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

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...

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Autores principales: Yoshida, Kohta, Kitano, Jun
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Public Library of Science 2021
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8081341/
https://www.ncbi.nlm.nih.gov/pubmed/33861748
http://dx.doi.org/10.1371/journal.pgen.1009502
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author Yoshida, Kohta
Kitano, Jun
author_facet Yoshida, Kohta
Kitano, Jun
author_sort Yoshida, Kohta
collection PubMed
description 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.
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spelling pubmed-80813412021-05-06 Tempo and mode in karyotype evolution revealed by a probabilistic model incorporating both chromosome number and morphology Yoshida, Kohta Kitano, Jun PLoS Genet Research Article 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. Public Library of Science 2021-04-16 /pmc/articles/PMC8081341/ /pubmed/33861748 http://dx.doi.org/10.1371/journal.pgen.1009502 Text en © 2021 Yoshida, Kitano https://creativecommons.org/licenses/by/4.0/This is an open access article distributed under the terms of the Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0/) , which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
spellingShingle Research Article
Yoshida, Kohta
Kitano, Jun
Tempo and mode in karyotype evolution revealed by a probabilistic model incorporating both chromosome number and morphology
title Tempo and mode in karyotype evolution revealed by a probabilistic model incorporating both chromosome number and morphology
title_full Tempo and mode in karyotype evolution revealed by a probabilistic model incorporating both chromosome number and morphology
title_fullStr Tempo and mode in karyotype evolution revealed by a probabilistic model incorporating both chromosome number and morphology
title_full_unstemmed Tempo and mode in karyotype evolution revealed by a probabilistic model incorporating both chromosome number and morphology
title_short Tempo and mode in karyotype evolution revealed by a probabilistic model incorporating both chromosome number and morphology
title_sort tempo and mode in karyotype evolution revealed by a probabilistic model incorporating both chromosome number and morphology
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8081341/
https://www.ncbi.nlm.nih.gov/pubmed/33861748
http://dx.doi.org/10.1371/journal.pgen.1009502
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