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Peruvian Genome Project Sheds Light on Native American Population History

NEW YORK (GenomeWeb) – A team from the US, Peru, and Brazil has analyzed the genomes of 280 Native American individuals from Peru, revealing historical and modern-day population patterns in the area.

"By providing the largest high-coverage genomic dataset of Native American haplotypes to date, this work lays the foundation for understanding the evolutionary history of the Peruvian region and the genomic medical needs for Native American ancestry populations worldwide," corresponding authors Heinner Guio, a biotechnology and molecular biology researcher with Peru's National Institute of Health, and Timothy O'Connor, a genome sciences researcher at the University of Maryland, and their colleagues wrote.

As part of the Peruvian Genome Project, the researchers analyzed high-quality, whole-genome sequence data for 150 Native American or mestizo individuals, along with array-based genotyping profiles for 130 Native American and mestizo representatives from Peru. The results, appearing online this week in the Proceedings of the National Academy of Sciences, suggest that Native American populations from the Amazon, Andes, and coastal regions arrived in Peru roughly 12,000 years ago and continued to migrate and diverge within the country.

The team's analyses indicated that these populations subsequently mixed with one another and with populations arriving from other parts of the world, contributing to the ancestry of present-day populations that describe themselves as mestizo.

"We find that the Native American populations possess distinct ancestral divisions, whereas the mestizo groups were admixtures of multiple Native American communities that occurred before and during the Inca Empire and Spanish rule," the authors wrote, noting that "mestizo communities also show Spanish introgression largely following Peruvian Independence, nearly 300 years after Spain conquered Peru."

Past studies suggest that Native American populations spread rapidly down the coast and beyond after moving into the Americas via Beringia more than 14,000 years ago, the researchers explained. Even so, they said, the precise population dynamics involved in peopling Peru and other parts of South America remain poorly understood.

"The Amazon, Andes, and coast populations in South America likely descend from one major population movement from Central America, [approximately 12,000 to 15,000 years ago]," the authors wrote. "However, the route Native American ancestors took once entering South America is unknown."

The analysis centered on 280 Peruvian Genome Project participants from 13 present-day populations identifying themselves as Native American or mestizo. Most of these participants had at least 90 percent Native American ancestry, the team noted.

Using Illumina HiSeq X instruments and Illumina 2.5M arrays, the researchers sequenced 150 individuals to an average depth of 35-fold and genotyped the remaining 130 individuals, respectively. They then analyzed the genome-wide data for the Peruvians in conjunction with data from phase 3 of the 1,000 Genomes Project and Human Genome Diversity Panel representatives assessed using the Human Origins Array.

The team's analysis put the age of the people of Peru at around 11,684 to 12,915 years ago, while offering a look at subsequent population migrations and fine-scale population structure in relation to the region's geography. There were hints that populations in the Andes tended to move towards the coast or to lower-altitude regions in the Amazon, for example, while mestizo populations showed signs of admixture that preceded the arrival of additional populations from Spain, West Africa, and other parts of Europe and Africa. 

"[W]e present a detailed model of the evolutionary dynamics which impacted the genomes of modern-day Peruvians and a Native American ancestry dataset that will serve as a beneficial resource to addressing the underrepresentation of Native American ancestry in sequencing studies," the authors wrote.

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