Abstract
The uniparentally inherited mitochondrial DNA (mtDNA) is in the limelight for the past two decades, in studies relating to demographic history of mankind and in forensic kinship testing. In this study, human mtDNA hypervariable segments 1, 2, and 3 (HV1, HV2, and HV3) were analyzed in 248 unrelated Malay individuals in Peninsular Malaysia. Combined analyses of HV1, HV2, and HV3 revealed a total of 180 mtDNA haplotypes with 149 unique haplotypes and 31 haplotypes occurring in more than one individual. The genetic diversity was estimated to be 99.47%, and the probability of any two individuals sharing the same mtDNA haplotype was 0.93%. The most frequent mtDNA haplotype (73, 146, 150, 195, 263, 315.1C, 16140, 16182C, 16183C, 16189, 16217, 16274, and 16335) was shared by 11 (4.44%) individuals. The nucleotide diversity and mean of pair-wise differences were found to be 0.036063 ± 0.020101 and 12.544022 ± 6.230486, respectively.
Similar content being viewed by others
References
Anderson S, Bankier AT, Barrell BG, Bruijn MHL, Coulson AR, Drouin J, Eperon IC, Nierlich DP, Roe BA, Sanger F, Schreier PH, Smith AJH, Staden R, Young IG (1981) Sequence mitochondrial genome. Nature 290:457–464
Andrew RM, Kubacka I, Chinnery PF, Lightowlers RN, Turnbull DM, Howell N (1999) Reanalysis and revision of the Cambridge reference sequence for human mitochondrial DNA. Nat Genet 23:147
Pakendorf B, Stoneking M (2005) Mitochondrial DNA and human evolution. Annu Rev Genomics Hum Genet 6:165–183
Nik Hassan Suhaimi NAR (1998) The encyclopedia of Malaysia: early history, vol 4. Archipelago Press, Singapore, pp 6–11
Zafarina Z, William G (2004) Mitochondrial DNA profiling of modern Malay and Orang Asli populations in Peninsular Malaysia. Int Congr Ser 1261:428–430
Edinur HA, Zafarina Z, SpÎnola H, Nurhaslindawaty AR, Panneerchelvam S, Norazmi MN (2009) HLA polymorphism in six Malay subethnic groups in Malaysia. Hum Immunol 70:518–526
Wong HY, Tang JS, Budowle B, Allard MW, Syn CKC, Tan-Siew WV, Chow ST (2007) Sequence polymorphism of the mitochondrial DNA hypervariable regions I and II in 205 Singapore Malays. Legal Med 9:33–37
Maruyama S, Nohira-Koike C, Minaguchi K, Nambiar P (2010) mtDNA control region sequence polymorphisms and phylogenetic analysis of Malay population living in or around Kuala Lumpur in Malaysia. Int J Legal Med 124(2):165–170
Tajima F (1989) Statistical methods for testing the neutral mutation hypothesis by DNA polymorphism. Genetics 123:585–595
Stoneking M, Hedgecock D, Higuchi RG, Vigilant L, Erlich HA (1991) Population variation of human mtDNA control region sequences detected by enzymatic amplification and sequence-specific oligonucleotide probes. Am J Hum Genet 48:370–382
Excoffier L, Laval G, Schneider S (2006) Arlequin version 3.1: An integrated software package for population genetics data analysis. Computational and Molecular Population Genetics Lab (CMPG) Switzerland: Institute of Zoology, University of Berne
Syed HA (1979) Orang Melayu: Masalah dan masa depannya. Penerbit Adabi Kuala Lumpur, pp 1–3
Melton T (2004) Mitochondrial DNA heteroplasmy. Forensic Sci Rev 16:1
Forster L, Forster P, Gurney SMR, Spencer M, Huang C, Röhl A, Brinkmann B (2010) Evaluating length heteroplasmy in the human mitochondrial DNA control region. Int J Legal Med 124(2):133–143
Irwin JA, Saunier JL, Strouss KM, Diegoli TM, Sturk KA, O’Callaghan JE, Paintner CD, Hohoff C, Brinkmann B, Parsons TJ (2008) Mitochondrial control region sequences from a Vietnamese population sample. Int J Legal Med 122:257–259
Lee HY, Yoo JE, Park MJ, Chung U, Shin KJ (2006) Mitochondrial DNA control region sequences in Koreans: identification of useful variable sites and phylogenetic analysis for mtDNA data quality control. Int J Legal Med 120:5–14
Irwin JA, Saunier JL, Beh P, Strouss KM, Paintner CD, Parsons TJ (2009) Mitochondrial DNA control region variation in a population sample from Hong Kong, China. Forensic Sci Int 3(4):e119–e125
Zhang YJ, Xu QS, Zheng ZJ, Lin HY, Lee JB (2005) Haplotype diversity in mitochondrial DNA hypervariable region I, II and III in northeast China Han. Forensic Sci Int 149:267–269
Hill C, Soares P, Mormina M, Macaulay V, Clarke D, Blumbach PB, Vizuete-Forster M, Forster P, Bulbeck D, Oppenheimer S, Richards M (2007) A mitochondrial stratigraphy for Island Southeast Asia. Am J Hum Genetics 80:29–43
Tajima A, Sun CS, Pan IH, Ishida T, Saitou N, Horai S (2003) Mitochondrial DNA polymorphisms in nine aboriginal groups of Taiwan: implications for the population history of aboriginal Taiwanese. Hum Genet 113:24–33
Kivisild T, Tolk H, Parik J, Wang Y, Papiha S, Bandelt HJ, Villems R (2002) The emerging limbs and twigs of the East Asian mtDNA tree. Mol Bio Evol 19(10):1737–1751
Carracedo A, Bär W, Lincoln P, Mayr W, Morling N, Olaisen B, Schneider P, Budowle B, Brinkmann B, Gill P, Holland M, Tully G, Wilson M (2000) DNA commission of the international society for forensic genetics: Guidelines for mitochondrial DNA typing. Forensic Sci Int 110:79–85
Acknowledgments
Special thanks to the Ministry of Higher Education, Malaysia, for funding this research under the Fundamental Research Grant Scheme (203/PPSK/6171005).
Ethical standards
The conducted experiments comply with the current law practice in Malaysia.
Conflict of interest
The authors have no conflict of interest.
Author information
Authors and Affiliations
Corresponding author
Electronic supplementary material
Below is the link to the electronic supplementary material.
ESM 1
Electronic supplementary material (DOC 178 kb)
Rights and permissions
About this article
Cite this article
Nur Haslindawaty, A.R., Panneerchelvam, S., Edinur, H.A. et al. Sequence polymorphisms of mtDNA HV1, HV2, and HV3 regions in the Malay population of Peninsular Malaysia. Int J Legal Med 124, 415–426 (2010). https://doi.org/10.1007/s00414-010-0469-x
Received:
Accepted:
Published:
Issue Date:
DOI: https://doi.org/10.1007/s00414-010-0469-x