Models and Methods for Analyzing Phenotypic Evolution in Lineages and Clades

In this chapter we discuss methods for analyzing continuous traits, with an emphasis on those approaches that rely on explicit statistical models of evolution and incorporate genealogical information (ancestor–descendant or phylogenetic relationships). After discussing the roles of models and genealogy in evolutionary inference, we summarize the properties of commonly used models including random walks (Brownian motion), directional evolution, and stasis. These models can be used to devise null-hypothesis tests about evolutionary patterns, but it is often better to fit and compare models equally using information criteria and related approaches. We apply these methods to a published data set of dental measurements in a sequence of ancestor–descendant populations in the early primate Cantius , with the particular goal of determining the best-supported mode of evolutionary change in this lineage. We also assess a series of questions about the evolution of femoral dimensions in several clades of dinosaurs, including testing for a trend of increasing body size (Cope's Rule), testing for correlations among characters, and reconstructing ancestral states. Finally, we list briefly some additional models, approaches, and issues that arise in genealogically informed analyses of phenotypic evolution.