A Gutsy Approach to Lemur Science

By Sheena Faherty, biology Ph.D. candidate

Can the microorganisms living in a baby lemur’s gut help it grow up to be a vegetarian or an omnivore?

A new study appearing May 13 in Plos One shows that baby lemurs’ gut bacteria have different, diet-dependent strategies for reaching adult mixtures of microbes.  This, in turn, might contribute to why some lemurs are strictly leaf-eaters, while some nosh on just about everything.

lemur eating flowers

A black and white ruffed lemur (Varecia variegata) finds North Carolina’s vegetation as delicious as it is beautiful. (Duke Lemur Center, David Haring)

Erin McKenney, lead author on the study and a Ph.D. candidate in the Biology department, is looking at the patterns of how the bacteria colonize the gut of their lemur host and why this is essential for helping the adult lemurs navigate their environment — and their diets.

“This study is important because all mammals are born with basically sterile guts,” McKenney said. “But by the time we’re adult mammals, there are 20 trillion bacteria living in the gut. (The bugs are an) adaptive super organ that has co-evolved with the host and dictated the host’s evolution. We want to know more about how that happens.”

This “microbiome” of the gut is a jack-of-all-trades, performing jobs like protecting the host’s body from pathogens and helping it digest food. When the gut’s microbes digest foods that are high in fiber — like plant matter — some of the digestion by-products are absorbed by the intestine, which provides nutrition for the body. Humans get up to 10 percent of our daily nutritional requirements from fiber breakdown by bacteria.

Erin McKenney

Erin McKenney scooping lemur poop for SCIENCE!

“Mammals don’t secrete the enzymes that are necessary, so no mammal can digest fiber on its own,” McKenney said. “These microbes are performing an incredibly important life process for us.”

At the Duke Lemur Center, McKenney collected fecal samples from three different species of lemur that evolved to eat different foods—a strict leaf-eater, and two omnivores. Using DNA sequencing, she determined the communities of bacteria that are living in their guts at different life stages from birth to adulthood.

Watching microbiomes through time may enable her to answer the question of how the microbiome of each species becomes teeming with 20 trillion bacteria, and if the patterns differ based on diet.

lemur eating pokeweed

Vegetarian lemurs can eat a surprising variety of stuff we’d find nasty, like pokeweed and even poison ivy. (Duke Lemur Center, David Haring)

The results suggest that all species of baby lemurs, when they are born and nursing from their mothers have similar microbiome profiles that are much less complex than adult profiles. But leaf-eaters that eat the most fiber show adult microbiome profiles as soon as solid foods are introduced, which is in contrast to the other two species that take longer to reach adult microbiome profiles. Additionally, leaf-eaters have more complex microbial communities, which allows them to digest fiber-rich foods.

“So when you start to think about the really big picture, beyond everything the gut microbes do for the hosts they live inside of, we find the microbes have done an incredible service to mammalian speciation. The only way that we have leaf-eaters is because of these gut microbes,” McKenney said.

Researcher Goes to the Dogs, Lands on TV

Fresh off a visiting teaching gig at Duke-Kunshan University and a sabbatical in Australia, canine and primate cognition researcher Brian Hare is about to land in your living room.

Hare, an associate professor of Evolutionary Anthropology and founder of Duke’s canine cognition lab and the Triangle startup Dognition.com, is now a television host too.

He’ll be hosting a three-part series on Nat Geo WILD at 10 p.m. ET this Friday, Saturday and Sunday nights called “Is Your Dog a Genius?”

Hare will introduce viewers to some of the latest knowledge about what our dogs think and understand, as well as sharing some at-home games you can use to reveal your dog’s personality. He’ll also visit with some ordinary and extraordinary dogs to see their problem-solving in action.

Friday’s episode is titled ” Doggy See Doggy Do.” Saturday is “Who’s Your Doggy.” And Sunday is “Talk Doggy to Me.”

