Giant Beaver Fever

Below, we describe the harrowing history of the world's most complete Giant Beaver fossil and the story behind our crossing continents to sequence the Giant Beaver mitochondrial genome.

The World’s Most Complete Fossil Giant Beaver In 1889, a neighborhood of farmers was digging a seven-mile-long ditch to drain a swampy tract called the "Dismal," when the contractor uncovered a large skeleton with massive incisors, crouched in lifelike form. The skeleton was found on the farm of Jno M. Turner, who contacted Professor Joseph Moore at Earlham College for identification. Indeed, Dr. Moore had read an article describing a fragment of tooth and jaw that matched this fossil and was attributed to a Giant Beaver. With enthusiasm, Joseph purchased the skeleton for $20 and asked if there were any other bones to complete the skeleton. He accompanied the farmer to the discovery site and proceeded to recover a few remaining pieces, resulting in a skeleton that is considered the world's most complete Giant Beaver specimen ever found, at 7/8ths complete. Joseph Moore shared the discovery with the scientific world in two publications and displayed her for visitors to see at the Earlham campus museum in 1892.

Tragedy struck on October 23, 1924 when a night watchman noticed that Lindley Hall, containing the museum, was on fire. Students dashed in to rescue specimens from the blaze after realizing the building was doomed.

J Wendell wrote to tell his parents about it that same night-- Dear Mother and Dadi – I spose you’ve got Dorothy’s letter by now telling about the terrible thing that happened here early this morning. I’d been in my room working and then I’d gone around to see Charley Edmundson and check up with him on my acc- ounting problems and by the time I got to bed it was 12:15. I just got in bed and was dozing off when I heard Glenn yelling up on third. I didn’t pay any attention at first until I heard some one say Lindley on fire, then I got out

of it in a hurry. I put on my oldest clothes and hurried over to the fire and stretched hose and held it for awhile then I went in and helped get out the records from the Registrars and business offices. I stayed in there until all the things were out and it was too hot for comfort then I got out and went over to the museum. It was so full of smoke that no one could stay in any time at all but Gordon Bowles and I went in and got the mummy out then we went back and got the beaver fossil out

its worth $25,000 [scratched out] by itself as its the only one in existence anywhere.. By that time the fire was getting pretty hot so we stayed out. We tryed to get the paintings out of Prexy’s office but when I opened the door the fire was coming in through the other wall so we couldn’t do any thing. Then I was around on the west side near Chase Stage and some of the firemen were working close in to the wall and some of it fell and two of the men were under the bricks

one of them was almost instantly killed and he was badly burnt while the other (scratched out ) was saved by his helmet. That sort

of shook me up so I didn’t sleep the rest of the nite so I’m ready to go to bed so I’ll stop now. Its going to be terrible to have to run all over town to classes but thats about what will happen the rest of this year. Too Tired to Continue J. Wendell

The Quest to Sequence the Giant Beaver

I’m Dr. Heather R.L. Lerner, an evolutionary biologist and I’ve been the Director of the Joseph Moore Museum for nine years. From my very first days at Earlham College, I could see the promise of the museum collections and immediately began building an ancient DNA lab. In my first year on campus, I worked with two students, Kat Hardy and Martin Moon, to transform a filthy storage space full of all manners of field gear into a sterile room with fume hoods and a UV chamber. Thanks to the support of Dean Greg Mahler, we even installed a glass door so museum visitors can see us working and ask questions. This was my introduction to the quirky nature of Earlham students and after a few pranks, I learned to password-protect my phone!

In my first summer research experience for undergrads, we were set to begin working in the ancient DNA lab when an unexpected campus-wide power outage locked us out of the new ancient DNA lab for half of our research period. We quickly designed a new research project that could be conducted remotely (from the coffeshop!), leaving the giant beaver for another summer project. See the results of that summer project here. https://www.biotaxa.org/Zootaxa/article/view/zootaxa.4216.4.1/25606

During the next research period, Sonia Kabra and Rachel Wadleigh read research articles and scanned the museum database to find promising candidates for giant beaver ancient DNA. It turns out that modern beavers are distinct enough both genetically and physically, that there were several competing hypotheses for which rodents are their closest relatives. Sonia, Rachel, Emily Buttrum, Maren Schroeder and I all examined other rodents in the collection for similarities to beavers.

