DNA Degradation and Destructive Drilling

In our third week of research we headed to the paleontology collections room looking for the actual giant beaver specimens.  We found 12 specimens apart from the mounted individual on exhibit in the museum. The specimens consist of a variety bones including a skull, ulna, vertebra, and assorted teeth.  As we photographed the specimens we considered each one’s potential for containing ancient DNA.  If the specimens were recent we would be able to easily extract DNA from any of the bones.  However, as time passes the DNA degrades and becomes fragmented.  Any remaining DNA is most likely to be present and intact in the most protected locations of the bones.

 Areas within the densest bones and underneath the tooth enamel best protect the DNA from changing elements that damage DNA like temperature, humidity and UV light.  Since our specimens were collected as early as the mid-1800s and were actually alive over 10,000 years ago, we have to be careful to select the best location for sampling.

After taking pictures of the specimens we consulted with Dr. Beth Rinaldi, a researcher who specializes in Giant Beaver morphology, about the best place to drill each specimen so as to preserve features that are informative for morphological study. We decided that the best way to determine where to drill into the two skull specimens was to obtain a CT scan which would show the densest areas which would be the most lucrative in DNA.  In the meantime we decided on three specimens to sample: a vertebra, a molar (or “cheek tooth”), and a lower jawbone (or “ramus”).

Giant Beaver Molar

Giant Beaver Molar

Giant Beaver Ramus (Jawbone)

Giant Beaver Ramus (Jawbone)

Giant Beaver Vertabra

Giant Beaver Vertabra

We drilled into the bones and took a small sample for DNA extraction, a form of “destructive sampling”.  The decision to do destructive sampling considers both the value of preserving the specimens for the future and the value of using them to further our knowledge of this incredible extinct species.  We chose to sample bones for which we had multiple samples and took only what we needed for an extraction (~100mg).  We are taking great time and care with this project as we consider the value that the specimens hold.  There are not many specimens of the Giant Beaver in collections today, so we want to be especially careful with those that we have. It was incredible to consider as we handled the bones, that some were collected by Joseph Moore himself.

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