The largest primate study ever has revealed surprises about humanity and our closest relatives, providing insight into which genes separate us from other primates and which do not. The huge international study also yielded new data for a wide range of disciplines, including human health, conservation biology and behavioral science.
Today, there are more than 500 species of primates, including humans, monkeys, apes, lemurs, tarsiers, and apes. Many of them are threatened by climate change, habitat loss and illegal hunting. The researchers sequenced the genomes of nearly half of all primate species and examined more than 800 genomes from 233 species from around the world, representing all 16 primate families. The work was published in a series of articles in Science and Science Advances this week (1-10).
"The more we understand primate genomics, the more we understand human genomics," says primatologist Alison Behie of the Australian National University in Canberra. "There's the potential to do a lot more really interesting work when they increase the sample size to bring in more species."
Huge expansion
Five years ago, scientists sequenced the genomes of less than 10% of primate species, says one of the project's leaders, Dong-Dong Wu, an evolutionary biologist at the Chinese Academy of Sciences in Kunming.
The effort began after a team led by Kyle Farh at San Diego, California-based sequencing company Illumina developed a way to predict whether mutations in the human genome cause disease by looking for the same mutations in great apes. The work relied on monkey genomes sequenced by Tomàs Marquès Bonet, a comparative genomics researcher at the University of Pompeu Fabra in Barcelona, Spain, and his colleagues, and demonstrated the power of looking beyond the human genome in the study of human disease.
"Kyle called me one day and basically asked me if I had more genomes in the queue for sequencing," says Marquès Bonet. The resulting project quickly attracted researchers from 24 countries who wanted to contribute samples and perform sequencing. "There is an opportunity for the conservation, evolution and understanding of the human genome," says Marquès Bonet.
"I'm particularly proud of the primatologists in Brazil and India," he says, because these hotspots for primate biodiversity have previously been underrepresented in genetic studies. "It's really a Herculean effort," he says.
Sequencing continues. "It's not the end of this project, it's just the beginning," says Wu. However, Marquès Bonet says it is becoming increasingly difficult to track down samples from species that have not yet been sequenced. "We're reaching a plateau," he says. "Going from 233 to 300 is extremely difficult."
Human insights
The primate resource promises to help researchers improve their understanding of human biology and disease. In one study by Marquèse Bonet et al., the genomes of 233 primate species were used to classify the 4.3 million common gene variants present in the human genome. By assessing how common these variants were across species, the researchers were able to deduce that approximately 98.7% of the variants they checked were likely to be benign in humans. This information could be used to identify disease-causing mutations in people whose entire genome or their exome—the protein-coding part of the genome—has been sequenced.
In another study, Wu and his colleagues compared the genomes of 50 species to map how the primate lineage evolved. They identified thousands of genetic sequences that became dominant over the course of evolution in different branches of the tree. For example, genes involved in brain development arose in the common ancestor of humans, great apes, and New World monkeys, setting the stage for the rapid evolution of large brains in humans. "The expansion of the brain started a long time ago," says Wu.
Meanwhile, a large cache of gene variants thought to be unique to humans because they are found in Homo sapiens but not in archaic human relatives called Neanderthals and Denisovans has been shown to be widespread among primates. Almost two-thirds of the variants considered exclusively human were present in at least one other primate species, and more than half were found in two or more.
Genetics of social structure
The ambition of the behavioral sciences is to identify the genetic mechanisms that explain specific behaviors. One of the studies drew this link. Xiao-Guang Qi, a behavioral ecologist at Northwestern University in Xi'an, China, says the five species of snub-nosed monkeys are among a handful of primates — including humans — that form complex, multi-level societies composed of large units. smaller family units. Two of the five – the snub-nosed monkey (Rhinopithecus roxellana) and the black-and-white snub-nosed monkey (Rhinopithecus bieti) – live in larger groups in cold, high-altitude environments.
By comparing the genomes of social proboscis monkeys with those of less socially related monkeys, known as baboons, and with those of more distantly related primates, Qi and his colleagues identified genes that appear to be associated with the formation of large multilevel societies. The team found that climate changes more than six million years ago led to a shift in ape social structure from small groups with one male and a few females to complex societies with multiple males and females.
"It's not the current environment that neatly explains their social organization; what happened in the past is probably as important or even more important," says co-author Cyril Grueter, an evolutionary anthropologist at the University of Western Australia in Perth.
Qi says changes in the brain hormones dopamine and oxytocin were involved. These neurotransmitters are key to forming social bonds, and Qi says colder conditions require a tighter bond between females and their young to ensure survival. This led to more monkeys and larger group sizes, he says.
Grueter says the evolutionary origins of other behaviors, such as mating, could also be investigated using this approach.
Analysis of the genomes of all 233 species also has conservation implications. For example, it shows that genetic diversity within a species is not consistent with its extinction risk. That's surprising, Behie says, because the lower genetic diversity that can result from inbreeding when population size shrinks is widely seen as a sign that a species is at risk of extinction. The finding suggests that for some endangered species, populations declined so quickly that there was no time for inbreeding. This points to factors other than inbreeding – such as habitat destruction – that are a greater threat to the species' resilience.
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