Meet the Scientist Extracting Ancient DNA From Squirrels and Lemurs

Every Groundhog Day, millions in North America wait for a small brown rodent to predict when winter will end. The groundhog is a member of the squirrel family (Sciuridae), a group that includes backyard favorites like the gray squirrel, the chipmunk and nearly 280 other species that roam the treetops and burrow into the hillsides of every continent except Antarctica.

At the Smithsonian National Museum of Natural History, Curator of Mammals Melissa Hawkins studies squirrels, other small mammals and lemurs by extracting DNA from century-old museum specimens and going on field expeditions to collect new ones. In this month’s “Meet a SI-entist,” we talk with Hawkins about her research and about how we’re still discovering new mammals even today.

What questions guide your research?

I’m always interested in how things are related across space and time. It’s also interesting how much we are surprised by animals that we think we know about, especially mammals. People kind of think, yeah, the ‘Age of Discovery’ of mammals is over. That's just simply not the case —there are many groups of mammals where species are regularly being described. That's what a lot of my work entails. There's a lot of degradation to forested habitats across the world, especially in the tropics, but we don't even know how many species live in those forests. If we don't know they exist, we can't protect them. The overarching goal of my research program is to shine more light on some of these species and figure out how many of them there are and where they live.

Tell me about the animals you study, and how you study them. What projects are you working on right now?

Most of my work is on small mammals, particularly rodents like squirrels. I do a lot of work on tree squirrels in Southeast Asia, which are a little bit more exciting than the tree squirrels in our backyard here. They’re very colorful, and variable in that some species are widespread while others are restricted to a single mountaintop. There’s a lot going on with this group.

Right now, I am continuing work from my PhD on a group called the “beautiful squirrels,” Callosciurus. I'm also working on projects that I started during my postdoc on a type of lemur called sifakas — they have been featured in many David Attenborough documentaries. And then the other thing we're working on is trying to figure out if we can detect historic viruses from the specimens we have here in the museum, in light of the COVID-19 pandemic.

Wow — how are you using museum specimens to look for historic viruses?

I do a lot of molecular work from specimens we have at the museum. Typically, I use skeletal remains or skins, and search for DNA from the animals itself. But for this project, we are looking for the viruses from the animal, and we're using what we call our fluid collections. These are when you take an animal and store it preserved in ethanol. It’s the entire animal— like you may have seen for dissections in school, where an animal is fixed in formalin, all internal organs are preserved and then stored in an alcohol solution. We then dissect a piece of the organ and do different types of molecular lab work to get [viral] RNA and DNA out of those specimens.

How old are some of the specimens you’re trying to pull genetic material from, and how hard is it to get good DNA from them?

We refer to it as using “ancient DNA”, but they're not ancient samples. They are generally from the late 1800s to the mid-1900s. Scientists didn’t know that DNA was a hereditary molecule until the 1950s, and most of our collections predate that. Before that, [scientists] were just collecting animal specimens to study their shape and appearance, so because of the way that they're stored we process them in ancient DNA facilities because the DNA is in degraded, short pieces. Today, if we took a sample from an animal, we could put it in liquid nitrogen and freeze it to preserve it right now and the DNA would be much higher quality. It's all about the quantity and quality of the DNA, and as soon as it's been stored for about 50 years at room temperature, the concentration of DNA is very low and it's broken up into little, tiny pieces.

So, you make extensive use of the historical specimens at the museum. Do you also go out into the field to gather samples to add to the museum's collections?

Yes. For my PhD research, I spent about six months climbing mountains in Borneo and trapping squirrels, mice, rats and things like that. There are a lot of people who think there is no need to collect any specimens anymore, but we still collect because we can ask a lot of cool questions by comparing modern DNA signatures with historic DNA signatures. It’s actually really important to continue doing that work, because, like I mentioned, there's still so much unknown about mammals in terms of biodiversity around the world and especially in tropical regions.

A lot of people are familiar with lemurs — they’re super cute, and they’re often the stars of nature documentaries. What are some things people might not know about them?

Some people see them and just think, oh, what a cool, exotic pet, when they are not good pets. And a lot of people probably think that they’re monkeys. They’re not monkeys, and while they are primates, they belong to a group of primates called the strepsirrhines. They've been isolated on Madagascar for a very long time and have diversified into different species adapted to the variable climate and habitat across the island. They crossed over to Madagascar something like 40 million years ago — way before many modern mammals existed.

There are five different families of lemurs, and over 100 species with more getting described every day. Many types of lemurs exist that people have never heard of or seen, and many of those species cannot be kept in captivity.

Do you have a favorite thing about being a scientist at the museum?

One of my favorite things is that I can just go open a cabinet and travel around the world and look at all sorts of animals. I can open cabinets and look at echidnas and platypus, the egg laying mammals. And I can turn around and then there are bats from all over the world. I can walk down another hall and we have 100,000 squirrels. It’s amazing that you can transport so easily in this one building to look at the diversity of mammals. And you know, these cabinets hold things that are still waiting to be discovered. In a lot of the work I do, I'm discovering new species, but not necessarily from me going and physically catching animals in remote corners of the world. Many are already here in the museum, just waiting to be described.

This interview has been edited for length and clarity.

Meet a SI-entist: The Smithsonian is so much more than its world-renowned exhibits and artifacts. It is a hub of scientific exploration for hundreds of researchers from around the world. Once a month, we’ll introduce you to a Smithsonian Institution scientist (or SI-entist) and the fascinating work they do behind the scenes at the National Museum of Natural History.

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Tess Joosse | | READ MORE

Tess Joosse is an intern in the Smithsonian National Museum of Natural History’s Office of Communications and Public Affairs. Her writing has appeared in Science, Scientific American, Inside Science, Eos, Mongabay and the Mercury News, among other outlets. Tess recently graduated from the University of California, Santa Cruz with an MS in science communication. She also holds a BA in biology from Oberlin College. You can find her at https://www.tessjoosse.com/.