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New Primate Genomes Study Deepens Understanding of Humans

NEW YORK – Several teams of international researchers have analyzed the genomes of 233 non-human primate species, with findings that have implications ranging from developing conservation strategies for endangered species to understanding human diseases.

In a series of eight papers published in Science on Thursday, along with two accompanying papers in Science Advances, the investigators described their results.

"The analysis of nonhuman primate genomes has long been motivated by a desire to understand human evolutionary origins, human health, and disease," the authors of one paper wrote.

One study that laid the foundation for some of the other analyses, led by Lukas Kuderna and Kyle Kai-How Farh at Illumina, Jeffrey Rogers at Baylor College of Medicine, and Tomas Marques Bonet at Pompeu Fabra University in Spain, took a close look at the genomes of more than 800 individuals from 233 primate species, which include 86 percent of primate genera and all 16 primate families.

DNA samples for this project came from primates across the globe and included the world's most endangered species such as the western black crested gibbon and the northern sportive lemur as well as lorises, galagos, and monkeys of the Americas, which were largely underrepresented in previous studies, the researchers said.

The researchers sequenced the genomes of 703 individuals from 211 primate species on the Illumina NovaSeq 6000 platform and later included datasets of 106 individuals representing 29 species from previously published studies to maximize phylogenetic diversity.  

"Altogether, we compiled data from 809 individuals from 233 primate species, amounting to 47 percent of the 521 currently recognized species," the authors wrote.

The data were used to evaluate heterozygosity within species, which indicates genetic diversity. The golden snub-nosed monkey was found to have the lowest level of diversity, compared to other primates.

The researchers also found that the genetics of primates did not always match their taxonomy. "We found several cases in which relationships among primate species are best described as complex and network-like rather than simple branching trees," they wrote.

The study also investigated whether genetic diversity estimates correlated with extinction risk in primates, a subject of previous debate, according to the authors. They did not find a relationship between numerically coded International Union for Conservation of Nature extinction risk categories and estimated heterozygosity.

With dwindling numbers of animals among many species, driven by climate change, loss of habitat, illegal trading, and hunting by humans, the study could also guide conservation strategies, the authors noted. "The analysis of whole-genome sequences allows estimation of genetic  diversity and evaluation of its association with ecological traits, degrees of inbreeding, and phylogenetic relationships, all metrics relevant to primate conservation genomics," the authors wrote.

 At present, 60 percent of the world's primate species are threatened with extinction, and current trends are likely to exacerbate the rates of biodiversity loss in the near future, they wrote.

The study also found that of 647 missense mutations that occur with high frequency in humans and were thought to be human-specific, 63 percent were present in at least one other primate species, and 55 percent in more than two, suggesting that "mutational recurrence generally might be widespread across primates," according to the authors.

Meanwhile, an accompanying study revealed a unique hybridization event among primate species. It found that the gray snub-nosed monkey was a descendent species from the hybridization between a morphologically differentiated species, the golden snub-nosed monkey, the common ancestor of black-white snub-nosed monkey, and the black snub-nosed monkey.

"To our knowledge, this is the first time that a hybrid speciation event is recorded in primates," said Li Yu, a researcher at Yunnan University in China and one of the corresponding -authors of the study.

Yet another paper used the new genomic data to understand primate social systems. Xiao-Guang Qi of Northwest University in China and colleagues studied Asian colobines, which consist of seven genera and 55 species. These primates are distributed from tropical rainforests to snow-covered mountains and exhibit four distinct types of social organization.

The researchers reconstructed the speciation process of this group using the full genome data and found a strong correlation between the environmental temperature and group size of the species. "The primate species living in colder environments tend to live in larger groups," they noted.