Data from: Cladogenetic and anagenetic models of chromosome number evolution: a Bayesian model averaging approach

Chromosome number is a key feature of the higher-order organization of the genome, and changes in chromosome number play a fundamental role in evolution. Dysploid gains and losses in chromosome number, as well as polyploidization events, may drive reproductive isolation and lineage diversification. The recent development of probabilistic models of chromosome number evolution in the groundbreaking work by Mayrose et al. (2010, ChromEvol) have enabled the inference of ancestral chromosome numbers over molecular phylogenies and generated new interest in studying the role of chromosome changes in evolution. However, the ChromEvol approach assumes all changes occur anagenetically (along branches), and does not model events that are specifically cladogenetic. Cladogenetic changes may be expected if chromosome changes result in reproductive isolation. Here we present a new class of models of chromosome number evolution (called ChromoSSE) that incorporate both anagenetic and cladogenetic change. The ChromoSSE models allow us to determine the mode of chromosome number evolution; is chromosome evolution occurring primarily within lineages, primarily at lineage splitting, or in clade-specific combinations of both? Furthermore, we can estimate the location and timing of possible chromosome speciation events over the phylogeny. We implemented ChromoSSE in a Bayesian statistical framework, specifically in the software RevBayes, to accommodate uncertainty in parameter estimates while leveraging the full power of likelihood based methods. We tested ChromoSSE’s accuracy with simulations and re-examined chromosomal evolution in Aristolochia, Carex section Spirostachyae, Helianthus, Mimulus sensu lato (s.l.), and Primula section Aleuritia, finding evidence for clade-specific combinations of anagenetic and cladogenetic dysploid and polyploid modes of chromosome evolution.

染色体数目是基因组高阶组织的关键特征，其数目改变在生物演化进程中发挥着基础性作用。非整倍性的染色体数目增减事件与多倍化事件，均可推动生殖隔离的形成与谱系分化。梅罗斯等人（Mayrose et al., 2010）在其开创性研究中开发的染色体数目演化概率模型（ChromEvol），首次实现了基于分子系统发育树的祖先染色体数目推断，重新激发了学界对染色体改变在演化中作用的研究兴趣。然而，ChromEvol模型假设所有染色体数目改变均沿线系前进演化（anagenetic，即沿物种树分支发生），并未针对物种形成事件特有的分支演化（cladogenetic）改变构建模型。若染色体改变可引发生殖隔离，则大概率会出现分支演化改变。本文提出一类全新的染色体数目演化模型（命名为ChromoSSE），该模型同时整合了前进演化与分支演化两类改变模式。ChromoSSE模型可用于解析染色体数目演化的模式：染色体演化主要发生在谱系内部，还是主要发生在谱系分化节点，亦或是两类模式按支系特异性组合出现？此外，我们还可估算系统发育树上各类潜在染色体物种形成事件的发生位置与时间节点。我们在贝叶斯统计框架下实现了ChromoSSE模型，并专门依托RevBayes软件完成部署，以在充分利用似然推断方法全部优势的同时，兼容参数估计过程中的不确定性。我们通过模拟实验验证了ChromoSSE模型的准确性，并重新审视了马兜铃属（Aristolochia）、螺旋穗薹草组（Carex section Spirostachyae）、向日葵属（Helianthus）、广义沟酸浆属（Mimulus sensu lato, s.l.）以及报春花属Aleuritia组（Primula section Aleuritia）的染色体演化历程，最终在多个类群中均发现了兼具前进演化与分支演化模式的非整倍性及多倍性染色体演化的证据