Mark PAGEL, University of Reading, UK.

"A model of pattern-heterogeneity for inferring phylogenetic trees and investigating sequence evolution"

Conventional models of gene-sequence evolution assume that all sites evolve according to a single homogeneous model of evolution or that rates of evolution vary among sites according to some statistical distribution, such as the gamma. I describe a likelihood-based model that can accommodate cases in which different sites in the alignment evolve in qualitatively different ways, such as might be expected of different genes in a concatenated alignment or of different regions of the same gene, such as the stems and loops of ribosomal RNA. We call such variability 'pattern-heterogeneity'. The method we describe can detect pattern-heterogeneity without prior partitioning of the data by the investigator, and simplifies to the gamma rates or homogeneous models as special cases. It therefore always improves upon these methods and frequently considerably so. I discuss examples based on an implementation of the model in a Bayesian MCMC framework.