DNA records effects of conquest, slave trade in the Americas

The Internet and modern genetics have been a pair of high-wattage searchlights slicing through one of the darkest periods of modern human history: more than three centuries of conquest, slave trade and population displacement in the Americas.

Historians now can sort through ship manifests once scattered across continents and even search a database for the names of slaves uprooted from Africa and brought across the Atlantic. And anyone who can afford it can trace their ancestry through commercially available DNA tests.

But just as spotlights dissipate over distance, these modern methods often turn up broadly hazy answers.

A spate of recent studies, however, have added more subtle details to genetic mixing across four continents. The latest, published online Tuesday in the journal Nature Communications, charts the strength of African and European genetic influence in the Americas and turns up hitherto unidentified ancestry traces, such as Basque lineages in South America.

“In the past, people have been comparing a European sample and an African sample,” said study coauthor Cristian Capelli, a geneticist from the University of Oxford. “We tried to see if within these populations there was additional information that was missed.”

Instead of lumping genomes by relatively broad national and geographic regions, the researchers sorted 1,414 individual whole genomes by genetic patterns -- sets of individual DNA variations that tend to be inherited together, called haplotypes.

That method grouped genomes into more than 70 clusters. For example, genomes that would previously have been termed “Spanish” were sorted into five clusters, two of which appeared to have no influence on any of the genomes sampled in the Americas, the study found.

Africans were grouped in 33 clusters, some of them in well-documented areas where slaves were traded. The Yoruba from Nigeria, for example, were in a single large cluster, and the Mandenka from Senegal formed two. But elsewhere, there were 20 clusters from east, south and southwest Africa.

That pattern shows “the slave trade was much more complex than just taking people from central Africa,” Capelli said.

Using the haplotype-based approach, researchers were able to separate European genomes into 37 clusters. They then compared the clustered data with the genomes from 2,500 people of mixed ancestry from the Americas to determine their ancestry influences.

The method helped them identify fine-scale ancestry sources, such as Basque DNA patterns from Spain, rather than France. They also identified small traces of ancestry influence from Sicily, Sardinia and other Mediterranean islands, as well as the southern part of the Italian peninsula.

“I’m Italian, so it was quite surprising to find Italian DNA in some of these regions,” Capelli said.

The genome analysis, however, can’t date when small traces of Italian DNA variants began to show up in the Americas in such places as Colombia and Puerto Rico. But Italians emigrated in large numbers to North and South America during the 19th century, he noted.

“That’s one limitation of this work -- we can’t really date when this happened,” he said.

Overall, the African influence was strongest in the Caribbean and weakest in the continental populations, the study found.

Barbados showed the strongest influence from African clusters (.87), particularly the Yoruba, which also was the strongest influence on the African American genomes in the mainland U.S., the study found. Britain was the biggest European influence on both.

Colombia and Puerto Rico showed the strongest contributions from the Spanish clusters, according to the study.

Traces of French DNA variants also showed up among African Americans, likely from French rule of the former Louisiana territory. But the study lacked details about the precise geographic origin of the African American donors, a gap researchers hope to fill in their future studies.

The most evenly mixed contributions appeared to be in Mexico, which had nearly equal influences from Spain and from pre-Colombian populations.

A genome-wide study of the Mexican population last year found a stunning diversity of influences, and revealed that regional mixtures of European and native DNA mapped the country’s pre-Colombian settlement patterns.

The same Stanford University-based researchers also have examined the genomic variation in the Caribbean, revealing that Amazonians apparently mixed with islanders and Mesoamerican mainlanders even before European conquerors arrived and slave traders brought a wide variety of Africans to the New World.

Those efforts have attempted to rectify a gap in genomic studies, which have focused heavily on Europeans and left out vast swaths of Africa and the Americas.

If science is in your DNA, follow me on Twitter: @LATsciguy