Summary Changes in chromosome numbers are a prominent driver of plant evolution, impacting ecological diversification, stress tolerance, and phenotypes. ChromEvol is a widely used software tool for deciphering patterns of chromosome‐number change along a phylogeny of interest. It evaluates the fit of alternative models to the data, estimates transition rates of different types of events, and infers the expected number of events along each branch of the phylogeny. We introduce ChromEvol v.3, featuring multiple novel methodological advancements that capture variation in the transition rates along a phylogeny. This version better allows researchers to identify how dysploidy and polyploidy rates change based on the number of chromosomes in the genome, with respect to a discrete trait, or at certain subclades of the phylogeny. We demonstrate the applicability of the new models on the Solanaceae phylogeny. Our analyses identify four chromosome‐number transition regimes that characterize distinct Solanaceae clades and demonstrate an association between self‐compatibility and altered dynamics of chromosome‐number evolution. ChromEvol v.3, available at https://github.com/anatshafir1/chromevol, offers researchers a more flexible, comprehensive, and accurate tool to investigate the evolution of chromosome numbers and the various processes affecting it.

中文翻译：

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ChromEvol v.3：染色体数量进化中的建模率异质性


摘要 染色体数量的变化是植物进化的重要驱动力，影响生态多样化、抗逆性和表型。ChromEvol 是一种广泛使用的软件工具，用于破译沿目标系统发育的染色体数量变化模式。它评估替代模型与数据的拟合度，估计不同类型事件的转换率，并推断系统发育每个分支的预期事件数量。我们介绍了 ChromEvol v.3，它具有多项新的方法学进步，可捕获系统发育中转换速率的变化。此版本使研究人员能够更好地识别异倍体和多倍体速率如何根据基因组中的染色体数量、离散性状或系统发育的某些亚分支而变化。我们证明了新模型在茄科系统发育上的适用性。我们的分析确定了四种染色体数转换机制，这些机制表征了不同的茄科分支，并证明了自交性与染色体数进化动力学改变之间的关联。ChromEvol v.3 可在 https://github.com/anatshafir1/chromevol 获得，它为研究人员提供了一种更灵活、更全面、更准确的工具，用于研究染色体数量的进化以及影响它的各种过程。