title: The impact of recombination on dN/dS within recently emerged bacterial clones.
abstract: The development of next-generation sequencing platforms is set to reveal an unprecedented level of detail on short-term molecular evolutionary processes in bacteria. Here we re-analyse genome-wide single nucleotide polymorphism (SNP) datasets for recently emerged clones of methicillin resistant Staphylococcus aureus (MRSA) and Clostridium difficile. We note a highly significant enrichment of synonymous SNPs in those genes which have been affected by recombination, i.e. those genes on mobile elements designated "non-core" (in the case of S. aureus), or those core genes which have been affected by homologous replacements (S. aureus and C. difficile). This observation suggests that the previously documented decrease in dN/dS over time in bacteria applies not only to genomes of differing levels of divergence overall, but also to horizontally acquired genes of differing levels of divergence within a single genome. We also consider the role of increased drift acting on recently emerged, highly specialised clones, and the impact of recombination on selection at linked sites. This work has implications for a wide range of genomic analyses.
authors.affiliation: Department of Biology and Biochemistry, University of Bath, Claverton Down, Bath, United Kingdom.
authors.forename: Santiago
authors.initials: S
authors.lastname: Castillo-Ramírez
authors.forename: Simon R
authors.initials: SR
authors.lastname: Harris
authors.forename: Matthew T G
authors.initials: MT
authors.lastname: Holden
authors.forename: Miao
authors.initials: M
authors.lastname: He
authors.forename: Julian
authors.initials: J
authors.lastname: Parkhill
authors.forename: Stephen D
authors.initials: SD
authors.lastname: Bentley
authors.forename: Edward J
authors.initials: EJ
authors.lastname: Feil
mesh_terms: D016360:Clostridioides difficile / Q000235:genetics*; D019143:Evolution, Molecular; D005798:Genes, Bacterial / Q000502:physiology*; D055624:Methicillin-Resistant Staphylococcus aureus / Q000235:genetics*; D020641:Polymorphism, Single Nucleotide; D011995:Recombination, Genetic