Identifying new lineages in the Y chromosome of Colombian Amazon indigenous populations

Abstract

Objectives: The Y chromosome has highly informative markers, such as singlenucleotide polymorphisms (SNPs), that are useful for making historical inferences about the settlement of the Americas. However, the scarcity of these markers has limited their use. This study aims to identify new SNPs and increase the phylogenetic resolution of haplogroup Q for the Americas, mainly focusing on the lineages of the Amazon region. Materials and Methods: Next-generation sequencing was performed on two Y chromosomes belonging to haplogroup Q-M3 using samples with divergent short tandem repeat haplotypes from the Colombian Amazon, and 14 of the new variants identified were selected for characterization in 207 samples of indigenous Colombians belonging to haplogroup Q-M3. Results: This methodology allowed us to establish nine new lineages within Q-M3, including its paragroups. The most basal lineages were predominant in communities of Andean origin, such as the Embera-Katio, the Nasas, and the Pastos. In contrast, the most distal lineages were restricted to inhabitants of the Amazon region of Vaupés. Discussion: The SNPs reported here advance the development of subhaplogroups of Q-M3 with a higher level of phylogenetic resolution than has been previously reported, which allowed the differentiation between populations that inhabit two regions of Vaupes area: the Pirá-Paraná region and the upper and middle sections of the Vaupés River, and the region encompassing the Papurí River and the lower Vaupés. They are very useful for the microevolutionary analysis of the Amerindian populations of Colombia and of the Americas.

New Y-SNPs in QM3 indigenous populations of Colombia

“…In a previous study by Rivera et al [21], the complete genome of two indigenous samples from the Colombian Amazon was sequenced. From the results of these sequences, only the Y chromosome data were filtered and used to search for new variants of phylogenetic importance.…”

“…The 24 selected variants were typed by allele-specific PCR in all samples from the communities studied (Tucano, Pasto, Nasa, Embera katio, Kogu ¨i and Arhuaco). In addition to the samples from the Colombian Caribbean (Arhuaco and Kogu ¨i), the 14 SNPs reported by Rivera et al [21] were typified. The SNPs CO17, CO25, CO26 and Z5915 were typed individually, and the PCR reaction was performed under the following conditions 1X buffer, 4.00mM MgCl2, 0.025mM dNTPs, 0.32μM primers, 0.017U/μL Taq polymerase and 10 ng DNA in a 15μL reaction.…”

“…Two Y chromosomes belonging to haplogroup Q-M3 were used for phylogenetic analyses. The new SNPs of this work were included, those reported by Rivera et al [21] and those described in other studies and present in this investigation. For its construction, the parameters defined by the Y Chromosome Consortium [46] were used, which include the haplogroup hierarchy and nomenclature.…”

“…The tree version proposed by [21,41] was considered as a base, to which the new variants observed in the present study were added. SNPs and subhaplogroups were considered valid if they fulfilled the ISOGG inclusion criteria [46].…”

“…Its settlement has been the subject of extensive debate at the level of evolutionary studies for more than 100 years [1][2][3][4]. A large number of genetic-population studies have been carried out on Amerindians, revealing some aspects of evolution and the various migrations that have taken place throughout history and prehistory [5][6][7][8][9][10][11][12][13][14][15][16][17][18][19][20][21]. However, questions related to the time of arrival, number of migrations, and migration patterns across the continent continue to be debated in the scientific community.…”