Chimpanzee Voices From the Past Go Digital, Open Access

By Karl Leif Bates

A treasure trove of chimpanzee audio recordings from the 1970s has been posted on an open access site for study by a team that includes Evolutionary Anthropology chair Anne Pusey, who also directs Duke’s Jane Goodall Institute Research Center.

An image from the  Scientific Data paper shows the bulky, analog field gear used for making recordings in the 70s.

An image from the Scientific Data paper shows the bulky, analog field gear used for making recordings in the 70s.

Announced this week in the open access journal Scientific Data, the collection includes more than 1,100 recordings made of 17 immature chimpanzees, totaling 10 hours. The recordings were made between 1971 and 1973 by the late Hetty van de Rijt-Plooij and Frans X. Plooij, Dutch researchers working at Goodall’s study site in Gombe National Park, Tanzania.

Though the Plooij collection was catalogued and annotated — notes which Frans then translated from Dutch to English with support from the National Evolutionary Synthesis Center in Durham — the massive collection has never been studied. Preparation of the metadata for the audio recordings was supported by the National Science Foundation (LTREB-1052693).

What the newly digitized recordings represent is the opportunity to study the development of vocalization over a chimpanzee’s lifetime, Pusey explained. Many of the individuals who were recorded as infants and adolescents subsequently turn up in recordings made by Peter Marler in 1967, Charlotte Uhlenbroek in 1991–1993, and Lisa O’Bryan in 2009–2010.

The authors say, “comparing their adult recordings with their infant/juvenile recordings might be an especially effective way of studying vocal development.”

They’re also just kind of fun to listen to. (Browse the entire catalog here.)

Jane Goodall visited Anne Pusey and the archive of Gombe field notes at Duke in 2011. (Duke Photo)

Jane Goodall visited Anne Pusey and the archive of Gombe field notes at Duke in 2011. (Duke Photo)

This work is the latest in a trend of Duke becoming one of the world’s great centers of longitudinal primate studies. Pusey’s work on this audio collection joins the more than 50 years of observational notes and data from Gombe now housed at Duke; Susan Alberts has led the assembly of life history data from nine different primate field studies into a single database. And nearly 50 years of captive lemur data from the Duke Lemur Center was digitized and just posted a few weeks ago. (Pro version on Scientific Data.)

Math and Comp Sci Junior Studies Fruit Flies

By Ashley Mooney

dorsal closure

Dorsal closure is a stage in fruitfly embryonic development that is used to study wound-healing.

Roger Zou, a computer science and math major from Solon, Ohio, is working on creating more efficient ways to study wound-healing in fruit flies. It turns out that the way fruit flies heal actually has implications for how mammals heal too.

The junior is developing computational methods that can more accurately quantify cellular properties of fruit flies. As fruit fly embryos develop, he tracks cells through space and time to learn more about a process called dorsal closure. It’s a developmental stage that is similar to wound healing, where a gap in the embryo’s epithelium—which is like its skin—is closed by the coordinated effort of different types of cells. (see movie below)

Roger Zou is a junior spending the summer in Dan Kiehart's lab.

Roger Zou is a junior spending the summer in Dan Kiehart’s lab.

“It’s fun to study the morphological forces because it’s not entirely understood how organisms develop,” Zou said.

In his analysis, Zou uses a laser under a microscope to make cuts on areas of the fly embryos. After making cuts, Zou uses computational methods to measure the wound healing.

Beyond collecting such data, Zou is developing a computer program that analyzes images from the microscope more accurately.

Zou has worked in Biology Professor Daniel Kiehart’s lab since his freshman year. His project was originally a component of a graduate student’s dissertation, but after she graduated, he continued some aspects of her research.

His project has been funded by the Dean’s Summer Research Fellowship for two consecutive summers. He also has done several independent study projects. Although Zou is planning on publishing his research this summer, he will likely use the data eventually to do a senior thesis.

Several of Zou’s math and computer science classes have given him a background in the techniques needed to use a computer to analyze large sets of image data, he said.

“My favorite thing about my research is the ability to learn new things independently,” Zou said. “[Kiehart] is very good at leading me in the right direction but allowing me to be very independent and I think because of that I’ve been able to learn a lot more and learn from my mistakes.”

