Identifying lineage effects when controlling for population structure improves power in bacterial association studies
SG Earle, CH Wu, J Charlesworth, N Stoesser… - Nature …, 2016 - nature.com
Bacteria pose unique challenges for genome-wide association studies because of strong
structuring into distinct strains and substantial linkage disequilibrium across the genome 1, 2. …
structuring into distinct strains and substantial linkage disequilibrium across the genome 1, 2. …
The McDonald–Kreitman test and slightly deleterious mutations
J Charlesworth, A Eyre-Walker - Molecular biology and evolution, 2008 - academic.oup.com
It is possible to estimate the proportion of substitutions that are due to adaptive evolution using
the numbers of silent and nonsilent polymorphisms and substitutions in a McDonald and …
the numbers of silent and nonsilent polymorphisms and substitutions in a McDonald and …
The rate of adaptive evolution in enteric bacteria
J Charlesworth, A Eyre-Walker - Molecular biology and evolution, 2006 - academic.oup.com
Here we estimate the rate of adaptive substitution in a set of 410 genes that are present in 6
Escherichia coli and 6 Salmonella enterica genomes. We estimate that more than 50% of …
Escherichia coli and 6 Salmonella enterica genomes. We estimate that more than 50% of …
[HTML][HTML] Mobile elements drive recombination hotspots in the core genome of Staphylococcus aureus
…, H Larner-Svensson, J Charlesworth… - Nature …, 2014 - nature.com
Horizontal gene transfer is an important driver of bacterial evolution, but genetic exchange
in the core genome of clonal species, including the major pathogen Staphylococcus aureus, …
in the core genome of clonal species, including the major pathogen Staphylococcus aureus, …
Severe infections emerge from commensal bacteria by adaptive evolution
…, E Liu, AE Sheppard, S Perera, J Charlesworth… - elife, 2017 - elifesciences.org
10.7554/eLife.30637.001 Bacteria responsible for the greatest global mortality colonize the
human microbiota far more frequently than they cause severe infections. Whether mutation …
human microbiota far more frequently than they cause severe infections. Whether mutation …
HierCC: A multi-level clustering scheme for population assignments based on core genome MLST
Motivation Routine infectious disease surveillance is increasingly based on large-scale
whole-genome sequencing databases. Real-time surveillance would benefit from immediate …
whole-genome sequencing databases. Real-time surveillance would benefit from immediate …
Genome reduction is associated with bacterial pathogenicity across different scales of temporal and ecological divergence
GGR Murray, J Charlesworth, EL Miller… - Molecular Biology …, 2021 - academic.oup.com
Emerging bacterial pathogens threaten global health and food security, and so it is important
to ask whether these transitions to pathogenicity have any common features. We present a …
to ask whether these transitions to pathogenicity have any common features. We present a …
Accurate reconstruction of bacterial pan-and core genomes with PEPPAN
Bacterial genomes can contain traces of a complex evolutionary history, including extensive
homologous recombination, gene loss, gene duplications, and horizontal gene transfer. To …
homologous recombination, gene loss, gene duplications, and horizontal gene transfer. To …
The other side of the nearly neutral theory, evidence of slightly advantageous back-mutations
J Charlesworth, A Eyre-Walker - Proceedings of the …, 2007 - National Acad Sciences
We argue that if there is a category of slightly deleterious mutations, then there should be a
category of slightly advantageous back-mutations. We show that when there are both slightly …
category of slightly advantageous back-mutations. We show that when there are both slightly …
EnteroBase: hierarchical clustering of 100 000s of bacterial genomes into species/subspecies and populations
…, Z Zhou, J Charlesworth… - … Transactions of the …, 2022 - royalsocietypublishing.org
The definition of bacterial species is traditionally a taxonomic issue while bacterial populations
are identified by population genetics. These assignments are species specific, and …
are identified by population genetics. These assignments are species specific, and …