Newly Sequenced Genome of Extinct Giant Lemur Sheds Light on the Animal’s Biology, May Offer Insight on Impacts on Madagascar’s Ecosystems

AMHERST, Mass. – Using an unusually well-preserved subfossil jawbone, a multi-national team of researchers has sequenced for the first time the nuclear genome of the koala lemur (Megaladapis edwardsi), one of the largest of the 17 or so giant lemur species that went extinct on the island of Madagascar between about 500 and 2,000 years ago. The findings reveal new information about this animal’s position on the primate family tree and how it interacted with its environment, which could help in understanding the impacts of past lemur extinctions on Madagascar’s ecosystems.

Image

The results of the work of the of 16 researchers, including Laurie Godfrey, professor emerita of anthropology at the University of Massachusetts Amherst, has been published by the journal Proceedings of the National Academy of Sciences.

“More than 100 species of lemurs live on Madagascar today, but in recent history, the diversity of these animals was even greater,” said George Perry, associate professor of anthropology and biology at Penn State and co-author of the study. “From skeletal remains and radiocarbon dating, we know that at least 17 species of lemurs have gone extinct, and that these extinctions happened relatively recently. What’s fascinating is that all the extinct lemurs were bigger than the ones that survived, and some substantially so; for example, the one we studied weighed about 180 pounds.”

Perry explained that much is unknown about the biology of these extinct lemurs and what their ecosystems were like. There is even uncertainty about how they were related to each other and to the extant lemurs that are alive today. This is due, in part, he said, to the difficulty inherent in working with ancient DNA, especially from animals that lived in tropical and sub-tropical locations.

“While many nuclear genomes of extinct animals have now been sequenced since the first extinct animal — the woolly mammoth — had its nuclear genome sequenced at Penn State in 2008, relatively few of these species have been from warmer climates due to faster DNA degradation in these conditions,” said Perry. “For example, to date, Penn State’s Ancient DNA Laboratory has screened hundreds of extinct lemur subfossils [or ancient bones that have not yet gone through the process of turning into rock]. Yet only two of our samples had sufficient DNA preservation for us to attempt to sequence the nuclear genome. The M. edwardsi jawbone was the best preserved.”

Part of the collection of the Laboratory of Primatology and Paleontology at Madagascar’s University of Antananarivo, the jawbone that the team used in its study had originally been discovered at Beloha Anavoha in southern Madagascar. Carbon-14 dating, a commonly used method for determining the age of archeological artifacts of a biological origin, revealed that the M. edwardsi jawbone was about 1,475 years old.

The team used a fragment of the jawbone to sequence the nuclear genome of M. edwardsi. Nuclear DNA contains information about both parents, whereas mitochondrial DNA, which is also used to study extinct species, only contains information about the mother.

They also sequenced the genomes of two extant — or currently living — lemur species: the weasel sportive lemur (Lepilemur mustelinus) and the red-fronted lemur (Eulemur rufifrons). The new study confirmed previous observations of the phylogenetic placement of Megaladapis to be more closely related to Eulemur than to Lepilemur.

In addition to extant lemur species, the team also compared M. edwardsi’s genome to the genomes of dozens of more distantly related species, including golden snub-nosed colobine monkeys, which are folivores, and horses, which are herbivores. The researchers found similarities between M. edwardsi and these two species in some of the genes that encode protein products that function in the biodegradation of plant toxins and in nutrient absorption, consistent with dental evidence suggesting that M. edwardsi was folivorous.

“This partnership has opened for me new windows into the past – new ways to test my ideas about how the giant lemurs behaved, their evolutionary relationships, and how they exploited resources available to them in their environments,” says Godfrey, a paleontologist who has worked in Madagascar for five decades, particularly on the bones of the recently extinct lemurs. While she has discovered new species, their preferred habitats and how climate change and human behavior impacted their populations, she is not a geneticist, and she says “the study of ancient DNA has begun to reveal more about evolutionary relationships than ever before, such as distinguishing between traits that are similar due to convergence and traits that are similar due to shared ancestry, and indeed more about how these animals actually behaved.”

In the future, the team plans to analyze DNA from additional extinct lemurs and non-lemur primates with the goal of continuing to fill in the gaps in the primate family tree.

Joining Godfrey and Perry in the research were study lead author Stephanie Marciniak, Mehreen Mughal and Richard Bankoff of Penn State; Heritiana Randrianatoandro, Jeannot Randrianasy, and Brigitte Raharivololona from Université d’Antananarivo; Christina Bergey of Rutgers University; Brooke Crowley of the University of Cincinnati; Midwestern University’s Kathleen Muldoon; Stephan Schuster of Singapore’s Nanyang Technological University; Ripan Malhi of the University of Illinois Urbana-Champaign; Edward Louis Jr., of the Omaha Henry Doorly Zoo; and Logan Kistler, of the Smithsonian Institution.

The research was supported by funding from the College of Liberal Arts and Huck Institutes of the Life Sciences at Penn State, the National Science Foundation and the Ahmanson Foundation.

The complete article, “Evolutionary and phylogenetic insights from a nuclear genome sequence of the extinct, giant, ‘subfossil’ koala lemur Megaladapis edwardsi,” is available online from PNAS.