A human, an octopus, and a coral may appear to have almost nothing in common, but their chromosomes still contain recognizable fragments inherited from an animal ancestor that lived more than 600 million years ago. Researchers at the University of Vienna have now traced how those ancient genomic pieces were reorganized as animal life diversified.
The study, published in Science Advances, suggests that animal genomes do not evolve through an unlimited number of possible routes. Instead, chromosome changes tend to move along a restricted set of irreversible pathways that the researchers describe as “evolutionary highways.” The findings may also provide a valuable foundation for efforts to understand and conserve animal biodiversity.
Tracing More Than 600 Million Years of Genome Evolution
Every living animal ultimately descends from a common ancestor that existed more than 600 million years ago. Since that time, chromosomes have repeatedly fused, separated, and been rearranged as new animal lineages emerged.
Thousands of animal genomes have now been sequenced, but comparing their long-term evolution has remained difficult. In this study, an international team led by University of Vienna researchers brought thousands of genomes together in a single large-scale comparison.
“Understanding these rules of evolution doesn’t just tell us about the past,” said Oleg Simakov, a professor at the University of Vienna who co-led the study. “It also lets us ask where genome evolution might go next and enables us to identify key measures for the conservation of animal biodiversity.”
Many sequenced genomes remain “drafts.” They can reveal which genes an animal possesses without showing exactly where those genes are positioned along its chromosomes. Chromosome-scale assemblies provide much more detail by arranging genes in their proper order across complete chromosomes. Producing these assemblies is considerably more difficult, and only recently have enough species been analyzed at this level to make a broad comparison across the animal kingdom possible.
Largest Chromosome Comparison Across the Animal Tree of Life
The researchers examined more than 5,800 publicly available chromosome-scale genomes representing 4,454 species from 19 animal phyla. According to the team, this is the largest comparison of its kind across the animal tree of life.
To organize such a vast amount of information, the scientists created a framework called evolutionary genome topology. It places the enormous variety of animal genome structures onto a single map.
That map revealed an important pattern. Genome architecture does not appear to change randomly. Instead, animal lineages tend to move along “evolutionary highways.” Evidence from hundreds of living species shows that different groups traveled along these routes or departed from them at different times and at different rates.
“For the first time, we can see thousands of genomes on a single map and trace the unique paths along which animals’ DNA evolved. Viewing the map as a whole gives us a picture of the patterns by which animal genomes have changed over time,” said Darrin Schultz, who led the work as a postdoctoral researcher at the University of Vienna and is now an Assistant Professor at Lehigh University and Lehigh Oceans. “And if we fold the map up in a different way, we can compare how different groups of animals took different paths from each other after splitting onto different evolutionary paths.”
Irreversible Chromosome Mixing Leaves a Genetic Record
A major force behind these patterns is a process the researchers previously named “fusion-with-mixing.” It occurs when two chromosomes join, and their genes become intermixed. Once this happens, the original arrangement cannot be restored.
That irreversibility makes such chromosome changes especially useful for reconstructing evolutionary history. Each event leaves a lasting genomic record that can serve as a marker of shared ancestry. Researchers have already used this type of evidence to help identify the sibling group to all other animals.
The team found that differences in chromosome numbers among animal groups can arise in two main ways. Ancestral chromosomes can combine, or they can separate. In either case, fusion-with-mixing can push different lineages onto very different evolutionary trajectories.
Animal Groups Occupy Distinct Genome Architecture Regions
Because the process cannot be reversed, a major chromosome detour can permanently influence where a lineage ends up in what researchers describe as “genome-architecture space.”
Once such a change (“fusion with mixing”) takes place, major animal groups can be shifted into distinct regions of this genomic landscape. As chromosome mixing accumulates over time, lineages continue to diverge. These changes can leave long-lasting effects across many genes, including important genes involved in controlling development.
Evolutionary genome topology focuses on the arrangement and structure of genomes rather than relying only on DNA sequences. This gives researchers a shared coordinate system for comparing the rapidly growing number of chromosome-scale animal genomes.
The framework could make it easier to identify unusual evolutionary lineages that deserve closer study. It may also help scientists investigate whether changes in chromosome structure are connected to differences in gene regulation, development, or biodiversity.
Identifying Some of the Most Distinctive Animal Genomes
The potential applications extend beyond reconstructing evolutionary history. Some clades occupy highly isolated parts of the genome map because their chromosome architecture has few close parallels.
Mosquitoes, glass sponges, and earthworms are among the lineages that stand out in this way. By highlighting groups with especially distinctive genome organization, the framework could help researchers identify evolutionarily unusual animals that may warrant greater scientific or conservation attention.
The system can also simulate possible future directions of genome evolution. That could give scientists a way to explore how animal genomes and biodiversity might continue to change over time.
Summary
- Researchers created the first unified “map” of animal genome organization by comparing more than 5,800 chromosome-scale genomes from 4,454 species across 19 major animal groups. It represents the largest analysis of its kind so far.
- The results suggest that animal genomes move along a limited set of “evolutionary highways.” Chromosome mergers and separations can produce changes that cannot be reversed, preventing genomes from simply returning to earlier arrangements.
- The new map reveals which animal lineages have particularly unusual genome architectures and can also be used to simulate possible future directions of genome evolution.
- Researchers may use the framework to identify unusual lineages for additional study and to test whether chromosome changes are associated with differences in gene regulation, development, or biodiversity.
- The findings may also provide an important scientific basis for conserving animal biodiversity.
Funding for this research was provided by the European Research Council (Horizon 2020 / European Union Research and Innovation Programme, grant No. 945026), the Austrian Science Fund (FWF, grant P32190), and the Rupert Riedl Prize of the Vienna Haus des Meeres Verein.