Can you give us some background on this research?

Evolutionary biology is founded on the concept that organisms share a common origin and have subsequently diverged through time. Phylogenies represent our attempts to reconstruct those evolutionary histories, and there is probably more interest in phylogenetic reconstruction today than at any time in the past. Phylogenies are central to virtually all comparisons among species, and they have found practical uses in tracing routes of infectious disease transmission (e.g., dental transmission of AIDS/HIV) and in identifying new pathogens such as the New Mexico hantavirus, just to mention a few examples.

The phylogeny problem—the estimation of the genealogy of organisms from DNA sequences—is not a standard statistical one. Hence one cannot simply consult statistical texts for a solution. Our research concentrates on how phylogeny can be estimated and how phylogenies can be used to address questions in evolutionary biology. In general, we have taken a Bayesian approach to the inference of phylogeny. Bayesian inference is a widely used method for making statistical inferences but has found only limited use in evolutionary biology. The technology we use to perform Bayesian analysis of DNA sequences is Markov chain Monte Carlo (MCMC). MCMC takes valid, albeit dependent samples from the probability distribution of interest and has made Bayesian inference practical for many scientific problems. Indeed, it turns out that Bayesian inference using MCMC is computationally vastly more efficient than previous statistical approaches to the phylogeny problem, generating a lot of interest in the Bayesian approach among evolutionary biologists.

The paper simply describes a computer program that other scientists can use to analyze DNA sequences that were sampled from different organisms of the same species or from different species. The program will provide the user with information on the best phylogenetic tree (or genealogy relating the species) along with information on the reliability of the tree. In order to reconstruct the phylogeny of a group of species, you need to make assumptions about how the DNA sequences evolve. The program allows the user to specify a large number of models (sets of assumptions) and explore the consequences of making different assumptions about how the DNA sequences evolve.