Saturday, October 10, 2015

Genome from 4,500 Years Ago Pulled from Ear in Africa

Seth Augenstein, Digital Reporter

John Arthur, of the Unviersity of South Florida St. Petersburg, excavates in the Mota Cave in southwestern Ethiopia in this undated photo. (USFSP)
John Arthur, of the Unviersity of South Florida St. Petersburg, excavates in the Mota Cave in southwestern Ethiopia in this undated photo. (USFSP)
Anthropologists have pulled a complete genome from a 4,500-year-old skeleton found in Ethiopia, a discovery which could have far-reaching implications for understanding prehistory in the region.

The ancient male remains were recovered from a cave in Ethiopia’s Gamo highlands in 2012 – and they could pull enough intact genetic information from the bones in the inner ear to make a full sequence,they announced in today’s issue of Science.
“We have given him the name Bayira, meaning ‘first born’ in the Gamo language in honor of the ethnic group that lives in the area today,” said John Arthur, the anthropologist from the University of South Florida St. Petersburg who led the team.
The genetic sequence has indicated that people from Europe and Asia had not yet mixed into the gene pool from that part of modern-day Ethiopia, the scientists said.
“Bayira’s genetic sequence does not contain any West Eurasia genes, supporting the idea that more recent population movements are responsible for Eurasian admixture into modern African populations,” Arthur added. “Thus, his genome is important for understanding the out-of-Africa expansion of Homo sapiens and later population movements between Africa and Europe.”
The genetics also show three genetic variants adapted to the high-altitude, low-oxygen environment of the highlands region – and the genes also resemble those of the people currently still living in the region, they added.
“Bayira is genetically closets to the Ari ethnic group, an Omotic-speaking society living in southwestern Ethiopia today,” said Kathryn Arthur, also of the scientific team.
“This is an extraordinary discovery, a contribution to the fields of anthropology and archaeology that will be recognized by scientists around the world,” added Sophia Wisniewska, the regional chancellor of USF.
DNA has provided insights into prehistorical dispersion of humans and hominids. Earlier this year a team from Harvard Medical School found genes from natives in South America that linked more closely with Australasian populations – which complicates the theory of a single population coming over the iced-over Bering Strait around 15,000 years ago.

Friday, October 9, 2015

Prehistoric Eurasians streamed into Africa, genome shows

This boy's ethnic group, the Ari, is closely related to a prehistoric African who lived in the Ethiopian highlands.

