Human Genetics

, Volume 133, Issue 9, pp 1169–1185 | Cite as

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
Original Investigation

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 genome-wide 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.

Supplementary material

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Copyright information

© Springer-Verlag Berlin Heidelberg 2014

Authors and Affiliations

  • Lian Deng
    • 1
  • Boon Peng Hoh
    • 2
  • Dongsheng Lu
    • 1
  • Ruiqing Fu
    • 1
  • Maude E. Phipps
    • 3
  • Shilin Li
    • 4
  • Ab Rajab Nur-Shafawati
    • 5
  • Wan Isa Hatin
    • 5
  • Endom Ismail
    • 6
  • Siti Shuhada Mokhtar
    • 2
  • Li Jin
    • 4
  • Bin Alwi Zilfalil
    • 7
  • Christian R. Marshall
    • 8
  • Stephen W. Scherer
    • 8
    • 9
  • Fahd Al-Mulla
    • 10
  • Shuhua Xu
    • 1
  1. 1.Max Planck Independent Research Group on Population Genomics, Chinese Academy of Sciences and Max Planck Society (CAS-MPG) Partner Institute for Computational Biology (PICB), Shanghai Institutes for Biological SciencesChinese Academy of SciencesShanghaiChina
  2. 2.Faculty of Medicine, Institute of Medical Molecular Biotechnology, Jalan HospitalUniversiti Teknologi MARASungai BulohMalaysia
  3. 3.Jeffrey Cheah School of Medicine and Health SciencesMonash University MalaysiaSelangorMalaysia
  4. 4.Ministry of Education (MOE) Key Laboratory of Contemporary Anthropology, School of Life Sciences and Institutes of Biomedical SciencesFudan UniversityShanghaiChina
  5. 5.Human Genome Center, School of Medical SciencesUniversiti Sains MalaysiaKelantanMalaysia
  6. 6.Faculty of Science and Technology, School of Biosciences and BiotechnologyUniversiti Kebangsaan MalaysiaBangiMalaysia
  7. 7.Department of Pediatrics, School of Medical SciencesUniversiti Sains MalaysiaKelantanMalaysia
  8. 8.The Centre for Applied GenomicsThe Hospital for Sick ChildrenTorontoCanada
  9. 9.McLaughlin Centre and Department of Molecular GeneticsUniversity of TorontoTorontoCanada
  10. 10.Department of Pathology, Faculty of MedicineKuwait UniversitySafatKuwait

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