期刊
TRENDS IN ECOLOGY & EVOLUTION
卷 30, 期 6, 页码 306-313出版社
ELSEVIER SCIENCE LONDON
DOI: 10.1016/j.tree.2015.03.009
关键词
bacteria; DNA virus; epidemiological models; evolutionary rate; infectious disease; phylodynamics
资金
- RAPIDD program of the Science and Technology Directorate of the US Department of Homeland Security
- National Institutes of Health (NIH) Fogarty International Center
- NIH [RO1 AI047498]
- Biotechnology and Biological Sciences Research Council (BBSRC) [BB/L010569/1]
- NSF [EF-0928690, OCE-1335657]
- European Research Council under the European Commission [614725-PATHPHYLODYN]
- National Institute for Health Research (NIHR) Health Protection Research Unit
- Directorate For Geosciences [1335657] Funding Source: National Science Foundation
- Division Of Ocean Sciences [1335657] Funding Source: National Science Foundation
- Biotechnology and Biological Sciences Research Council [BB/L010569/1, BB/L023458/1] Funding Source: researchfish
- Medical Research Council [MR/K010174/1B, MR/K010174/1] Funding Source: researchfish
- National Institute for Health Research [HPRU-2012-10080] Funding Source: researchfish
- BBSRC [BB/L010569/1, BB/L023458/1] Funding Source: UKRI
- MRC [MR/K010174/1] Funding Source: UKRI
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.
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