A comprehensive analysis of Y-chromosomal diversity in Colombian populations

An intense gene flow between Native, European, and African groups, since the colonial period, has led to complex admixture patterns throughout Colombia. To investigate this genetic structure, we analyzed 23 Y-STRs in 975 males from five major regions of the country: Andes, Pacific, Caribbean, Orinoquía, and Amazon. To explore the paternal lineages and to reconstruct the underlying historical and demographic processes, a subset of 175 individuals was genotyped for 859 Y-SNPs using massively parallel sequencing. A high haplotypic diversity was found for the 23 Y-STRs (0.9998), compared to other Latin American populations studied. Pairwise genetic distance analyses (F_ST and R_ST) showed a clearer differentiation among Colombian regions, when increasing the number of Y-STRs from 17 to 23. In population comparisons, Caribbean and Orinoquía regions clustered closer to European and Admixed populations, while the Pacific region moves towards African populations. The Amazon clustered with Peru and Ecuador that have high Native American ancestry. The predominant paternal ancestry in the Caribbean and Andes was European (79% and 87.9%, respectively), with macrohaplogroup R being the most frequent (39% and 64%, respectively). In the Caribbean region, sub-Saharan African lineages are the second most prevalent (16%), while in the Andean region the Native American lineages are the second most represented (7.6%), followed by a smaller proportion of sub-Saharan African lineages (4.5%). The results attest to the extensive regional genetic diversity within the country. The Y-STRs showed good intra and inter-population discrimination capabilities and support the establishment of specific regional databases for forensic purposes.