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）推断这一新兴可能性，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支系（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该问题：(1) 采用包含分配至每个末端支系的现存物种推断数量的小型骨干进化树；(2) 采用包含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收录的物种样本至少大致对应不同支系的实际物种多样性水平，这一点在多数主要被子植物支系中似乎成立。通过两种方法的分析，我们发现多样化速率转变与本次研究考察的主要命名支系并无直接关联，仅在GenBank巨型系统发育树分析中，豆科（Fabaceae）为唯一例外。这些结果的一致性令人备受鼓舞，或可支撑被子植物演化领域的一项普遍性规律：多样化速率的主要转变或许并不直接关联于主要命名支系，而是与嵌套于这些类群内部不远的支系相关。另一种解释则是，这些支系内早期分化支系的灭绝速率有所上升。基于我们的巨型系统发育树分析结果，多样化速率转变似乎在整个被子植物类群中分布得相当均匀。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潜力，但我们仍需投入更多精力以合理设定零假设预期（null expectation）。