Ancient DNA Summer Research Intro

My name is Maren Schroeder, and I’m a junior at Earlham. I’m lucky enough to be one of Heather’s research assistants this summer. I’m a neuroscience and comparative languages and linguistics double major. In my spare time, I enjoy horseback riding, wandering around outside, petting the barn cats, eating peppers, and thinking. I’m excited to work with ancient Giant Beaver DNA because I’ve never done anything like it before and I love learning about DNA. No matter how this project turns out, I’ll learn something and that’ll be cool.

As for the actual project, our science-y goal is to extract DNA from an ancient Giant Beaver (Castoroides ohioensis). If you’ve been to the Joseph Moore Museum or follow our blog, you probably already know that Giant Beavers are an extinct species of beavers that lived during the Pleistocene era. We aim to see how genetically similar the Giant Beaver is to the modern beaver.

Since we may or may not be successful in extracting Ancient Beaver DNA, we made some other goals. Our other goals are to do science for ourselves and not for our grades, improve our lab skills, understand the nuances of working with ancient DNA, maybe publish something, and have fun. If we fail to get a single base pair of ancient DNA, that failure will be purely a learning experience and not a GPA-tarnishing humiliation. We’ll all learn something and it will be fine.

On our first day, we did a mishmash of everything, from meeting each other, going over our goals, writing a schedule that was erased and rewritten multiple times, ordering oligonucleotides (short DNA sequences that will be attached to the ancient DNA), finding some modern beaver tissue to get DNA from, digesting the tissue, and leaving it in a tube to float in some hot water overnight.

As it turns out, it is very unlikely to successfully extract and analyze ancient DNA. DNA degrades and makes errors over time. Living organisms have cellular mechanisms to catch errors in DNA replication, which is why we’re still alive. However, dead things do not have this ability, so their DNA basically sits and messes itself up for thousands of years before we come along and try to analyze it. The DNA may be mixed with bacterial DNA from the outside environment, various proteins may chop the DNA up, there might be a T base pair where there was originally a C base pair, heat may degrade the DNA, and the list goes on. Therefore, any ancient DNA strands we get will be very short, likely less than 100bp. Depending on the environment, DNA that is 100,000-1,000,000 may be preserved. DNA will be better preserved in cold, dry environments.

After going over all of that, we got to work. We found some modern beaver tissue in a freezer, weighed it (about 21 mg), chopped it up into tiny pieces and put the pieces into a tube, added some enzymes, and left the tube to sit in a hot water bath overnight.

2016-05-09 16.03.12

Emily weighing out modern beaver tissue.

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Getting tiny bits of chopped up beaver tissue in a tube.

We read a paper about the evolution of swimming and tree-exploitation behavior in beavers, which found that swimming and woodcutting evolved in beavers only once, and had implications for how beavers might evolve/react to climate change in the future. The paper noted that beavers survive winter by creating food caches underwater from trees that they cut down themselves. The chemical defenses in Poplar trees probably evolved as defenses against beavers. If the earth becomes warmer and beavers stop creating caches, there could be secondary effects on the species that interact with beavers, including animals that live in the lakes created by beavers and the trees beavers predate.

 

That’s all for now! Thanks for reading!

Maren

 

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