A study published in Science Advances by researchers at the University of Vienna maps how genome architecture has been reshuffled across the animal kingdom, showing that animal genomes evolve along a limited set of irreversible “evolutionary highways.” The findings offer a new basis for conservation of animal biodiversity.
Since all animals split from a common ancestor more than 600 million years ago, their chromosomes have fused, split and rearranged repeatedly. Thousands of animal genomes have now been sequenced, but most are “draft” genomes that list an animal’s genes without showing how they’re arranged. Chromosome-scale assemblies, which place every gene in order along complete chromosomes, are harder to produce. Only recently have enough of them existed to allow a comparison across the animal tree of life.
The team analyzed more than 5,800 publicly available chromosome-scale genomes spanning 4,454 species across 19 animal phyla, the largest such comparison to date. They built a new framework called evolutionary genome topology that projects this diversity onto a single map. The approach showed that genomes don’t change at random. Instead, hundreds of present-day species carry evidence of traveling along, or diverging from, shared evolutionary highways 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,” said Darrin Schultz, who led the work. “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.”
Underlying these patterns is a process the team calls “fusion-with-mixing”: when two chromosomes fuse, their genes intermingle in a way that can’t be undone, leaving a permanent, one-directional record. Differences in chromosome number across animal groups trace back to either the combination or separation of ancestral chromosomes, and in both cases fusion-with-mixing pushes lineages onto distinct evolutionary paths, placing major animal groups in separate regions of “genome-architecture space” and leaving a lasting imprint on genes that control development.
Because the framework compares genome architecture rather than sequence alone, it gives researchers a shared coordinate system for the growing number of chromosome-scale genomes, useful for prioritizing unusual lineages and testing links between chromosome change and gene regulation, development or biodiversity. Some groups, including mosquitoes, glass sponges and earthworms, occupy isolated regions of the map with no close parallel, and the approach can also simulate possible future directions of genome evolution. “Understanding these rules of evolution doesn’t just tell us about the past,” said study co-leader Oleg Simakov. “It also lets us ask where genome evolution might go next and enables us to identify key measures for the conservation of animal biodiversity.”
Since all animals split from a common ancestor more than 600 million years ago, their chromosomes have fused, split and rearranged repeatedly. Thousands of animal genomes have now been sequenced, but most are “draft” genomes that list an animal’s genes without showing how they’re arranged. Chromosome-scale assemblies, which place every gene in order along complete chromosomes, are harder to produce. Only recently have enough of them existed to allow a comparison across the animal tree of life.
The team analyzed more than 5,800 publicly available chromosome-scale genomes spanning 4,454 species across 19 animal phyla, the largest such comparison to date. They built a new framework called evolutionary genome topology that projects this diversity onto a single map. The approach showed that genomes don’t change at random. Instead, hundreds of present-day species carry evidence of traveling along, or diverging from, shared evolutionary highways 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,” said Darrin Schultz, who led the work. “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.”
Underlying these patterns is a process the team calls “fusion-with-mixing”: when two chromosomes fuse, their genes intermingle in a way that can’t be undone, leaving a permanent, one-directional record. Differences in chromosome number across animal groups trace back to either the combination or separation of ancestral chromosomes, and in both cases fusion-with-mixing pushes lineages onto distinct evolutionary paths, placing major animal groups in separate regions of “genome-architecture space” and leaving a lasting imprint on genes that control development.
Because the framework compares genome architecture rather than sequence alone, it gives researchers a shared coordinate system for the growing number of chromosome-scale genomes, useful for prioritizing unusual lineages and testing links between chromosome change and gene regulation, development or biodiversity. Some groups, including mosquitoes, glass sponges and earthworms, occupy isolated regions of the map with no close parallel, and the approach can also simulate possible future directions of genome evolution. “Understanding these rules of evolution doesn’t just tell us about the past,” said study co-leader Oleg Simakov. “It also lets us ask where genome evolution might go next and enables us to identify key measures for the conservation of animal biodiversity.”