A History of Slavery and Genocide Is Hidden in Modern DNA

There are plenty of ways to study history. You can conduct archaeological digs, examining the artifacts and structures buried under the ground to learn about past lifestyles. You can read historical texts, perusing the written record to better understand events that occurred long ago.

But an international group of medical researchers led by Andrés Moreno-Estrada and Carlos Bustamante of Stanford and Eden Martin of the University of Miami are looking instead at a decidedly unconventional historical record: human DNA.

Hidden in the microscopic genetic material of people from the Caribbean, they’ve found, is an indelible record of human history, stretching back centuries to the arrival of Europeans, the decimation of Native American populations and the trans-Atlantic slave trade. By analyzing these genetic samples and comparing them to the genes of people around the world, they’re able to pinpoint not only the geographic origin of various populations but even the timing of when great migrations occurred.

As part of a new project, documented in a study published yesterday in PLOS Genetics, the researchers sampled and studied the DNA of 251 people living in Florida who had ancestry from one of six countries and islands that border the Caribbean—Cuba, Haiti, Dominican Republic, Puerto Rico, Honduras and Colombia—along with 79 residents of Venezuela who belong to one of three Native American groups (the Yukpa, Warao and Bari tribes). Each study participant was part of a triad that included two parents and one of their children who were also surveyed, so the researchers could track which particular genetic markers were passed on from which parents.

The researchers sequenced the DNA of these participants, analyzing their entire genomes in search of particular genetic sequences—called single-nucleotide polymorphisms (SNPs)—that often differ between unrelated individuals and are passed down from parent to child. To provide context for the SNPs they found in people from these groups and areas, they compared them to existing databases of sequenced DNA from thousands of people globally, such as data from the HapMap Project.

Tracing a person’s DNA to a geographical area is relatively straightforward—it’s well-established that particular SNPs tend to occur in different frequencies in people with different ancestries. As a result, sequencing the DNA of someone living in Florida whose family came from Haiti can reveal what proportion of his or her ancestors originally came from Africa and even where in Africa those people lived.

But one of the most amazing things about the state of modern genetics is that it also allows scientists to draw chronological conclusions about human migration, because blocks of these SNPs shorten over time at a generally consistent rate.  ”You can essentially break the genome up into European chunks, Native American chunks and African chunks,” Martin says. “If each of these regions are longer, it suggests they arrived in the gene pool more recently, because time tends to break up the genome. If these chunks are shorter, it suggests there’s been a lot of recombination and mixing up of the genome, which suggests the events were longer ago.”

Modeling their DNA data with these assumptions built in, the researchers created a portrait of Caribbean migration and population change that stretches back to before the arrival of Columbus. One of their most interesting findings was just how few Native Americans survived the arrival of Europeans, based on the DNA data. “There was an initial Native American genetic component on the islands,” Martin says, “but after colonization by the Europeans, they were almost decimated.”

This decimation was the result of European attacks and enslavement, as well as the disease and starvation that came in their wake. The DNA analysis showed that the native population collapse of Caribbean islands happened almost immediately after the arrival of Columbus, within one generation of his first visits and the appearance of other Europeans. The gene pool on the mainland, by contrast, shows a more significant Native American influence, indicating that they didn’t die off at the same rates.

What replaced the missing Native American genes in island populations? The answer reflects the conquering Europeans’ solution to diminishing populations available for labor: slaves kidnapped and imported from Africa. The DNA analysis showed a heavy influence from characteristically African SNPs, but notably, it revealed two separate phases in the trans-Atlantic slave trade. “There were two distinct pulses of African immigration,” Martin says. “The first pulse came from one part of West Africa—the Senegal region—and the second, larger pulse came from another part of it, near the Congo.”

This corresponds to written records and other historical sources, which show an initial phase of slave trade starting around 1550, in which slaves were mostly kidnapped from the Senegambia area of the Mali Empire, covering modern-day Senegal, Gambia and Mali (the orange area in the map at right). This first push accounted for somewhere between 3 and 16 percent of the total Atlantic slave trade. It was followed by a second, much heavier period that made up more than half of the trade and peaked during the late 1700s, in which slaves were largely taken from what is now Nigeria, Cameroon, Gabon and the Congo (the red and green areas).

The genetic analysis can also look at genes that are passed down on the X chromosome in particular, revealing the historical influence of different ancestries on both the female and male sides of the genome. They found that, in the populations studied, Native American SNPs were more prevalent on the X chromosome than the others, reflecting the history of both marriage and rape of Native American women by Spanish men who settled in the area.

As medical researchers, the scientists are primarily interested in using the findings to advance research into the role of genetics in diseases that disproportionately affect Hispanic populations. Similar research on genetics and ethnicity has revealed that, for instance, Europeans are much more likely to suffer from cystic fibrosis, or sickle-cell anemia tends to strike people of African ancestry.

“Hispanics are extremely diverse genetically—they originate from countries all over the world,” Martin says. “So that poses great challenges in genetic studies. We can’t just lump all Hispanics into a group and think of them as homogenous, so we’re trying to look more deeply into their genetic heritage and where it came from.”

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Joseph Stromberg was previously a digital reporter for Smithsonian.