Revell Liam J, Schliep Klaus P, Mahler D Luke, Ingram Travis
Department of Biology, University of Massachusetts Boston, Boston, MA, United States.
Facultad de Ciencias, Universidad Católica de la Santísima Concepción, Concepción, Chile.
J Evol Biol. 2024 Dec 2;37(12):1591-1602. doi: 10.1093/jeb/voae119.
Many hypotheses in the field of phylogenetic comparative biology involve specific changes in the rate or process of trait evolution. This is particularly true of approaches designed to connect macroevolutionary pattern to microevolutionary process. We present a method to test whether the rate of evolution of a discrete character has changed in one or more clades, lineages, or time periods. This method differs from other related approaches (such as the "covarion" model) in that the "regimes" in which the rate or process is postulated to have changed are specified a priori by the user, rather than inferred from the data. Similarly, it differs from methods designed to model a correlation between two binary traits in that the regimes mapped onto the tree are fixed. We apply our method to investigate the rate of dewlap colour and/or caudal vertebra number evolution in Caribbean and mainland clades of the diverse lizard genus Anolis. We find little evidence to support any difference in the evolutionary process between mainland and island evolution for either character. We also examine the statistical properties of the method more generally and show that it has acceptable type I error, parameter estimation, and power. Finally, we discuss some general issues of frequentist hypothesis testing and model adequacy, as well as the relationship of our method to existing models of heterogeneity in the rate of discrete character evolution on phylogenies.
系统发育比较生物学领域的许多假设都涉及性状进化速率或过程的特定变化。旨在将宏观进化模式与微观进化过程联系起来的方法尤其如此。我们提出了一种方法来检验离散性状的进化速率在一个或多个进化枝、谱系或时间段内是否发生了变化。该方法与其他相关方法（如“协变”模型）的不同之处在于，速率或过程被假定发生变化的“状态”是由用户事先指定的，而不是从数据中推断出来的。同样，它与旨在模拟两个二元性状之间相关性的方法不同，因为映射到树上的状态是固定的。我们应用我们的方法来研究多样化的安乐蜥属在加勒比和大陆进化枝中喉扇颜色和/或尾椎数量的进化速率。我们几乎没有发现证据支持这两个性状在大陆和岛屿进化的进化过程中存在任何差异。我们还更全面地研究了该方法的统计特性，并表明它具有可接受的I型错误、参数估计和检验效能。最后，我们讨论了频率主义假设检验和模型适用性的一些一般问题，以及我们的方法与系统发育树上离散性状进化速率的现有异质性模型的关系。
