Genetic Structure of the Y-Chromosome in Colombia: An Analysis of Regional Diversity and Ancestry

Objective: To determine the genetic diversity and ancestry of male lineages across various regions of Colombia by analyzing Y-chromosome Short Tandem Repeats (STRs) and to explore how these genetic variations relate to the historical and migratory events that shaped the country's subpopulations. Materials and Methods: A total of 672 DNA samples from diverse Colombian populations were analyzed, and Y-chromosome STRs were genotyped using the Yfiler and Yfiler Plus amplification kits. Haplogroup assignments were performed using open-source software, and multivariate analyses were employed to facilitate intra- and interpopulation comparisons. Results: Substantial genetic diversity was observed among the haplotypes of the studied populations. Haplogroup R1b, of European origin, was predominant in the Andean region, while haplogroup E1b, associated with African ancestry, was more frequent in the Pacific and San Andrés regions. In relatively conserved populations, such as those from the Amazon and La Guajira, a high frequency of haplogroup Q, characteristic of Native American lineages, was detected. Multidimensional scaling (MDS) analyses showed clear genetic separations among regions, reflecting historical and geographical influences. Populations from the Pacific and Caribbean coasts clustered closely with African lineages, while those from the interior of the country exhibited a stronger European influence. In contrast, Indigenous communities and other more conserved populations, such as those in the Amazon, were clearly differentiated, underscoring the preservation of native lineages. Discussion: The results highlight the genetic complexity of Colombian populations, which have been shaped by the admixture of Native American, African, European, and, to a lesser extent, Middle Eastern lineages. These findings highlight the impact of historical processes, including European colonization, the transatlantic slave trade, and more recent migration events, on the country's genetic structure.