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Current sequencing technologies have created unprecedented opportunities for studying microbial populations. For pathogens with comparatively low per-site mutation rates, such as DNA viruses and bacteria, whole-genome sequencing can reveal the accumulation of novel genetic variation between population samples taken at different times. The concept of 'measurably evolving populations' and related analytical approaches have provided powerful insights for fast-evolving RNA viruses, but their application to other pathogens is still in its infancy. We argue that previous distinctions between slow- and fast-evolving pathogens become blurred once evolution is assessed at a genome-wide scale, and we highlight important analytical challenges to be overcome to infer pathogen population dynamics from genomic data.

Original publication

DOI

10.1016/j.tree.2015.03.009

Type

Journal article

Journal

Trends Ecol Evol

Publication Date

06/2015

Volume

30

Pages

306 - 313

Keywords

DNA virus, bacteria, epidemiological models, evolutionary rate, infectious disease, phylodynamics, Bacteria, Evolution, Molecular, Genome, Bacterial, Genome, Viral, Mutation Rate, Population Dynamics, RNA Viruses