UCalgary scientists use new research method to better understand monkey evolution

Although separated by millions of years of evolution, capuchin monkeys have evolved similar characteristics to humans, such as large brains, long lifespans, and the ability to adapt to significantly different habitats.

An international team of scientists, led by the University of Calgary, sequenced the genome of a capuchin monkey to uncover new genetic clues about the evolution of the species’ large brain size and longevity. They also developed a new research method, FecalFACS (fluorescence activated cell sorting of feces) to generate non-invasive, high-coverage genomes from monkeys living in different habitats to look at adaptation to drought and food shortage.

Recently published in The Proceedings of the National Academy of Sciences, the research took place over several years and was the result of a substantial international effort spanning Canada, Costa Rica, Spain, the U.K., Japan, the U.S., and more.

Genetic underpinnings explored

“We wanted to look at capuchins in a comparative context across other primates and mammals to see if we could find signatures of selection on traits that make capuchins unique amongst monkeys, and that are also trademarks of human evolution,” says senior author Dr. Amanda Melin, PhD, associate professor, Department of Anthropology and Archaeology and Canada Research Chair at the University of Calgary.

Scattered widely across Central and South America, capuchin monkeys have the largest relative brain size of any monkey and a lifespan that can exceed 50 years despite their small body size. These features, and their other human characteristics such as complex foraging skills, well-developed cognitive capacity, and dextrous handling skills, make them an informative primate to study.

Comparing capuchins in rainforests and dry forests

By looking at capuchin monkeys’ genome using a comparative genomic approach, including humans and a wide range of other mammals, researchers identified genes underlying brain size and longevity that are under positive selection.

“Although we should be cautious about the biological significance of our findings, it is tempting to speculate that, like in other species, changes to specific aging-related genes or pathways could contribute to the longevity of capuchins,” explains study collaborator Dr. João Pedro de Magalhães, researcher at the University of Liverpool studying aging, longevity and genome biology.

Furthermore, the researchers worked with Dr. Roman Krawetz, PhD, associate professor, Cumming School of Medicine, to develop a new research method, fecalFACS, to recover capuchin intestinal skin cells from feces. The cells gathered through the newly developed technique allowed researchers to sequence high-quality whole genomes by adapting flow cytometry, which is regularly used in cancer research, for a completely different purpose, sorting cells found in primate feces.

Using whole genome sequencing from fecal-sourced cells, researchers compared the genomes of capuchin monkey populations in tropical dry forests and lowland rainforests. They identified local adaptations and divergence in genes involved in water balance, kidney function, and metabolism.

Non-invasive technique

“By putting the monkey feces through a flow cytometer, we were able to pull out epithelial cells that had passed through the gut and use them for genome sequencing. This technique made it much more like working with high-quality tissue samples but from a safe, non-invasive origin,” says the study’s lead author, Dr. Joseph Orkin, PhD, who at the time of the research was a postdoctoral scholar in the Department of Anthropology and Archaeology and Alberta Children’s Hospital Research Institute at the University of Calgary.

Now Orkin is a La Caixa postdoctoral junior leader at Universitat Pompeu Fabra in Barcelona. “Using fecalFACS is a new way to study the population and conservation genomics of wild animals that before was prohibitively expensive and difficult to do.”

Support future conservation efforts

With the creation of fecalFACS, the UCalgary team has established a new non-invasive research method that is cost-effective and will help future conservation efforts through the research of genomics.

“There is a lot that needs to be done for conservation, but as people who study genomics, one of the things we really try to do is understand the genetic health of these populations so we can help to inform conservation management,” says Orkin. “The hope here, aside from our own narrow interests, is that this could be a real benefit for future mammalian conservation.”