Understanding Angiosperm Diversification Using Small and Large Phylogenetic Trees 1
Understanding Angiosperm Diversification Using Small and Large Phylogenetic Trees 1
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影响因子：
3.9
通讯作者：
Stephen A. Smith;Jeremy M Beaulieu;A. Stamatakis;M. Donoghue
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作者：
Stephen A. Smith;Jeremy M Beaulieu;A. Stamatakis;M. Donoghue
开花植物在全球的成功是整个群体的某些特征的函数，还是它真的反映了一个或多个被子植物亚群的成功（例如，Sanderson and Donoghue，1994）？这些明显的成功，无论发生在什么层面，最好用关键创新或关键机会来解释（例如，摩尔和多诺霍，2007年），以及差异灭绝如何影响我们对问题的看法？这些问题的答案取决于对系统发育关系和物种丰富度如何在整个树中分布的见解。幸运的是，在过去的十年里，我们对被子植物发生学的认识有了很大的提高（当然，我们仍然需要很长时间才能知道每一个被子植物物种之间的关系。鉴于我们对可预见的未来的不完全了解，研究多样化率变化的最佳策略是什么？一种方法是将这种分析建立在主干树的基础上，主干树描述了一个感兴趣的分支内主要谱系之间的“已建立“关系。在这种情况下，每个终端都被分配了被认为是由“范例物种”代表的物种数量，并且分析必须绕过多样性在这些终端谱系中的分布（例如：这有一个明显的缺点，即不能确定在一个大的终端进化枝中可能发生了多样化的转变，并且它可能导致一种特殊的错误：归因于这种复合终端的多样化的转变实际上可能是由于在该进化枝中发生的转变（“涓滴“效应的一种形式;摩尔等人，2004年）。另一种可能的方法，尚未详细探讨，是使用一个系统发育树，其中包括所有物种的相关系统发育数据是可用的，简单地对待每个终端作为一个单一的物种。在使用这种方法时，人们必须希望有足够的代表性的利益分支的数据是可用的，物种的样本可用于系统发育分析或多或少准确地反映了潜在的物种多样性的分布。这种方法有一个明显的缺点，即由于底层数据集中特定分支的过度或不足，可能会导致结果出现偏差。人们希望这两种不同的方法在很大程度上会产生类似的结果，...
Is the global success of the fl owering plants a function of some feature of the group as a whole, or does it really refl ect the success of one or more angiosperm subgroups (e.g., Sanderson and Donoghue, 1994)? Are such apparent successes, at whatever level they occur, best explained by key innovations or by key opportunities (e.g., Moore and Donoghue, 2007), and how has differential extinction infl uenced our perception of the problem? Answers to these questions depend on insights about phylogenetic relationships and about how species richness is distributed throughout the tree. Fortunately, our knowledge of angiosperm phylogeny has improved dramatically over the past decade (e.ever, it will still be a long time before we know the relationships of every angiosperm species with any level of confi dence. In view of our incomplete knowledge for the foreseeable future, what are the best strategies for studying shifts in diversifi cation rate? One approach has been to base such analyses on a backbone tree that depicts " established " relationships among the major lineages within a clade of interest. In this case, each terminal is assigned the number of species thought to be represented by an " exemplar species, " and the analysis necessarily bypasses how diversity is distributed within these terminal lineages (e. This has the obvious drawback of not being able to identify where shifts in diversifi cation may have occurred within a large terminal clade, and it can result in a particular kind of mistake: a shift in diversifi cation attributed to such a composite terminal might actually be due to a shift that occurred within that clade (a form of the " trickle-down " effect; Moore et al., 2004). Another possible approach, which has not yet been explored in detail, is to use a phylogenetic tree that includes all species for which relevant phylogenetic data are available, simply treating each terminal as a single species. In using this approach, one has to hope that there are enough representatives of the clade of interest for which data are available and that the sample of species available for phylogenetic analysis more-or-less accurately refl ects the distribution of the underlying species diversity. This approach has the obvious drawback of potentially biasing the results due to the over-or underrepresentation of particular clades in the underlying data set. One would hope that these two different approaches would largely yield similar results, …