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Genetic testing of people with Caribbean ancestry reveals evidence of indigenous population collapse and specific waves of slave trade. Image via Wikimedia Commons/NASA

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Featuring article
A History of Slavery and Genocide Is Hidden in Modern DNA
November 15, 2013 | Posted By: Joseph Stromberg | Original online publication Smithsonian.com

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.

Reference paper originally published on PloS Genetics
Reconstructing the Population Genetic History of the Caribbean

Author Summary
Latinos are often regarded as a single heterogeneous group, whose complex variation is not fully appreciated in several social, demographic, and biomedical contexts. By making use of genomic data, we characterize ancestral components of Caribbean populations on a sub-continental level and unveil fine-scale patterns of population structure distinguishing insular from mainland Caribbean populations as well as from other Hispanic/Latino groups […]

 

University Report
Researchers home in on roots of Caribbean populations using new DNA analysis method
NOV. 14, 2013 | BY KRISTA CONGER | Original online publication Stanford School of Medicine

Those of us who want to learn about our ancestors — who they were, where they came from and how they mingled (or didn’t) with others around them — often turn to historical records or elderly family members for answers. But a new study by researchers at the Stanford University School of Medicine and the University of Miami Miller School of Medicine indicates that the answers can also be found within our own genes […]

Further reading about
Senegambia and the Atlantic slave trade

by B. Barry
Library of Congress – Cambridge University Press

TK

Amerikanisches_Mittelmeer_NASAGenetic testing of people with Caribbean ancestry reveals evidence of indigenous population collapse and specific waves of slave trade. Image via Wikimedia Commons/NASA

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A History of Slavery and Genocide Is Hidden in Modern DNA

November 15, 2013 | Posted By: Joseph Stromberg | Original online publication Smithsonian.com | PDF A History of Slavery and Genocide Is Hidden in Modern DNA | Surprising Science

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.

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The regions of Africa most heavily raided for slaves. Image via Wikimedia Commons

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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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Reference paper

Reconstructing the Population Genetic History of the Caribbean

Andrés Moreno-Estrada, Simon Gravel, Fouad Zakharia, Jacob L. McCauley, Jake K. Byrnes, Christopher R. Gignoux, Patricia A. Ortiz-Tello, Ricardo J. Martínez, Dale J. Hedges, Richard W. Morris, Celeste Eng, Karla Sandoval, Suehelay Acevedo-Acevedo, Paul J. Norman, Zulay Layrisse, Peter Parham, Juan Carlos Martínez-Cruzado, Esteban González Burchard, Michael L. Cuccaro, Eden R. Martin, Carlos D. Bustamante

Published: Nov 14, 2013 | DOI: 10.1371/journal.pgen.1003925

Abstract

The Caribbean basin is home to some of the most complex interactions in recent history among previously diverged human populations. Here, we investigate the population genetic history of this region by characterizing patterns of genome-wide variation among 330 individuals from three of the Greater Antilles (Cuba, Puerto Rico, Hispaniola), two mainland (Honduras, Colombia), and three Native South American (Yukpa, Bari, and Warao) populations. We combine these data with a unique database of genomic variation in over 3,000 individuals from diverse European, African, and Native American populations. We use local ancestry inference and tract length distributions to test different demographic scenarios for the pre- and post-colonial history of the region. We develop a novel ancestry-specific PCA (ASPCA) method to reconstruct the sub-continental origin of Native American, European, and African haplotypes from admixed genomes. We find that the most likely source of the indigenous ancestry in Caribbean islanders is a Native South American component shared among inland Amazonian tribes, Central America, and the Yucatan peninsula, suggesting extensive gene flow across the Caribbean in pre-Columbian times. We find evidence of two pulses of African migration. The first pulse—which today is reflected by shorter, older ancestry tracts—consists of a genetic component more similar to coastal West African regions involved in early stages of the trans-Atlantic slave trade. The second pulse—reflected by longer, younger tracts—is more similar to present-day West-Central African populations, supporting historical records of later transatlantic deportation. Surprisingly, we also identify a Latino-specific European component that has significantly diverged from its parental Iberian source populations, presumably as a result of small European founder population size. We demonstrate that the ancestral components in admixed genomes can be traced back to distinct sub-continental source populations with far greater resolution than previously thought, even when limited pre-Columbian Caribbean haplotypes have survived.

