Indigenous Ancestry and Admixture in the Uruguayan Population

Abstract

The Amerindian group known as the Charrúas inhabited Uruguay at the timing of European colonial contact. Even though they were extinguished as an ethnic group as a result of a genocide, Charrúan heritage is part of the Uruguayan identity both culturally and genetically. While mitochondrial DNA studies have shown evidence of Amerindian ancestry in living Uruguayans, here we undertake whole-genome sequencing of 10 Uruguayan individuals with self-declared Charruan heritage. We detect chromosomal segments of Amerindian ancestry supporting the presence of indigenous genetic ancestry in living descendants. Specific haplotypes were found to be enriched in “Charrúas” and rare in the rest of the Amerindian groups studied. Some of these we interpret as the result of positive selection, as we identified selection signatures and they were located mostly within genes related to the infectivity of specific viruses. Historical records describe contacts of the Charrúas with other Amerindians, such as Guaraní, and patterns of genomic similarity observed here concur with genomic similarity between these groups. Less expected, we found a high genomic similarity of the Charrúas to Diaguita from Argentinian and Chile, which could be explained by geographically proximity. Finally, by fitting admixture models of Amerindian and European ancestry for the Uruguayan population, we were able to estimate the timing of the first pulse of admixture between European and Uruguayan indigenous peoples in approximately 1658 and the second migration pulse in 1683. Both dates roughly concurring with the Franciscan missions in 1662 and the foundation of the city of Colonia in 1680 by the Spanish.

Testing the existence of an unadmixed ancestor from a specific population t generations ago

“…We applied the hypothesis test onto a real data set, originated in the context of the project Urugenomes. In this project, 10 Uruguayan individuals of known Amerindian ancestry (probably Charru ´as) were analyzed; these are the same 10 individuals that were studied in [1]. The inclusion criteria to be part of the study was to have at least one indigenous great grandfather or great great grandfather, according to social anthropological studies and family records and genealogies.…”

“…For t = 2, c 1 i will be a recombination of a P 1 -complete chromosome and a P 2 -complete chromosome (as in Fig 1). We observe that the length of each tract is distributed as exp (1), and tracts alternate between P 1 and P 2 . Let N i be the amount of P 1 -tracts in c 1 i .…”

“…Our previous study has shown that there is non-negligible indigenous ancestry in this particular data set, indigenous percentages range from 7% to almost 40%. Also, mitochondrial DNA haplogroups show indigenous haplogroups such as B or C. Admixture results together with admixture graphs show a genomic affinity with Amazonian and one Andean indigenous group [1].…”

“…With genomic information we can build more precise and reliable genealogies and even calculate the proportions of our ancestries. For instance, there can be a discordance between the self-declared ancestry and the ancestry estimated from a genome study, as shown in [1]. Even if the exact genealogy of an individual is known, it is very difficult to estimate the proportion of a particular ethnic group, since the amount of genetic material that is yielded from one generation to the next one is highly variable [2,3].…”

“…We applied this test on a data set that includes the genomes of 20 Uruguayan individuals (ten descendants of the past local indigenous groups [1] and ten afro-descendants). According to historical records, most Uruguayan Amerindian were exterminated in 1831 [12].…”