Germs, genomes and genealogies.
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 epidemiolog...Expand abstract
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