Shafir Anat, Halabi Keren, Escudero Marcial, Mayrose Itay
School of Plant Sciences and Food Security, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, 69978, Israel.
Department of Plant Biology and Ecology, University of Seville, Reina Mercedes, ES-41012, Seville, Spain.
New Phytol. 2023 May;238(4):1733-1744. doi: 10.1111/nph.18805. Epub 2023 Mar 8.
Changes in chromosome numbers, including polyploidy and dysploidy events, play a key role in eukaryote evolution as they could expediate reproductive isolation and have the potential to foster phenotypic diversification. Deciphering the pattern of chromosome-number change within a phylogeny currently relies on probabilistic evolutionary models. All currently available models assume time homogeneity, such that the transition rates are identical throughout the phylogeny. Here, we develop heterogeneous models of chromosome-number evolution that allow multiple transition regimes to operate in distinct parts of the phylogeny. The partition of the phylogeny to distinct transition regimes may be specified by the researcher or, alternatively, identified using a sequential testing approach. Once the number and locations of shifts in the transition pattern are determined, a second search phase identifies regimes with similar transition dynamics, which could indicate on convergent evolution. Using simulations, we study the performance of the developed model to detect shifts in patterns of chromosome-number evolution and demonstrate its applicability by analyzing the evolution of chromosome numbers within the Cyperaceae plant family. The developed model extends the capabilities of probabilistic models of chromosome-number evolution and should be particularly helpful for the analyses of large phylogenies that include multiple distinct subclades.
染色体数目的变化，包括多倍体和非整倍体事件，在真核生物进化中起着关键作用，因为它们可以加速生殖隔离并有可能促进表型多样化。目前，在系统发育中解读染色体数目变化模式依赖于概率进化模型。所有目前可用的模型都假设时间齐性，即整个系统发育过程中的转变速率是相同的。在这里，我们开发了染色体数目进化的异质性模型，该模型允许多种转变模式在系统发育的不同部分起作用。系统发育到不同转变模式的划分可以由研究人员指定，或者使用顺序检验方法来识别。一旦确定了转变模式中变化的数量和位置，第二个搜索阶段会识别具有相似转移动力学的模式，这可能表明趋同进化。通过模拟，我们研究了所开发模型检测染色体数目进化模式变化的性能，并通过分析莎草科植物家族内染色体数目的进化来证明其适用性。所开发的模型扩展了染色体数目进化概率模型的能力，对于分析包括多个不同亚分支的大型系统发育应该特别有帮助。
