Ancient DNA retells Story of Caribbean's First People
Florida Museum of Natural History 3 Dec 2020
GAINESVILLE, Fla. --- "The history of the Caribbean's original islanders comes into sharper focus in a new Nature study that combines decades of archaeological work with advancements in genetic technology.
"An international team led by Harvard Medical School's David Reich analyzed the genomes of 263 individuals in the largest study of ancient human DNA in the Americas to date. The genetics trace two major migratory waves in the Caribbean by two distinct groups, thousands of years apart, revealing an archipelago settled by highly mobile people, with distant relatives often living on different islands.
"Reich's lab also developed a new genetic technique for estimating past population size, showing the number of people living in the Caribbean when Europeans arrived was far smaller than previously thought - likely in the tens of thousands, rather than the million or more reported by Columbus and his successors.
"For archaeologist William Keegan, whose work in the Caribbean spans more than 40 years, ancient DNA offers a powerful new tool to help resolve longstanding debates, confirm hypotheses and spotlight remaining mysteries. "This "moves our understanding of the Caribbean forward dramatically in one fell swoop," said Keegan, curator at the Florida Museum of Natural History and co-senior author of the study. "The methods David's team developed helped address questions I didn't even know we could address."
"Archaeologists often rely on the remnants of domestic life - pottery, tools, bone and shell discards - to piece together the past. Now, technological breakthroughs in the study of ancient DNA are shedding new light on the movement of animals and humans, particularly in the Caribbean where each island can be a unique microcosm of life.
"While the heat and humidity of the tropics can quickly break down organic matter, the human body contains a lockbox of genetic material: a small, unusually dense part of the bone protecting the inner ear. Primarily using this structure, researchers extracted and analyzed DNA from 174 people who lived in the Caribbean and Venezuela between 400 and 3,100 years ago, combining the data with 89 previously sequenced individuals.
"The team, which includes Caribbean-based scholars, received permission to carry out the genetic analysis from local governments and cultural institutions that acted as caretakers for the human remains. The authors also engaged representatives of Caribbean Indigenous communities in a discussion of their findings.
"The genetic evidence offers new insights into the peopling of the Caribbean. The islands' first inhabitants, a group of stone tool-users, boated to Cuba about 6,000 years ago, gradually expanding eastward to other islands during the region's Archaic Age. "Where they came from remains unclear - while they are more closely related to Central and South Americans than to North Americans, their genetics do not match any particular Indigenous group. However, similar artifacts found in Belize and Cuba may suggest a Central American origin," Keegan said.
"About 2,500-3,000 years ago, farmers and potters related to the Arawak-speakers of northeast South America established a second pathway into the Caribbean. Using the fingers of South America's Orinoco River Basin like highways, they travelled from the interior to coastal Venezuela and pushed north into the Caribbean Sea, settling Puerto Rico and eventually moving westward. Their arrival ushered in the region's Ceramic Age, marked by agriculture and the widespread production and use of pottery.
"Over time, nearly all genetic traces of Archaic Age people vanished, except for a holdout community in western Cuba that persisted as late as European arrival. Intermarriage between the two groups was rare, with only three individuals in the study showing mixed ancestry.
"Many present-day Cubans, Dominicans and Puerto Ricans are the descendants of Ceramic Age people, as well as European immigrants and enslaved Africans. But researchers noted only marginal evidence of Archaic Age ancestry in modern individuals.
"That's a big mystery," Keegan said. "For Cuba, it's especially curious that we don't see more Archaic ancestry."
"During the Ceramic Age, Caribbean pottery underwent at least five marked shifts in style over 2,000 years. Ornate red pottery decorated with white painted designs gave way to simple, buff-colored vessels, while other pots were punctuated with tiny dots and incisions or bore sculpted animal faces that likely doubled as handles. Some archaeologists pointed to these transitions as evidence for new migrations to the islands. But DNA tells a different story, suggesting all of the styles were developed by descendants of the people who arrived in the Caribbean 2,500-3,000 years ago, though they may have interacted with and took inspiration from outsiders.
"That was a question we might not have known to ask had we not had an archaeological expert on our team," said co-first author Kendra Sirak, a postdoctoral fellow in the Reich Lab. "We document this remarkable genetic continuity across changes in ceramic style. We talk about 'pots vs. people,' and to our knowledge, it's just pots."
"Highlighting the region's interconnectivity, a study of male X chromosomes uncovered 19 pairs of "genetic cousins" living on different islands - people who share the same amount of DNA as biological cousins but may be separated by generations. In the most striking example, one man was buried in the Bahamas while his relative was laid to rest about 600 miles away in the Dominican Republic.
"Showing relationships across different islands is really an amazing step forward," said Keegan, who added that shifting winds and currents can make passage between islands difficult. "I was really surprised to see these cousin pairings between islands."
