Tracing Bai-Yue Ancestry in Aboriginal Li People on Hainan Island

Abstract

As the most prevalent aboriginal group on Hainan Island located between South China and the mainland of Southeast Asia, the Li people are believed to preserve some unique genetic information due to their isolated circumstances, although this has been largely uninvestigated. We performed the first whole-genome sequencing of 55 Hainan Li (HNL) individuals with high coverage (∼30–50×) to gain insight into their genetic history and potential adaptations. We identified the ancestry enriched in HNL (∼85%) is well-preserved in present-day Tai-Kadai speakers residing in South China and North Vietnam, i.e., Bai-Yue populations. A lack of admixture signature due to the geographical restriction exacerbated the bottleneck in the present-day HNL. The genetic divergence among Bai-Yue populations began ∼4,000–3,000 years ago when the proto-HNL underwent migration and the settling of Hainan Island. Finally, we identified signatures of positive selection in the HNL, some outstanding examples included FADS1 and FADS2 related to a diet rich in polyunsaturated fatty acids. In addition, we observed that malaria-driven selection had occurred in the HNL, with population-specific variants of malaria-related genes (e.g., CR1) present. Interestingly, HNL harbors a high prevalence of malaria leveraged gene variants related to hematopoietic function (e.g., CD3G) that may explain the high incidence of blood disorders such as B cell lymphomas in the present-day HNL. The results have advanced our understanding of the genetic history of the Bai-Yue populations and have provided new insights into the adaptive scenarios of the Li people.

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

“…All F2517 lineages were observed in Li people, which was consistent with a recent whole-genome sequencing study [55]. Chen et al found O1b1a1a was the dominant lineage in southern East Asians, which diverged from others 10998 years ago, and the F2517 sublineages were further divided into O1b1a1a1a1b2a1a1a and O1b1a1a1a1b2a1a1b clades at 2828 years ago [55]. Sun et al also found most sublineages of M119, including our identi ed F1759, Z23420 and Z23266, contributed to the ancient gene pool of modern Tai-Kadai, Austronesian and southern Han Chinese [10].…”

“…Sublineages of O1b1a1a1a1b2a1a1-F2517 (23), O1b1a2a1-F1759 (10), O1a1a1b-Z23420 (15) and O1a1a2a1a-Z23266 (11) had undergone population expansion recently. All F2517 lineages were observed in Li people, which was consistent with a recent whole-genome sequencing study [55]. Chen et al found O1b1a1a was the dominant lineage in southern East Asians, which diverged from others 10998 years ago, and the F2517 sublineages were further divided into O1b1a1a1a1b2a1a1a and O1b1a1a1a1b2a1a1b clades at 2828 years ago [55].…”

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

“…Sublineages of O1b1a1a1a1b2a1a1-F2517 (23), O1b1a2a1-F1759 (10), O1a1a1b-Z23420 (15) and O1a1a2a1a-Z23266 (11) had undergone population expansion recently. All F2517 lineages were observed in Li people, which was consistent with a recent whole-genome sequencing study [64]. Chen et al found O1b1a1a was the dominant lineage in southern East Asians, which diverged from others 10998 years ago, and the F2517 sublineages were further divided into O1b1a1a1a1b2a1a1a and O1b1a1a1a1b2a1a1b clades at 2828 years ago [64].…”

“…All F2517 lineages were observed in Li people, which was consistent with a recent whole-genome sequencing study[64]. Chen et al found O1b1a1a was the dominant lineage in southern East Asians, which diverged from others 10998 years ago, and the F2517 sublineages were further divided into O1b1a1a1a1b2a1a1a and O1b1a1a1a1b2a1a1b clades at 2828 years ago[64]. Sun et al also found most sublineages of M119, including our identified F1759, Z23420 and Z23266, contributed to the ancient gene pool of modern Tai-Kadai, Austronesian and southern Han Chinese[10].We could also identify the shared paternal lineages among Li, southern Han and Gelao people in the distribution of M119 mutations.…”

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

“…We collected population data from all different HM ethnicity identities, which included the Miao Large-scale high-coverage WGS projects aiming at East Asians, including the ChinaMAP, NyuWa genomic resources, and other single population admixture history reconstructions focused on Li, Tibetan, Hui and others [5,6,47,48], have provided insights into fine-scale genetic stratification, genetic diversity, dispersal, and admixture landscape. However, HM-speaking populations were a significant lack in the early genomic projects, which are essential for better understanding the genetic diversity of South China and Mainland Southeast Asia.…”