Mammals are an extraordinarily diverse and successful group of animals, from the tiniest pygmy shrew to the mighty blue whale, and including, of course, ourselves. In a special issue of the journal Science published today (April 27), the Zoonomia Consortium shows how comparing the genomes of 240 modern mammals sheds light on mammalian evolution, with implications for conservation and understanding human and animal health.

The new studies identify regions of mammalian genomes, sometimes just single bases, or letters, of DNA, that are the least changed across mammalian species and millions of years of evolution — regions that are likely biologically important.

The Zoonomia Consortium is led by the Broad Institute of MIT and Harvard University and affiliated with the Earth BioGenome Project, headquartered at the University of California, Davis. The goal of the Earth BioGenome Project is to sequence the DNA of all eukaryotic life on Earth.

“The Zoonomia Consortium was formed around the idea that comparative genomics would reveal important details of mammalian evolution at the genomic level and provide a powerful new tool for understanding human diseases,” said Harris Lewin, distinguished professor of evolution and ecology at UC Davis and collaborator in the consortium. Lewin also chairs the executive working group of the Earth BioGenome Project. “With the incredible set of papers published this week, the consortium has fulfilled its promise and is poised to make more breakthrough discoveries as additional mammalian genomes are sequenced to a higher standard of quality.”

One of the papers in the collection, co-authored by Lewin, used genomic data from modern mammals to reconstruct the evolution of the group since the first mammalian ancestor appeared about 180 million years ago. Lead authors on the paper are Nicole Foley and William Murphy at Texas A&M University.

Timeline for mammal evolution

Mammals lived alongside the dinosaurs for 120 million years and survived the mass extinction that killed off all dinosaurs except the ancestors of modern birds. An open question has been whether placental mammals diversified before the mass extinction, or afterward, with dinosaurs out of the way.

From the Zoonomia project data on modern mammals, Foley, Murphy, UC Davis postdoctoral researcher Joana Damas, Lewin and colleagues constructed a molecular clock, allowing them to attach dates to the appearance of common ancestors of groups of mammals.

“The molecular clock gives us the power to precisely understand when and where different lineages of mammals last shared common ancestors, even in the absence of a fossil record,” Murphy said.

They found that mammals began diversifying before the Cretaceous-Tertiary mass extinction, as the result of continental drift that caused the Earth’s land masses to drift apart and come back together over millions of years.

Another pulse of diversification occurred immediately following the extinction of the dinosaurs, when mammals had more room, resources and stability. This accelerated rate of diversification led to the rich diversity of mammal lineages such as carnivores, primates and hoofed animals that share the Earth today. 

“This is the first time that the timing of chromosome rearrangements in mammalian evolution was able to help resolve important issues in mammalian phylogenetics,” Lewin said. “These data, provided as part our collaboration with the Murphy group and the Zoonomia Consortium, have clarified the relationships of two mammalian orders to other groups. We think that this approach is going to be helpful to resolving disputed phylogenetic relationships in many other parts of the eukaryotic tree of life.”  

Other highlights from the special issue include:

• At least 10% of the human genome is highly conserved across other mammals, indicating regions vital to life and fundamental processes
• Pinpointing genomic regions related to exceptional traits, such as hibernation, brain size  or superlative sense of smell
• Mammals with fewer genetic changes at conserved sites in the genome were at greater risk for extinction, enabling identification of species in need of protection
• From comparisons with other animals, identifying mutations linked to both rare and common human diseases

The Zoonomia consortium is led by Elinor Karlsson, director of the vertebrate genomics group at the Broad Institute and a professor of bioinformatics and integrative biology at the UMass Chan Medical School, and Kerstin Lindblad-Toh, scientific director of vertebrate genomics at the Broad Institute and a professor of comparative genomics at Uppsala University, Sweden. This work was supported in part by the National Institutes of Health, the Swedish Research Council, the Knut and Alice Wallenberg Foundation, and the National Science Foundation.