Paternal lineage affinity of the Malay subethnic and Orang Asli populations in Peninsular Malaysia


Peninsular Malaysia is populated by the Malays, Chinese, Indians, and Orang Asli. We have analyzed 17 Y-STRs loci for 243 randomly unrelated individuals, which include 153 Malays (7 Acheh, 13 Champa, 11 Rawa, 9 Kedah, 23 Minang, 15 Bugis, 43 Kelantan, 14 Jawa, and 18 Bugis) and 90 Orang Asli [54 Semang (16 Kensiu, 13 Lanoh, 25 Bateq); 30 Senoi (21 Semai, 9 Che Wong); and 6 Proto-Malay (6 Orang Kanaq)] from selected settlements in Peninsular Malaysia using the AmpFlSTR Yfiler™ kit (Applied Biosystems™). The overall haplotype diversity is 0.9966, i.e., 0.9984 for the Malays and 0.9793 for the Orang Asli. A total of 158 haplotypes (65.02%) were individually unique. The p value and pairwise Rst analysis was calculated to show the genetic structure of the samples with other world populations (from YHRD website). Based on the Y-STR data, Champa, Acheh, Kedah, Minang, and Kelantan are clustered together. Lanoh and Kensiu (Semang) are very closely related, suggesting similar paternal ancestry. Jawa Malays and Indonesian Java, plus the Bugis Malays and Australian Aborigines shared high degree of paternal lineage affinity. This study presents data for very precious relict groups, who are the earliest inhabitants of Peninsular Malaysia.

This is a preview of subscription content, log in to check access.

Change history

  • 13 November 2017

    The original version of this article contains an error. The Author Abd Rashid Nur Haslindawaty has been added as to the above author group as third author. The original article was corrected.


  1. 1.

    Milner A (2010) The Malays (the peoples of South-East Asia and the Pacific). John Wiley and Sons Ltd, United Kingdom

  2. 2.

    Halim-Fikri H, Etemad A, Latif AZA, Merican AF, Baig AA, Annuar AA, Ismail E, Salahshourifar I, Liza-Sharmini AT, Ramli M, Shah MI, Johan MF, Hassan NNN, Abdul-Aziz NM, Noor NHM, Nur-Shafawati AR, Hassan R, Bahar R, Zain RB, Yusoff SM, Yusoff S, Tan SG, Thong M-K, Wan-Isa H, Abdullah WZ, Mohamed Z, Latiff ZA, Zilfalil BA (2015) The first Malay database toward the ethnic-specific target molecular variation. BMC Res Notes 8(1):176.

  3. 3.

    Bellwood P (1997) Prehistory of the Indo-Malaysian Archipelago. Univ. of Hawaii Press, Honolulu

    Google Scholar 

  4. 4.

    Nicholas C (2006) In: Hood S (ed) The Orang Asli: origins, identity and classification. Archipelago Press, Kuala Lumpur, pp 20–21

    Google Scholar 

  5. 5.

    JHEOA (2002) Kehidupan, budaya dan pantang larang orang asli. Department of Orang Asli, Kuala Lumpur

    Google Scholar 

  6. 6.

    Peakall R, Smouse PE (2006) GENALEX 6: genetic analysis in Excel. Population genetic software for teaching and research. Mol Ecol Notes 6:288–295

    Article  Google Scholar 

  7. 7.

    Nei M (1987) Molecular evolutionary genetics. Columbia University Press, New York

    Google Scholar 

  8. 8.

    Kayser M, Knijff PD, Dieltjes P, Kraweczak M, Nagy M, Zerjal T et al (1997) Applications of microsatellite-based Y-chromosome haplotyping. Electrophoresis 18:1602–1607

    CAS  Article  Google Scholar 

  9. 9.

    Kayser M, Caglia A, Corach D, Fretwell N, Gehrig C, Graziosi G et al (1997) Evaluation of Y-chomosomal STRs: a multicenter study. Int J Legal Med 110:125–133 41-49

    CAS  Article  Google Scholar 

  10. 10.

    Chang YM, Perumal R, Keat PY, Kuehn DLC (2007) Haplotype diversity of 16 Y-chromosomal STRs in three main ethnic populations (Malays, Chinese and Indians) in Malaysia. Forensic Sci Int 167:70–76

    CAS  Article  Google Scholar 

  11. 11.

    Willuweit S, Roewer L (2015) The new Y chromosome haplotype reference database. Forensic Sci Int Genet 15:43–48

    CAS  Article  Google Scholar 

  12. 12.

