Measurably evolving pathogens in the genomic era

Biek, R. , Pybus, O. G., Lloyd-Smith, J. O. and Didelot, X. (2015) Measurably evolving pathogens in the genomic era. Trends in Ecology and Evolution, 30(6), pp. 306-313. (doi:10.1016/j.tree.2015.03.009) (PMID:25887947) (PMCID:PMC4457702)

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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.

Item Type:Articles
Status:Published
Refereed:Yes
Glasgow Author(s) Enlighten ID:Biek, Dr Roman
Authors: Biek, R., Pybus, O. G., Lloyd-Smith, J. O., and Didelot, X.
College/School:College of Medical Veterinary and Life Sciences > Institute of Biodiversity Animal Health and Comparative Medicine
Journal Name:Trends in Ecology and Evolution
Publisher:Elsevier
ISSN:0169-5347
ISSN (Online):1872-8383
Copyright Holders:Copyright © 2015 Elsevier, Ltd.
First Published:First published in Trends in Ecology and Evolution 30(6):306-313
Publisher Policy:Reproduced in accordance with the copyright policy of the publisher.

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Project CodeAward NoProject NamePrincipal InvestigatorFunder's NameFunder RefLead Dept
639191Joint estimation of epidemiological and genetic processes for Mycobacterium bovis transmission dynamics in cattle and badgersRowland KaoBiotechnology and Biological Sciences Research Council (BBSRC)BB/L010569/1RI BIODIVERSITY ANIMAL HEALTH & COMPMED
473964Phylogeography and spatial dynamics of epidemic rabiesRoman BiekNational Institute of Health (NIH-GA)5 R01 AI047498-RI BIODIVERSITY ANIMAL HEALTH & COMPMED