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Population Genetic Study of the Americas Reflects Historical Events

NEW YORK – Researchers from Estonia, Brazil, the UK, and elsewhere have retraced the genomic consequences of European colonization events, the Atlantic slave trade, and other migrations that irrevocably altered and sculpted populations in North, Central, and South America.

"We revealed a high degree of complexity underlying the genetic contribution of European and African populations in North and South America, from both geographic and temporal perspectives, identifying previously unreported sources related to Italy, the Middle East, and to specific regions of Africa," the researchers wrote in a paper appearing in Current Biology today.

The authors, led by senior author Francesco Montinaro, a researcher affiliated with the Institute of Genomics Estonian Biocentre and the University of Oxford, noted that "the fine-scale composition here reported is important for the future development of epidemiological, translational, and medical studies."

For their study, the researchers genotyped on more than 12,000 participants from a dozen American countries. With the help of a haplotype-based analysis that included data for another 6,000 or so individuals from other parts of the world, the investigators uncovered genetic signatures stemming from populations in Europe and Africa that lined up with known historical events, including patterns related to migrations and mixing events over the past couple centuries.

"[W]e demonstrated that the European and African genomic ancestries in American populations are composed of several different sources that arrived in the Americas in the last six centuries, dramatically affecting their demography and mirroring historical events," the authors reported.

Although the peopling of the Americas started some 15,000 years ago, the team explained, many of the populations living there now have ancestry from groups that arrived relatively recently — some reflecting slave trading that persisted into the 19th century and others originating from European populations that arrived in waves over hundreds of years.

"[I]t has been estimated that more than 32 million individuals reached the United States at the end of the 1800s and the beginning of the 1900s," the authors noted, "and similar estimates are available for other American countries."

For their analyses, the researchers relied on analytical methods based on allele frequency and haplotype clues gleaned from array-based genotypes for 17,722 individuals from around the world — a group that included roughly 12,000 participants from the Americas and around 6,000 individuals from other parts of the world, particularly Africa, Europe, Asia, and Oceania.

After defining population clusters within Africa and Europe, the team took a closer look at the "ancestral mosaic" of 21 groups contributing at least 2 percent ancestry apiece to 22 populations in the Americas — from Argentina stretching up to the northern US.

In African American participants and individuals from Barbados, parts of the Caribbean, and Brazil, for example, the researchers saw significant ancestry from sub-Saharan Africa, while African ancestry in other parts of South America was more heterogeneous.

On the European side, British and French populations were significant sources of the European ancestry detected in the US and Barbados, they reported, though European ancestry was diverse. Ancestry corresponding to clusters from Iberia — Spain and Portugal — was more prominent in other American populations.

The team noted that Native American ancestry tended to increase in samples from more southerly sites in the Americas, with some exceptions. It also picked up Jewish and Middle Eastern or North African ancestry in parts of Mexico, Colombia, Peru, Chile, and Brazil.

Through a series of additional analyses, the authors looked at everything from sex-biased gene flow to the timing, dynamics, and demographics of admixture events in the Americas, though they noted that additional data will be needed to get a more complete population picture of the Americas.

"The analysis of high-quality genomes from the American continents, combined with the analysis of ancient DNA and denser sampling, will be crucial to better clarify the genetic impact of these dramatic events," they wrote.