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Research group sequences DNA of long-extinct giant beaver

February 03, 2020

Earlham College scientists traveled back in time and all the way to Germany using specimens from both the living and the dead to sequence the code of life of the extinct giant beaver.

Heather Lerner, Ph.D., director of Earlham’s Joseph Moore Museum, conducted the study with three undergraduate research assistants, Mayeesha Ahmed, Jacob Harris and Rachel Wadleigh, who have since graduated, with contributions from a host of European collaborators. The study, co-authored by the Earlham team, has been published in Current Biology. The project was inspired by the giant beaver skeleton in the museum’s collection that is thought to be the most complete skeleton ever found.

“This is the first-ever DNA sequence for this extinct species,” Lerner says, noting that the findings provide clarity and offer doors of opportunity for additional learning.

“This shows that giant beavers are more closely related to modern beavers than previously understood,” Lerner says. Protein sequences had indicated that the giant beaver was not the closest relative of the modern beaver. “There was the idea that giant beavers were more closely related to 13-lined ground squirrels. This also gives us an idea of when modern beavers evolved. When we have a date, we can look at what’s going on in the environment to see why one species might have flourished and why another may have not.”

Heather LernerLerner (pictured right) was hired as Joseph Moore Museum director in 2011 and created the ancient-DNA lab. Lerner came from the Smithsonian Conservation Biology Institute's Center for Conservation Genomics. “This has been a dream since I first visited Earlham,” Lerner says.

Isolating and sequencing the DNA were not easy tasks because of the difficulties presented in working with ancient DNA. “There’s far less of it, and what’s left is often damaged,” says Lerner.

Research to sequence DNA from the museum’s giant beaver collection began in 2012. In 2015 Lerner, Ahmed and Harris drilled subsamples from the museum’s giant beaver specimens, including teeth and jawbones, and took them to the ancient-DNA lab at the University of Potsdam in Germany to attempt sequencing.

“We found 11 fossils of giant beaver in the JMM collections that could potentially contain ancient DNA for us to work with,” Ahmed says. “After DNA extraction, four samples showed evidence of ancient DNA.”

At that point there was no way of knowing if the DNA came from giant beavers or was contamination that had occurred during the samples’ thousands of years of existence. To verify that the DNA was indeed giant beaver DNA, the group had to sequence it through a time-consuming and expensive process that required copying and using modern beaver DNA as bait.

“Out of the four samples that contained ancient DNA, we were able to isolate ancient giant beaver DNA from only one sample,” Ahmed says. “Whew. This was a huge accomplishment given all the challenges we faced.”

“We spent the next several weeks isolating and amplifying DNA of the extinct giant beaver, working late hours and navigating holiday weekends, and once searching through the trash cans of the lab for a misplaced tube that contained all of our giant beaver DNA,” Lerner says. “In a harrowing series of events, the tube was located and the DNA was recovered and purified in a series of chemical washes.”

Another harrowing event in the story of Earlham’s giant beaver skeleton took place in 1924 when students and Richmond firefighters abandoned their attempts to save the building and rescued the giant beaver fossil skeleton and the Egyptian mummy during a fire that destroyed Lindley Hall, which housed the Joseph Moore Museum. The museum’s stuffed birds and mastodon were charred but reparable.

Earlham secured the giant beaver skeleton from a Randolph County farmer who in 1889 discovered the fossil while draining swampy land called “the dismal.” Having never seen an animal that would match the skull, the farmer was advised to take the skull to Dr. Joseph Moore at Earlham College.

“The existence of an extinct giant beaver had been postulated about 50 years prior to this discovery, but all of the remains that were found were just small fragments or an isolated skull,” Lerner says. “Moore accompanied the farmer to the location of its discovery and proceeded to uncover a few remaining bones, resulting in a skeleton that we think is still the world's most complete specimen ever found, at 7/8ths complete.”

Moore then assembled the giant beaver skeleton in 1892 for display at the museum on campus and published a lengthy description of the specimen.

The giant beaver fossil that was sequenced in Germany was collected by Earlham geologist Jim Thorpe in 1970 in Darke County and preserved in the museum collections.

“We were lucky that we had so many giant beaver fossil remains in our collections to work with, especially so we didn’t need to sacrifice part of our assembled skeleton, which is such a significant specimen,” Lerner says. “One of the best parts of museum collections is when they are carefully protected, they can be used by future scientists in ways that were not even imaginable when they were first collected.”

Lerner thinks Moore and Thorpe would be delighted with the sequencing project, its ramifications for science, and the opportunities it offered the students who were involved.

“While giant beavers may be unrelated to pharmacy, the sequencing techniques I learned about are similar to the ones used for pharmacogenomics, which is a growing field with a lot of potential,” says Ahmed, who is in her first professional year of pharmacy school at the University of Cincinnati.

“I worked on getting the ancient-DNA lab at Earlham set up and took part in the first DNA extraction from a giant beaver fossil in the lab,” says Wadleigh. “This project, and the opportunity to work closely with Heather as a research mentor, was what first got me interested in research. I learned valuable lessons about the scientific method and the process of research in general. Heather’s guidance throughout the process helped me to build a solid foundation, learning not only about genetic work, but how to conduct research, and why it is important and exciting.”

Wadleigh is a Ph.D. candidate at the University of Michigan, working in the Evolutionary Biology department. “I’m interested in avian dispersal and what kind of barriers and species-specific traits affected how they move around. I explore these types of questions using both genetic and behavioral data.”

Harris is currently an English-language teaching assistant in South Korea as part of the Fulbright scholarship he was awarded in 2019.  

 

— EC —

Earlham College, a national liberal arts college located in Richmond, Indiana, is a College That Changes Lives. We aspire to provide the highest quality undergraduate education in the liberal arts and sciences. We expect our students to think rigorously, value directness and genuineness, and actively seek insights from differing perspectives. The values we practice at Earlham are rooted in centuries of Quaker tradition, but they also constitute the ideal toolkit for contemporary success.

Princeton Review ranks Earlham in the Top 15 nationally for Best Classroom Experience, and U.S. News & World Report recognizes the College as one of the nation’s “Most Innovative Schools,” and ranks EC 7th for the percentage of international students on campus, 25th for “Best Undergraduate Teaching” and 34th for “Best Value.”

Brian Zimmerman is director of media relations at Earlham College. He can be reached at 765-983-1256 and zimmebr@earlham.edu.

 

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