An ancient rodent Morganucodon is the ancestor of all mammals including humans, study finds

The genome organization of the oldest mammal common ancestor has been recreated by an international research team.

A new study shows the reconstruction of the ancestral genome may aid in both the study of mammalian evolution and the preservation of contemporary species.

This fossilized animal, Morganucodon, which lived approximately 200 million years ago, most likely resembled the earliest mammal progenitor. The results of the study have been published in PNAS on September 26.

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

The research was carried out by using 32 living species genome samples including humans and chimps, wombats and rabbits, manatees, domestic cattle, rhinos, bats, and pangolins. The analysis also included the chicken and Chinese alligator genomes as comparison groups.

As suggested by the University of California, Davis, some of these genomes are being generated as part of the Earth BioGenome Project and other large-scale biodiversity genome sequencing initiatives. The Earth BioGenome Project Working Group is chaired by Lewin.

According to Joana Damas, the first author of the study and a postdoctoral researcher at the UC Davis Genome Center, the reconstruction reveals that the mammal ancestor had two sex chromosomes and 19 autosomal chromosomes, which govern the inheritance of an organism's traits aside from those controlled by sex-linked chromosomes.

More than 320 million years

In all 32 genomes, the scientists found 1,215 clusters of genes that always appear in the same order and on the same chromosome.

“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,” Lewin 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,” explained Professor William Murphy, Texas A&M University, who was not an author of the paper, referring to rearrangements and sequence duplications, which are major drivers of genome evolution.

“This provides the foundation for assessing the role of natural selection in chromosome evolution across the mammalian tree of life,” he also added.

The ancestral chromosomes from the common ancestor could be traced by the researchers forward in time. They discovered that there were variations in chromosomal rearrangement rates among mammal lineages.

Abstract:

Decrypting the rearrangements that drive mammalian chromosome evolution is critical to understanding the molecular bases of speciation, adaptation, and disease susceptibility. Using 8 scaffolded and 26 chromosome-scale genome assemblies representing 23/26 mammal orders, we computationally reconstructed ancestral karyotypes and syntenic relationships at 16 nodes along the mammalian phylogeny. Three different reference genomes (human, sloth, and cattle) representing phylogenetically distinct mammalian superorders were used to assess reference bias in the reconstructed ancestral karyotypes and to expand the number of clades with reconstructed genomes. The mammalian ancestor likely had 19 pairs of autosomes, with nine of the smallest chromosomes shared with the common ancestor of all amniotes (three still conserved in extant mammals), demonstrating a striking conservation of synteny for ∼320 My of vertebrate evolution. The numbers and types of chromosome rearrangements were classified for transitions between the ancestral mammalian karyotype, descendent ancestors, and extant species. For example, 94 inversions, 16 fissions, and 14 fusions that occurred over 53 My differentiated the therian from the descendent eutherian ancestor. The highest breakpoint rate was observed between the mammalian and therian ancestors (3.9 breakpoints/My). Reconstructed mammalian ancestor chromosomes were found to have distinct evolutionary histories reflected in their rates and types of rearrangements. The distributions of genes, repetitive elements, topologically associating domains, and actively transcribed regions in multispecies homologous synteny blocks and evolutionary breakpoint regions indicate that purifying selection acted over millions of years of vertebrate evolution to maintain syntenic relationships of developmentally important genes and regulatory landscapes of gene-dense chromosomes.