Outside of his research, Zou is a teaching assistant for the computer science class Data Structures and Algorithms. He also tutors  Duke students in organic chemistry and middle school children in math through the America Reads*America Counts program. And he also does web development for The Chronicle, Duke University’s independent student newspaper.

After graduating, Zou said he hopes to pursue a PhD in either computational biology or computer science or maybe go for a combined MD-PhD program. No matter which program he chooses, Zou said he wants to continue doing research.

Duke Undergrads Sink Their Teeth into Evolution Research

Undergraduates Ben Schwartz (left) and Amalia Cong (center) have spent the past year studying enamel evolution in the labs of Christine Wall (right) and Greg Wray (not pictured).

Undergraduates Ben Schwartz (left) and Amalia Cong (center) have spent the past year studying enamel evolution in the labs of Christine Wall (right) and Greg Wray (not pictured).

By Erin Weeks

The evolution of thick tooth enamel helped turn our species into hard food-chomping omnivores, and two undergraduates are taking a bite out of research to unravel how that happened. Amalia Cong and Ben Schwartz are building on the work of a recent paper that identified precisely where in the human genome natural selection worked to give our species thick tooth enamel. The original study looked only at the potential role of four genes with a known role in tooth development — so now the team is broadening their scope.

“They’re really excited to expand out and push the envelope on new genes,” said Christine Wall, associate research professor of evolutionary anthropology and one of the authors of the paper, along with professor of biology Greg Wray.

Cong and Schwartz arrived in the Wall and Wray labs last summer through a special research session at Duke, the Howard Hughes Vertical Integration Partners (VIP) Program. For ten weeks, they received a crash course in primate evolutionary genomics.

“They had very little time, and the progress they made was astounding,” Wall said. “The success that they had is really a testament to how hard they worked. This has developed into their own research.”

“We’ve begun to expand our tooth enamel gene analysis to include proteins in conjunction with the RNA in order to gain a more holistic understanding of the evolutionary differences that exist between chimpanzees and humans,” Schwartz said. He will continue to work in the lab through this summer, turning the work into a senior thesis.

“One of our goals was to look at the relative expression of these few genes,” Schwartz said, which they’ve done by comparing tooth development in primates of different ages. “Our results correlated very heavily with known functions of these genes in other animals, such as rats.”

The experience has given both students a taste for research, which they hope to continue doing after graduating from Duke. Cong, who hails from a small city outside of Toronto, will be attending dental school in the fall, while Baltimore native Schwartz is interested in pursuing a joint MD/PhD.

Hey, Tone it Down Little Man

By Karl Leif Bates

If your preferred method of attracting a mate is to bob your head vigorously and flash your chin-fan, you’d better tone it down a notch when there are predators around, lest you become lunch and not Dad.

The fan-waving, head-bobbing social display of a frisky male Anole sagrei tends to be more subtle and subdued …

The fan-waving, head-bobbing social display of a frisky male Anole sagrei tends to be more subtle and subdued …

That’s the take-away advice generated by biology assistant professor Manuel Leal and graduate student David Steinberg in a new paper appearing the week of May 19 in the Proceedings of the National Academy of Sciences. (Visit their lab.)

On nine tiny islands in the Snake Creek region of Great Abaco Island in the Bahamas, the biologists videotaped and observed the social mating behavior of head-bobbing, fan-waving  Anole sagrei studs. Five of the islands also harbored the anoles’ predator, the curly-tailed lizard Leiocephalus carinatus, who is a bit bigger and mostly stays on the ground.

When the predators were present, the anoles chose to do their displays twice as high off the ground and they reduced the amplitude of their head bobs by as much as 60 percent.

...when his major predator, the curly-tailed lizard Leiocephalus carinatus is at large. (credits: Manuel Leal)

…when his major predator, the curly-tailed lizard Leiocephalus carinatus is at large. (credits: Manuel Leal)

The anoles spent just as much time displaying when the predators were around, but doing so a little less flamboyantly may mean the females have to be closer to catch the signal, Leal said. And that, in turn, may affect mating success and how the anole males set up their territories.