    Hatin WI, Nur-Shafawati AR, Zahri M-K, Xu S, Jin L, Tan S-G et al (2011) Population genetic structure of Peninsular Malaysia Malay sub-ethnic groups. PLoS One 6:e18312

  13. 13.

    Wink A (2004) Indo-Islamic society: 14th–15th centuries. Oxford University Press, Oxford, England, UK

  14. 14.

    Schwerdtner Máñez K, Ferse SCA (2010) The history of Makassan trepang fishing and trade. PLoS ONE 5(6):e11346

  15. 15.

    Norhalifah HK, Syaza FH, Chambers GK, Edinur HA (2016) The genetic history of Peninsular Malaysia. Gene 586:129–135

    CAS  Article  Google Scholar 

  16. 16.

    Bellwood P (2005) First farmers: the origins of agricultural societies. Blackwell, Victoria

    Google Scholar 

  17. 17.

    Tumonggor MK, Karafet TM, Hallmark B, Lansing JS, Sudoyo H, Hammer MF et al (2013) The Indonesian archipelago: an ancient genetic highway linking Asia and the Pacific. J Hum Genet 58:165–173

    CAS  Article  Google Scholar 

  18. 18.

    Macaulay V, Hill C, Achilli A, Rengo C, Clarke D, Meehan W et al (2005) Single, rapid coastal settlement of Asia revealed by analysis of complete mitochondrial genomes. Science 308:1034

    CAS  Article  Google Scholar 

  19. 19.

    Nicholas C (2000) The Orang Asli and the contest for resources: indigenous politics, development and identity in Peninsular Malaysia. International Work Group on Indigenous Affairs (IWGIA), Denmark

    Google Scholar 

  20. 20.

    JHEOA (2008) Data Maklumat Asas Jabatan Hal Ehwal Orang Asli Tahun. Bahagian Penyelidikan dan Perancangan Jabatan Hal Ehwal Orang Asli, Kuala Lumpur

  21. 21.

    Baer A (1999) Health, disease and survival: a biomedical and genetic analysis of the Orang Asli of Malaysia COAC, Kuala Lumpur

  22. 22.

    Hill C, Soares P, Mormina M, Macaulay V, Meehan W, Blackburn J, Clarke D, Raja JM, Ismail P, Bulbeck D, Oppenheimer S, Richards M (2006) Phylogeography and ethnogenesis of aboriginal southeast Asians. Mol Biol Evol 23(12):2480–2491

  23. 23.

    Andaya LY (2001) The search for the ‘origins’ of Melayu. J Southeast Asian Stud 32:315–330

    Article  Google Scholar 

  24. 24.

    Chang YM, Swaran Y, Phoon YK, Sothirasan K, Sim HT, Lim KB et al (2009) Haplotype diversity of 17 Y-chromosomal STRs in three native Sarawak populations (Iban, Bidayuh and Melanau) in East Malaysia. Forensic Sci Int Genet 3:e77–e80

    CAS  Article  Google Scholar 

  25. 25.

    Poetsch M, Bajanowski T, Pfeiffer H (2012) The publication of population genetic data in the International Journal of Legal Medicine: guidelines. Int J Legal Med 126:489–490

    Article  Google Scholar 

Download references


The authors acknowledge the Department of Orang Asli Development (JAKOA), Ministry of Higher Education Malaysia and Universiti Sains Malaysia (Long-Term Research Grant Scheme: 304/PPSK/6150115/U132) (Orang Asli samples), and FRGS Top Down 203/PPSK/ 249 6171005 (Malay samples).

Author information



Corresponding author

Correspondence to Zainuddin Zafarina.

Ethics declarations

Informed consents were obtained from each participant before the blood samples were collected. Ethical approvals were obtained from Universiti Teknologi MARA and Universiti Sains Malaysia Human Ethics Committee (FWA Reg. No: 00007718; IRB Reg. No: 00004494) with Ref. No: USMKK/PPPJEPeM [254.4.129/].

Additional information

The original version of this article was revised: The original version of this article contains an error. The Author Abd Rashid Nur Haslindawaty has been added as to the above author group as third author.

Electronic supplementary material


(PDF 199 kb)

Rights and permissions

Reprints and Permissions

About this article

Verify currency and authenticity via CrossMark

Cite this article

SharifahNany RahayuKarmilla, S., Aedrianee, A.R., Nur Haslindawaty, A.R. et al. Paternal lineage affinity of the Malay subethnic and Orang Asli populations in Peninsular Malaysia. Int J Legal Med 132, 1087–1090 (2018).

Download citation


  • Y-STR
  • Malay
  • Orang Asli
  • Peninsular Malaysia