The genome sequencing of 233 primate species would provide a wealth of information for understanding primates’ genetic diversity and evolutionary history. Scientists can learn about the genetic similarities and differences between primate species by comparing their genomes, as well as identify genes and genetic variations that are unique to certain species or shared by multiple species.
Researchers from 24 countries examined the genomes of 809 individuals from 233 primate species, creating the most comprehensive catalog of genomic data on our closest relatives to date. The project, which consists of a series of studies in which researchers from the German Primate Center – Leibniz Institute for Primate Research (DPZ) participated, sheds new light on the evolution and diversity of primates, including humans.
Hybridization and gene flow between different species in baboons, for example, occurred in the past and continue to occur in several regions of their range. Baboons are thus an excellent model for the evolution of early human lineages both within and outside of Africa. In addition, using a specially designed AI algorithm, the genomic data enable new insights into the genetic causes of human diseases (Science, Special Issue).
Primates show great genetic diversity that varies between species and geographic regions. “Studying this diversity is crucial also for understanding human evolution, the causes of human diseases, and for preserving our closest relatives,” says Christian Roos, a scientist in the Primate Genetics Laboratory at the German Primate Center and one of the authors. Led by researchers from Universitat Pompeu Fabra, Spain, Baylor College of Medicine, USA, and Illumina Inc, USA, the genomes of 809 individuals from 233 primate species have been sequenced. This covers nearly half of the extant primate species and increases the number of available primate genomes fourfold.
Studying this diversity is crucial also for understanding human evolution, the causes of human diseases, and for preserving our closest relatives. This covers nearly half of the extant primate species and increases the number of available primate genomes fourfold.
Christian Roos
New insights into primate evolution and the uniqueness of humans
The comparative analyses provide important insights into what distinguishes humans from other primates as well as fundamental information on the genetic diversity and evolutionary history of primates. The number of genomic variants thought to be unique to humans has been cut in half thanks to genomic data.
“This makes it easier to look for mutations that we do not share with other primates and that could therefore be the basis for the traits that make us human,” says Dietmar Zinner, a scientist in the Cognitive Ethology Laboratory at the German Primate Center and one of the authors. One of the studies digs deeper into baboon evolution and discovers previously unknown instances of hybridization and gene flow between baboon species.
“We found that baboons from western Tanzania are the first nonhuman primates to have received input from three genetic lineages,” said Liye Zhang, a doctoral student at the German Primate Center and one of the study’s lead authors. “These findings suggest that the genetic structure of the baboon population and its history of genetic exchange between species is more complex than previously thought, and they demonstrate that baboons are an excellent model for similar processes in the evolution of early human lineages in and outside of Africa,” says Dietmar Zinner.
Species conservation with the help of genome data
Species with high genetic diversity can better adapt to changing environmental conditions and pathogens. There is a risk of inbreeding, which reduces genetic diversity, especially in small populations. Already, 63 percent of all primate species are threatened with extinction, and genetic diversity analysis reveals which species, at least genetically, require the most urgent protection. “We found particularly low genetic diversity in the golden snub-nosed monkey of China and the aye-aye of Madagascar,” Christian Roos says.
Rare mutations can increase disease risk
One of the current limitations in human and clinical genetics is the inability to identify disease-causing mutations among hundreds of thousands. Many common diseases, such as diabetes and heart disease, have unknown genetic causes due to a lack of genetic information or the large number of genetic and other factors involved. By comparing primate genomes, researchers have discovered 4.3 million mutations that may alter protein function and thus cause disease in humans.
Six percent of the 4.3 million identified mutations are common in primates and are thus thought to have little impact on human disease because they are tolerated in these animals. Disease-causing mutations can now be identified more accurately thanks to Illumina Inc’s PrimateAI-3D deep-learning algorithm. “It’s a kind of ChatGPT for genetics that uses genome sequences instead of human language,” says Kyle Farh, vice director of the AI group at Illumina Inc, the world leader in DNA sequencing.
