Uniparental Lineages from the Oldest Indigenous Population of Ecuador: The Tsachilas

Genes 2021, 12(8), 1273; https://doi.org/10.3390/genes12081273

Received: 29 June 2021 / Revised: 12 August 2021 / Accepted: 16 August 2021 / Published: 20 August 2021

Abstract
Together with Cayapas, the Tsachilas constitute the oldest population in the country of Ecuador and, according to some historians, they are the last descendants of the ancient Yumbos. Several anthropological issues underlie the interest towards this peculiar population: the uncertainty of their origin, their belonging to the Barbacoan linguistic family, which is still at the center of an intense linguistic debate, and the relations of their Yumbo ancestors with the Inca invaders who occupied their ancient territory. Our contribution to the knowledge of their complex past was the reconstruction of their genetic maternal and paternal inheritance through the sequencing of 70 entire mitochondrial genomes and the characterization of the non-recombinant region of the Y chromosome in 26 males. For both markers, we built comprehensive datasets of various populations from the surrounding geographical area, northwestern South America, NW, with a known linguistic affiliation, and we could then compare our sample against the overall variability to infer relationships with other Barbacoan people and with other NW natives. We found contrasting patterns of genetic diversity for the two markers, but generally, our results indicated a possible common origin between the Tsachilas, the Chachi, and other Ecuadorian and Colombian Barbacoans and are suggestive of an interesting ancient linkage to the Inca invaders in Yumbo country.

3.2. Y Chromosome

The Y-STRs profiles revealed that 24 of the 26 male individuals belong to the native Q haplogroup, and the remaining two belong to Eurasian haplogroups (Table S8). We only considered the Q haplotypes for Y-SNPs characterization, and we found the native Q-M3 with one individual assigned to the Q-M19 sub-branchas unique lineage, which had previously only been described in Peruvian Amazon and Argentina [39,66,67]. The standard diversity indices calculated for the Y-STRs profiles indicates that the haplotype diversity of the Tsachilas (0.9) is similar to the average of the other Ecuadorian, Peruvian, and Colombian populations used as comparison (Table S2).
The network of Y-STRs haplotypes was only built with the Q-M3* haplotypes selected from the Y chromosome dataset since it was the unique haplogroup detected in our sample (Figure 4). The absence of shared nodes between Tsachilas individuals and other haplotypes is a common trait between the two uniparental markers. If compared tothe MJ network obtained from mitochondrial haplotypes, the phylogenetic relationships of male lineages highlighted a closer relationship between some Tsachilas and Peruvian Quechua nodes (including Peruvians of Inca kinship, published by Sandoval et al. [55]), while the other haplotypes show a relatedness with the Ecuadorian Cañar and Pasto and the Guambiano from Colombia (all affiliated with the Barbacoans)."

3.1. mtDNA

We generated 70 novel sequences of complete mitochondrial genomes. All of the mtDNA profiles belonged to the main Native American haplogroups A2, B2, C1, and D1.
Mitochondrial haplogroups B2 and D1 were the most frequent lineages in Tsachilas samples, as shown in Table S3, which also summarizes the haplogroup frequencies for 53 Native populations from all over northern South America. The entire mtDNA genomes also allows the identification of sub-haplogroup frequency in our Tsachilas sample, as shown in Table S4: it can be noticed that the most represented mitochondrial sublineage is A2ac, one of the ancient native lineages that is also detected in North and Central America and dated back to 15–12 Kya [28].