In Search of DNA
A semester in the Disotell Lab
Dr. Todd Disotell (Professor, NYU) has famously searched for the DNA of many things: Bigfoot, Neanderthals, enigmatic primates, and modern humans. As an accomplished molecular anthropologist he typically succeeds in his quest… with the exception of Bigfoot. After spending a semester doing a NYCEP internship in his lab we all gained a newfound respect for the methods behind collecting, analyzing, and interpreting genetic data.
On the first day we collected our own samples from cheek swabs and blood, to extract our DNA for later analyses. Over the first few meetings, we went through the steps of amplifying the hyper variable region 1 (HVR1) of our mitochondrial genome (mtDNA) using PCR (polymerase chain reaction). As all of us were newcomers to genetics laboratory work, we initially ran into a few problems ranging from the mathematical to mechanical. To improve our skills, we had a few sessions in genetics lab boot camp making gels, pipetting dye into wells, and diluting buffers. Afterwards we felt ready to snap on our gloves and get back in the game.
Dr. Disotell moved us along to extraction of baboon (Papio anubis) DNA from fecal samples collected by Dr. Clifford Jolly (Professor Emeritus, NYU) in Uganda. These particular samples were taken north of Lake Albert, an interesting biogeographical region that is currently unrepresented in Dr. Jolly and colleague’s Papio dataset. mtDNA is easier to extract from fecal samples than nuclear DNA, and has previously given researchers insight into the sex-biased hybridization of baboon species. Though the rest of the analyses will be completed by postdoctoral researcher Dr. Andrew Burrell, learning how to extract and amplify DNA from feces was an important step for us to practice, as some of us will be applying this methodology to our own research.
Now more experienced in genetics wet lab techniques we advanced closer to our ultimate goal of sequencing our own mtDNA samples. PCR: successful, ExoSAP: no sweat, cycle sequencing: a piece of cake, and finally ethanol precipitation: ultimately a success. We then sat with Dr. Disotell to go over our results and compared the ~200 base pairs from the HVR1 of our mtDNA sequenced against other published whole mitochondrial genomes using GenBank to determine our maternal haplogroup. The returned searches were both fun and interesting. Megan Petersdorf matched with individuals from Germany, Margaret Bryer with individuals from Ukraine and Poland, Kristen Ramirez with individuals from Zambia and Namibia, and Susie Lee with individuals from Finland and China. A discussion followed about using haplogroups to trace genetic patterns of human variation. We were reminded again that any interpretation of ancestry from isolated data needs to be taken with a grain of salt, but it was an entertaining and thought-provoking discussion nonetheless.
We thank Dr. Disotell for the opportunity to work in his genetics wet lab. After a semester of learning how to navigate our way around the genetics laboratory, understanding the feasibility and timelines of different techniques, and getting hands-on training in methodology, our eclectic group has expanded its anthropological horizons into molecular primatology.
Written by the Fall 2014 Disotell Lab interns:
- Kristen Ramirez is a Ph.D. student at CUNY Graduate Center/NYCEP concentrating on the evolution of the upper limb in the genus Homo.
- Megan Petersdorf is a Ph.D. student at NYU/NYCEP concentrating on sexual selection and communication.
- Margaret Bryer is a Ph.D. student at CUNY Graduate Center/NYCEP focusing on primate nutritional ecology and behavior.
- Susie Lee is a Ph.D. student at NYU/NYCEP studying behavioral dynamics in primate mother-offspring pairs
Kristen Ramirez, Megan Petersdorf, Margaret Bryer, and Susie Lee