Journal Article

The evolutionary genomics of pathogen recombination

Awadalla, Philip

2003

Overview

Key Points The frequency and rate of genetic recombination in several species, specifically in microbes and pathogens, is unknown. For pathogens, the rate at which populations recombine can help to explain the dynamics of drug resistance and pathogenicity. Furthermore, recombination is necessary for genetic mapping and for the ability of population genetic studies to locate genes that underlie important phenotypes (for example, genes that are associated with virulence, transmission and immune evasion). Finally, although almost all organisms engage in some form of recombination, our understanding of why recombination occurs and is maintained remains controversial. Recombination allows genomic sites or regions to have different evolutionary histories. As a result, the presence of recombination complicates phylogenetic reconstruction and several phylogenetic methods that are used to infer population parameters. Several non-parametric methods are available to detect and estimate recombination in systems that do not conform to standard assumptions, such as having constant population size and an infinite number of sites. Many of these methods have successfully revealed the action of recombination in several viruses, and in bacterial and protozoan species. Unlike non-parametric methods, model-based approaches allow the population recombination rate to be inferred. Model-based estimates of the population recombination rate seem to be consistent with experimental estimates, at least in bacteria. Although species certainly vary, there seem to be some phylogenetic consistencies between recombination rates, relative to the population mutation rates, across broad phylogenetic groupings of taxa. The rates of recombination are often substantial and are correlated with life history, such as endemicity in a population. It is reasonable to suggest that recombination has an active role in the life history and fitness of many pathogens. A pressing problem in studying the evolution of microbial pathogens is to determine the extent to which these genomes recombine. This information is essential for locating pathogenicity loci by using association studies or population genetic approaches. Recombination also complicates the use of phylogenetic approaches to estimate evolutionary parameters such as selection pressures. Reliable methods that detect and estimate the rate of recombination are, therefore, vital. This article reviews the approaches that are available for detecting and estimating recombination in microbial pathogens and how they can be used to understand pathogen evolution and to identify medically relevant loci.

• Publisher: Nature Publishing Group UK,Nature Publishing Group
• Subject: Agriculture / Animal Genetics and Genomics / Animals / Bacteria - genetics / Bacteria - pathogenicity / Bacteriology / Biological and medical sciences / Biological Evolution / Biomedical and Life Sciences / Biomedicine / Cancer Research / Disease control / Drug resistance / Drug Resistance - genetics / Eukaryota - genetics / Eukaryota - pathogenicity / Evolution / Fundamental and applied biological sciences. Psychology / Gene Function / Genetic engineering / Genetics / Genic rearrangement. Recombination. Transposable element / Genomes / Genomics / HIV / Human Genetics / Human immunodeficiency virus / Likelihood Functions / Microbiology / Molecular and cellular biology / Molecular genetics / Mutation / Organisms / Pathogens / Phylogenetics / Phylogeny / Population / Recombination, Genetic / review-article / Transcription. Transcription factor. Splicing. Rna processing / Virulence / Virulence - genetics / Viruses / Viruses - genetics / Viruses - pathogenicity / Yeast