Data from: Linking the investigations of character evolution and species diversification

Variation in diversification rates is often studied by investigating traits related to species' ecology and life history. Often, however, it is unknown whether these traits evolve gradually or in punctuated bursts during speciation. Using phylogenetic data and species' present-day trait information, we present a novel approach to assess the mode of character change while accounting for trait-dependent speciation and extinction. Our model, "Binary-State Speciation and Extinction - node enhanced state shift" (BiSSE-ness), estimates both the rate of change occurring along lineages and the probability of change occurring during speciation, as well as independent speciation and extinction rates for each character state. Using simulations, we found that BiSSE- ness is able to distinguish along-lineage and speciational change and to estimate accurately the parameters associated with character change and diversification rates. We applied BiSSE-ness to an empirical primate data set, finding evidence for along-lineage changes in primate mating systems and social behaviours, whereas shifts in habitat were associated with speciation. In cases where trait changes may be linked to the speciation process itself (e.g., niche-related traits), BiSSE-ness provides a suitable framework in which to simultaneously address questions regarding species' diversification and character change.

物种分化速率的变异通常通过探究与物种生态学及生活史相关的性状展开研究。然而，学界往往难以明确这些性状是在物种形成过程中逐步演化，还是以间断爆发的方式发生改变。本研究结合系统发育数据与物种现存性状信息，提出一种全新方法，在评估性状演化模式的同时，纳入性状依赖的物种形成与灭绝过程。我们所提出的模型为"二元状态物种形成与灭绝-节点增强状态转移"（Binary-State Speciation and Extinction - node enhanced state shift，简称BiSSE-ness），该模型可同时估算沿谱系发生的性状变化速率、物种形成过程中的性状变化概率，以及对应各性状状态的独立物种形成与灭绝速率。通过模拟实验验证，我们发现BiSSE-ness能够有效区分沿谱系发生的性状变化与物种形成过程中的性状变化，并可精准估算与性状演化及分化速率相关的参数。我们将BiSSE-ness应用于灵长类实证数据集，结果显示，灵长类的交配系统与社会行为的性状变化主要沿谱系发生，而栖息地的转移则与物种形成过程相关。当性状变化可能与物种形成过程本身存在关联时（例如与生态位相关的性状），BiSSE-ness提供了一套合适的研究框架，可同时解答物种分化与性状演化相关的科学问题。