The non-recombining nature of the Y chromosome and the well-established
phylogeny of Y-specific Single Nucleotide Polymorphisms (Y-SNPs) make them
useful for defining haplogroups with high geographical specificity; therefore,
they are more apt than the Y-STRs to detect population stratification in
admixed populations from diverse continental origins. Different Y-SNP typing
strategies have been described to address issues of population history and
movements within geographic territories of interest. In this study, we
investigated a set of 41 Y-SNPs in 1217 unrelated males from the five
Brazilian geopolitical regions, aiming to disclose the genetic structure of
male lineages in the country. A population comparison based on pairwise FST
genetic distances did not reveal statistically significant differences in
haplogroup frequency distributions among populations from the different
regions. The genetic differences observed among regions were, however,
consistent with the colonization history of the country. The sample from the
Northern region presented the highest Native American ancestry (8.4%), whereas
the more pronounced African contribution could be observed in the Northeastern
population (15.1%). The Central-Western and Southern samples showed the higher
European contributions (95.7% and 93.6%, respectively). The Southeastern
region presented significant European (86.1%) and African (12.0%)
contributions. The subtyping of the most frequent European lineage in Brazil
(R1b1a-M269) allowed differences in the genetic European background of the
five Brazilian regions to be investigated for the first time