Author Summary

Latinos are often regarded as a single heterogeneous group, whose complex variation is not fully appreciated in several social, demographic, and biomedical contexts. By making use of genomic data, we characterize ancestral components of Caribbean populations on a sub-continental level and unveil fine-scale patterns of population structure distinguishing insular from mainland Caribbean populations as well as from other Hispanic/Latino groups. We provide genetic evidence for an inland South American origin of the Native American component in island populations and for extensive pre-Columbian gene flow across the Caribbean basin. The Caribbean-derived European component shows significant differentiation from parental Iberian populations, presumably as a result of founder effects during the colonization of the New World. Based on demographic models, we reconstruct the complex population history of the Caribbean since the onset of continental admixture. We find that insular populations are best modeled as mixtures absorbing two pulses of African migrants, coinciding with the early and maximum activity stages of the transatlantic slave trade. These two pulses appear to have originated in different regions within West Africa, imprinting two distinguishable signatures on present-day Afro-Caribbean genomes and shedding light on the genetic impact of the slave trade in the Caribbean.

___ Read through PLOS Genetics ( open access )

___ PDF PLOS Genetics: Reconstructing the Population Genetic History of the Caribbean

Further Reading and Links

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Researchers home in on roots of Caribbean populations using new DNA analysis method

NOV. 14, 2013 | BY KRISTA CONGER | Original online publication Stanford School of Medicine | PDF Researchers home in on roots of Caribbean populations using new DNA analysis method – Office of Communications & Public Affairs – Stanford University School of Medicine

Those of us who want to learn about our ancestors — who they were, where they came from and how they mingled (or didn’t) with others around them — often turn to historical records or elderly family members for answers. But a new study by researchers at the Stanford University School of Medicine and the University of Miami Miller School of Medicine indicates that the answers can also be found within our own genes.

The researchers compared patterns of genetic variation found in populations in and around the Caribbean, which has had a particularly tumultuous past since Christopher Columbus stumbled into the Bahamas in 1492. Not only did they identify an influx of European genes into the native population that occurred within a generation of Columbus’ arrival, but they also discovered two geographically distinct pulses of African immigration that correspond to the beginning and height of the transatlantic slave trade.

The study demonstrates how deciphering genetic echoes from the distant past can illuminate human history. But it also helps explain why some populations, like Latinos, who may be classified by medical researchers as a single group, display marked differences among populations in susceptibility to diseases or responses to therapeutic drugs.

“If we don’t understand the origin of our genetic variants, we won’t be able to design personalized, or even population-level, medicine,” said Andres Moreno-Estrada, MD, PhD, a life sciences research associate at Stanford. “Until recently, Latinos have been considered as a single group of people, when in fact they are very heterogeneous. We wanted to know what are the roots of the Caribbean people. Where do they come from? Clearly the population history of the region is very complex.”

Moreno-Estrada is the lead author of the study, published Nov. 14 in PLOS Genetics. Carlos Bustamante, PhD, professor of genetics at Stanford, shares senior authorship with Eden Martin, PhD, of the University of Miami.

“Until recently, researchers have tried to extract this type of information from ancient DNA, which can be very difficult to find and to analyze, and can’t show the full range of Caribbean diversity,” Moreno-Estrada said. “We wanted to approach the question from the other end — starting from the present day and going back in time.”

The group, led by Bustamante and Martin, documented genetic variants found in 251 people of Caribbean descent — representing Cuba, Puerto Rico, Haiti, the Dominican Republic, Honduras and Colombia — living in South Florida, and 79 Venezuelans representing three native South American tribes. They then compared the genetic variants with those found in more than 3,000 Native Americans, Europeans and Africans.

“For us, this is a very important project,” Bustamante said. “Hispanic/Latinos, are the second-largest ethnic group in the United States, with people tracing their national origins to more than two dozen countries. Yet they are largely under-represented in medical genetic studies. An often-cited reason for this is that we do not know enough about genetic differences within and among groups to effectively design multi- and trans-population studies. Dr. Martin and I were very fortunate to receive NIH funding for the GOAL project [Genetic Origins and Admixture of Latinos], which develops novel medical and population genetic approaches that we hope will improve the design and, ultimately, the outcome of medical genetic studies in this group.”

To conduct the research, the team devised a new way of analyzing DNA to infer genetic ancestry at a fine geographic scale. Using this approach, they were able to estimate not just what proportion of each individual’s genome was derived from each continent, but also to determine the closest ancestral group at a more-regional level.

