Y chromosome haplogroup diversity in a Mestizo population of Nicaragua

Forensic Sci Int Genet. 2012 Dec;6(6):e192-5. doi: 10.1016/j.fsigen.2012.06.011. Epub 2012 Jul 6.


Y chromosome single nucleotide polymorphisms (Y-SNPs) are indispensable markers for haplogroup determination. Since Y chromosome haplogroups show a high specific geographical distribution, they play a major role in population genetics but can also benefit forensic investigations. Although haplogroup prediction methods based on Y chromosome short tandem repeats (Y-STRs) exist and are frequently used, precaution is required in this regard. In this study we determine the Y chromosome haplogroups of a Nicaraguan population using several Y-SNP multiplex reactions. Y chromosome haplogroups have been predicted before, but our results show that a confirmation with Y-SNP typings is necessary. These results have revealed a 4.8% of error in haplogroup prediction based on Y-STR haplotypes using Athey's Haplogroup Predictor. The Nicaraguan Mestizo population displays a majority of Eurasian lineages, mainly represented by haplogroup R-M207 (46.7%). Other Eurasian lineages have been observed, especially J-P209 (13.3%), followed by I-M170 (3.6%) and G-M201 (1.8%). Haplogroup E-P170 was also observed in 15.2% of the sample, particularly subhaplogroup E1b1b1-M35. Finally, the Native American haplogroup Q-M242 was found in 15.2% of the sample, with Q1a3a-M3 being the most frequent.

MeSH terms

  • Chromosomes, Human, Y*
  • DNA Fingerprinting
  • Ethnicity / genetics*
  • Gene Frequency
  • Genetic Loci
  • Genetics, Population*
  • Haplotypes*
  • Humans
  • Microsatellite Repeats
  • Multiplex Polymerase Chain Reaction
  • Nicaragua
  • Polymorphism, Single Nucleotide*