Africa is the birthplace of our species and the source of ancient migrations that spanned the globe. But it has missed out on a revolution in understanding human origins: the study of ancient DNA. Although researchers have managed to sequence the genomes of Neandertals from Europe, prehistoric herders from Asia, and Paleoindians from the Americas, Africa's hot and humid climate has left little ancient DNA intact for scientists to extract. As a result, “Africa was left out of the party,” says anthropological geneticist Jason Hodgson of Imperial College London.
Until now. A paper published online this week in Science( reveals the first prehistoric genome from Africa: that of Mota, a hunter-gatherer man who lived 4500 years ago in the highlands of Ethiopia. Named for the cave that held the remains, the Mota genome “is an impressive feat,” says Hodgson, who was not involved in the work. It “gives our first glimpse into what an African genome looked like prior to many of the recent population movements.” And when compared with the genomes of living Africans, it implies something startling. Africa is usually seen as a source of outward migrations, but the genomes suggest a major migration into Africa by farmers from the Middle East, possibly about 3500 years ago. These farmers' DNA reached deep into the continent, spreading even to groups considered isolated, such as the Khoisan of South Africa and the pygmies of the Congo.
Anthropologists John and Kathryn Arthur of the University of South Florida, St. Petersburg, discovered the skeleton in 2012 at Mota Cave in southwest Ethiopia after local Gamo elders led the pair to the cave, a hiding place for the Gamo during wartime. The Arthurs unearthed the skeleton of an adult male beneath a stone layer and dated it to 4500 years ago using radiocarbon. The researchers analyzed the petrous bone of the inner ear, which can sometimes preserve more DNA than other bones.
DNA had indeed survived in the ear bone, perhaps aided by the cool temperatures in the highland cave. Researchers were able to sequence each DNA base more than 12.5 times on average, considered a high-quality genome. When population geneticist Andrea Manica and graduate student Marcos Gallego Llorente at the University of Cambridge in the United Kingdom analyzed the sequence, they found that the Mota man had brown eyes and dark skin, as well as three gene variants associated with adaptation to high altitudes; some peaks in the highlands reach 4500 meters, as high as the Matterhorn.
By comparing 250,000 base pairs from Mota's genome with the same sites in individuals from 40 populations in Africa and 81 populations from Europe and Asia, the team found that Mota was most closely related to the Ari, an ethnic group that still lives nearby in the Ethiopian highlands. They zeroed in on the DNA that the Ari carry but Mota doesn't, which was presumably added during the past 4500 years. They found that Mota lacks about 4% to 7% of the DNA found in the Ari and all other Africans examined. This new DNA most closely matches that of modern Sardinians and a prehistoric farmer who lived in Germany. Hints of these early farmers' DNA previously had turned up in some living Africans, but Mota helped researchers zero in on the farmer's genetic signature in Africa, and to establish when it arrived.
Manica suggests that both the European farmers and living Africans inherited this DNA from the same source—a population in the Middle East, perhaps Anatolia or Mesopotamia. Some of these Middle Easterners headed into Europe and Asia starting 8000 years ago, and were the first farmers of Europe (Science, 20 February, p. 814). But other descendants of this population migrated into Africa, likely after Mota lived. This fits with traces of Middle Eastern grains found in Africa and dated to 3000 to 3500 years ago.
Because so many far-flung Africans still carry the farmers' DNA, the study suggests a “huge” migration, Manica says. Farming had already been established in Africa by this time, but the newcomers likely had some advantage that explains why their genes spread. “It must have been lots of people coming in or maybe they had new crops that were very successful,” Manica says.
Population geneticist David Reich of Harvard University is struck by the magnitude of the mixing between Africans and Eurasians. He notes that “a profound migration of farmers moving from Mesopotamia to North Africa has long been speculated.” But, he says, “a western Eurasian migration into every population they study in Africa—into the Mbuti pygmies and the Khoisan? That's surprising and new.”
Migrations into and out of Africa were likely complex and ongoing. “This study is significant on its own,” Hodgson says. “But hopefully it is only just the beginning of ancient African genomics”.

Scientists Recover First Genome of Ancient Human From Africa - The New York Times


A skeleton found in the Mota cave in Ethiopia yielded a complete assemblage of DNA. CreditKathryn and John Arthur

A team of scientists reported on Thursday that it had recovered the genome from a 4,500-year-old human skeleton in Ethiopia — the first time a complete assemblage of DNA has been retrieved from an ancient human in Africa.
The DNA of the Ethiopian fossil is strikingly different from that of living Africans. Writing in the journal Science, the researchers conclude that people from the Near East spread into Africa 3,000 years ago. In later generations, their DNA ended up scattered across the continent.
“It’s a major milestone for the field,” said Joseph Pickrell, an expert on ancient DNA at the New York Genome Center who was not involved in the study. For decades, scientists had doubted that ancient DNA could survive in the tropics. The study raises hopes that scientists can recover far older human genomes from Africa — perhaps dating back a million years or more.
“I would bet it’s not that far in the future,” said Lee Berger, a paleoanthropologist at the University of the Witwatersrand who recently announced the discovery of an ancient humanlike species called Homo naledi.
In the 1980s, few scientists would have believed it possible to reconstruct an entire genome from the DNA in a fossil. Once a human or other animal dies, its DNA starts to fall apart. Bacteria swiftly colonize the corpse, overwhelming it with their own DNA.
But by the 1990s scientists were beginning to retrieve fragments of DNA and piece them together into longer segments. In 2010, researchers assembled the genome of a Neanderthal from 38,000-year-old fossils from Croatia. In many other cases, researchers failed to find ancient DNA in human fossils. Because it was widely suspected that the heat and humidity in the tropics would destroy genetic material, many scientists flocked to places like Siberia to seek ancient DNA.
That skepticism proved to be unwarranted. In recent years, Ron Pinhasi, an archaeologist at University College Dublin, and his colleagues have been surveying different bones to see if any are particularly good for preserving DNA. They found that the bone surrounding the inner ear can hold an abundance of genetic material even when other bones have lost theirs.