Trove of genetic data yields insights into primates’ evolution

A new dataset of genetic information collected from 233 primate species, the largest and most complete of its kind, promises to yield insights into primates’ evolutionary biology and how genetics influences their behavior, says Yale biological anthropologist Eduardo Fernandez-Duque.

The dataset, assembled by a consortium that includes dozens of researchers from institutions worldwide, includes samples from 30 owl monkeys inhabiting a field site in northeastern Argentina established by Fernandez-Duque in 1996 on 2,500 acres of forest in the country’s Chaco region of Formosa Province. It provided the basis for three separate studies published June 2 in the journal Science, two of which Fernandez-Duque coauthored.

All told, the researchers compiled data from 809 individuals representing 233 of the 521 recognized primate species, covering all 16 primate families and 86% of genera — the classification that falls between family and species. More than half of the species in the dataset are threatened with extinction, according to the International Union for the Conservation of Nature.

Importantly, more than 72% of individuals represented in the dataset — including all the owl monkeys that Fernandez-Duque sampled — were born in the wild, he said.

“The dataset’s high number of wild-born individuals is novel and extremely valuable,” said Fernandez-Duque, a professor of anthropology in Yale’s Faculty of Arts and Sciences and the Yale School of the Environment.

The owl monkeys, which entirely comprise the family Aotidae, is the only primate species in the Americas with nocturnal habits. Some species are entirely nocturnal while others are both nocturnal and diurnal. The new dataset could help researchers better understand, among other things, the genetics behind the activity patterns and circadian biology of owl monkeys and other primates.

The fact that the genomic information came from wild-born individuals (as opposed to those in captivity) offers researchers an important advantage, Fernandez-Duque explained.

“We know where the individuals we sampled live in the wild. We’ve studied what they eat, where they move, and whether they have reproduced,” he said. “If you’re sequencing genes related to activity patterns from individuals in captivity, you’re lacking basic ecological information — such as the climate and altitude of their habitat in the wild — that is extremely important in understanding their genomes, which presumably adapted through exposure to specific environments.”

In one of the papers co-authored by Fernandez-Duque, researchers combined the new dataset with information from the fossil record to create the most complete, time-calibrated phylogeny, or evolutionary tree, of primates that exists. Using this detailed evolutionary tree, researchers estimated that the divergence between humans and chimpanzees, our closest living relatives, occurred between 9 million and 6.9 million years ago, which is slightly older than other recent analyses have concluded.

Of particular interest to Fernandez-Duque, the new evolutionary tree was unable to pinpoint where owl monkeys fit among its branches.

“It continues to be unclear where owl monkeys belong in the primate phylogeny in relation to other families of monkeys in the Americas,” he said. “We can’t decide if they are more closely related to cebids, atelids, or pitheciids. You do not have those kinds of uncertainties for any other primate genus or family. Even with this unprecedented dataset, the question is unresolved, which is interesting.”

The same study also found that within-species genetic diversity across primate families and geographic regions is associated with climate of their habitats and their sociality, but not with their risk of extinction. The new dataset also allowed researchers to explore the uniqueness of the human genome relative to other primates. They found that missense mutations — alterations in the DNA that results in a different amino acid being incorporated into the structure of a protein — previously thought to be exclusive to humans occur extensively in other primate species.

In the second study on which Fernandez-Duque is listed as a coauthor, the researchers used the dataset to better understand the potential effects of human genetic variants and their relationship to the risk of contracting diseases. Their analysis showed that 4.3 million common genetic variants are associated with benign effects in humans given their high frequency and non-deleterious presence in primate populations.