The field of phylogenetics is entering a new era in which trees of historical relationships
between species are increasingly inferred from multilocus and genomic data. A major …

Recently, researchers in several areas of ecology and evolution have begun to change the
way in which they analyze data and make biological inferences. Rather than the traditional …

What are the models used in phylogenetic analysis and what exactly is involved in Bayesian
evolutionary analysis using Markov chain Monte Carlo (MCMC) methods? How can you …

Passive transfer of broadly neutralizing HIV antibodies can prevent infection, which suggests
that vaccines that elicit such antibodies would be protective. Thus far, however, few broadly …

PhyML is a phylogeny software based on the maximum-likelihood principle. Early PhyML
versions used a fast algorithm performing nearest neighbor interchanges to improve a …

The program MODELTEST uses log likelihood scores to establish the model of DNA
evolution that best fits the data. AVAILABILITY: The MODELTEST package, including the …

We present here a framework for the study of molecular variation within a single species.
Information on DNA haplotype divergence is incorporated into an analysis of variance …

Phylogeography is a discipline concerned with various relationships between gene
genealogies—phylogenetics—and geography. The word “phylogeography” was coined in …

Episodes of population growth and decline leave characteristic signatures in the distribution
of nucleotide (or restriction) site differences between pairs of individuals. These signatures …

We previously developed a cladistic approach to identify subsets of haplotypes defined by
restriction endonuclease mapping or DNA sequencing that are associated with significant …