Mitochondrial DNA analysis of five Pathan tribes from Pakistan

Paper Details

Research Paper 01/05/2016
Views (257) Download (3)
current_issue_feature_image
publication_file

Mitochondrial DNA analysis of five Pathan tribes from Pakistan

Sadia Tabassum, Habib Ahmad, Muhammad Ilyas, Ikram Muhammad, Amanda Owings, Hongjie Lee
Int. J. Biosci.8( 5), 262-273, May 2016.
Certificate: IJB 2016 [Generate Certificate]

Abstract

Substantial genetic diversity exists in Pakistani human population and understanding the evolution of this diversity is complicated due to several waves of migration from populations in the North and Northwest. Pathans are one of the largest ethnic groups of Pakistan inhabiting the vast geographical areas, specifically the northwestern part. In the present study, we assessed the extent of genetic diversity using mtDNA sequence analysis of HVI (Hyper variable I) control region of the Pathan populations of Mardan and Charsada districts. A total of 165 buccal swabs were collected from five major populations of the two geographically adjacent districts, Charsada and Mardan. Mitochondrial control region HVI data was generated for all the samples. mtDNA haplogroups were assigned to each sample using a phylotree (www.phylotree.org). Principle Coordinate (PCoA) plot was generated by combining our data set with other published datasets from neighboring populations of central Asia, Middle East, Europe and South Asia. The most frequent mtDNA HVI macro haplogroups R (63.4%), M (26.8%) and N (8.6%) were observed among Pathan populations. Some novel mitochondrial haplogroups (mtDNA Hgs) of M and R sub-clades have also been detected that had not been observed in previous investigation of Pathans. The clustering pattern when compared on the basis of mitochondrial HVI data sets of different neighboring populations depicts less female mediated gene flow among populations. In addition, the mitochondrial genetic structure of some sub-populations may be influenced by Turkish invasion.

VIEWS 9

Abu-Amero KK, José ML, Vicente MC, Ana MG. 2008. Mitochondrial DNA structure in the Arabian Peninsula. BMC Evolutionary Biology 8, 45. http://dx.doi.org/10.1186/1471-2148-8-45

Andrews RM, Kubacka I, Chinnery PF, Lightowlers RN, Turnbull DM, Howell N. 1999. Reanalysis and revision of the Cambridge reference sequence for human mitochondrial DNA. Nature Genetics 23(2), 147. http://dx.doi.org/10.1038/13779

Caroe O. 1984. The  Pathans:  500 B.C.-A.D.  1957. (Oxford in Asia Historical Reprints). Oxford University Press.1976.

Caroe O. 1984. The Pathans: 500 B.C.-A.D. 1957 (Oxford in Asia Historical Reprints). Oxford University Press.1976.

Comas D, Calafell F, Mateu E, Pe’rez-Lezaun A, Bertranpetit J. 1996. Geographic Variation in Human Mitochondrial DNA Control Region Sequence: The Population History of Turkey and its Relationship to the European Populations. Molecular Biology and Evolution 13(8), 1067-1077.

Derenko M, Malyarchuk B, Bahmanimehr A, Denisova G, Perkova M, Farjadian S, Yepiskoposyan L. 2013. Complete Mitochondrial DNA Diversity in Iranians. PLOS One 8(11), e80673. http://dx.doi.org/10.1371/journal.pone.0080673

Elahi S. 1996. Sayyid. Encyclopedia of world cultures. Encyclopedia.com. 29 Mar. 2016 http://www.encyclopedia.com/topic/Sayyid.aspx#1

Excoffier L, Lischer HEL. 2010. Arlequin suite ver 3.5: A new series of programs to perform population genetics analyses under Linux and Windows. Molecular Ecology Resources 10, 564-567. http://dx.doi.org/10.1111/j.1755-0998.2010.02847.x

Hall TA. 1999. BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT Nucleic Acids Symposium Series 41, 95-98.

Hayat S, Akhter T, Siddiqi MH, Rakha A, Haider N, Tayyab M, Abbas G, Ali A, Bokhari SYA, Tariq MA, Khan FM. 2015. Mitochondrial DNA Control region sequences study in Saraiki population from Pakistan. Legal Medicine 17, 140-144.

Hunley KL, Healy ME, Long JC. 2009. The Global Pattern of Gene Identity Variation Reveals a History of Long-Range Migrations, Bottlenecks, and Local Mate Exchange: Implications for Biological Race. American Journal of physical Anthropology 139, 35– 46. http://dx.doi.org/10.1002/ajpa.20932

Irwin J, Saunier J, StroussK, Paintner C, Diegoli T, Sturk K, Kovatsi L, Brandstatter A, Cariolou MA, Parson W, Parsons TJ. 2008. Mitochondrial control region sequences from northern Greece and Greek Cypriots. International Journal of Legal Medicine 122(1), 87-8. http://dx.doi.org/10.1016/j.fsigen.2014.06.013

Kayser M, Brauer S, Weiss G, Schiefenhövel W, Underhill P, Shen P, Oefner P, Tommaseo-Ponzetta M, Stoneking M. 2003. Reduced Y-chromosome, but not mtDNA, diversity in human populations from West New Guinea. American Journal of Human Genetics 72, 281–302. http://dx.doi.org/10.1086/346065

