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.
, , , # Data from: Topological mixing and irreversibility in animal chromosome evolution

This repository contains data from multiple related studies investigating chromosome evolution across Metazoa using ancestral linkage group (ALG) analyses and phylogenetic methods. This dataset contains pairs of BCnS loci that are stable, unstable, or close in a selection of clades. This is Supplementary Table 16 in the manuscript https://doi.org/10.1101/2024.07.29.605683

* Original DOI: [https://doi.org/10.5061/dryad.m905qfvbv](https://doi.org/10.5061/dryad.m905qfvbv)

## Brief Description

This dataset includes:

1. **Topological mixing and irreversibility analysis** (`SupplementaryTable_16.xlsx`): Data on clade-defining locus pairs that demonstrate topological linkage and mixing in animal chromosome evolution
2. **Comprehensive phylogenetic analysis workflow** (`newick_and_timetree_20251118/`): Complete analytical pipeline including phylogenetic trees, chromosome evolution analyses, and temporal patt..., ,