Giant Beaver Fever (a fanatical love of the Giant Beaver) is highly contagious, and two new students joined my research team in 2015. Mayeesha Ahmed and Jacob Harris drilled subsamples from 10 of the museum's Giant Beaver specimens. The story of their summer research is below:

In a country far, far away, four scientists set forth to capture DNA from an extinct Giant Beaver. George, Heather, Jacob and Mayeesha met in Potsdam, Germany to begin their mission in June 2015. Five fossils of giant beaver teeth were their best hope. They ground the bones to a fine powder, digested them in solution overnight and returned the next morning to finish extracting the DNA. But, no separation column existed that could handle the massive amount of digested Beaver samples. Undaunted, our fearless scientists crammed together pieces from two different kits to make the perfect column system. Early signs were good: four of the extracted bones showed evidence of ancient DNA. That is, short fragments of ~100 nucleotides in length.

There was no way to know if that DNA belonged to a Giant Beaver unless they actually sequenced it. Our scientists knew they would need a lot more copies of each DNA fragment in the samples to be able to sequence them. But this copying process would be risky. At any step, a simple mistake could mean that all of the DNA was lost. Over three days, they attached strings of known DNA (barcodes and adaptors) to the ancient DNA in each tube. Using those known strings as “primers” and a DNA copying enzyme (polymerase), they attempted to copy the ancient DNA. Signs were again good, four of the remaining samples still showed evidence of ancient DNA! An ice cream celebration ensued with much joy. Our intrepid scientists faced another challenge: DNA sequencing is too expensive to waste time and money on sequences that aren’t Giant Beaver. They would have to somehow pull out only sequences that were likely to be Giant Beaver. “What else might be in that tube?” you might ask. The most likely contaminants are bacteria, any humans who had handled the samples, and any DNA that might have been floating around the lab or in the chemicals they used. They called on another scientist, Johanna, to help them solve this problem. She proposed capturing Giant Beaver DNA with a trap made of modern beaver DNA. Using a similar copying process as before (i.e. PCR), the scientists essentially made a series of baits from modern beaver DNA to capture the Giant Beaver DNA. When the two types of DNA were mixed, strands of DNA that were similar would be attracted to each other. As the strands paired up (i.e. hybridized), one strand would be made from modern beaver DNA and the other from extinct Giant Beaver. They faced yet another challenge: to separate the captured beaver DNA from contaminating DNA. Brilliantly, they had modified their original modern beaver DNA by attaching a molecule that sticks to special enhanced magnetic beads (i.e. biotin). By applying a magnet to each tube, they could pull the hybridized strands to the side and pipette everything else—that is, all the contaminants--away! One final challenge remained: How would they get their ancient DNA unattached from the modern DNA baits, (which would be too expensive to sequence)? Luckily, it is easy to get DNA strands to separate by just heating them up. Again, that magnetic bead came in handy: after heating the tubes, they used the same magnet and pipetted off the ancient DNA that had once been trapped by the modern beaver DNA. It was time to check again to see if they had been successful. This was an important moment after three arduous weeks of challenges, including several mishaps in which they all believed the project had been lost (see Heather’s notes below). This time, three of the samples showed evidence of short strands of ancient DNA! After copying the DNA again and carefully calculating its quantity, our heroes determined that one sample was their best chance: collected in 1970 in Darke County by Earlham geologist Jim Thorpe, this specimen VP-73 was estimated to be 11,500 years old.

Over the course of 24 hours, a DNA sequencer read each DNA base using flashes of light to tell their order. On Friday, June 12, our heroes had cause for major celebration—their DNA sequence was not modern beaver or any other animal recorded to date. But it did most closely match modern beaver, pretty strong evidence that it came from a Giant Beaver! Watch the video to learn more about the careful work the team used to be sure it really was Giant Beaver DNA and how they used the DNA to study ancient beaver behavior. https://www.youtube.com/watch?v=zQ8yiZypB5o&feature=youtu.be You can also read the museum research students' blog posts about the project over the years on our museum blog: https://josephmooremuseum.wordpress.com/category/research-2/. Let us know what burning questions we should address next in our research by sending us an email!