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Y-Chromosomal DNA Variation in Pakistan
Open accessAbstract
Eighteen binary polymorphisms and 16 multiallelic, short-tandem-repeat (STR) loci from the nonrecombining portion of the human Y chromosome were typed in 718 male subjects belonging to 12 ethnic groups of Pakistan. These identified 11 stable haplogroups and 503 combination binary marker/STR haplotypes. Haplogroup frequencies were generally similar to those in neighboring geographical areas, and the Pakistani populations speaking a language isolate (the Burushos), a Dravidian language (the Brahui), or a Sino-Tibetan language (the Balti) resembled the Indo-European-speaking majority. Nevertheless, median-joining networks of haplotypes revealed considerable substructuring of Y variation within Pakistan, with many populations showing distinct clusters of haplotypes. These patterns can be accounted for by a common pool of Y lineages, with substantial isolation between populations and drift in the smaller ones. Few comparative genetic or historical data are available for most populations, but the results can be compared with oral traditions about origins. The Y data support the well-established origin of the Parsis in Iran, the suggested descent of the Hazaras from Genghis Khan's army, and the origin of the Negroid Makrani in Africa, but do not support traditions of Tibetan, Syrian, Greek, or Jewish origins for other populations.
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TL;DR
Y-chromosome binary and STR markers in 718 Pakistani males from 12 ethnic groups identify 11 haplogroups and 503 haplotypes, with frequencies broadly similar to neighboring regions but substantial population substructure. The Y data support Iranian origin of the Parsis, Mongolian/Genghis Khan–related descent of the Hazaras, and an African contribution to the Negroid Makrani, but not Tibetan, Syrian, Greek, or Jewish origins for other tested populations.
Key findings
- Among 718 males, 18 binary polymorphisms and 16 Y-STRs identified 11 stable haplogroups and 503 combination binary-marker/STR haplotypes; 5 haplogroups accounted for 92% of the sample.
- Haplogroup frequencies were generally similar to neighboring areas, and the language-isolate Burusho, Dravidian-speaking Brahui, and Sino-Tibetan-speaking Balti resembled the Indo-European-speaking majority; median-joining networks nevertheless showed population-specific clusters and substructuring.
- Admixture estimates supported external contributions for Hazaras from Mongolia (Long’s WLS .67, mR .52, mρ .41), Kalash from Greece (.4, .32, .23), Negroid Makrani from sub-Saharan Africa (.12, .12, .13), and Parsis from Iran (1.21, 1.06, 1), but not for Baluch from Syria, Balti from Tibet, Burusho/Pathan from Greece, or Kashmiri/Pathan from Jews (estimates 0 or negative).
- BATWING TMRCA estimates included Pakistani haplogroup 28 at ~7,000 years (95% CI 4,000–14,000), the Parsi-specific haplogroup 28 cluster at 1,800 years (600–4,500), and Hazara-specific haplogroup 1 and 10 clusters at 400 years (120–1,200) and 100 years (6–600), respectively.
Methods
- The study analyzed 718 unrelated male subjects from 12 ethnic groups of Pakistan; DNA was extracted from Epstein-Barr virus–transformed lymphoblastoid cell lines, with informed consent obtained.
- Samples were typed for 18 binary Y-chromosome markers (15 SNPs, an Alu insertion, a LINE1 insertion, and the 12f2 deletion) and 16 multiallelic Y-STR loci.
- Analyses included principal-components analysis, admixture estimation by Long’s weighted least-squares, mR, and mρ, AMOVA/population pairwise F_ST, median-joining networks, and BATWING TMRCA estimation.
Limitations
- The paper states that some population samples were small (e.g., Balti n=13, Kashmiri n=12, Hazara n=23), that origin conclusions assume modern source populations are representative of ancient populations, and that BATWING confidence intervals account for mutation-rate, growth, and subdivision uncertainty but not generation-time uncertainty.
- Evident from the text: the Punjabi-speaking majority was not analyzed, only 12 ethnic groups were included, some haplogroups were rare or absent (with F_ST set to 1 in some pairwise comparisons), and admixture estimates could be negative or zero, indicating limited resolution.
- The study uses only Y-chromosome data, so it captures male-specific history and cannot by itself resolve maternal or autosomal contributions; the authors note that mitochondrial DNA and other loci would help clarify histories such as those of the Negroid Makrani and Balti.
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73 Own result · 38 Own interpretation · 10 Check pending · 7 No full text of the sources · 6 Not checked yet · 6 Own method · 5 Sources not found · 1 No basis given
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“haplogroup 3 was present in all except the Hazaras”
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“The diversity of Y-STR haplotypes (table 4) was lowest for the Hazara (0.893) as suggested by previous analyses (Ayub et al. 2000).”
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- Check pendingcites Ayub et al. 2000 source
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“The remaining haplotypes were shared by 2-18 individuals (details are given in the online-only supplementary table).”
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“Southwestern populations show higher frequencies of hg 9 and the YAP + haplogroups 21 and 8 than northeastern populations (figs. 1 D-E )”
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“Clusters of Kalash, Burusho, and-to a lesser degree-Baluch chromosomes are also evident”
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“The Hazaras of Pakistan have a Mongol origin (Qamar et al. 2002)”
From The Genetic Legacy of the Mongols (2003) · cites this paper as Qamar et al. 2002
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Metadata
- Authors
- Qamar, R., Ayub, Q., Mohyuddin, A., Helgason, A., Mazhar, K., Mansoor, A., Zerjal, T., Tyler-Smith, C., & Mehdi, S. Q.
- Affiliations
- University of Oxford (GB)
- deCODE Genetics (Iceland) (IS)
- Venue
- The American Journal of Human Genetics
- Publisher
- Elsevier BV
- Published
- 2002-05
- Volume
- 70
- Issue
- 5
- Pages
- 1107-1124
- ISSN
- 0002-9297 (ISSN-L)
- PMC
- PMC447589
- OpenAlex
- W2093557681
- Cited by
- 236
- References
- 60
- Citations by year
- 2025: 3 · 2024: 3 · 2023: 7 · 2022: 7 · 2021: 11 · 2020: 9 · 2019: 10 · 2018: 5 · 2017: 10 · 2016: 7 · 2015: 16 · 2014: 16 · 2013: 10 · 2012: 8
- FWCI
- 5.21
- Type
- journal article
- Language
- en
- Open access
- bronze
- doi.org
- Licence
- Locations
- The American Journal of Human Genetics (publishedVersion)
- PubMed (publishedVersion)
- PubMed Central (publishedVersion)
- Funders
- Aga Khan Foundation
- Wellcome Trust
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Forensic and Genetic Research
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic diversity and population structure
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic Associations and Epidemiology
- Keywords
- Y-chromosome haplogroups, population structure, Brahui, Bălţi, Parsis, Hazara, paternal origin, oral tradition
- MeSH terms
- Alleles, Ethnicity, Gene Frequency, Haplotypes, Humans, Male, Pakistan, Phylogeny, Polymorphism, Genetic, Genetic Variation, Y Chromosome, Sample Size, Tandem Repeat Sequences
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