Underwater Cave is a Lemur Treasure Trove

Guest post by Gregg Gunnell, Division of Fossil Primates

(A version of this column originally appeared in the Duke Lemur Center newsletter)

Lagerstätten – that word sends a shiver of excitement up and down the spine of every paleontologist.

In German the word means ‘storage place’ or ‘deposits,’ but in paleontology it has come to mean a very rich fossil deposit that contains complete or nearly complete specimens that sample a wide variety of the creatures living at a certain time.

cave diver

A cave diver and subfossil specimen in Aven Cave, Madagascar. The plastic triangle is a scale for photographs of the specimen in situ. (Image by Phillip Lehman and Pietro Donaggio-Bitner)

As you might imagine, Lagerstätten are quite rare. Some of the more famous examples are the Burgess Shale in Canada which preserves soft body outlines of ancient (530 million years ago) Cambrian animals; the Jurassic (150 Ma) Solenhofen limestones in Germany where the famous Archaeopteryx is found; and the middle Eocene (45 Ma) Messel Oil Shale in Germany which preserves whole skeletons of many birds, mammals, reptiles, amphibians, and insects.

I have had the good fortune to be in on the discovery of two Lagerstätten in addition to studying specimens from two others. The first one our team discovered was in 1998 in Pakistan, a place we named Gandhera Quarry. It preserves a remarkable wealth of early Eocene (52 Ma) mammals from Balochistan Province – an assemblage that has yet to completely studied.

But the latest and most exciting to me as Director of the Division of Fossil Primates in the Duke Lemur Center happened late last year in Southwest Madagascar.

The discovery of subfossils at a place called Aven Cave was known to local people, but not reported to the scientific community until an Australian cave diver named Ryan Dart saw it. The cave and its specimens are underwater. The specimens are called subfossils, because they aren’t old enough to have completed (or in some cases even started) the fossilization process.

A joint team from the University of Antananarivo, Duke University, University of Massachusetts, Brooklyn College and Midwestern University led an expedition to this cave site in October 2014. Cave divers Phillip Lehman  and the Dominican Republic Speleological Society dive team helped us find a treasure trove of subfossils.

lemur skulls

Lemur skulls, as they were found in the cave, with a scale marker. (Photo courtesy of Phillip Lehman and Pietro Donaggio-Bitner)

Only a preliminary survey has been made of Aven Cave to date, but it is clear already that it is one of the richest subfossil sites ever discovered in Madagascar. The initial list of animal specimens found in the cave includes three genera of extinct lemurs (Pachylemur, Mesopropithecus, and Megaladapis) as well as one species of a living form, Lemur catta, the familiar ring-tailed lemur. In addition to the primates there are abundant specimens of bats (Hipposideros), carnivores (the extinct fossa Cryptoprocta spelea as well as a smaller, still living species, C. ferox), two species of rodents, an extinct pygmy hippopotamus, crocodiles, turtles, and two bird species including the extinct elephant bird Mullerornis.

Not only is there a diverse assembly of species coming from Aven Cave, the sample is also abundant, with many species represented by multiple specimens. Many specimens appear to be complete or nearly complete skeletons.

The expedition was aided by Mr. Lovasoa Dresy, the director of Tsimanampetsotsa National Park, and was generously supported by the National Science Foundation and the National Geographic Society.

We anticipate many more and surprising discoveries in the future. Stay tuned for updates from Aven Cave!

Mouse Lemur Quandary Stumps Researchers

By Sheena Faherty, Ph.D. Candidate in Biology

What does famous lemur researcher, Dame Alison Richard, do when she has a burning question she can’t answer?

She visits Duke and appeals to a room full of lemur enthusiasts to help out.

Richard’s question concerns the curious case of the mouse lemurs at Beza Mahafaly in southwestern Madagascar, where she has been involved in a wildlife-monitoring program since the mid-1990s.

Alison Richard (left) and Lemur Center Director Anne Yoder (right) lead a discussion in the 'Beach House' at DLC.

Alison Richard (left) and Lemur Center Director Anne Yoder (right) lead a discussion in the ‘Beach House’ at DLC.