"Uncovering such a high proportion of genetic cousins in a sample of fewer than 100 men is another indicator that the region's total population size was small," said Reich, professor of genetics in the Blavatnik Institute at HMS and professor of human evolutionary biology at Harvard. "When you sample two modern individuals, you don't often find that they're close relatives," he said. "Here, we're finding relatives all over the place."
"A technique developed by study co-author Harald Ringbauer, a postdoctoral fellow in the Reich Lab, used shared segments of DNA to estimate past population size, a method that could also be applied to future studies of ancient people. Ringbauer's technique showed about 10,000 to 50,000 people were living on two of the Caribbean's largest islands, Hispaniola and Puerto Rico, shortly before European arrival. "This falls far short of the million inhabitants Columbus described to his patrons, likely to impress them," Keegan said.
"Later, 16th-century historian Bartolomé de las Casas claimed the region had been home to 3 million people before being decimated by European enslavement and disease. While this, too, was an exaggeration, the number of people who died as a result of colonization remains an atrocity," Reich said. "This was a systematic program of cultural erasure. The fact that the number was not 1 million or millions of people, but rather tens of thousands, does not make that erasure any less significant," he said.
"For Keegan, collaborating with geneticists gave him the ability to prove some hypotheses he had argued for years - while upending others. "At this point, I don't care if I'm wrong or right," he said. "It's just exciting to have a firmer basis for reevaluating how we look at the past in the Caribbean. One of the most significant outcomes of this study is that it demonstrates just how important culture is in understanding human societies. Genes may be discrete, measurable units, but the human genome is culturally created."
Daniel Fernandes of the University of Vienna and the University of Coimbra in Portugal was also co-first author of the study. Other co-senior authors are Alfredo Coppa of the Sapienza University of Rome, Mark Lipson of HMS and Harvard and Ron Pinhasi of the University of Vienna.
An earlier article from June 2020
Illustration of one of the early settlers in the Caribbean. Image credit: Tom Björklund.
Humans Colonized Caribbean Islands in Three Waves: Study
Jun 5, 2020 Sci News
An international team of researchers has sequenced and analyzed the genomes of 93 ancient Caribbean islanders and found evidence of at least three separate population dispersals into the region: two early dispersals into the Western Caribbean, one of which seems connected to earlier population dispersals in North America; and a third, more recent wave from South America.
The Caribbean Islands were one of the last regions in the Americas to be settled by humans.
The earliest archeological evidence suggests that the Caribbean’s first residents arrived roughly 8,000 years ago, and by 5,000 years ago, were widely dispersed.
However, how, when and from where the region’s first colonists came to the islands of the Antilles isn’t well understood.
Much of the Caribbean’s settlement history has heavily relied on interpretations from archaeological findings, such as the stylistic comparison of artifact collections between Caribbean sites and those from the surrounding mainland.
While these approaches have illuminated broad-scale population movements, many of the more nuanced aspects of Caribbean population history remain unknown.
To fill these gaps, Kathrin Nägele from the Max Planck Institute for the Science of Human History and colleagues analyzed genome-wide data from 93 ancient Caribbean islanders who lived between 400 and 3,200 years ago using bone fragments excavated from 16 different archaeological sites across the Caribbean.
The analysis provided new genetic evidence of at least three separate colonization events, including two early dispersals into the Western Caribbean – one of which was previously unknown and may have been connected to radiation events in North America that predate the diversification of Central and South American populations.
Afterward, a later expansion of groups from South America arrived and brought new technologies, including pottery, supporting previous archaeological interpretations.
“The new data give us a fascinating glimpse of the early migration history of the Caribbean,” said senior co-author Dr. Hannes Schroeder, a researcher in the Globe Institute at the University of Copenhagen. “We find evidence that the islands were settled and resettled several times from different parts of the American mainland.”
“Big bodies of water are traditionally considered barriers for humans and ancient fisher-hunter-gatherer communities are usually not perceived as great seafarers,” Nägele said. “Our results continue to challenge that view, as they suggest that there was repeated interaction between the islands and the mainland.”
“The new data support our previous observations that the early settlers of the Caribbean were biologically and culturally diverse, adding resolution to this ancient period of our history,” said co-author Dr. Yadira Chinique de Armas, a researcher at the University of Winnipeg.
The team’s results also revealed distinct genetic differences between the ancestors of the region’s earliest settlers and the newcomers from South America.
Despite coexisting for centuries, the scientists found almost no evidence of admixture, raising intriguing new questions about their interactions.
“Although different groups were present in the Caribbean at the same time, we found surprisingly little evidence of admixture between them,” said co-author Dr. Cosimo Posth, a researcher at the Max Planck Institute for the Science of Human History.
“The results of this study provide yet another layer of data that highlights the diverse and complex nature of pre-Columbian Caribbean societies and their connections to the American mainland prior to the colonial invasion,” said co-author Professor Corinne Hofman, a scientist at Leiden University.
The findings were published in the journal Science. Kathrin Nägele et al. Genomic insights into the early peopling of the Caribbean. Science, published online June 4, 2020
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