‘Game changing’ research reveals the full genome sequences of hundreds of primates

The rich genetic diversity and evolutionary history of primates – the group that includes monkeys, apes, lemurs and humans ourselves – has been revealed in full for the first time in a new research paper published today.  And the results will help us gain a better understanding of genetic diseases, human health, how we evolved, and even the mutations that make us uniquely human.

Academics from around the world, including the University of Salford, have sequenced the genomes of more than 200 primate species, nearly half of the current total, to create the first ever global catalogue of genetic diversity among primates. Published today in the journal Science, the new data will open up a new era in primate research. Whereas previous genetic research into primates has mainly focused on relatively small parts of the genome, such as specific genes, this study is the first to publish a diverse sample of whole genomes across the primate family tree. As a comparison, if genes are paragraphs and chromosomes are chapters, the whole genome is the entire book that includes all of an organism’s DNA.

Working with 75 colleagues in Spain, Germany, the US, Brazil, among another 20 countries, the team from Salford contributed 205 samples totalling 77 species, or more than 30% of the species analysed in the new study, from their large primate genetic collection, the only of its kind in Europe. The Salford team also used information from the fossil record in combination with the genome sequences to produce a new best primate family tree to date. The results have created an accurate picture of how all the different branches, including humans, are related to each other, and when these branches split from each other.

Professor Jean Boubli, Chair in Tropical Ecology and Conservation at the University of Salford, one of the papers authors and one of the leading researchers in the Primate Conservation Sequencing Consortium (PCSC) that led this research said: “This is a real game changer in studying many aspects of primate evolution. And it touches on conservation. Many of these species are under threat and the results here could help with conservation efforts. It is a fantastic collaboration that is going to open up a lot of doors to future research.”

Dr Robin Beck, Reader in Biology at the University of Salford, is an expert in fossils and phylogenetics and co-author on the paper. He said: “This study shows the power of whole genomes for understanding primate diversity, and how primates have evolved through time. We now have a high quality family tree of primates, using by far the biggest dataset ever published. It shows how primates have diversified over the last 60 million years, from their origin a few million years after the extinction of the dinosaurs to the present day. For the first time, we have a truly robust timescale for these evolutionary events, and we can now start to try to identify what might have caused them.”

Dr Dorien de Vries is a postdoctoral researcher at the University of Salford who used her expertise in the primate fossil record to identify fossils that could be used to help calculate the timescale of the new primate family tree. She said: “Knowing the timeline of primate evolution provides a great framework for many kinds of future research.  For example, only then can you calculate and compare mutation rates between different primate groups (as we did in the paper) which has important implications for rates of evolution, and what differences there are between small and large primates, among many other questions.”

Dr. Mareike Janiak, a former Salford postdoctoral researcher now at the Canadian Centre of Computational Genomics, combined these fossil data with the genomic data to calculate when different primate groups developed, an analysis that was only possible by using a large supercomputer. Because of the immense size of the data involved, even on a supercomputer the analysis required a full month to complete. She said: “This was a large collaborative effort that was made possible by combining the expertise of researchers from many backgrounds, including field biologists, fossil experts, and computer scientists. Just a few years ago, only around 20 primate genomes were available, so this is a massive leap forward for the field.”

Professor Ian Goodhead, Associate Dean for Research and Innovation for the School of Science, Engineering and Environment and Genomics researcher, said: “This study highlights how effective it is bringing together multiple disciplines to help answer some of the toughest scientific questions. Salford University has invested close to £1m in computational and molecular biology over the past few years, and it’s great to see this pay off to both researchers and students; studies like this highlight how future biologists will be working. Over the next few years we hope to expand this work further to make further contributions to conservation efforts in the Amazon, and more widely.”