| Summary: | Genetic diversity in pathogen species contains information about evolutionary and epidemiological processes, including the origins and history of disease, the nature of the selective forces acting on pathogen genes and the role of recombination in generating genetic novelty. Here, we review recent developments in these fields and compare the use of population genetic, or population-model based, approaches to phylogenetic, or population-model free, methodologies. We show how simple epidemiological models can be related to the ancestral, or coalescent, process underlying samples from pathogen species, enabling detailed inference about pathogen biology from patterns of molecular variation.
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