A series of global studies of genomes of primates have revealed key features of their evolution, human disease, and biodiversity conservation.
After generating the most complete catalogue of genomic information for primates ever produced, the studies involving researchers from 24 countries have compared the genomes of 809 individuals from 233 species of primates.
The Institute of Evolutionary Biology, Pompeu Fabra University, Illumina, and Baylor College of Medicine have led a series of global new studies on primate genomes which is published in the journal Science.
The CSIR-Centre for Cellular and Molecular Biology (CCMB), Hyderabad is the Indian collaborator and analysed the Indian primate species.
According to the CCMB, the studies have helped to create a new AI algorithm with clinical applications to identify new insights into the genetic causes of human disease using the primate genomic data.
These studies have discovered DNA sequence variants and developed phylogenies for primate species that will provide new data on primate and human evolution, as well as primate biodiversity.
Two new investigations combined genome sequencing of over 800 individuals from 233 primate species, covering nearly half of all existing primate species on Earth, with the study of fossil remains and multiplying by four-fold the number of primate genomes available to date.
“This also included 83 samples from 19 major primate species in India also studied by scientists at CSIR-CCMB. The study provides new information about primates’ genetic diversity and evolution, which is important for understanding and conserving the biodiversity of the closest species to our own,” the CCMB said.
By comparing the genomes of 809 non-human primate individuals from 233 species to the human genome, the research has identified 4.3 million common missense mutations. Such mutations affect the composition of amino acids and can alter the function of proteins, leading to many human diseases. According to researchers, only rare missense mutations can raise the risk of disease.
One of the current limitations of human and clinical genetics is the inability to detect, among hundreds of thousands of mutations, those that cause diseases. Currently, the genetic causes of many common diseases, such as diabetes and heart diseases, are unknown, both due to the lack of genetic information and the large number of genetic factors involved.
Some diseases are thought to originate when a set of mutations with mild effects act together to cause a disease of polygenic origin, like diabetes or cancer.
“We have identified 6 per cent of the 4.3 million missense mutations, and these are abundant in primates. We consider these to be ‘potentially benign’ in human diseases, given that their presence is tolerated in these animals,” stated Kyle Farh, Vice President of Artificial Intelligence at Illumina.
The identification of disease-causing mutations has been achieved thanks to the PrimateAI-3D deep learning algorithm. PrimateAI-3D is an artificial intelligence (AI) algorithm developed by Illumina, the world’s leading company in DNA sequencing. The algorithm is a kind of ChatGPT for genetics that uses genome sequence instead of human language.
The publication of this unique dataset includes the most complete catalogue of primate genomic information produced so far, covering nearly half of all existing primate species on Earth. It contains information of primates from Asia, America, Africa, and Madagascar. This catalogue has enabled the investigators to compare genomes, to improve the understanding of the evolutionary history of primates and it has provided key insights into what makes us human.
According to Govindhaswamy Umapathy, Senior Principal Scientist at CSIR-CCMB whose group, include Shivakumara Manu and Mihir Trivedi, contributed to this research from India, primates have a great genetic diversity that varies between the different geographical regions and taxonomies. “The study of this diversity is crucial for human evolutionary studies, human disease, and for their future conservation.”
Further, he added that the study also found that the western hoolock gibbon, the only ape from India and lion-tailed macaques from northeastern India and Western Ghats, respectively had low genetic diversity among the global primates examined in this study. He stated that these primates need to be given highest priority both in situ and ex situ conservation efforts in India.
These studies have also indicated that the genetics of primates does not always correspond with their current classification system. The research found several cases in which relationships among primate species are best described as complex and network-like rather than simple branching trees.
“These studies provide clues as to which species are in most dire need of conservation efforts, and could help to identify the most effective strategies to preserve them,” CCMB Director, Vinay Kumar Nandicoori said.
The new genomic catalogue has halved the number of genomic signatures that were believed to be exclusively human. This observation facilitates the identification of those mutations not shared with primates that might be the foundation of the characteristics that make us human, the CCMB added.
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