Data from: Comparing the rates of speciation and extinction between phylogenetic trees

Over the past decade or so it has become increasingly popular to use reconstructed evolutionary trees to investigate questions about the rates of speciation and extinction. Although the methodology of this field has grown substantially in its sophistication in recent years, here I’ll take a step back to present a very simple model that is designed to investigate the relatively straightforward question of whether the tempo of diversification (speciation and extinction) differs between two or more phylogenetic trees, without attempting to attribute a causal basis to this difference. It is a likelihood method, and I demonstrate that it generally shows type I error that is close to the nominal level. I also demonstrate that parameter estimates obtained with this approach are largely unbiased. Since this method can be used to compare trees of unknown relationship, it will be particularly well-suited to problems in which a difference in diversification rate between clades is suspected, but in which these clades are not particularly closely related. Since diversification methods can easily take into account an incomplete sampling fraction, but missing lineages are assumed to be missing at random, this method is also appropriate for cases in which we’ve hypothesized a difference in the process of diversification between two or more focal clades, but in which many un-sampled groups separate the few of interest. The method of this study is by no means an attempt to replace more sophisticated models in which, for instance, diversification depends on the state of an observed or unobserved discrete or continuous trait. Rather, my intention is to provide a complementary approach for circumstances in which a simpler hypothesis is warranted and of biological interest.

近十余年来，借助重建进化树（reconstructed evolutionary trees）探究物种形成与灭绝速率相关科学问题的研究愈发流行。尽管近年来该领域的方法论体系在复杂度与严谨性上均有长足进展，本文仍将回归本源，提出一个极简模型，用于直接检验两类或多类系统发育树（phylogenetic trees）间的多样化（物种形成与灭绝）速率模式是否存在差异，且不对该差异的因果机制作出归因。该方法属于似然法（likelihood method），本文验证其一类错误（type I error）通常趋近于预设的名义显著性水平。同时，该方法得到的参数估计值整体无偏。鉴于该方法可用于比较亲缘关系未知的树群，其尤其适用于以下研究场景：怀疑不同演化支（clades）间的多样化速率存在差异，但这些演化支的亲缘关系并不十分紧密。此外，尽管多样化分析方法通常可纳入不完全采样比例的考量（默认未采样类群为随机缺失），本方法同样适用于如下情形：我们推测两类或多类目标演化支间的多样化过程存在差异，但目标类群之间存在大量未被采样的类群。本研究提出的方法绝非意图取代更为复杂的模型——例如那些将多样化过程与观测或未观测的离散、连续性状状态相关联的模型。相反，本文旨在为那些需要更简洁研究假设且具备生物学意义的场景，提供一种互补的分析路径。