Data from: Topological mixing and irreversibility in animal chromosome evolution

Animal chromosome homology can persist over hundreds of millions of years,
in spite of fusions and translocations. The frequency and pace of these
major genomic changes, as well as their impact, remain unclear. Using a
multi-scale manifold representation of pan-animal genome homology, we
compare 3,631 whole chromosomal genomes spanning all major animal clades.
This ‘evolutionary genome topology’ reveals irreversible genomic
configurations at both chromosomal and subchromosomal levels. We show that
accumulation of such states over macro-evolutionary time scales results in
distinct evolutionary trajectories with intermediate positions associated
with major phylogenetic groups emergence. We show that key developmental
gene loci are impacted by this process, associating regulatory innovations
with major evolutionary transitions.