Phylogenetic approaches to the study of comparative data have a long history in the field of animal behaviour (e.g. Lorenz 1941; Greene & Burghardt 1978; Gittleman 1981). However, since the publication in 1991 of Brooks & McLennan’s Phylogeny, Ecology and Behavior and Harvey & Pagel’s The Comparative Method in Evolutionary Biology, there has been a huge increase in the use of phylogenetic metho...

Conservation biologists and palaeontologists are increasingly investigating the phylogenetic distribution of extinctions and its evolutionary consequences. However, the dearth of palaeontological studies on that subject and the lack of methodological consensus hamper our understanding of that major evolutionary phenomenon. Here we address this issue by (i) reviewing the approaches used to quant...

A principal objective for phylogenetic experimental design is to predict the power of a data set to resolve nodes in a phylogenetic tree. However, proactively assessing the potential for phylogenetic noise compared with signal in a candidate data set has been a formidable challenge. Understanding the impact of collection of additional sequence data to resolve recalcitrant internodes at diverse ...

The relationships between diversity and ecosystem functioning have become a major focus of science. A crucial issue is to estimate functional diversity, as it is intended to impact ecosystem dynamics and stability. However, depending on the ecosystem, it may be challenging or even impossible to directly measure ecological functions and thus functional diversity. Phylogenetic diversity was recen...

Comparative analyses of microbial communities increasingly involve the assay of 16S rRNA (or other gene) sequences from environmental DNA. Determining whether the composition of two or more communities differ in their phylogenetic composition involves testing for covariation between phylogeny and community type. This approach requires estimating the phylogenetic relationships among all sampled ...

Phylogenetic analysis has shown that Escherichia coli is composed of four main phylogenetic groups (A, B1, B2 and D). Characterization of phylogenetic groups is of clinical interest, as group A and B1 generally associated with commensals, whereas most enteropathogenic isolates are assigned to group D, and group B2 is associated with extra-intestinal pathotype. One hundred E. coli strains recove...