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SNP Study Reveals Migration, Ancestry Patterns in South American Latino Populations

NEW YORK (GenomeWeb) - A recently published PLOS Genetics paper illustrates ancestral patterns and population histories in admixed Latino individuals in South America.

Using array-based genotyping profiles for more than 400 admixed individuals from five South American countries, researchers from the US, Spain, Mexico, and elsewhere delved into the migration and mixing events that have shaped these populations. By comparing SNP patterns in the individuals with those from several populations that had previously been profiled, they uncovered ancestry patterns reflecting historical migrations in different parts of the continent.

Past studies suggest Native Americans arrived in South America in a single migration wave more than 14,000 years ago, the team noted. After that, populations in the Andes, the Brazilian Amazon, and elsewhere became genetically differentiated as tribes spread out and settled throughout the continent.

Historical events like the arrival of Spanish conquistadors in the early 16th century, slave trading from West Africa to the Americas, and bursts of immigration from Europe — particularly to Argentina — in the 19th and 20th centuries also left their mark on South American populations, the researchers explained.

To look at the influence of such events on ancestry patterns in various admixed Latino populations, the team used Illumina OMNI1 arrays to assess patterns at almost 700,000 SNPs in 266 admixed individuals from Peru, Chile, and Argentina. They also added publicly available SNP and/or genome sequence data for individuals from Peru, Chile, Argentina, Ecuador and Colombia, bringing their tally of genotyped Latinos to 436: 175 Argentines, 119 Peruvians, 27 Chileans, 19 Ecuadorians, and 96 Colombians.

Through comparisons with reference panels for hundreds of Europeans, West Africans, Han Chinese individuals, and Native Americans profiled for studies such as POPRES and the 1000 Genomes Project, the team teased apart the proportion — and, when possible, the source — of Native American, European, African, and Asian ancestry tracts in admixed Latinos from the countries considered.

For example, individuals from Peru tended to have the highest proportions of Native American and Asian ancestry, while Argentines had the highest European ancestry proportions. Moreover, Native American ancestry in Peruvians most closely matched indigenous populations from the Andes region, such as the Quechua and Aymara in the Andes.

On the other hand, individuals from other South American populations often had Native American ancestry tracts resembling those in Southern or Amazonian tribes, though Native American ancestry in Argentina spanned both groups.

The source of European ancestry in South American mainly stemmed from the Iberian Peninsula, though the team also saw significant Italian ancestry in Argentina, likely reflecting migration during the 1800s and 1900s. And the vast majority of Argentines had relatively low proportions of African ancestry.

Further, the researchers used migration models that accounted for ancestry tract length to determine that the first influx of European ancestry to South America was later than European arrival in Mexico or the Caribbean, a finding consistent with documented movement by the conquistadors. The genetic data supported a second round of more recent European migration to the area.

And as in populations from other colonized regions, the team saw sex-biased ancestry in South America, including higher-than-usual levels of Native American ancestry on the female sex chromosome, reflecting largely male migration from Europe mixing with Native American females.

Authors of the study believe such findings will have implications for interpreting genome-wide association studies in Latino populations from South America. "The extensive structure observed in sub-continental ancestry between different populations … suggests that medically relevant genetic variation may vary between populations, demonstrating the need to ensure representation of diverse populations in future genetic association studies," they wrote.