Forensic and genetic characterization of mtDNA from Pathans of Pakistan

Abstract

Complete mitochondrial control region data were generated for 230 unrelated Pathans from North West Frontier Province and Federally Administered Tribal Areas of Pakistan. To confirm data quality and to explore the genetic structure of Pathans, mitochondrial DNA haplogroup affiliation was determined by shared haplogroup-specific polymorphisms in the control region and by the analysis of diagnostic coding region single-nucleotide polymorphisms using a multiplex system for the assignment of eight haplogroups: M, N1'5, W, R, R0, T, J, and U. Sequence comparison revealed that 193 haplotypes were defined by 215 variable sites when major insertions were ignored at nucleotide positions 16193, 309, and 573. From a phylogenetic perspective, Pathans have a heterogeneous origin, displaying a high percentage of West Eurasian haplogroups followed by haplogroups native to South Asia and a small fraction from East Asian lineages. In population comparisons, this ethnic group differed significantly from several other ethnic groups from Pakistan and surrounding countries. These results suggest that frequency estimates for mtDNA haplotypes should be determined for endogamous ethnic groups individually instead of pooling data for these subpopulations into a single dataset for the Pakistani population. Data presented here may contribute to the accuracy of forensic mtDNA comparisons in the Pathans of Pakistan.

West Eurasian mtDNA lineages in India: an insight into the spread of the Dravidian language and the origins of the caste system

“…Apart from complete sequence phylogeny, we noticed that the matches of Indian H2a1, H2a1a, H2b, H5a1, H6a1a, H7b, H9, H14a, H15a1a1, HV6, HV12b1, HV12b1a, U3, U4, and U5 mtDNA HVS-I haplotypes were found in the populations of the Caucasus, Armenia, Anatolia, Turkey, Iran, Iraq, Georgia, Jordan, Syria, Arabia Peninsula, Kuwait, Pakistan, central Asia, Tajikistan, Uzbekistan, Siberia, Slovaks, and Russia (Comas et al 1998Macaulay et al 1999;Richards et al 2000;Nasidze and Stoneking 2001;Loogväli et al 2004;Nasidze et al 2004;Quintana-Murci et al 2004;Roostalu et al 2007;Abu-Amero et al 2008;Malyarchuk et al 2008;Nasidze et al 2008;Rakha et al 2011;Al-Zahery et al 2011;Terreros et al 2011;Derenko et al 2013).…”

“…W3a1 and W3a1b lineages are sparsely distributed in India. Notably, W3a1b lineages are found specifically in India and Pakistan (Quintana-Murci et al 2004;Rakha et al 2011). Subclade W3a2 is very rare and only three complete sequences have been reported so far (Olivieri et al 2013).…”

“…The near eastern origin R0 haplogroup-derived R0a and R0a2 lineages were proposed based on their presence in the Arabian Peninsula, Iran, Iraq, Kuwait and Pakistan (Quintana-Murci et al 2004;Abu-Amero et al 2008;Rakha et al 2011;Al-Zahery et al 2011;Scheible et al 2011), whereas in India, only R0a2 has been found mostly in Muslim communities from Gujarat and Tamil Nadu, and generally absent or rare in non-Muslim Indian populations. Surprisingly, we have detected the R0a2 lineages in Brahmin populations from northern India-Uttar Pradesh (supplementary table S1) which clustered phylogenetically with Iranian and Somalian samples (Cerný et al 2011;Derenko et al 2013).…”

Haplogrouping mitochondrial DNA sequences in Legal Medicine/Forensic Genetics

“…In a similar way, one could fine-classify the control-region profile PK-044 from [16] allocated to haplogroup W3. This sample shows four variants 16209C, 16255A, 119C, and 185A not covered by the motif of haplogroup W3.…”

“…To exemplify these strategies, consider the control-region profiles PK-187, PK-189, PK-249 of [16], all sharing the rare variant 16179del, which were allocated by the authors to haplogroup M30 but not classified further. In order to explore the control-region variation within this haplogroup, one could enter the Website http://www.ianlogan.co.uk/ sequences_by_group/m30_genbank_sequences.htm and immediately find a complete mtDNA sequence (GenBank accession number AY922256) within haplogroup M30d1 listed with this particular deletion.…”