The Primate Genome Project reveals hidden evolutionary secrets

In a groundbreaking investigation, scientists have delved deep into the genomes of 233 nonhuman primate species, casting new light on primate evolution, human disease, and biodiversity conservation. 

The multinational research endeavor, led by the Human Genome Sequencing Center at Baylor College of Medicine, the Institute of Evolutionary Biology, Pompeu Fabra University in Barcelona, Spain, and Illumina, Inc., generated a trove of new information. The experts have now published their findings in a series of studies in a special issue of the scientific journal Science.

Nearly half of all primates represented

This initiative, known as the Primate Genome Project, resulted in the most comprehensive collection of primate genomic information to date. Nearly half of all primate species on Earth are represented within this catalog. Over 800 individual primates from these 233 species were studied by researchers hailing from 24 countries. A staggering 4.3 million common missense mutations were identified in this process.

These studies uncovered previously unknown DNA sequence variants and created phylogenies – essentially family trees – for primate species. This wealth of data enriches our understanding of primate and human evolution and expands our knowledge of primate biodiversity. 

Moreover, the research team mined the primate genomic data to uncover new insights into the genetic roots of human disease. A novel algorithm was also developed to predict pathogenic variants in humans.

Dr. Jeffrey Rogers, lead investigator and associate professor at the Human Genome Sequencing Center at Baylor, emphasized the significance of these findings. “The simultaneous publication of this broad array of papers on primate genomics demonstrates the value and the power of comparative genetics. When we investigate the genomics of nonhuman primates, we not only learn about these species, which is important and timely, but we can also place human genetics into its proper comparative context, which provides new insights into human health and human evolution.”

Varying genetic diversity

Genetic diversity among primates varies significantly across geographical regions and taxonomies, as noted by Dr. Tomàs Marquès-Bonet, lead investigator from Pompeu Fabra. “The study of this diversity is crucial for human evolutionary studies, human disease and for their future conservation.”

The urgency of conservation efforts is underscored by the findings, which highlight which primate species are in the most desperate need. Dr. Lukas Kuderna, lead investigator from the Institute of Evolutionary Biology, commented, “Our studies show which species are in most dire need of conservation efforts and can help identify the most effective strategies for preserving these species.”

One particular study in the consortium turned the spotlight onto baboons. Utilizing whole genome sequence data from 225 baboons, researchers discovered new geographic sites of gene flow between different populations. 

The research revealed that yellow baboons from western Tanzania are the first nonhuman primates known to have received genetic input from three distinct lineages. This discovery prompts us to reconsider the evolutionary dynamics of early hominins, which may be far more complex than previously assumed.

“These results suggest that the population genetic structure and history of introgression among baboon lineages is more complex than was previously thought, and that shows that the baboons are a good model for the evolution of humans, Neanderthals and Denisovans,” Rogers said.

Predicting human disease through primate mutations

The team also looked at how primate mutations can be used to predict the risk of human disease. Out of the 4.3 million missense mutations identified in the primates studied, researchers found 6% to be likely benign in human disease, as their high frequency in primate populations seems to be benign. 

In the other 94% of cases, the PrimateAI-3D deep learning algorithm was deployed to predict pathogenicity in human disease. This artificial intelligence algorithm was developed by the team at Illumina.

Dr. Kyle Farh, lead investigator from Illumina, shed light on the findings, saying, “We discovered that if a ‘rare’ mutation cannot be found in the primate genome, it is very likely to cause a human disease. In addition, some of these rare mutations can cause, by themselves, some diseases considered polygenic.”

Significant contribution to science and the world

The newfound genomic catalog significantly impacts our understanding of genetic evolution (see image here). The number of genomic innovations previously thought to be exclusively human has been cut in half by the findings from these studies. This enables easier identification of mutations not shared with primates, which may be unique to human evolution and the characteristics that set us apart as a species.

Dr. Richard Gibbs, founding director of the Human Genome Sequencing Center and Wofford Cain Chair and Professor of Molecular and Human Genetics at Baylor, praised the series of studies. “These studies bring comparative genomics to new heights, and we can predict the impact on both understanding of human biology and on practical clinical diagnostic issues,” said Dr. Gibbs.

More about genome sequencing

Genome sequencing is a laboratory process that determines the complete DNA sequence of an organism’s genome at a single time. This complex task involves sequencing all of an organism’s chromosomal DNA as well as DNA contained in the mitochondria and, for plants, in the chloroplast.

The Human Genome Project, completed in 2003, marked the successful execution of the first full sequencing of the human genome. This ambitious international research effort began in 1990, aiming to map and understand all the genes of human beings. All our genes together are known as our “genome.”

In genome sequencing, the precise order of the four chemical building blocks – adenine, guanine, cytosine, and thymine – that make up the DNA molecule is determined. The human genome, for instance, contains about 3 billion of these base pairs, which reside in the 23 pairs of chromosomes within the nucleus of all our cells.

Modern sequencing technology, known as next-generation sequencing (NGS), allows for sequencing multiple DNA strands in parallel, resulting in huge amounts of data generated quickly and at a lower cost than traditional methods. These technological advancements have allowed genomics to become a significant tool in biological research, medical diagnostics, evolutionary studies, and many other fields.

There are a few different methods for sequencing genomes. Sequencing by synthesis, for example, involves synthesizing a complementary strand of DNA based on the sequence of the original strand. Another common method, called nanopore sequencing, pushes a DNA strand through a tiny pore and reads the sequence based on changes in electrical conductivity.

Genome sequencing can have numerous applications. It can be used to study genetic diseases, trace ancestry, understand and combat hereditary disorders, guide personalized medicine, and even in fields like forensic science. It has helped to uncover numerous genetic variants responsible for certain diseases, track the evolution of different species, and has been a cornerstone in understanding our own human biology and health.

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