For example, DNA from one African region may be under-represented in the US because so many slaves from there died of malaria on American plantations.
The grim results from a paper, which appeared in the American Journal of Human Genetics, compiled genetic data from 50,000 consenting research participants from both sides of the Atlantic.
It cross-referenced these with detailed records from slave ships that transported 12.5 million men, women and children between 1515 and 1865. Some two million died on the journey.
“We wanted to compare our genetic results to those actual shipping manifest to see how they agreed and how they disagreed,” Steven Micheletti, a population geneticist at 23andMe, which recruited most of the participants, told AFP.
“And in some cases, we see that they disagree, quite strikingly,” he added.
The researchers found that while the genetic contributions from major African populations largely correspond to what they expected based on historic records, there are major exceptions.
For instance, most Americans of African descent have roots in Angola and the Democratic Republic of the Congo, in line with the major slave route.
But Nigerian ancestry was over-represented in African Americans in the US, probably because of the intra-continental slave trade which brought them from the Caribbean.
By contrast, there were fewer genetic connections between African Americans and the Senegambia region than would be expected given the number who disembarked on slave ships in North America.
The probable reasons are grim.
“Because Senegambians were commonly rice cultivators in Africa, they were often transported to rice plantations in the US,” said Micheletti.
“These plantations were often rampant with malaria and had high mortality rates, which may have led to the reduced genetic representation of Senegambia in African Americans today.”
Government and slave-owner practices had an enormous impact on African genetics too.
Despite the fact that more than 60 percent of enslaved people brought to the Americas were men, comparisons of genetics reveal a strong bias toward African female contributions in the modern gene pool of African heritage people across the region.
Much of this can be attributed to the rape of enslaved African women by white men, and other forms of sexual exploitation, like the promise of freedom if they birthed enough children.
But the imbalance is even more pronounced in Latin America, where 70 percent of the slaves who survived the ship voyages disembarked, compared to the United States, the new study showed.
In the US, slave-owners promoted marriages among slaves to ensure their children would form the next generation of the forced labor pool.
In countries like Brazil and Cuba, though, the governments implemented immigration policies in the 1900s, which involved women with African ancestry marrying whites.
These whitening or “branqueamento” policies were meant to cleanse or purify Black people toward a supposed ideal of whiteness.
“We have some regions that are essentially showing 17 African females reproducing for every one African male. We never expected the ratio to be that high,” said Micheletti.
In the British-colonized Americas, the ratio is closer to 1.5 or two African women for every African man contributing to the gene pool.
The researchers also found evidence of frequent mixing between enslaved indigenous people with enslaved Africans in Latin America, something which previous work has shown to be the case in the US.
The researchers said they hoped to not only help people of African descent find their roots, but also to understand the historic experiences that had shaped their genes today.