Odd lemur’s habitat limits its gene pool

PENN STATE (US) — Sequencing the complete genomes of three populations of aye-ayes—a type of lemur—reveals how disappearing forests threaten their survival.

The International Union for the Conservation of Nature recently re-classified the aye-aye—found only on the island of Madagascar in the Indian Ocean—as “endangered.”


“The aye-aye is one of the world’s most unusual and fascinating animals,” says George H. Perry, assistant professor of anthropology and biology at Penn State.

“Aye-ayes use continuously growing incisors to gnaw through the bark of dead trees and then a long, thin, and flexible middle finger to extract insect larvae, filling the ecological niche of a woodpecker. Aye-ayes are nocturnal, solitary, and have very low population densities, making them difficult to study and sample in the wild.”

Perry adds that he and other scientists are concerned about the long-term viability of aye-ayes as a species, given the loss and fragmentation of natural forest habitats in Madagascar. Their findings appear in the Proceedings of the National Academy of Sciences.

“Aye-aye population densities are very low, and individual aye-ayes have huge home-range requirements,” says Perry. “As forest patches become smaller, there is a particular risk that there won’t be sufficient numbers of individual aye-ayes in a given area to maintain a population over multiple generations.

“We were looking to make use of new genomic-sequencing technologies to characterize patterns of genetic diversity among some of the surviving aye-aye populations, with an eye towards the prioritization of conservation efforts.”

Genetic ‘distance’

Edward Louis, with his team at Omaha’s Henry Doorly Zoo and Aquarium and the Madagascar Biodiversity Partnership, worked to locate aye-ayes and collect DNA samples from three separate regions of Madagascar: the northern, eastern, and western regions.

To discover the extent of the genetic diversity in present-day aye-ayes, the researchers generated the complete genome sequences of 12 individual aye-ayes. They then analyzed and compared the genomes of the three populations.

They found that, while eastern and western aye-ayes are somewhat genetically distinct, aye-ayes in the northern part of the island and those in the east show a much more significant amount of genetic distance, suggesting an extensive period of time during which interbreeding has not occurred between the populations in these regions.

“Our next step was to compare aye-aye genetic diversity to present-day human genetic diversity,” explains Webb Miller, professor of biology and of computer science and engineering at Penn State. “This analysis can help us to gauge how long the aye-aye populations have been geographically separated and unable to interbreed.”

To make the comparison, the team gathered 12 complete human DNA sequences—the same number as the individual aye-aye sequences generated—from publicly available databases for three distinct human populations: African agriculturalists, individuals of European descent, and Southeast Asian individuals.

Using Galaxy—an open-source, web-based computer platform designed at Penn State for data-intensive biomedical and genetic research—the team developed software to compare the two species’ genetic distances.

Long-term separation

They found that present-day African and European human populations have a smaller amount of genetic distance than that found to exist between northern and eastern aye-aye populations, suggesting that the aye-aye populations were separated for an especially lengthy period of time by geographic barriers.

“We believe that northern aye-ayes have not been able to interbreed with other populations for some time. Although they are separated by a distance of only about 160 miles, high and extensive plateaus and major rivers may have made intermingling relatively infrequent,” explains Miller.

He adds that the results of the team’s data further suggest that the separation of the two aye-aye populations stretches back much longer than 2,300 years, which is when human settlers first arrived on the island and started burning the aye-ayes’ forest habitat and hunting lemurs.

The team members hope that their findings will help to guide future conservation efforts for the species. “This work highlights an important region of aye-aye biodiversity in northern Madagascar, and this unique biodiversity is not preserved anywhere except in the wild,” says Louis.

“There is tremendous historical loss of habitat in northern Madagascar that is continuing at an unsustainable rate today.”

The authors add that, in future research, they would like to sequence the genomes of other lemur species—more than 70 percent of which are considered endangered or critically endangered—as well as aye-ayes from the southern reaches of the island of Madagascar.

In addition to Perry, Miller, and Louis, additional scientists contributed to the research from Penn State, the Center for Conservation and Research at Omaha’s Henry Doorly Zoo and Aquarium; and the University of Calgary in Alberta, Canada.

Conservation International, the Primate Action Fund, and the Margot Marsh Biodiversity Foundation funded the aye-aye sample collection. The Ahmanson Foundation and the Theodore F. and Claire M. Hubbard Family Foundation provided logistical support.

The National Institutes of Health, the National Science Foundation, the Pennsylvania Department of Health, and the College of the Liberal Arts at Penn State also supported the study.

Source: Penn State