Data from: A unifying comparative phylogenetic framework including traits coevolving across interacting lineages

Models of phenotypic evolution fit to phylogenetic comparative data are widely used to make inferences regarding the tempo and mode of trait evolution. A wide range of models is already available for this type of analysis, and the field is still under active development. One of the most needed development concerns models that better account for the effect of within- and between-clade interspecific interactions on trait evolution, which can result from processes as diverse as competition, predation, parasitism, or mutualism. Here, we begin by developing a very general comparative phylogenetic framework for (multi)-trait evolution that can be applied to both ultrametric and nonultrametric trees. This framework not only encapsulates many previous models of continuous univariate and multivariate phenotypic evolution, but also paves the way for the consideration of a much broader series of models in which lineages coevolve, meaning that trait changes in one lineage are influenced by the value of traits in other, interacting lineages. Next, we provide a standard way for deriving the probabilistic distribution of traits at tip branches under our framework. We show that a multivariate normal distribution remains the expected distribution for a broad class of models accounting for interspecific interactions. Our derivations allow us to fit various models efficiently, and in particular greatly reduce the computation time needed to fit the recently proposed phenotype matching model. Finally, we illustrate the utility of our framework by developing a toy model for mutualistic coevolution. Our framework should foster a new era in the study of coevolution from comparative data.适配于系统发育比较数据的表型进化模型，被广泛用于推断性状进化的速率与模式。当前已有大量适用于此类分析的模型，且该领域仍处于活跃发展阶段。当前最亟需的一类发展方向，是构建能够更好地考量支系内与支系间种间相互作用对表型进化影响的模型——此类相互作用可源于竞争、捕食、寄生、互利共生等多样的生态学过程。本研究首先构建了一套极具普适性的比较系统发育框架，用于（多）性状进化分析，该框架可同时应用于超度量树（ultrametric tree）与非超度量树（nonultrametric tree）。此框架不仅涵盖了诸多已有的连续单变量与多变量表型进化模型，更为考虑更为广泛的一类谱系协同进化模型铺平了道路——这类模型中，某一谱系的性状变化会受到其他相互作用谱系的性状值影响。随后，我们提供了一套标准方法，用于推导该框架下末端分支处性状的概率分布。研究表明，对于纳入种间相互作用的大类模型而言，其性状分布仍服从多元正态分布。我们的推导过程可实现各类模型的高效拟合，尤其大幅缩短了近期提出的表型匹配模型所需的计算时长。最后，我们通过构建一个互利共生协同进化的示例模型，展示了本框架的应用价值。本框架有望推动基于比较数据的协同进化研究迈入全新阶段。