Topological mixing and irreversibility in animal chromosome evolution
4 affiliations
- 1Department of Neuroscience and Developmental Biology, University of Vienna, Vienna 1010, Austria
- 2Department of Neuroscience and Developmental Biology, University of Vienna, Vienna 00, Austria
- 3Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT 06520, USA
- 4Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT 0650, USA
Abstract
/Summary Paragraph Animal chromosomes can persist with recognizable homology over hundreds of millions of years, in spite of homology-obfuscating processes such as chromosomal fusion and translocation. The frequency and pace of these major genome structural changes are unknown, and it remains unclear whether or how they impact long-term genome evolution. Here, we compare whole chromosomal sequences of 3,631 genomes from 2,291 species spanning all major animal clades and show that animal karyotypes evolve primarily via karyotype contraction, associated with increased rates of chromosomal fusion-with-mixing and dispersion that largely obey chromosomal algebra 1 , or karyotype expansion, which breaks up ancestral linkage groups and forms new chromosomal elements via non-algebraic changes. We show that chromosomal changes can be associated with major extinction events. Using a multi-scale encoding of pan-animal genome homology and a manifold representation of genomic changes, we find that genome evolution is not only driven by changes at the chromosomal level, but that subchromosomal mixing and irreversibility define clade-specific evolution. Using this ‘evolutionary genome topology’ approach, we calculate extrema of irreversible genomic configurations and identify species that occupy intermediate manifold positions, providing evidence for distinct macro-evolutionary trajectories. We propose that investigation of mixed state accumulation around important gene loci (such as Hox) will be crucial in capturing and further study of clade-specific regulatory innovations.
Related
- Anvaya: phylogenomic analysis of chromosome fusion-and-mixing characters and detection of shared whole-genome duplication
- Patterns of base chromosome numbers, genome size and rDNA loci evolution in the genus Capsicum (Solanaceae)
- Cytogenetic constraints on hybridization: a meta-analysis investigating the role of chromosome number in monocot hybrid evolution using a newly developed tool, the ploidy deviation index (PDI)
- A chromosome-level genome assembly of the classical model nematode Panagrellus redivivus for comparative studies of parasitism evolution
- Interchromosomal Translocations and Large Deletions Drive the Evolution of the Outlier Chromosome in the Smallest Photosynthetic Eukaryote
BibTeX
@article{schultz2026topological,
title = {{Topological mixing and irreversibility in animal chromosome evolution}},
author = {Darrin T. Schultz and Arno Blümel and Dalila Destanović and Fatih Sarigol and Oleg Simakov},
journal = {Science Advances},
year = {2026},
month = aug,
doi = {10.1126/sciadv.adz5561},
url = {https://doi.org/10.1126/sciadv.adz5561},
note = {CC BY},
}
RIS
TY - JOUR
TI - Topological mixing and irreversibility in animal chromosome evolution
AU - Darrin T. Schultz
AU - Arno Blümel
AU - Dalila Destanović
AU - Fatih Sarigol
AU - Oleg Simakov
PY - 2026
DA - 2026/08/19
JO - Science Advances
DO - 10.1126/sciadv.adz5561
UR - https://doi.org/10.1126/sciadv.adz5561
AB - /Summary Paragraph Animal chromosomes can persist with recognizable homology over hundreds of millions of years, in spite of homology-obfuscating processes such as chromosomal fusion and translocation. The frequency and pace of these major genome structural changes are unknown, and it remains unclear whether or how they impact long-term genome evolution. Here, we compare whole chromosomal sequences of 3,631 genomes from 2,291 species spanning all major animal clades and show that animal karyotypes evolve primarily via karyotype contraction, associated with increased rates of chromosomal fusion-with-mixing and dispersion that largely obey chromosomal algebra 1 , or karyotype expansion, which breaks up ancestral linkage groups and forms new chromosomal elements via non-algebraic changes. We show that chromosomal changes can be associated with major extinction events. Using a multi-scale encoding of pan-animal genome homology and a manifold representation of genomic changes, we find that genome evolution is not only driven by changes at the chromosomal level, but that subchromosomal mixing and irreversibility define clade-specific evolution. Using this ‘evolutionary genome topology’ approach, we calculate extrema of irreversible genomic configurations and identify species that occupy intermediate manifold positions, providing evidence for distinct macro-evolutionary trajectories. We propose that investigation of mixed state accumulation around important gene loci (such as Hox) will be crucial in capturing and further study of clade-specific regulatory innovations.
SN - 2375-2548
ER -