The population genomic landscape of human genetic structure, admixture history and local adaptation in Peninsular Malaysia

Lian Deng, Boon Peng Hoh, Dongsheng Lu, Ruiqing Fu, Maude E. Phipps, Shilin Li, Ab Rajab Nur-Shafawati, Wan Isa Hatin, Endom Ismail, Siti Shuhada Mokhtar, Li Jin, Bin Alwi Zilfalil, Christian R. Marshall, Stephen W. Scherer, Fahd Al-Mulla, Shuhua Xu

Research output: Contribution to journalArticle

14 Citations (Scopus)

Abstract

Peninsular Malaysia is a strategic region which might have played an important role in the initial peopling and subsequent human migrations in Asia. However, the genetic diversity and history of human populations - especially indigenous populations - inhabiting this area remain poorly understood. Here, we conducted a genomewide study using over 900,000 single nucleotide polymorphisms (SNPs) in four major Malaysian ethnic groups (MEGs; Malay, Proto-Malay, Senoi and Negrito), and made comparisons of 17 world-wide populations. Our data revealed that Peninsular Malaysia has greater genetic diversity corresponding to its role as a contact zone of both early and recent human migrations in Asia. However, each single Orang Asli (indigenous) group was less diverse with a smaller effective population size (Ne) than a European or an East Asian population, indicating a substantial isolation of some duration for these groups. All four MEGs were genetically more similar to Asian populations than to other continental groups, and the divergence time between MEGs and East Asian populations (12,000-6,000 years ago) was also much shorter than that between East Asians and Europeans. Thus, Malaysian Orang Asli groups, despite their significantly different features, may share a common origin with the other Asian groups. Nevertheless, we identified traces of recent gene flow from non-Asians to MEGs. Finally, natural selection signatures were detected in a batch of genes associated with immune response, human height, skin pigmentation, hair and facial morphology and blood pressure in MEGs. Notable examples include SYN3 which is associated with human height in all Orang Asli groups, a height-related gene (PNPT1) and two blood pressure-related genes (CDH13 and PAX5) in Negritos. We conclude that a long isolation period, subsequent gene flow and local adaptations have jointly shaped the genetic architectures of MEGs, and this study provides insight into the peopling and human migration history in Southeast Asia.

Original languageEnglish
Pages (from-to)1169-1185
Number of pages17
JournalHuman Genetics
Volume133
Issue number9
DOIs
Publication statusPublished - 2014

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Metagenomics
Genetic Structures
Malaysia
Medical Genetics
Human Migration
History
Gene Flow
Population
Genes
Blood Pressure
Skin Pigmentation
Southeastern Asia
Genetic Selection
Population Density
Population Groups
Ethnic Groups
Hair
Single Nucleotide Polymorphism

ASJC Scopus subject areas

  • Genetics(clinical)
  • Genetics

Cite this

The population genomic landscape of human genetic structure, admixture history and local adaptation in Peninsular Malaysia. / Deng, Lian; Hoh, Boon Peng; Lu, Dongsheng; Fu, Ruiqing; Phipps, Maude E.; Li, Shilin; Nur-Shafawati, Ab Rajab; Hatin, Wan Isa; Ismail, Endom; Mokhtar, Siti Shuhada; Jin, Li; Zilfalil, Bin Alwi; Marshall, Christian R.; Scherer, Stephen W.; Al-Mulla, Fahd; Xu, Shuhua.

In: Human Genetics, Vol. 133, No. 9, 2014, p. 1169-1185.

Research output: Contribution to journalArticle

Deng, L, Hoh, BP, Lu, D, Fu, R, Phipps, ME, Li, S, Nur-Shafawati, AR, Hatin, WI, Ismail, E, Mokhtar, SS, Jin, L, Zilfalil, BA, Marshall, CR, Scherer, SW, Al-Mulla, F & Xu, S 2014, 'The population genomic landscape of human genetic structure, admixture history and local adaptation in Peninsular Malaysia', Human Genetics, vol. 133, no. 9, pp. 1169-1185. https://doi.org/10.1007/s00439-014-1459-8
Deng, Lian ; Hoh, Boon Peng ; Lu, Dongsheng ; Fu, Ruiqing ; Phipps, Maude E. ; Li, Shilin ; Nur-Shafawati, Ab Rajab ; Hatin, Wan Isa ; Ismail, Endom ; Mokhtar, Siti Shuhada ; Jin, Li ; Zilfalil, Bin Alwi ; Marshall, Christian R. ; Scherer, Stephen W. ; Al-Mulla, Fahd ; Xu, Shuhua. / The population genomic landscape of human genetic structure, admixture history and local adaptation in Peninsular Malaysia. In: Human Genetics. 2014 ; Vol. 133, No. 9. pp. 1169-1185.
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