“What do I know about mouse lemurs?” she questioned a group that gathered at the Duke Lemur Center on March 3 as the first of three talks she held at Duke this week as part of the Von der Heyden Fellows Program. “Probably less than you do. But I am incredibly interested in what is going on with them at Beza Mahafaly.”

Everywhere else in Madagascar, mouse lemurs that look indistinguishable are classified as different species due to big variations at the genetic level. But at Beza Mahafaly, Richard is finding that mouse lemurs with major deviations in appearance are genetically the same.

Dame Alison Richard (Photo: HHMI)

Dame Alison Richard (Photo: HHMI)

For a long time, the general view was that there were two species of mouse lemur in the forests of Beza Mahafaly : the gray-brown mouse lemur and the gray mouse lemur (both being exceptionally adorable).

A few studies in the mid-1990s and early 2000s compared the shapes of certain features such as jawbone shape and leg length, and confirmed this view. Then, researchers started noticing a few trapped animals that had very noticeable differences in coat coloration. These animals were redder than the other two known species. Was this a possible third species?

In 2006, Duke Lemur Center Director, Anne Yoder, and her former Ph.D. student Kellie Heckman examined this same population of mouse lemurs from a genetic standpoint. Comparing sequences of DNA they expected to find major genetic differences between the two known species, and possibly confirm the existence of a third species.

“The genetic data was a disaster for the mouse lemurs,” Richard said.

All the samples collected from animals at Beza Mahafaly, regardless of the animal’s outward appearance, sorted together and seemed to be one species.

Dame Alison and the bedeviled mouse lemur of Beza Mahafaly

Dame Alison and the bedeviled mouse lemur of Beza Mahafaly

“There’s a part of me that’s very distressed about this, but there’s a part of me that thinks this is great,” Richard said. “At Beza Mahafaly we swim upstream. We’re contrarians,” she said laughing. “But we still don’t know how to best explain the diversity that we do see.”

She offered up some suggestions: A glimpse of an ongoing process of change? A replacement by one species over another? The beginning of a new species?

Flashing a picture of a mouse lemur displaying ominous eye shine from a headlamp, she said: “The mouse lemurs are waiting with an evil gleam in their eye to be told the truth about themselves. The question is how should we take this forward?”

Madagascar’s Conservation Superhero to Visit Campus

Guest Post By Sheena Faherty, Ph.D. Candidate in Biology

Dame Alison Richard is the epitome of someone who puts her money where her mouth is. And her dedication is directed precisely where it’s needed most.

Richard, a protector of lemurs, artisanal salt entrepreneur and endless optimist, is not just doing something about Madagascar’s conservation crisis. She’s doing everything about it.

Alison Richard (Photo: HHMI)

Alison Richard (Photo: HHMI)

She’ll visit Duke March 3-5 to give three-part lecture series discussing her role in over forty years of community-based conservation efforts in Madagascar.

Members of the Duke community know all too well that our beloved lemurs— many of which can only be found at the Duke Lemur Center or in Madagascar—are in dire straights.

Their plight has been a life’s work for Richard, who is best known for her research on sifakas in the spiny forests of Madagascar.  But she also lays claim to having been the first female vice-chancellor at Cambridge. She has now returned to Yale, where she spent most of her career, as a senior research scientist and professor emerita.

“Sometimes I think that because I’m covering so many bases, I end up doing nothing very well,” Richard said. “But it’s what I do and I can’t imagine not doing any of them—so it’s too bad,” she said laughing.

Richard is a conservationist who understands that without considering the local people’s well-being, all attempts to save wildlife habitats will fail.

“There are a variety of ways in which we are trying to facilitate socio-economic enhancements to people’s lives,” Richard said. “[On a recent trip to Madagascar] I met with the association of women salt producers, who are producing artisanal salt by techniques that have been in place for hundreds of years.”

In collaboration with a start-up company that is highly focused on sustainability, she recently shipped the first 500 kilos of the Madagascan salt to the U.S.

