Introduction

Due to its haploid nature and advantageous location within the non-recombining region, Y-chromosomal specific markers are commonly applied in forensic investigations and population genetic research [1]. The forensic application of this type of markers depends on the availability of haplotypic data that allows an accurate estimation of the weight of evidence. Nonetheless, haplotype data for Y-chromosomal STRs (Y-STRs) included in the kits currently used in forensics are still scarce for Colombian populations.

Colombia is located in northwestern South America, sharing borders with Ecuador and Peru to the south, and Venezuela and Brazil to the east. It faces the Pacific Ocean to the west and the Caribbean Sea to the north. The country comprises 32 administrative departments and a Federal District, and it is geographically divided into six natural regions: Caribbean, Andes, Orinoquía, Pacific, Amazon, and Insular.

Colombia exhibits high ethnic diversity, primarily resulted from extensive admixture between the Native American populations and people arriving in the territory during the Spanish colonization that started in the 16th century. During this period, the Native American people faced enslavement, displacement, or extermination. Subsequently, during the transatlantic slave trade, Africans arrived in the Colombian territory, mainly through the port of Cartagena. Initially, enslaved African people that were taken to Cartagena came mainly from Upper Guinea [2]. In the mid-17th century, Angola became the main source of enslaved individuals, a situation that lasted until 1640, when the Spanish lost access to Portuguese trade entrepôts for human trafficking [2]. After that, the enslaved Africans arriving in Cartagena were brought mainly from the Gold Coast and Bight of Benin regions, until the beginning of the 18th century [2]. In the last century, migratory movements were mainly from neighboring countries [3].

In 2024, the Colombian population was approximately 53 million. According to the latest census conducted by the Colombian Administrative Department of Statistics in 2018 [4], the Colombian population is largely concentrated in urban areas, with 77.1% living in municipal capitals and 15.8% are in rural zones. The population is mostly concentrated in the Andean region, followed by the Caribbean. The forested regions of Colombia, comprising the Orinoquía and Amazon, are the largest in land area but remain the least densely populated. The indigenous population, self-declared within 115 distinct ethnic groups, corresponds to 4.4% of the total population [4]. They are distributed across 24 departments, mainly covering rural areas, with smaller proportions in urban centers. The indigenous population is prevalent in the eastern departments of the Orinoquía and Amazon regions, accounting for more than 57% of the population. In the province of La Guajira, in the Caribbean region, the indigenous population is also significant, corresponding to approximately 48% of the population. Afro-descendant groups represent 9.34% of the total Colombian population, and are concentrated in the Caribbean and Pacific Coasts, as well as in the Insular region.

As for most South American populations, a high genetic diversity has been reported in Colombia. Studies using ancestry-informative autosomal markers (AIMs) show distinct admixture patterns across the country. In admixed populations, the European component generally predominates, except in the Amazon and Pacific regions, where the Native American and African components are, respectively, higher [5].The Native American component is the second most prevalent throughout the country, except in the Caribbean region, where the African component is higher than the Native American one [5–8]. Contrasting results have been reported when analyzing the non-recombining mtDNA and Y-chromosomal genomes in admixed populations. A predominance of maternal lineages from Native American ancestry have been reported in populations from the Andean, Caribbean and Pacific regions [9–11]. For the paternal lineages, European ancestry prevails in most populations, except for those on the Insular region [9, 10, 12–16].

The main aim of this study was to expand Y-STR haplotype data for forensic use in admixed Colombian populations. A single study was identified that report Colombian population data [17] for the currently used forensic Y-STR kits, namely the Yfiler Plus (Thermo Fisher Scientific) and the PowerPlexY23 (Promega Corporation). Most studies included a subset of the loci in current forensic kits [9, 12, 18–28], and only a few analyzed all the 17 loci present in the Yfiler kit (Thermo Fisher Scientifc) [14, 16, 29, 30]. Moreover, for the Yfiler Plus and PowerPlex 23 kits, no Colombian data are currently available at the Y-Chromosome Haplotype Reference Database (YHRD, Release R69; https://yhrd.org). Data included in the YHRD comprise shorter datasets, namely 1,507 Y17 profiles, 1,857 Y12 profiles, and 3,453 profiles for the Minimal haplotype (Release R69).

In this study, a sample of 975 unrelated admixed individuals from the five main regions of Colombia (Amazon, Andean, Caribbean, Orinoquía, and Pacific) was selected and genotyped for the 23 Y-STRs included in the PowerPlex 23 kit (PPY23). This allowed the dataset available for forensic and population studies in Colombia to be considerably expanded, both in terms of the geographic scope of previous studies and the number of loci analyzed. Particularly, (i) samples from the Orinoquía were included, a region that had only been previously analyzed for 6 Y-STRs [9]; (ii) data for the Pacific and Insular regions was only available for a set of 17 Y-STRs (n = 58 [17], and n = 54 [14], respectively); (iii) Yfiler Plus data is only available for Andes, Caribbean and Amazon (n = 699 [16, 17, 30], n = 353 [17, 29], n = 65 [17], respectively); and (iv) no data were previously available for the full set of Y-STRs from the PowerPlexY23.

Given the distinct admixture processes from various continental origins that contributed to the present-day Colombian population, differences are expected in the genetic composition of populations from different regions of the country. Population substructure affects accuracy of forensic parameters and should be considered in haplotype databases. Therefore, to evaluate male-mediated admixture patterns, a subset of 175 samples from this study were also genotyped for 859 Y-SNPs, using the Ion AmpliSeq™ HID Y-SNP Research Panel v1 [31].