Inferring Chromosome Number Changes Along a Phylogeny Using chromEvol

Anna Rice, Itay Mayrose

Research output: Chapter in Book/Report/Conference proceedingChapterpeer-review

Abstract

Chromosome numbers have long been used for the identification of key genomic events such as polyploidy and dysploidy. These inferences are often challenging, particularly when applied to large phylogenies, or clades in which more than a few chromosome number transitions had occurred. Here we describe the chromEvol computational framework that infers shifts in chromosome numbers along a phylogeny using probabilistic models of chromosome number change. Given chromosome count data and an associated phylogeny, chromEvol identifies such patterns by fitting probabilistic models of chromosome number evolution to the data. We describe the chromEvol workflow using available online tools, including the specification of the desired models, the examination of model fit to the data, and the inference of ploidy levels. The pipeline can be used by the wide scientific community and requires no previous computational or programming skills.

Original languageEnglish
Title of host publicationMethods in Molecular Biology
Pages175-187
Number of pages13
DOIs
StatePublished - 2023

Publication series

NameMethods in Molecular Biology
Volume2545

Keywords

  • CCDB
  • chromEvol
  • Chromosome number
  • Dysploidy
  • OneTwoTree
  • Phylogenetics
  • Polyploidy
  • Polyploidy

All Science Journal Classification (ASJC) codes

  • Molecular Biology
  • Genetics

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