Inferring Process from Pattern In Fungal Population Genetics

Our focus in this review is on powerful new methods for determining population patterning over time and space and how from this, the dynamic processes leading to population divergence and speciation can be inferred. We focus on fungal populations, but draw from the wider literature on population genetics, evolutionary statistics, and, of course, phylogeography (see Avise, 2000). We discuss the problems of gene duplication, paralogy, orthology, and deep coalescence as challenges to finding the interface between population divergence and speciation. Our main objective, however, is to guide the reader through the key phylogenetic, nested phylogenetic, coalescent and Bayesian operations with the aid of a set of figures based on a simple, hypothetical dataset of DNA haplotypes. Phylogenetic and compatibility approaches are presented with the goal of not only detecting recombination, but of detecting recombination when it is not widespread throughout a phylogeny. This is a major challenge in fungal systems with substantial asexual reproduction or with significant selfed sexual reproduction in a haploid genome. The key feature here is that recombination can be " localized " in some but not all clades in a phylogeny and that these clades can be identified. From this, contemporary versus historical patterns of recombination can be inferred from a phylogeny. Phylogenetic approaches based on conversion of the phylogeny to a nested hierarchical statistical design are presented for fuller exploration of associations between each nested level of the phylogeny and any variable, such as geographical location, host, or symptom type. The basic operations for both testing for population subdivision based on geographical associations, and for cladistic inference of population processes are presented. Our hypothetical dataset is also used to demonstrate how genealogical relationships and population parameters can be inferred using coalescent and Bayesian methods. The basic principles of these approaches are graphically presented, along with useful references and comments on key assumptions implicit in methods currently available. 1. INTRODUCTION Population genetics is the study of the structure of populations and of the evolutionary processes that shape these structural patterns. The patterns of distinct, divergent populations are inferred from the genetic diversity of contemporary samples made from " the field " , including clinical patient populations. The evolutionary processes include mutation, gene flow, recombination, selection, and drift. Population divergence resulting from such evolutionary processes, as well as from hybridization or vicariance (fragmentation of the environment that can lead to fragmentation of populations), eventually results in speciation. …