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Genome-scale rates of evolutionary change in bacteria
- Source :
- Microbial Genomics, Microbial Genomics, 2016, 2 (11), pp.e000094. ⟨10.1101/069492⟩, Microbial Genomics, Society for General Microbiology, 2016, 2 (11), pp.e000094. ⟨10.1101/069492⟩
- Publication Year :
- 2016
-
Abstract
- Estimating the rates at which bacterial genomes evolve is critical to understanding major evolutionary and ecological processes such as disease emergence, long-term host-pathogen associations, and short-term transmission patterns. The surge in bacterial genomic data sets provides a new opportunity to estimate these rates and reveal the factors that shape bacterial evolutionary dynamics. For many organisms estimates of evolutionary rate display an inverse association with the time-scale over which the data are sampled. However, this relationship remains unexplored in bacteria due to the difficulty in estimating genome-wide evolutionary rates, which are impacted by the extent of temporal structure in the data and the prevalence of recombination. We collected 36 whole genome sequence data sets from 16 species of bacterial pathogens to systematically estimate and compare their evolutionary rates and assess the extent of temporal structure in the absence of recombination. The majority (28/36) of data sets possessed sufficient clock-like structure to robustly estimate evolutionary rates. However, in some species reliable estimates were not possible even with “ancient DNA” data sampled over many centuries, suggesting that they evolve very slowly or that they display extensive rate variation among lineages. The robustly estimated evolutionary rates spanned several orders of magnitude, from 10−6 to 10−8 nucleotide substitutions site-1 year-1. This variation was largely attributable to sampling time, which was strongly negatively associated with estimated evolutionary rates, with this relationship best described by an exponential decay curve. To avoid potential estimation biases such time-dependency should be considered when inferring evolutionary time-scales in bacteria.
- Subjects :
- 0301 basic medicine
0106 biological sciences
Mechanisms of Evolution
Evolutionary change
Genome scale
Bacterial genome size
phylogeny
Genome
010603 evolutionary biology
01 natural sciences
Orders of magnitude (bit rate)
Evolution, Molecular
03 medical and health sciences
Phylogenetics
evolution
Molecular clock
Evolutionary dynamics
030304 developmental biology
Whole genome sequencing
Genetics
0303 health sciences
biology
Bacteria
Models, Genetic
molecular clock
Genetic Variation
General Medicine
biology.organism_classification
Biological Evolution
030104 developmental biology
Ancient DNA
13. Climate action
Evolutionary biology
time-dependency
Microbial Evolution and Epidemiology
Mutation
Human genome
[SDV.SPEE]Life Sciences [q-bio]/Santé publique et épidémiologie
substitution rates
Genome, Bacterial
Research Paper
Subjects
Details
- ISSN :
- 20575858
- Database :
- OpenAIRE
- Journal :
- Microbial Genomics, Microbial Genomics, 2016, 2 (11), pp.e000094. ⟨10.1101/069492⟩, Microbial Genomics, Society for General Microbiology, 2016, 2 (11), pp.e000094. ⟨10.1101/069492⟩
- Accession number :
- edsair.doi.dedup.....abf047934cf565a07c7de69d1b5b8c76