The genomes of 233 primate species reveal key features of human evolution, human disease and the conservation of their biodiversity
A joint study by Spanish and international scientists brings new information about the genetic diversity and phylogeny of primates, important for understanding and conserving diversity and preventing the extinction of the species closest to ours. But in addition, it identifies a new way of finding genetic mutations that may be responsible for many human diseases.
The research led by Tomàs Marquès-Bonet, ICREA Researcher at IBE (CSIC-UPF) and Professor of Genetics at the Department of Medicine and Life Sciences (MELIS) at Pompeu Fabra University (UPF); doctor Kyle Farh (Illumina) and Dr. Jeffrey Rogers (Baylor College of Medicine), combines the genome sequencing of more than 809 individuals from 233 primate species, covering nearly half of all primate species on Earth. Earth, including the study of fossil remains and multiplying by 4 the number of primate genomes available so far.
Rare mutations may increase disease risk
One of the limitations of human and clinical genetics is the current inability to detect, among hundreds of thousands of mutations, those that cause disease. The genetic causes of many common diseases, such as diabetes and heart disease, are currently unknown due to a lack of genetic information or the large number of genetic factors involved. Some diseases are believed to arise when a set of genetic variations or mutations with a ‘soft’ effect work together to cause a disease of polygenic origin, such as diabetes or cancer.
By comparing the genome of 809 individuals from 233 species of non-human primates with the human genome, the research identified 4.3 million “missense” mutations that affect the composition of amino acids and can alter the function of the protein. These mutations identified in primates are the basis for comparative studies with human variants and for identifying these key variants in many human diseases.
“Six percent of these mutations are abundant in primates and therefore are considered ‘potentially benign’ in human disease, as their presence is tolerated in these animals,” says Kyle Farh, vice president of Artificial Intelligence at Illumina and co-author of the leading publications. .
Identification of disease-causing mutations was achieved thanks to the PrimateAI-3D deep learning algorithm. An artificial intelligence (AI) algorithm developed by Illumina, the world’s leading DNA sequencing company, which is a kind of ChatGPT for genetics that uses the genome sequence instead of human language.
New insights into primate evolution and human uniqueness
The publication of this project contains the most comprehensive catalog of primate genomic information produced to date, covering nearly half of all primate species on Earth. Contains information on primates from Asia, America, Africa and Madagascar.
According to Tomàs Marquès-Bonet, “humans are primates. The study of hundreds of non-human primate genomes, given their phylogenetic position, is highly valuable for human evolutionary studies, to better understand the human genome and the bases of our uniqueness, including the bases of human diseases, and for its future conservation”.
These studies also indicated that primate genetics do not always match their taxonomy. We found several cases in which relationships between primate species are described more as complex networks than simple tree branches.
Another study investigates the evolution of baboons, a large and diverse group of apes, showing that there have been several episodes of hybridization and gene flow between species not previously recognized. Furthermore, we found that the yellow baboons of western Tanzania are the first non-human primates to receive genetic information from three different lineages. “These results suggest that the population genetic structure and history of introgression among baboon lineages is more complex than previously thought, demonstrating that baboons are a good model for the evolution of humans, Neanderthals and Denisovans. says Jeffrey Rogers, an associate professor in the Center for Human Genome Sequencing and Department of Molecular and Human Genetics at Baylor College of Medicine, who co-led this study.
“Our studies provide clues about which species are most urgently in need of conservation efforts and can help identify the most effective strategies to preserve them,” says Lukas Kuderna, first author of one of the studies.
Finally, the new genomic catalog halved the number of genomic innovations once thought to be uniquely human. This observation facilitates the identification of those mutations not shared with primates that, consequently, may be unique to human evolution and the characteristics that make us human.
Source: POMPEU FABRA UNIVERSITY – BARCELONA