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，而染色体数目改变在演化过程中发挥着基础性作用。染色体数目的非整倍体增减事件以及多倍化事件，可能推动生殖隔离与世系分化。Mayrose等人于2010年的开创性研究中开发的染色体数目演化概率模型（ChromEvol），已实现基于分子系统发育树推断祖先染色体数目，并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系统发育分支以前进演化（anagenetic）模式发生，并未对专门的分支发生型（cladogenetic）事件进行建模。若染色体数目改变可引发生殖隔离，则这类分支发生型改变理应存在。为此，我们提出一类全新的染色体数目演化模型（命名为ChromoSSE），该模型同时涵盖前进演化与分支发生型两种改变模式。借助ChromoSSE模型，我们可明确染色体数目演化的模式：染色体演化主要发生在世系内部？还是主要发生在世系分裂之时？亦或是两类模式的支系特异性组合？此外，我们还可在系统发育树上估算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（具体依托RevBayes软件）实现了ChromoSSE模型，在充分利用似然法全部效能的同时，可容纳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，并重新分析了马兜铃属（Aristolochia）、螺序薹草组（Carex section Spirostachyae）、向日葵属（Helianthus）、广义沟酸浆属（Mimulus sensu lato, s.l.）以及Aleuritia报春花组（Primula section Aleuritia）的染色体演化过程，结果发现支系特异性的前进演化与分支发生型非整倍体、多倍体染色体演化模式组合的相关证据。