Monday, May 26, 2014

Rhinos, eDNA, and Turtles

Rachel Dalton-- The Wilds

Name: Rachel Dalton
Class Year: 2016
Hometown: Columbus, OH
Internship: Conservation Science Research Intern, the Wilds
Location: Cumberland, OH


Hello again! It’s been a busy few days here at the Wilds. With orientation complete, project work is in now full swing.

As I mentioned in my first post, I am studying Indian rhino eDNA extraction and detection via qPCR (also known as “real time” PCR). The little “e” in front of DNA stands for “environmental”. Environmental DNA is the DNA that is naturally released by organisms into their environment—this may occur via metabolic waste, shedding skin cells or other tissue fragments, etc. Previous work has demonstrated that this DNA can be detected from bodies of water the organisms have been in via a technique known as PCR: polymerase chain reaction. In a nutshell, the process of PCR allows you to amplify (make a lot of copies of) very specific DNA sequences, and can be used to determine whether a specific sequence is present. The successful (or unsuccessful) amplification of specific DNA sequences can be used to address a lot of different research questions. In the context of my study, PCR will be used to essentially determine if rhino eDNA can be successfully detected from water samples from various lakes within the rhino pasture, and whether differences exist in the amounts of eDNA detected from the different lakes (ex: do lakes that are more downstream tend to collect higher concentrations of the eDNA, etc).

Why does this matter? Unfortunately, Indian rhinos are a threatened species—classified as Vulnerable by the IUCN-- and have experienced very significant habitat loss and fragmentation in their home range of north eastern India and Nepal. 

This is an Indian rhino! Image courtesy of Arkive.

Many of the population surveillance techniques commonly used to monitor Indian rhino populations (and populations of other species) are contingent on actually seeing the animals—whether in person or via camera traps. The beautiful thing about potentially using eDNA detection as a monitoring technique is that in theory you could assess whether a species was present in an area without having to actually see the species. For attempting to monitor populations of threatened/endangered as well as more recluse species, this would be a really big deal. Additionally, a lot of eDNA survellience research to date has focused on species that live in the water, such as marine mammals and fishes. There has not been much work published yet regarding terrestrial mammal species—like rhinos J So, I am very excited to get to work on a project that has such significant implications for helping to monitor and conserve wild populations! Additionally, it is a pretty new area of study—the vast majority of the eDNA primary literature I've found so far has been published within the last 5-10 years. Cool beans on all fronts. J

After helping to care for the hellbenders this morning, I spent a couple of hours in the lab this afternoon learning how to do the process of DNA extraction from the awesome Caitlin Byrne. Caitlin is one of the Conservation Science staff members, and also does a lot of research involving eDNA. What I learned today is actually step 2 in the lab work process of analyzing samples potentially containing eDNA. First, you have to filter the water samples, then you do the DNA extraction process, then you run PCR.

Another fabulous aspect of being a Conservation Science intern is that you have the opportunity to metaphorically (or literally, in the case of stream-based projects J) dip your toes in other projects as well. I really appreciate this because we have the opportunity to learn about a lot of different research, field work, and ecological issues! On Friday, we all went out in the field with the interns who are working on turtle, snake, and salamander species diversity surveys. One of our finds was a ~13 pound female snapping turtle! I was particularly excited about this, as I have a soft spot for snappers J We learned about how to safely pick up and move a snapping turtle in the field (which is quite a bit different from how one would handle smaller species, like box turtles). We were taught to hold the turtle by both the tail and a leg so that its weight is distributed in a way that is safer for the turtle, and to be sure to hold it far away from you—snapping turtles have a bite force capable of biting off fingers and breaking broom handles!

The snapping turtle and I!
Also note how I am sporting extremely glamorous field work/anti-tick fashion here with my socks pulled up over my khakis. :)

A very small painted turtle we also found.