Data from: Phylogenetic evidence for cladogenetic polyploidization in land plants

Premise of the study: Polyploidization is a common and recurring phenomenon in plants and is often thought to be a mechanism of "instant speciation." Whether polyploidization is associated with the formation of new species ("cladogenesis") or simply occurs over time within a lineage ("anagenesis") has never, however, been assessed systematically. Methods: Here, we tested this hypothesis using phylogenetic and karyotypic information from 235 plant genera (mostly angiosperms). We first constructed a large database of combined sequence and chromosome number data sets using an automated procedure. We then applied likelihood models (ClaSSE) that estimate the degree of synchronization between polyploidization and speciation events in maximum likelihood and Bayesian frameworks. Key results: Our maximum likelihood analysis indicated that 35 genera supported a model that includes cladogenetic transitions over a model with only anagenetic transitions, whereas three genera supported a model that incorporates anagenetic transitions over one with only cladogenetic transitions. Furthermore, the Bayesian analysis supported a preponderance of cladogenetic change in four genera but did not support a preponderance of anagenetic change in any genus. Conclusions: Overall, these phylogenetic analyses provide the first broad confirmation that polyploidization is temporally associated with speciation events, suggesting that it is indeed a major speciation mechanism in plants, at least in some genera.研究背景：多倍化是植物界普遍且反复出现的演化现象，常被视为“瞬时物种形成”的重要机制。然而，多倍化究竟是参与新物种的形成过程（即分支成种（cladogenesis）），还是仅在单一演化线系内随时间逐步发生（即线系演化（anagenesis）），此前尚未得到系统性的评估。研究方法：本研究依托235个植物属（绝大多数为被子植物（angiosperms））的系统发育与核型信息，对上述假说开展检验。我们首先通过自动化流程构建了整合序列与染色体数数据集的大型数据库，随后应用似然模型（ClaSSE），在最大似然（maximum likelihood）与贝叶斯（Bayesian）框架下估算多倍化与物种形成事件的同步发生程度。主要结果：本次最大似然分析结果显示，35个属支持包含分支成种过程的模型，而非仅包含线系演化过程的模型；另有3个属支持包含线系演化过程的模型，而非仅包含分支成种过程的模型。此外，贝叶斯分析支持4个属以分支成种为主要演化过程，但未发现任何属以线系演化作为主导过程。研究结论：综合上述系统发育分析结果，本研究首次在广泛尺度上证实了多倍化与物种形成事件存在时间上的关联性，表明至少在部分植物属中，多倍化确实是一类重要的物种形成机制。