Male lineage strata of Brazilian population disclosed by the simultaneous analysis of STRs and SNPs

Highlights • High values of Y-STR haplotype diversity and Y-SNP haplogroup diversity found in 605 unrelated males from Rio de Janeiro. • The study revealed a high percentage of European haplogroups, together with a noticeable proportion of African haplogroups. • Population comparisons showed significant differences between Brazilian South Eastern and Northern populations. • Large samples necessary to statistically support small differences between populations, or detect population stratification. • The combined analysis of Y-STR and Y-SNP markers proved to be a good strategy to predict population sub-structure.