CITATION: “Predation-associated modulation of movement-based signals by a Bahamian lizard,” David S. Steinberg, Jonathan B. Losos, Thomas W. Schoener, David A. Spiller, Jason J. Kolbe and Manuel Leal. Proceedings of the National Academy of Sciences, week of May 19, 2014. DOI: 10.1073/pnas.1407190111

Some Animals Move Through The Treetops With Help From A Stiff Back

Guest post from Robin A. Smith, Duke Lemur Center

Some tree-dwelling animals move through the forest with the help of an unlikely tool — a stiff back. A more rigid spine seems to help  stabilize their trunks as they reach across gaps in the canopy, according to Duke researchers.

Slender Loris

The slender loris (Loris tardigradus) is able to exploit tender tips of tree branches by moving slowly and keeping a stiff back rather than leaping from branch to branch. (Credit: David Haring, Duke Lemur Center)

The findings appear in the March 2014 issue of the Journal of Morphology.

Animals that live in the treetops need to be good at crossing gaps between trees in order to move and forage in the canopy without constantly climbing up and down. Some animals leap, hop or bound from branch to branch, flying through the forest in a feat of aerial acrobatics. But others move more slowly and deliberately, reaching out and grabbing onto the tips of the nearest tree to form a bridge and pulling themselves across.

The latter strategy helps some animals venture onto slender branch tips where young leaves and fruits are often found –- perches that are too thin and delicate to leap off without buckling, said lead author Michael Granatosky, a grad student in Evolutionary Anthropology.

To investigate the anatomical traits that help some animals bridge rather than bound between branches, Granatosky and colleagues pored over skeletons in museums and took measurements of the spines and ribs of 22 species — including lemurs, treeshrews, anteaters, opossums and squirrels. Some of the species move slowly and cautiously through the treetops, while others leap and jump.

The researchers also analyzed the bridging behavior of two pairs of closely-related species — the bare-tailed woolly opossum versus the gray short-tailed opossum, and the fat-tailed dwarf lemur versus the slender loris — while the animals negotiated custom-made jungle gyms.

The opossum study was part of a previous experiment by co-authors Daniel Schmitt and Pierre Lemelin at Duke, and the primate study was conducted at the Duke Lemur Center.

The researchers found that the species that bridged more often, or for longer periods of time, had narrower spaces between adjacent ribs and vertebrae.

Their more tightly-woven spines limit their ability to bend side-to-side, but enable them to hold their body out straight to span openings in the canopy without relying on brute muscle strength alone, Granatosky said.

The study was funded by the Force and Motion Foundation and by a National Science Foundation Graduate Research Fellowship to Michael Granatosky.

CITATION: “Functional and evolutionary aspects of axial stability in Euarchontans and other mammals,” Granatosky, M., et al. Journal of Morphology, March 2014. DOI: 10.1002/jmor.20216. http://onlinelibrary.wiley.com/doi/10.1002/jmor.20216/abstract

Seeing may not be perceiving—the neurobiology of perception

The elephant-nosed electric fish

The elephant-nosed electric fish

By Olivia Zhu

Larry Abbott argues that sensation is not perception. In a lecture presented on March 25th to the Department of Neurobiology at Duke, Dr. Abbott, of the Center for Neurobiology and Behavior at Columbia University, presented his model of integrated perception.

Dr. Abbott went into particular depth about how an organism can tell itself apart from its surroundings. Though we may take it for granted, self-identification is extremely important in many instances: for example, when a young, male zebra finch learns how to sing by copying his tutor, he must be able to distinguish his own song from other birds’ songs in order to properly listen to it and refine it.

Dr. Abbott studies self-perception in elephant-nosed electric fish. Electric fish have an organ in their body that sends out strong electric pulses. However, the fish also have a sensory organ to detect electric pulses from potential prey, which are several orders of magnitude lower than their own signals. Their own electric fields should diminish their sensitivity to external electricity; this interference, though, is prevented because their electricity-generating organ sends impulses to the sensory organ to inform it when it is firing. Essentially, the fishes’ neural circuits are tuned to cancel out the input they receive from their own electric pulses.

Ultimately, Dr. Abbott claimed that when you look at your friend, you’re not exactly seeing your friend: your mental image is a product of various mental manipulations of the original sensory input your brain receives. His mathematical, model-based approach attempts to redefine the way in which we view ourselves and our relation to the world.