Phylogenetic comparative methods comprise the general endeavor of using an estimated
phylogenetic tree (or set of trees) to make secondary inferences: about trait evolution …

The TreeBASE portal is an important and rapidly growing repository of phylogenetic data.
The R statistical environment has also become a primary tool for applied phylogenetic …

All comparative analyses rely on at least one phylogenetic hypothesis. However, the
reconstruction of the evolutionary history of species is not the primary aim of these studies. In …

Phylogenetic comparative methods are essential for addressing evolutionary hypotheses
with interspecific data. The scale and scope of such data have increased dramatically in the …

phytools: an R package for phylogenetic comparative biology (and other things) Page 1
APPLICATION phytools: an R package for phylogenetic comparative biology (and other things) …

We introduce phylodyn, an r package for phylodynamic analysis based on gene
genealogies. The package's main functionality is Bayesian nonparametric estimation of …

Phylogenies have emerged as central in evolutionary biology over the past three decades or
more, and an extraordinary expansion in the breadth and sophistication of phylogenetic …

Phylogenetic comparative methods are becoming increasingly popular for investigating
evolutionary patterns and processes. However, these methods are not infallible–they suffer …

Abstract Model‐based approaches are increasingly popular in ecological studies. A good
example of this trend is the use of joint species distribution models to ask questions about …

Recent computational and modeling advances have produced methods for estimating
species trees directly, avoiding the problems and limitations of the traditional phylogenetic …