Revealing the genome organization of the earliest common ancestor of all mammals

The results will help to understand the genetics behind adaptations.


From a platypus to a blue whale, all living mammals today are descendants of a single ancestor that existed around 180 million years ago. However, less is known about this animal.

Now, an international team has computationally reconstructed the organization of its genome. The reconstructed ancestral genome could help in understanding mammals’ Evolution and conservation of modern animals. The reconstructed ancestral genome could help in understanding mammals’ Evolution and conservation of modern animals.

The earliest mammal ancestor likely looked like the fossil animal “Morganucodon,” which lived about 200 million years ago.

Harris Lewin, distinguished professor of evolution and ecology at the University of California, Davis, said, “Our results have important implications for understanding the evolution of mammals and conservation efforts.”

Scientists drew on high-quality genome sequences from 32 living species representing 23 of the 26 known orders of mammals. They included chimpanzees, humans, wombats, domestic cattle, rhinos, bats, pangolins, and manatees. The genomes of the chicken and Chinese alligators were also analyzed as comparison samples. The Earth BioGenome Project and other extensive biodiversity genome sequencing initiatives produce some of these genomes. The Working Group for the Earth BioGenome Project is presided over by Lewin.

Joana Damas, the first author of the study and a postdoctoral scientist at the UC Davis Genome Center, said, “The reconstruction shows that the mammal ancestor had 19 autosomal chromosomes, which control the inheritance of an organism’s characteristics outside of those controlled by sex-linked chromosomes, (these are paired in most cells, making 38 in total) plus two sex chromosomes. The team identified 1,215 blocks of genes that consistently occur on the same chromosome in the same order across all 32 genomes. These building blocks of all mammal genomes contain genes critical to developing a normal embryo.”

The scientists found nine whole chromosomes or chromosome fragments in the mammal ancestor whose gene arrangement is similar to modern birds’ chromosomes.

Lewin said, “This remarkable finding shows the evolutionary stability of the order and orientation of genes on chromosomes over an extended evolutionary timeframe of more than 320 million years. In contrast, regions between these conserved blocks contained more repetitive sequences and were more prone to breakages, rearrangements, and sequence duplications, which are major drivers of genome evolution.”

Professor William Murphy, Texas A&M University, who was not an author of the paper, said, “Ancestral genome reconstructions are critical to interpreting where and why selective pressures vary across genomes. This study establishes a clear relationship between chromatin architecture, gene regulation, and linkage conservation. This provides the foundation for assessing the role of natural selection in chromosome evolution across the mammalian tree of life.”

Scientists could follow the ancestral chromosomes forward in time from the common ancestor. Scientists, in time, could trace ancestral chromosomes from the same ancestor. They discovered that there were variations in chromosomal rearrangement rates among mammal lineages. For instance, when an asteroid strike 66 million years ago wiped out the dinosaurs and gave rise to mammals, the rearrangement process in the ruminant lineage—which gave rise to contemporary cattle, sheep, and deer—accelerated.

Co-author Dr. Camilla Mazzoni said“The results will help to understand the genetics behind adaptations that have allowed mammals to flourish on a changing planet over the last 180 million years.”

Journal Reference:

  1. Damas J, Corbo M, Kim J, et al. Evolution of the ancestral mammalian karyotype and syntenic regions. PNAS 119, e2209139119. DOI: 10.1073/pnas.2209139119
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