Breakups and Hookups: a Markov model for karyotype evolution

Chromosome rearrangements represent a prominent form of genetic variation that plays a key role in creating genetic isolation between emergent species. Despite their significance, the mechanisms and constraints governing chromosome evolution remain poorly understood. Relatively few species have karyotypes with very high chromosome counts, and the chromosome sizes of most species tend to be narrowly distributed around the mean length. Here, we develop and analyze a Markov model for the evolution of chromosome number and relative sizes through fission and fusion events, exploring several alternative models for the dynamics of each as well as the effect of enforcing limits on chromosome length. We compare the distribution of chromosome lengths predicted by the Markov model to karyotype data for a range of Eukaryote species to identify the best-fitting fission/fusion dynamics. We find broad support for a model which (i) favours the breaking of long chromosomes, (ii) favours the fusion of pairs of small chromosomes, and (iii) does not require size limitations to provide a good fit to the data. However, there are exceptions. On the one hand, species with micro chromosomes fit best to models with more uniform rates of fission and/or fusion. On the other hand, many species have chromosome sizes that are much more narrowly distributed than our models predict, suggesting the need to explore alternative dynamics and/or limitations to chromosome lengths.