Detecting Genetic Ancestry and Adaptation in the Taiwanese Han People

Yun Hua Lo, Hsueh Chien Cheng, Chia Ni Hsiung, Show Ling Yang, Han Yu Wang, Chia Wei Peng, Chun Yu Chen, Kung Ping Lin, Mei Ling Kang, Chien Hsiun Chen, Hou Wei Chu, Chiao Feng Lin, Mei Hsuan Lee, Quintin Liu, Yoko Satta, Cheng Jui Lin, Marie Lin, Shu Miaw Chaw, Jun Hun Loo, Chen Yang ShenWen Ya Ko*

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

6 Scopus citations

Abstract

The Taiwanese people are composed of diverse indigenous populations and the Taiwanese Han. About 95% of the Taiwanese identify themselves as Taiwanese Han, but this may not be a homogeneous population because they migrated to the island from various regions of continental East Asia over a period of 400 years. Little is known about the underlying patterns of genetic ancestry, population admixture, and evolutionary adaptation in the Taiwanese Han people. Here, we analyzed the whole-genome single-nucleotide polymorphism genotyping data from 14,401 individuals of Taiwanese Han collected by the Taiwan Biobank and the whole-genome sequencing data for a subset of 772 people. We detected four major genetic ancestries with distinct geographic distributions (i.e., Northern, Southeastern, Japonic, and Island Southeast Asian ancestries) and signatures of population mixture contributing to the genomes of Taiwanese Han. We further scanned for signatures of positive natural selection that caused unusually long-range haplotypes and elevations of hitchhiked variants. As a result, we identified 16 candidate loci in which selection signals can be unambiguously localized at five single genes: CTNNA2, LRP1B, CSNK1G3, ASTN2, and NEO1. Statistical associations were examined in 16 metabolic-related traits to further elucidate the functional effects of each candidate gene. All five genes appear to have pleiotropic connections to various types of disease susceptibility and significant associations with at least one metabolic-related trait. Together, our results provide critical insights for understanding the evolutionary history and adaption of the Taiwanese Han population.

Original languageEnglish
Pages (from-to)4149-4165
Number of pages17
JournalMolecular Biology and Evolution
Volume38
Issue number10
DOIs
StatePublished - 1 Oct 2021

Keywords

  • Taiwanese Han
  • adaptation
  • admixture
  • ancestry
  • natural selection

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