Verreaux's Sifaka, a favorite of Richard's in Southwestern Madagascar. (Credit: Flickr user nomis-simon, CC)

Verreaux’s Sifaka, a favorite of Richard’s in Southwestern Madagascar. (Credit: Flickr user nomis-simon, CC)

Taking time away from protecting the lemurs and enhancing the lives of the Malagasy people, Richard said her Duke lectures will have broad appeal for anyone interested in conservation, or for those who just enjoy seeing adorable pictures of lemurs.

She hopes to focus on writing a book, the topic of which will draw from her public lecture on March 5 at 6:00 pm at the Great Hall of the Mary Duke Biddle Trent Semans Center for Health Education. This lecture is set to explore how an array of different sciences has changed our understanding of Madagascar’s history.

And the conservationist who said she does everything has some advice for conserving her own mental sanity.

“One thing I need to do going forward is to find things to stop doing,” she admits. “And I’m not good at that because they are all too interesting and seemingly too important,” she said.

So, what’s next for Alison Richard?

“More of doing everything!” she said.

Richard's installation as vice chancellor of Cambridge in November 2009 was occasioned by a visit from  her Majesty Queen Elizabeth II, who's husband, Prince Philip, is the chancellor.

Richard’s installation as vice chancellor of Cambridge in November 2009 was occasioned by a visit from her majesty Queen Elizabeth II, who’s husband, Prince Philip, is the chancellor.

Is it Computer Science or Biology? A Bit of Both

Guest Post By Chichi Zhu, NC School of Science and Math

The National Evolutionary Synthesis Center (NESCent), is tucked away behind the supermarkets and youth-infested restaurants on Ninth Street in Durham. It’s a National Science Foundation brainchild with the purpose of consolidating data collected on small scales to help evolutionary biologists answer larger scale questions.

Allen Rodrigo

Allen Rodrigo directs NESCent and is a professor of biology at Duke

NESCent pursues a variety of missions, from answering these big ideas to connecting evolutionary science to linguistics and religious and cultural studies. Behind NESCent’s day-to-day function is evolutionary biologist Allen Rodrigo.

As a response to the question “so, what exactly is it that you do?” Rodrigo laughs. Here at NESCent, he oversees all of the programs, managing NSF grant money and keeping each part of the center on track with its mission. But NESCent is coming to the end of its funded run, and Dr. Rodrigo himself does far more than direct this innovative program.

Rodrigo is also a professor at Duke University and a computational evolutionary biologist. As a student, he was interested in three areas of study: mathematics, computer science, and biology. He continued pursuing all three tracks throughout his higher education, and allowed coincidence to launch him into his field today. The timing of his post-doc perfectly coincided with a late-1980s boom in technologic and scientific advances. With the invention of PCR and the subsequent increase in ability to study genetics, there came a demand for people with the skill and ability to conduct studies computationally, thus propelling Dr. Rodrigo into this growing field.

“There are many benefits to using computational methods,” Rodrigo said. “Suppose you want to compare two potential hypotheses on how a system might look, what patterns you might see. A computational biologist can help you with that.” He advocates for his area of study with a digestible list of its merits: “It helps experimentalists, it helps make inferences, and it helps make predictions about patterns.”

Today Rodrigo teaches classes at Duke, including courses on statistics for biologists and courses on computational science. He applies his passions for computational biology to his own research.

He is currently using computational study to track the evolution of traits of cancer related to their malignancy. “We start with a small set of cells and develop simulations that tell us how these cells change, grow, and divide,” Rodrigo said. “We can simulate how mutations accumulate, and can simulate, for a given collection of cells, what patterns of evolution you’d obtain.”

Chichi Zhu

Chichi Zhu

Working with oncologists from Duke, his job is to use these computational and mathematical methods to search for patterns that oncologists can then use to collect laboratory data. “To do this all in a lab would take quite a long time,” he said. “To apply computational biology is much more efficient.”