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.推断超大型系统发育树（ultra-large phylogenies）的新兴可行性，将如何影响我们识别物种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) 采用仅包含少量主干类群的系统发育树，并为每个末端支系分配经推断的现存物种数量；(2) 采用涵盖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内的物种样本至少大致对应不同支系的实际物种多样性，这一现象在多数主要被子植物支系中均有体现。通过两种方法的分析对比，我们发现本次研究涉及的主要命名支系与多样化速率转变并无直接关联，仅在基于GenBank的巨型系统发育树分析中，豆科（Fabaceae）是唯一例外。上述结果的一致性令人备受鼓舞，或可支撑被子植物演化的一项普遍性规律：物种多样化的重大转变或许并不直接关联于主要命名支系，而是更倾向于发生在这些支系内部嵌套较浅的类群中。另一种可能的解释是，此类支系内早期分化的类群经历了更高的灭绝速率。基于我们构建的巨型系统发育树，物种多样化速率的转变似乎在整个被子植物类群中分布相对均匀。针对物种多样化的巨型系统发育研究（mega-phylogenetic studies）展现出揭示全新演化模式的巨大潜力，但我们仍需投入更多精力以合理设定零期望（null expectation）的相关标准。