Kivisild T, Rootsi  S, Metspalu M, Mastana S, Kaldma K, Parik J,  Metspalu E, Adojaan M, Tolk HV, Stepanov V, Gölge M, Usanga E, Papiha SS, Cinnioğlu C, King R, Cavalli-Sforza L, Underhill PA, Villems R. 2003. The Genetic Heritage of the Earliest Settlers Persists Both in Indian Tribal and Caste Populations. American Journal of Human Genetics 72(2), 313–332. http://dx.doi.org/10.1086/346068

Lott MT, Leipzig JN, Derbeneva O, Xie HM, Chalkia D, Sarmady M, Procaccio V, Wallace DC. 2013. mtDNA variation and analysis using MITOMAP and MITOMASTER. Current Protocols in Bioinformatics 1(123), 1-26.http://dx.doi.org/10.1002/0471250953

Malhi RS, Cybulski JS, Tito RY, Johnson J, Harry H, Dan C. 2010. Brief communication: mitochondrial haplotype C4c confirmed as a founding genome in the Americas. American Journal of Physical Anthropology 141(3), 494-7. http://dx.doi.org/10.1002/ajpa.21238

Marisi AIDAR, Sergio  Roberto Peres LINE. 2007. A simple and cost–effective protocol for DNA isolation from buccal epithelial cells. Brazilian Dental Journal 18(2), 148-152. http://dx.doi.org/10.1590/S010364402007000200012

McElreavey K, Quintana-Murci L. 2005. A population genetics perspective of the Indus Valley through uniparentally-inherited markers. Annals of Human Biology 32, 154–162.

Metspalu M, Kivisild T, Metspalu E, Parik J, Hudjashov G, Kaldma K, Serk P, Karmin M,Behar DM, Gilbert MT, Endicott P, Mastana S, Papiha SS, Skorecki K, Torroni A, Villems R. 2004. Most of the extant mtDNA boundaries in South and Southwest Asia were likely shaped during the initial settlement of Eurasia by anatomically modern humans. BMC Genetics 5(1), 26. http://dx.doi.org/10.1186/1471-2156-5-26

Nei M. 1987. Molecular Evolutionary Genetics, Columbia University Press, New York.

Peakall R, Smouse PE. 2006. GENALEX 6: genetic analysis in Excel. Population genetic software for teaching and research. Molecular Ecology Notes 6, 288-295. http://dx.doi.org/10.1111/j.1471-8286.2005.01155.x

Qamar R, Ayub Q, Khaliq S, Mansoor A, Karafet T, Mehdi SQ, Hammer MF. 1999. African and Levantine origins of Pakistani YAP+ Y chromosomes. Human Biology 71, 745–755.

Qamar R, Ayub Q, Mohyuddin A, Helgason A, Mazhar K, Mansoor A, Zerjal T, Tyler-Smith C, Mehdi SQ. 2002. Y-Chromosomal DNA Variation in Pakistan. American Journal of Human Genetics 70(5), 1107–24. http://dx.doi.org/10.1086/339929

Quintana-Murci L, Chaix R, Wells RS, Behar DM, Sayar H, Scozzari R, Rengo C, Al Zahery N, Semino O, Santachiara Benerecetti AS, Coppa A, Ayub Q, Mohyuddin A, Tyler-Smith C, Qasim Mehdi S, Torroni A, McElreavey K. 2004. Where west meets east: the complex mtDNA landscape of the southwest and Central Asian corridor. American Journal of Human Genetics 74, 827–845.

Rajkumar R, Banerjee J, Gunturi HB, Trivedi R, Kashyap VK. 2005. Phylogeny and antiquity of M macrohaplogroup inferred from complete mt DNA sequence of Indian specific lineages, BMC Evolutionary Biology 5, 26. http://dx.doi.org/10.1186/1471-2148-5-26

Rakha A, Shin KJ, Yoon JA, Kim NY, Siddique MH, Yang IS, Yang WI, Lee HY. 2011. Forensic and genetic characterization of mtDNA from Pathans of Pakistan. International Journal of Legal Medicine 125(6), 841–8. http://dx.doi.org/10.1007/s00414-010-0540-7

Rosenberg NA, Mahajan S, Gonzalez-Quevedo C, Blum MG, Nino-Rosales L, Ninis V, Das P, Hegde M, Molinari L, Zapata G, Weber JL, Belmont JW, Patel PI.  2006.   Low levels of genetic divergence across geographically and linguistically diverse populations from India. PLOS Genet 2, e215 http://dx.doi.org/ 10.1371/journal.pgen.0020215

Siddiqi HS, Akhter T, Rakha A, Abbas G, Ali A, Haider N, Ali A, Hayat S, Masooma S, Ahmad J, Tariq MA, Oven M, Khan FM. 2015. Genetic Characterization of Makrani People of Pakistan from mitochondrial DNA control-region data. Legal Medicine 17, 134-139.

Van Oven M, Kayser M. 2009. Updated comprehensive phylogenetic tree of global human mitochondrial DNA variation. Hum Mutatation 30(2), E386-E394. http://www.phylotree.org.

Wolpert S. 2000. A new history of India. New York: Oxford University Press.

Ye Y, Gao J, Fan G, Liao L, Hou Y.  2015. Population genetics for 23 Y-STR loci in Tibetan in China and confirmation of DYS448 null allele. Forensic Science International Genetics 16, e7–e10. http://dx.doi.org/10.1016/j.fsigen.2014.11.018