or ancient Hanben-related ancestry [41]. Han Chinese ancestry localized between the four ancestries mentioned above and showed a northern-to-southern genetic cline.…”