Until recently, it has been common practice for a phylogenetic analysis to use a single gene
sequence from a single individual organism as a proxy for an entire species. With …

We present a new open source, extensible and flexible software platform for Bayesian
evolutionary analysis called BEAST 2. This software platform is a re-design of the popular …

Elaboration of Bayesian phylogenetic inference methods has continued at pace in recent
years with major new advances in nearly all aspects of the joint modelling of evolutionary …

Background Effective population size (N e) is related to genetic variability and is a basic
parameter in many models of population genetics. A number of methods for inferring current …

The use of fossil evidence to calibrate divergence time estimation has a long history. More
recently, Bayesian Markov chain Monte Carlo has become the dominant method of …

Background Bayesian phylogenetic analysis generates a set of trees which are often
condensed into a single tree representing the whole set. Many methods exist for selecting a …

Estimates of the timing of divergence are central to testing the underlying causes of
speciation. Relaxed molecular clocks and fossil calibration have improved these estimates; …

Abstract Motivation Phylogenetic analysis like Bayesian MCMC or bootstrapping result in a
collection of trees. Trees are discrete objects and it is generally difficult to get a mental grip …

Background There is an increasing demand for rapid biodiversity assessment tools that
have a broad taxonomic coverage. Here we evaluate a suite of environmental DNA (eDNA) …

Under the multispecies coalescent model of molecular evolution, gene trees have
independent evolutionary histories within a shared species tree. In comparison, supermatrix …