MOTMOT: Models of trait macroevolution on trees (an update)

The disparity in species’ traits arises through variation in the tempo and mode of evolution over time and between lineages. Understanding these patterns is a core goal in evolutionary biology. Here we present the comprehensively updated r package MOTMOT: Models Of Trait Macroevolution On Trees that contains methods to fit and test models of continuous trait evolution on phylogenies of extant and extinct species. MOTMOT provides functions to investigate a range of evolutionary hypotheses, including flexible approaches to investigate heterogeneous rates and modes of evolution, models of trait change under interspecific competition and patterns of trait change across significant evolutionary transitions such as mass extinctions. We introduce and test novel algorithms of heterogeneous tempo and mode of evolution that allow for phylogeny-wide shifts in evolution at specific times on a tree. We use these new MOTMOT functions to highlight an exceptionally high rate of mammalian body mass evolution for 10 million years following the Cretaceous–Palaeogene mass extinction. These methods provide biologists and palaeontologists with the tools to analyse continuous trait data on phylogenies, including large trees of up to thousands of species.