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Human Genetics

, Volume 137, Issue 2, pp 161–173 | Cite as

Genomic structure of the native inhabitants of Peninsular Malaysia and North Borneo suggests complex human population history in Southeast Asia

  • Chee-Wei Yew
  • Dongsheng Lu
  • Lian Deng
  • Lai-Ping Wong
  • Rick Twee-Hee Ong
  • Yan Lu
  • Xiaoji Wang
  • Yunus Yushimah 
  • Farhang Aghakhanian
  • Mokhtar Siti Shuhada 
  • Hoque Mohammad Zahirul 
  • Christopher Lok-Yung Voo
  • Thuhairah Abdul Rahman
  • Jong Bhak
  • Maude E. Phipps
  • Shuhua Xu
  • Yik-Ying Teo
  • Subbiah Vijay Kumar
  • Boon-Peng Hoh
Original Investigation

Abstract

Southeast Asia (SEA) is enriched with a complex history of peopling. Malaysia, which is located at the crossroads of SEA, has been recognized as one of the hubs for early human migration. To unravel the genomic complexity of the native inhabitants of Malaysia, we sequenced 12 samples from 3 indigenous populations from Peninsular Malaysia and 4 native populations from North Borneo to a high coverage of 28–37×. We showed that the Negritos from Peninsular Malaysia shared a common ancestor with the East Asians, but exhibited some level of gene flow from South Asia, while the North Borneo populations exhibited closer genetic affinity towards East Asians than the Malays. The analysis of time of divergence suggested that ancestors of Negrito were the earliest settlers in the Malay Peninsula, whom first separated from the Papuans ~ 50–33 thousand years ago (kya), followed by East Asian (~ 40–15 kya), while the divergence time frame between North Borneo and East Asia populations predates the Austronesian expansion period implies a possible pre-Neolithic colonization. Substantial Neanderthal ancestry was confirmed in our genomes, as was observed in other East Asians. However, no significant difference was observed, in terms of the proportion of Denisovan gene flow into these native inhabitants from Malaysia. Judging from the similar amount of introgression in the Southeast Asians and East Asians, our findings suggest that the Denisovan gene flow may have occurred before the divergence of these populations and that the shared similarities are likely an ancestral component.

Notes

Acknowledgements

This study is funded by Ministry of Science, Technology and Innovation (MOSTI) erBiotek Grant # 100-RM/BIOTEK 16/6/2 B (1/2011) and [100-RMI/GOV 16/6/2 (19/2011] awarded to HBP, VK, and MEP for supporting the experimental work. HBP received the FRGS/1/2015/ST03/UCSI/01/1 for supporting the data analysis. MEP and FA acknowledge human genomics grant from Tropical Medicine and Biology platform, Monash University Malaysia. We thank all the indigenous participants, JAKOA, and the Sabah state authorities for their full cooperation and assistance during the various field trips, the medical team from Faculty of Medicine Universiti Teknologi MARA, for their involvement during sample collection, and all staffs who assisted. L.P.W., R.T.H.O., and Y.Y.T. acknowledge support by the National Research Foundation, Prime Minister’s Office, Singapore under its Research Fellowship (NRF-RF-2010-05) and administered by the National University of Singapore. S.X. is Max–Planck Independent Research Group Leader and member of CAS Youth Innovation Promotion Association. S.X. gratefully acknowledges support by the National Natural Science Foundation of China (NSFC) Grants (91331204, 31525014, 91731303, 31771388, 31501011, and 31711530221), the Chinese Academy of Sciences (CAS) (XDB13040100 and QYZDJ-SSW-SYS009), and the Program of Shanghai Academic Research Leader (16XD1404700). JB was supported by the Industrial Strategic technology development program, 10040231, “Bioinformatics platform development for the next generation bioinformation analysis” funded by the Ministry of Knowledge Economy (MKE, Korea)” and 2014 Research Fund (1.150014.01) of UNIST (Ulsan National Institute of Science & Technology).

Compliance with ethical standards

Conflict of interest

The authors declare that there is no conflict of interest.

Supplementary material

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Copyright information

© Springer-Verlag GmbH Germany, part of Springer Nature 2018

Authors and Affiliations

  • Chee-Wei Yew
    • 1
  • Dongsheng Lu
    • 2
  • Lian Deng
    • 2
  • Lai-Ping Wong
    • 3
  • Rick Twee-Hee Ong
    • 3
  • Yan Lu
    • 2
  • Xiaoji Wang
    • 2
  • Yunus Yushimah 
    • 4
  • Farhang Aghakhanian
    • 5
    • 6
  • Mokhtar Siti Shuhada 
    • 4
  • Hoque Mohammad Zahirul 
    • 7
  • Christopher Lok-Yung Voo
    • 1
  • Thuhairah Abdul Rahman
    • 8
  • Jong Bhak
    • 9
    • 10
    • 11
  • Maude E. Phipps
    • 5
  • Shuhua Xu
    • 2
    • 12
    • 13
  • Yik-Ying Teo
    • 3
    • 14
    • 15
    • 16
    • 17
  • Subbiah Vijay Kumar
    • 1
  • Boon-Peng Hoh
    • 18
  1. 1.Biotechnology Research InstituteUniversiti Malaysia SabahKota KinabaluMalaysia
  2. 2.Max Planck Independent Research Group on Population Genomics, Chinese Academy of Sciences and Max Planck Society Partner Institute for Computational Biology, Shanghai Institutes for Biological SciencesChinese Academy of Sciences ShanghaiShanghaiChina
  3. 3.Saw Swee Hock School of Public HealthNational University of SingaporeSingaporeSingapore
  4. 4.Faculty of Medicine, Institute of Medical Molecular BiotechnologyUniversiti Teknologi MARASg BulohMalaysia
  5. 5.Jeffrey Cheah School of Medicine and Health SciencesMonash University MalaysiaSunwayMalaysia
  6. 6.Tropical Medicine and Biology Platform, Monash University MalaysiaSunwayMalaysia
  7. 7.Faculty of Medicine and Health SciencesUniversiti Malaysia SabahKota KinabaluMalaysia
  8. 8.Clinical Pathology Diagnostic Centre Research Laboratory, Faculty of MedicineUniversiti Teknologi MARASg BulohMalaysia
  9. 9.Personal Genomics InstituteGenome Research FoundationSuwonRepublic of Korea
  10. 10.GeromicsUlsanRepublic of Korea
  11. 11.Biomedical Engineering Department, The Genomics InstituteUNISTUlsanRepublic of Korea
  12. 12.School of Life Science and TechnologyShanghaiTech UniversityShanghaiChina
  13. 13.Collaborative Innovation Center of Genetics and DevelopmentShanghaiChina
  14. 14.NUS Graduate School for Integrative Science and EngineeringNational University of SingaporeSingaporeSingapore
  15. 15.Life Sciences Institute, National University of SingaporeSingaporeSingapore
  16. 16.Department of Statistics and Applied ProbabilityNational University of SingaporeSingaporeSingapore
  17. 17.Genome Institute of SingaporeAgency for Science, Technology and ResearchSingaporeSingapore
  18. 18.Faculty of Medicine and Health SciencesUCSI UniversityKuala LumpurMalaysia

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