“We gathered genome-wide data from these populations and employed various analytical strategies to identify segments that looked like those found in Native Americans, others which were more African in origin, and so on,” Moreno-Estrada said. “We then looked within those segments to more precisely determine their geographic source within those larger groups.”

The approach allowed the researchers to categorize regions of DNA as not just European, for example, but Iberian. Or not just African, but West African. They could also estimate when each mixing event occurred by assuming longer segments had been incorporated more recently than shorter segments. That’s because, over time, our chromosomes randomly swap regions during cell division, breaking apart and mixing up formerly long, contiguous stretches of DNA. The more time that passes, the greater the likelihood that any one piece will be disrupted by this recombination process.

The research confirmed much of what is known about the history of the Caribbean islands. But it also answered some long-standing questions about the ancestry of native Caribbean people, the impact of European colonization, and the timing and geographic origins of forced African immigration.

The researchers found, for example, that the Caribbean was first populated by people from inland South America about 2,500 years ago. Their DNA mirrors that of Amazonian tribes in the interior of the continent, and this flow of genes matches what is known about how language spread across the region during that time.

The European component, which was introduced 16 to 17 generations ago (or about 500 years ago — roughly when Columbus reached the islands) matches, but does not exactly mirror, the range of genetic diversity in modern-day Iberia. This finding most likely indicates that a small number of Europeans settled in the Caribbean and contributed their DNA to future islanders. It also confirms that, after the initial colonization of the Caribbean islands, future waves of immigration from Europe primarily came to the mainland.

Finally, African genetic diversity was first introduced to the Caribbean population about 15 generations ago (about 1550), when the first enslaved Africans were brought to the islands. The second pulse occurred five to seven generations ago, during the late 18th century, at the height of the transatlantic slave trade. The origin of the first pulse arose from the north coast of West Africa, whereas the second originated from central coast of West Africa.

“The transatlantic slave trade involved the brutal and forced migration of over 12 million people,” Bustamante said. “They were the ancestors to and kin of many people who now live in the Americas, Africa and throughout the world today. We have tried to understand for years what role, if any, DNA can play in reconstructing these voyages. Realistically, we are just scratching the surface and seeing that we can find genetics signals that corroborate historical research. We are cautiously optimistic that as technology improves we can delve deeper and help reclaim more of this critically important history.”

As exciting as it is to use genetics to answer age-old historical mysteries, it’s the potential contribution of this knowledge to medicine that has captured the researchers’ interest.

“All this affects what we call a genetic-mapping strategy to identify disease variants specific to population subgroups,” Moreno-Estrada said. “For example, those individuals with more European influence may be at increased risk for certain diseases because that genetic contribution was made by only a few individuals. Or, perhaps Caribbeans with more African ancestry may share an increased risk of diseases with others from West Africa. We’re not yet at the point where we are able to say which populations are most likely to have specific diseases, but now we can begin to figure out the important components.”

Other Stanford co-authors include former postdoctoral scholar Simon Gravel, PhD; former graduate student Fouad Zakharia, PhD; postdoctoral scholars Jake Byrnes, PhD, and Karla Sandoval, PhD; graduate student Patricia Ortiz-Tello; senior research scientist Paul Norman, PhD; and Peter Parham, PhD, professor of structural biology and of microbiology and immunology.

The research was supported by the National Institutes of Health (grants 1R01GM090087, P60MD006902 and T32 GM007175), the Stanley J. Glaser Foundation and the George Rosenkranz Prize for Health Care Research in Developing Countries.

Information about Stanford’s Department of Genetics, which also supported the work, is available at http://genetics.stanford.edu.

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___Read through Stanford School of Medicine

by B. Barry
Library of Congress – Cambridge University Press

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Andrés Moreno-Estrada, Simon Gravel, Fouad Zakharia, Jacob L. McCauley, Jake K. Byrnes, Christopher R. Gignoux, Patricia A. Ortiz-Tello, Ricardo J. Martínez, Dale J. Hedges, Richard W. Morris, Celeste Eng, Karla Sandoval, Suehelay Acevedo-Acevedo, Paul J. Norman, Zulay Layrisse, Peter Parham, Juan Carlos Martínez-Cruzado, Esteban González Burchard, Michael L. Cuccaro, Eden R. Martin, & Carlos D. Bustamante (2013).
Reconstructing the Population Genetic History of the Caribbean
PloS Genetics DOI: 10.1371/journal.pgen.1003925

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