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USF St. Pete professors play key role in African genome discovery

University of South Florida St. Petersburg associate professors Kathryn Arthur, 49, and her husband John Arthur, 50, discovered a 4,500 year old corpse in Ethiopia. The body is first ancient genome sequenced from Africa. The two were pictured in John Arthur's science lab in the Science and Technology Building at the University of South Florida St. Petersburg Wednesday afternoon. [DIRK SHADD | Times]
Published Oct. 9, 2015

On a cool day in the lush Ethiopian mountains, John Arthur hunched over and picked through two feet of dirt. Three months of excavating in the Mota cave had turned up thousands of small artifacts that he and his wife, Kathryn Arthur, would teach about in their anthropology classes at the University of South Florida St. Petersburg.

John dug until he hit river gravel. Then, he found the remains of human feet. He shifted over and started working on the next square meter of dirt covered by a mound of brick-sized rocks. He removed them and unearthed a man's tomb.

It wasn't uncommon for the Arthurs to come across burials in their excavations. But soon they would learn that their find in June 2012 held special significance.

Geneticists from the University of Cambridge later determined that the skeleton dated back 4,500 years and held the first complete ancient African genome — a discovery that sheds light on early interactions between Africans and Eurasians, a lesser-known chapter in human history. The findings of the Arthurs and their team of 19 people were published in the journal Science on Thursday.

"(John) was kind of jumping in the hallway and told me about what they had discovered," recalled V. Mark Durand, interim regional vice chancellor for academic affairs at USFSP. "This is a discovery that anybody at USF in Tampa or Harvard or Stanford would be delighted to have."

There in the Ethiopian cave lay an ashy skeleton curled into a sleeping position, hands folded below the face, the skull resting on a stone pillow facing west.

The Arthurs named him Bayira (BI-ruh), meaning "first born" in the African language of Gamo. They believed him to be a 5-foot-tall hunter and gatherer who possibly lived to be 50. Bayira would later be sent off to Cambridge in England for DNA analysis.

The scientists decided not to release photos of the remains out of deference for their subject.

"Excavating an individual is probably one of the most tedious things you can do in archaeology," John Arthur explained. "There's some respect involved too. This was an individual that was living at one time and you want to treat his remains in a very respectful way."

The Arthurs' interest in the culture and origins of Ethiopian peoples date back long before their discovery of Bayira.

Naturally, they met in 1990 excavating a site where the Austin Convention Center in Texas stands today. John insisted on taking Kathryn on a date before she left on a four-month work trip to Africa.

Many letters crossed between Botswana and the Congo, where Kathryn worked, and the southwestern United States, where John was working. They married in 1993.

Soon after, the pair enrolled at the University of Florida for their doctorate degrees and decided to write their dissertations focusing on the Gamo highlands in southwestern Ethiopia, an area that had largely been ignored by researchers. Kathryn studied leather workers; John studied pottery. They completed their degrees in 2000.

Three years later, the Arthurs moved to St. Petersburg and joined the USFSP faculty as associate professors of anthropology. They began a new project in the Gamo highlands to study the material remains of the Gamo people and their oral traditions. Occasionally, they were accompanied to Ethiopia by an unofficial third anthropologist — their daughter, Hannah, now 12.

John, 50, and Kathryn, 49, traveled back and forth, conducting interviews with the natives and excavating the land.

Then, in 2011, Gamo elders led Kathryn to the Mota cave, a carved-out space at an altitude of 6,000 feet bordered by a rift valley and a beautiful cascading waterfall where locals hid during conflicts in the late 19th century and early 20th century. The space is slightly larger than a two-bedroom apartment with a ceiling clearance short of 5 feet.

Kathryn noticed the floor was dirt, not stone, and did a shovel test to find artifacts. The area was rife with obsidian stone tools, each no larger than a Cheerio. She told her husband, and in 2012, John and a colleague, Matthew Curtis, arrived in Ethiopia to begin excavating.

For three wet summer months, the team departed from their research station at 8 a.m. for a two-hour commute. They drove through dangerous mountainside roads, then hiked an hour to the cave, working until 4 p.m. to leave enough daylight for the journey home.

Bayira was found during the last week of their stay. Working from toe to head, it took five days to excavate the remains.

"You always find the good things at the end," Kathryn said.

As the sun set on their last day of work, it was time to remove Bayira's fragmented skull. John and a partner could not dig below the stone pillow, so they carefully wrapped the skull in layers of aluminum foil and duct tape.

Another colleague held the box for Bayira's skull. John and his partner carefully lifted the skull and flipped it over. It stayed intact. Geneticists later found the complete genome in a bone near Bayira's ear.

"That was like a moment of 'Wow, we're able to do that,' " John said. "It helped preserve DNA because we weren't touching it."

Geneticists found that Bayira's genetic sequence does not contain any West Eurasia genes, so he predates a migration of humans from West Eurasia into the Horn of Africa. His DNA closely matches those alive today in the Ari ethnic group in southwestern Ethiopia, confirming that the Aris have lived there for the last 4,500 years.

Most excavated DNA is only partially complete because it doesn't preserve, John said. If other ancient genomes are discovered, Bayira's genome can be compared to learn more about population movements and interactions through time.

"We're figuring out, really, human history and before that was kind of hidden," John said, "But the DNA is unlocking that, and that's what's remarkable on a global scale."

John is working on a grant to return to Ethiopia and conduct research on how the Gamo society developed from hunting and gathering to food production. Kathryn plans to work with the National Museum of Ethiopia, where Bayira is stored, to create an exhibit about the Gamo culture and history.

Knowing more about the human past, Kathryn said, "will help us increase the respect and our understanding of other people's cultures if we realize more and more genetically how we are similar."

She added: "I hope that will lead to people taking a little more time to sit down and figure out who I'm talking to and who I'm interacting with and give more respect."

Contact Colleen Wright at cwright@tampabay.com or (727) 893-8643. Follow @Colleen_Wright.

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