A human, an octopus, and a coral could hardly look more different — yet deep inside their cells, their chromosomes still carry recognizable pieces of a genome inherited from an animal ancestor that lived more than 600 million years ago. A study published today in Science Advances by researchers at the University of Vienna maps how those pieces have been reshuffled across the world of animals and reveals that animal genomes evolve along a limited set of irreversible "evolutionary highways". The latest findings provide an important basis for the conservation of animal biodiversity.

All living animals share a common ancestor from over 600 million years ago. Since then, their chromosomes have fused, split, and rearranged countless times. Today thousands of animal genomes have been sequenced. For the first time in this study an international team led by scientists from the University of Vienna set about comparing them all at once. So far it has been a major challenge to make sense of how their genomes changed over such vast timescales. "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."

Most sequenced genomes are "drafts" that show which genes an animal has but not how they are arranged. Chromosome-scale assemblies instead place every gene in order along complete chromosomes – they are much harder to produce, and only recently have enough animals been sequenced this way to allow a comparison across the world of animals.

Largest comparison across the animal tree of life to date

The team analyzed more than 5,800 publicly available chromosome-scale genomes spanning 4,454 species across 19 animal phyla — the largest such comparison across the animal tree of life to date. They developed a new framework, called evolutionary genome topology, that projects this enormous diversity onto a single map. The approach revealed that genomes do not change at random: instead, they travel along "evolutionary highways," a path revealed by hundreds of present-day species whose genomes have evidence of traveling on or "getting off" of the highway at different times and 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."

At the heart of these patterns is a process the team named "fusion-with-mixing" in an earlier study: when two chromosomes fuse, their genes intermingle in a way that cannot be undone, leaving a permanent record of the event. Because these changes run only one way, they serve as reliable markers of shared ancestry, evidence already used to reveal the sibling group to all other animals.

The researchers found that differences in chromosome number across animal groups arise either from the combination of ancestral chromosomes or from their separation, and that in both cases, fusion-with-mixing leads lineages along very different evolutionary paths.

Over time major animal groups get placed in distinct regions of "genome-architecture"

Because this process cannot be reversed, once such a detour ("fusion with mixing") occurred, it places major animal groups in distinct regions of "genome-architecture space". Over time, this progressive, one-way mixing shapes the diverging paths of animal genome evolution and leaves a lasting imprint on a broad range of genes, including key genes that control development.

Because evolutionary genome topology compares genome architecture rather than only DNA sequence, it gives researchers a way to turn the growing flood of chromosome-scale animal genomes into a shared coordinate system. That could help prioritize unusual lineages for deeper study and test whether chromosome changes are linked to shifts in gene regulation, development, or biodiversity.

The framework's relevance reaches beyond evolutionary biology. Because some clades occupy unique, isolated regions of the map — lineages whose genome architecture has no close parallel like mosquitos, glass sponges, or earthworms— the approach could help flag evolutionarily distinctive groups. It can also be used to simulate possible future directions of genome evolution, offering a way to explore how animal biodiversity may continue to change.

Summary:

• Researchers built the first single "map" of how animal genomes are organized, comparing more than 5,800 chromosome-scale genomes from 4,454 species across 19 major animal groups — the largest such comparison to date.
• Animals' genomes travel along a limited set of "evolutionary highways," driven by chromosome mergers and splits whose effects can never be reversed — genomes can't go back where they came from.
• The map shows which animal lineages are the most genomically unusual—and even lets researchers simulate where animal genomes might go next.
• The new system could help prioritize unusual lineages for deeper study and test whether chromosome changes are linked to shifts in gene regulation, development, or biodiversity.
• Furthermore, the latest findings provide an important basis for the conservation of 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.

About the University of Vienna:

At the University of Vienna, curiosity has been the core principle of academic life for more than 650 years. For over 650 years the University of Vienna has stood for education, research and innovation. Today, it is ranked among the top 100 and thus the top four per cent of all universities worldwide and is globally connected. With degree programmes covering over 180 disciplines, and more than 10,000 employees we are one of the largest academic institutions in Europe. Here, people from a broad spectrum of disciplines come together to carry out research at the highest level and develop solutions for current and future challenges. Its students and graduates develop reflected and sustainable solutions to complex challenges using innovative spirit and curiosity.