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Patagonian Hunter-Gatherer Study Points to Continuity Between Ancient, Modern Groups

NEW YORK (GenomeWeb) – At least some of the Native American populations living in Patagonia have retained strong genetic ties to the populations that came before them, a new sequencing study suggests.

Researchers from Chile, Denmark, Mexico, and elsewhere did array-based genotyping and/or genome sequencing on samples from four ancient hunter-gatherers from maritime sites in Patagonia and another 61 individuals currently residing in south-central Chile and Argentinean Patagonia. Their findings, appearing online this week in the Proceedings of the National Academy of Sciences, pointed to population persistence in Patagonia over 1,000 years or more.

The current Kawéskar and Yámana groups in Patagonian appeared to share the closest genetic ties to the ancient hunter-gatherers, the team noted. Other modern-day mainland populations in Patagonia shared ancestry with the maritime hunter-gatherers as well, though historical splits between populations introduced some genetic structure to Native American populations in Patagonia.

"We found a strong affinity between modern and ancient individuals from the region, providing evidence of continuity in the region for the last ~1,000 years and regional genetic structure within Southern South America," co-corresponding authors Mauricio Moraga and Ricardo Verdugo, human genetics researchers at the University of Chile, and their colleagues wrote. "In particular, the analysis of these ancient genomes helps address questions related to the maritime tradition in the region and its diversification posterior to the split from terrestrial hunter-gatherers."

Microarray- and sequencing-based profiling methods have untangled large swaths of human, and archaic hominin, history. But the team noted that such approaches have not been deployed as extensively in the Patagonia region of South America, which is believed to have been the last area accessed by Native American ancestors migrating from Siberia through the Americas some 15,000 to 20,000 years ago.

"Exploring the genomic diversity within Patagonia is not just a valuable strategy to gain a better understanding of the history and diversification of human populations in the southernmost tip of the Americas, but it would also improve the representation of Native American diversity in global databases of human variation," the authors wrote.

With that in mind, the team used Illumina HiSeq 2000 to tackle ancient DNA from hunter-gatherer individuals from maritime sites where Kawéskar and Yámana populations currently reside, generating sequences that spanned the genomes to average depths of between nearly twofold and more than nine-fold coverage from samples stretching back up to 1,300 years.

The researchers analyzed those genome sequences alongside new genotypes generated with Affymetrix Axiom LAT1 arrays for 61 modern-day individuals from south-central Chile and Patagonia, along with historical genome sequences from Patagonia and array-based variant profiles for a broader population reference panel that spanned more than 2,300 individuals.

Prior studies indicated that hunter-gatherer populations reached northern Patagonia an estimated 14,500 years ago, the authors explained, though the earliest available evidence of populations specialized to life at coastal marine sites on or around the Patagonian archipelago comes from around 6,000 years ago. By the time Europeans arrived in the 16th century, the region was home to three main maritime hunter-gatherer groups and three mainland hunter-gatherer populations.

With the newly generated genomic data, the researchers saw clustering by locale, with groups in south-central Chile and Patagonia clustering together apart from individuals in the Andes and other parts of South America. Digging into the data further, they found pronounced ties between ancient maritime hunter-gatherers and the current Yámana population, followed by another maritime group, the Selk'nam.

Modern-day members of the Kawéskar population shared a slightly closer relationship with populations in other parts of Patagonia than the Yámana, Selk'nam, and ancient individuals. And overall, the results were consistent with a historical split between terrestrial and maritime hunter-gatherer, followed by diversification in the populations residing in coastal territories.

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