Detection of novel Y SNPs provides further insights into Y chromosomal variation in Pakistan

J Hum Genet. 2006;51(4):375-378. doi: 10.1007/s10038-005-0357-2. Epub 2006 Feb 10.


Biallelic polymorphisms on the Y chromosome have been extensively used to study the history, evolution, and migration patterns of world populations. In this study we screened 8.5 kb of Y chromosomal DNA for single nucleotide polymorphisms (SNPs) in a panel of 95 male individuals belonging to different haplogroups. Five novel Y-SNPs (PK1-5) were identified, four in the Pakistani sample and one in an African sample. The ancestral state of each SNP was determined in two chimpanzee samples and a variety of Pakistani ethnic groups. In addition to these novel Y-SNPs 77 additional markers on the Y chromosome were analyzed to place the SNPs on the phylogenetic tree of Y chromosomal lineages and to further investigate extant human Y chromosomal variation within Pakistan. BATWING analysis gave an estimate of between 2,500 and 7,300 YBP for population expansion in Pakistan which coincides with the period of the Indus Valley civilizations.

Publication types

  • Comparative Study

MeSH terms

  • Alleles
  • Animals
  • Base Pairing
  • Black People / ethnology
  • Chromatography, High Pressure Liquid
  • Chromosomes, Human, Y*
  • DNA / genetics
  • Databases, Genetic
  • Emigration and Immigration
  • Evolution, Molecular
  • Genetic Markers
  • Genetic Variation*
  • Haplotypes
  • Humans
  • Male
  • Nucleic Acid Amplification Techniques
  • Pakistan / epidemiology
  • Pan troglodytes / genetics
  • Phylogeny
  • Polymorphism, Single Nucleotide*


  • Genetic Markers
  • DNA