Field Journal: The Business End Of A DNA Database

by AMNH on

From the Field posts

Mary Blair, assistant director for research and strategic planning at the Museum’s Center for Biodiversity and Conservation, is blogging from the field during this summer’s expedition to Vietnam. Read about her 2013 expedition here.

I watched it fall from the tree with anticipation… and with glee saw it make a satisfying splat on the ground. It was loris poop, and it was filled with priceless primate DNA.

Loris Sample
Sometimes we are lucky enough to get a fecal sample from a loris.
© AMNH/M. Blair

Okay, I know, most people aren’t going to share my excitement for animal bowel movements. Taking your dog outside and picking up after him is a chore. But for a primatologist, a modest dropping could contain an invaluable trove of biological information.

In the past, I’ve collected hundreds of primate fecal samples for my dissertation fieldwork on squirrel monkeys in Costa Rica. Looking back, I didn’t realize how good I had it; squirrel monkeys have one of the highest metabolic rates of all primates for their body size, and they defecate several times a day. Not only are they veritable poop machines, they also travel in groups of up to 70 monkeys, which means there’s a pretty good chance that one of them is defecating at any given moment.

Douc Image
A male red-shanked douc (Pygathrix nemaeus) whose group we came across while marking trails for night surveys in Son Tra Nature Reserve.
© AMNH/M. Blair

It’s not uncommon for primates to be cooperative with poop-collecting researchers. This red-shanked douc (above) we came across during a daytime hike made deposits right in front of our research team, as did several of his colleagues. While the assist is appreciated, we’re not focusing on red-shanked doucs during this trip. 

We’re looking for lorises, and unfortunately, lorises don’t make many trips to the figurative forest "bathroom." These primates poop maybe once a day, are mostly solitary, and are nocturnal! So, we are extremely lucky to get any loris fecal samples in the wild. Every sample is precious, and collecting it feels like striking gold.

The Center for Biodiversity and Conservation team, co-led by Dr. Minh Le, a conservation genetics researcher at Vietnam National University, is attempting to amass the most comprehensive genetic sample of slow lorises in Vietnam to date. His student Giang Cao is with us in the field now to help with sampling, and has just completed her undergraduate thesis on the conservation genetics of slow lorises using the samples we have collected previously. And no, not all the samples stink.

Our growing database of genetic information is extremely important for two reasons:

First, we still know very little about loris biogeography in Southeast Asia. Biogeography is the study of the geographic distribution of organisms in space and time, and is a common research focus at the Museum. Why did such high levels of biodiversity evolve in Southeast Asia? What explains the current distribution of species and populations? Finding the answers to these and other biogeographic questions can help us target the best ways to conserve biodiversity into the future—by helping us understand how to conserve not just species themselves, but also the processes that allow species and systems to respond to ongoing environmental change. 

Customers buy dried squid and other items at a busy Vietnamese market.
© AMNH/M. Blair

Second, we know that loris populations are under pressure from commercial concerns, like the meat, medicine, and pet trades. A DNA database that can be used for forensic identification of the origin of illegal pet lorises and products would be extremely helpful for enforcement of wildlife trafficking cases. It could also to help us understand where and how to release healthy animals confiscated from trade back into the wild.

Because obtaining fecal and other genetic samples (such as hair) from lorises in the wild is so difficult, we supplement them with samples from rescue centers and confiscations. However, the exact provenance of these animals is unknown, so their value to our study is more limited. So far, the most valuable samples for an early database have come from museum collections, both in the U.S. and in Vietnam.

Museum collection specimens are vouchered, georeferenced, and sometimes have accompanying drawings, photographs, and morphological descriptions, so they are ideal to answer biogeographic questions. And now, we can use advanced genomic techniques to extract DNA from even the oldest museum specimens. During this project, for instance, we successfully sequenced DNA from a specimen collected in 1903. This way, we’re growing the database with specimens old and new alike, taking DNA samples from museum shelves and fresh from loris "deposits."