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Tempo and mode in karyotype evolution revealed by a probabilistic model incorporating both chromosome number and morphology

Citation

Yoshida, Kohta; Kitano, Jun (2021), Tempo and mode in karyotype evolution revealed by a probabilistic model incorporating both chromosome number and morphology, Dryad, Dataset, https://doi.org/10.5061/dryad.s4mw6m966

Abstract

Karyotype, including the chromosome and arm numbers, is a fundamental genetic characteristic of all organisms and has long been used as a species-diagnostic character. Additionally, karyotype evolution plays an important role in divergent adaptation and speciation. Centric fusion and fission change chromosome numbers, whereas the intra-chromosomal movement of the centromere, such as pericentric inversion, changes arm numbers. A probabilistic model simultaneously incorporating both chromosome and arm numbers has not been established. Here, we built a probabilistic model of karyotype evolution based on the “karyograph”, which treats karyotype evolution as a walk on the two-dimensional space representing the chromosome and arm numbers. This model enables analysis of the stationary distribution with a stable karyotype for any given parameter. After evaluating their performance using simulated data, we applied our model to two large taxonomic groups of fish, Eurypterygii and series Otophysi, to perform maximum likelihood estimation of the transition rates and reconstruct the evolutionary history of karyotypes. The two taxa significantly differed in the evolution of arm number. The inclusion of speciation and extinction rates demonstrated possibly high extinction rates in species with karyotypes other than the most typical karyotype in both groups. Finally, we made a model including polyploidization rates and applied it to a small plant group. Thus, the use of this probabilistic model can contribute to a better understanding of tempo and mode in karyotype evolution and its possible role in speciation and extinction.

Methods

We upload scripts for phylogenetic comparative methods and subsequent analyses using our probabilistic model of karyotype evolution described in Yoshida and Kitano (2021, PLoS Genet). We also upload data set used for the analysis.

Usage Notes

Please read "Ducuments_Yoshida_and_Kitano_2021.doc" for detailed information.

Funding

Japan Society for the Promotion of Science, Award: 17KT0028

Japan Society for the Promotion of Science, Award: 19H01003

Japan Science and Technology Agency, Award: CREST JPMJCR20S2