Data from: Understanding angiosperm diversification using small and large phylogenetic trees

How will the emerging possibility of inferring ultra-large phylogenies influence our ability to identify shifts in diversification rate? For several large angiosperm clades (Angiospermae, Monocotyledonae, Orchidaceae, Poaceae, Eudicotyledonae, Fabaceae, and Asteraceae), we explore this issue by contrasting two approaches: (1) using small backbone trees with an inferred number of extant species assigned to each terminal clade and (2) using a mega-phylogeny of 55473 seed plant species represented in GenBank. The mega-phylogeny approach assumes that the sample of species in GenBank is at least roughly proportional to the actual species diversity of different lineages, as appears to be the case for many major angiosperm lineages. Using both approaches, we found that diversification rate shifts are not directly associated with the major named clades examined here, with the sole exception of Fabaceae in the GenBank mega-phylogeny. These agreements are encouraging and may support a generality about angiosperm evolution: major shifts in diversification may not be directly associated with major named clades, but rather with clades that are nested not far within these groups. An alternative explanation is that there have been increased extinction rates in early-diverging lineages within these clades. Based on our mega-phylogeny, the shifts in diversification appear to be distributed quite evenly throughout the angiosperms. Mega-phylogenetic studies of diversification hold great promise for revealing new patterns, but we will need to focus more attention on properly specifying null expectation.超大型系统发育树（ultra-large phylogenies）推断技术的日渐成熟，将如何影响我们识别多样化速率转变的能力？针对多个大型被子植物演化支（被子植物门Angiospermae、单子叶植物纲Monocotyledonae、兰科Orchidaceae、禾本科Poaceae、真双子叶植物纲Eudicotyledonae、豆科Fabaceae以及菊科Asteraceae），我们通过对比两种研究方法探讨这一议题：(1) 采用为每个末端演化支赋予现存物种推断数量的小型框架树；(2) 采用收录了GenBank中55473种种子植物的巨型系统发育树（mega-phylogeny）。该巨型系统发育树方法假设，GenBank收录的物种样本量至少与不同演化支的实际物种多样性大致成正比，这一假设在多数主要被子植物演化支中均成立。通过两种方法开展分析后，我们发现本研究考察的主要命名演化支与多样化速率转变并无直接关联，仅在GenBank巨型系统发育树的分析中，豆科（Fabaceae）为唯一例外。上述结果的一致性令人备受鼓舞，或可为被子植物演化的普遍性规律提供支撑：多样化速率的重大转变或许并不直接对应主要命名演化支，而是与隶属于这些类群、嵌套层级较浅的演化支相关。另一种可能的解释是，这些演化支内早期分化的演化支存在灭绝速率上升的情况。基于本次研究的巨型系统发育树结果，多样化速率转变在整个被子植物类群中分布相对均匀。针对多样化速率的巨型系统发育研究在揭示全新演化模式方面极具应用前景，但我们仍需投入更多精力，以合理设定零假设预期（null expectation）。