title: Measurably evolving pathogens in the genomic era.
abstract: 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.
authors.affiliation: Boyd Orr Centre for Population and Ecosystem Health, Institute of Biodiversity, Animal Health and Comparative Medicine, College of Medical, Veterinary, and Life Sciences, University of Glasgow, Glasgow, UK; Fogarty International Center, National Institutes of Health, Bethesda MD, USA. Electronic address: roman.biek@glasgow.ac.uk.
authors.forename: Roman
authors.initials: R
authors.lastname: Biek
authors.affiliation: Department of Zoology, University of Oxford, Oxford, UK.
authors.forename: Oliver G
authors.initials: OG
authors.lastname: Pybus
authors.affiliation: Fogarty International Center, National Institutes of Health, Bethesda MD, USA; Department of Ecology and Evolutionary Biology, University of California at Los Angeles, Los Angeles, CA 90095, USA.
authors.forename: James O
authors.initials: JO
authors.lastname: Lloyd-Smith
authors.affiliation: Department of Infectious Disease Epidemiology, Imperial College, London, UK.
authors.forename: Xavier
authors.initials: X
authors.lastname: Didelot
mesh_terms: D001419:Bacteria / Q000235:genetics; D019143:Evolution, Molecular; D016680:Genome, Bacterial; D016679:Genome, Viral; D059645:Mutation Rate; D011157:Population Dynamics; D012328:RNA Viruses / Q000235:genetics
keywords: DNA virus; bacteria; epidemiological models; evolutionary rate; infectious disease; phylodynamics