Is it Just Us?

Plankzooka, on the left there, is two big tubes strapped on either side of the autonomous undersea rover Sentry.

Plankzooka, on the left there, is two big tubes strapped on either side of the autonomous undersea rover Sentry.

We certainly admired the news Friday coming out of a marine science cruise that hasn’t even ended: They found a shipwreck a mile down while also pioneering a new device for gently and precisely sampling plankton at those crushing and dark depths.

But we couldn’t help but notice the “plankzooka’s” uncanny resemblance to a familiar cartoon character.  Here’s an example of some of the juvenile plankton it collected around a methane seep on the sea floor.


A sampling of juvenile plankton from the deep sea.


Summer Data+ Groups Pursue Pigs and Purchases

Many students spend their summer breaks going on vacations and relaxing, but not the 40 students selected to participate in Data+, a summer research program at Duke.

They meet twice a week for lunch to share their work on the third floor of Gross Hall.

A pair of pigs and their piglets. Photo by Alan Fryer via Wikimedia commons

A pair of pigs and their piglets. Photo by Alan Fryer via Wikimedia commons

Mercy Fang and Mike Ma are working on a research project involving prolific pigs, those that make a lot of piglets. They are trying to determine if the pigs are being priced rationally, whether or not the livestock market is efficient and the number of offspring per pig.

Fang said the most challenging part is the research data. “Converting PDF files of data into words has been hard,” said Fang.
The students are using four agricultural databases to determine the information on the pigs, including pedigrees.

Most of the students in Data+ are rising sophomores and juniors majoring in a variety of majors that include math, statistics, sociology and computer science. The program started in mid-May and runs for 10 weeks and allows students to work on projects using different research methods.

Another group of student that presented on June 18 is working on a research project involving data on food choices.

A produce stand in New York City, photo by Anderskev via Wikimedia Commons.

A produce stand in New York City, photo by Anderskev via Wikimedia Commons.

Kang Ni, Kehan Zhang and Alex Hong are using quantitative methods of study using the “clustering process” to determine a recommendation system for consumers to help them choose healthier food choices. The students are working with The Duke-UNC USDA Center for Behavioral Economics and Healthy Food Choice Research (BECR) center.

“Consumers already recognize a system to get a certain snack,” said Zhang. “We want to re-do a system to help consumers make better choices.”

The students are basing their research on nutrition information and food purchases from the BECR Data warehouse, which comes from consumer information from throughout the US. This includes food purchases and nutrition information from 2008-2012.

Zhang added that the hardest part was keeping up with information.
“It’s a lot of data in the future, and it will be challenging putting it into use,” said Zhang.

Students in attendance said the food choices data research group provided good information.

“I liked the quantitative methods they used to categorize food,” said Ashlee Valante.

The Data+ research program is sponsored and hosted by the Information Initiative at Duke (iiD) and the Social Science Research Institute (SSRI).  The funding comes from Bass Connections and from a National Science Foundation grant managed by the Department of Statistical Science.

Warren_Shakira_hed100Guest post by Shakira Warren, NCCU Summer Intern

Bird Consortium Wants to Run the Table

Just a few months after rolling out a huge package of studies on the genomics of 48 members of the bird family tree, an international consortium of scientists is announcing their new goal: sequencing all 10,000 species of birds in the next five years.

Erich Jarvis

Erich Jarvis is an associate professor of neurobiology in the medical school and a Howard Hughes Medical Institute investigator.

Called B10K for short, this effort should be the first attempt to sequence the genomes of all living species in a single class of vertebrates – and the most species-rich one at that.

The consortium announced their intentions in a letter appearing June 4 in Nature.

A genomic-level tree of life of the entire class should reveal links between genetic and phenotypic variation, perhaps reveal the evolution of biogeographical and biodiversity patterns across a wide-range of species, and maybe show the influences of ecology and human activity on species evolution.

But consortium co-leader, Erich Jarvis of Duke neurobiology, just loves birds for their minds. He is involved with the project to enhance his use of songbird brains as models of human speech.

Having proven the technical feasibility of the project and redrawn the bird phylogeny already, the consortium is now expanding to include experts in museum science, biogeography and ecology from the Kunming Institute of Zoology and Institute of Zoology of Chinese Academy of Science in Beijing; the Smithsonian Institution in the USA; and the Center of Macroecology, Evolution and Climate in Denmark. The complete list of contributing institutions and collaborators is listed on the B10K site.

B10K bird phylogeny

The new bird family tree drawn on complete genome sequencing of 48 species representing each major order. Painting by Jon Fjeldså.

“Given the small size and less complex features of bird genomes relative to other vertebrates, the ongoing advances in sequencing technologies, and the extensive availability of high quality tissue samples from birds deposited in museums around the world, reaching this ambitious goal is not only possible but also practical,” the consortium said in a prepared statement.

We look forward to many more exciting findings from B10K, but hopefully not all at once like last time.

-By Karl Leif Bates

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, 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!