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（Polyploidization）是植物中普遍且反复出现的演化现象，常被认为是一种"瞬时成种"机制。然而，多倍化究竟是与新物种形成（分支成种，cladogenesis）相关，还是仅在一个演化支系内随时间发生（线系演化，anagenesis），此前从未得到系统性的评估。

研究方法：本研究利用235个植物属（多数为被子植物）的系统发育与核型信息对该假说进行验证。首先，我们通过自动化流程构建了整合序列与染色体数目数据集的大型数据库。随后，我们应用似然模型（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之间的同步程度。

主要结果：我们的最大似然分析显示，35个属支持包含分支成种转变的模型，相较于仅支持线系演化转变的模型；另有3个属支持包含线系演化转变的模型，相较于仅支持分支成种转变的模型。此外，贝叶斯分析支持4个属中以分支成种转变为主的演化模式，但未发现任何属存在以线系演化转变为主的情况。

研究结论：总体而言，本项系统发育分析首次在大范围尺度上证实了多倍化与物种形成事件在时间维度上存在关联，表明至少在部分植物属中，多倍化确实是一类重要的成种机制。