title: Phylogenetic relationships among Staphylococcus species and refinement of cluster groups based on multilocus data.
abstract: BACKGROUND
  Estimates of relationships among Staphylococcus species have been hampered by poor and inconsistent resolution of phylogenies based largely on single gene analyses incorporating only a limited taxon sample. As such, the evolutionary relationships and hierarchical classification schemes among species have not been confidently established. Here, we address these points through analyses of DNA sequence data from multiple loci (16S rRNA gene, dnaJ, rpoB, and tuf gene fragments) using multiple Bayesian and maximum likelihood phylogenetic approaches that incorporate nearly all recognized Staphylococcus taxa.
  
  
  RESULTS
  We estimated the phylogeny of fifty-seven Staphylococcus taxa using partitioned-model Bayesian and maximum likelihood analysis, as well as Bayesian gene-tree species-tree methods. Regardless of methodology, we found broad agreement among methods that the current cluster groups require revision, although there was some disagreement among methods in resolution of higher order relationships. Based on our phylogenetic estimates, we propose a refined classification for Staphylococcus with species being classified into 15 cluster groups (based on molecular data) that adhere to six species groups (based on phenotypic properties).
  
  
  CONCLUSIONS
  Our findings are in general agreement with gene tree-based reports of the staphylococcal phylogeny, although we identify multiple previously unreported relationships among species. Our results support the general importance of such multilocus assessments as a standard in microbial studies to more robustly infer relationships among recognized and newly discovered lineages.
authors.affiliation: Burnett School of Biomedical Sciences, University of Central Florida College of Medicine, 4000 Central Florida Boulevard, Orlando, FL 32816, USA.
authors.forename: Ryan P
authors.initials: RP
authors.lastname: Lamers
authors.forename: Gowrishankar
authors.initials: G
authors.lastname: Muthukrishnan
authors.forename: Todd A
authors.initials: TA
authors.lastname: Castoe
authors.forename: Sergio
authors.initials: S
authors.lastname: Tafur
authors.forename: Alexander M
authors.initials: AM
authors.lastname: Cole
authors.forename: Christopher L
authors.initials: CL
authors.lastname: Parkinson
mesh_terms: D001499:Bayes Theorem; D004269:DNA, Bacterial / Q000235:genetics; D016013:Likelihood Functions; D008957:Models, Genetic; D058885:Multilocus Sequence Typing; D010802:Phylogeny; D017422:Sequence Analysis, DNA; D013210:Staphylococcus / Q000145:classification* / Q000235:genetics
chemical_list: D004269:DNA, Bacterial