title: Population genetics of microbial pathogens estimated from multilocus sequence typing (MLST) data.
abstract: The inference of population recombination (rho), population mutation (Theta), and adaptive selection is of great interest in microbial population genetics. These parameters can be efficiently estimated using explicit statistical frameworks (evolutionary models) that describe their effect on gene sequences. Within this framework, we estimated rho and Theta using a coalescent approach, and adaptive (or destabilizing) selection under heterogeneous codon-based and amino acid property models in microbial sequences from MLST databases. We analyzed a total of 91 different housekeeping gene regions (loci) corresponding to one fungal and sixteen bacterial pathogens. Our results show that these three population parameters vary extensively across species and loci, but they do not seem to be correlated. For the most part, estimated recombination rates among species agree well with previous studies. Over all taxa, the rho/Theta ratio suggests that each factor contributes similarly to the emergence of variant alleles. Comparisons of Theta estimated under finite- and infinite-site models indicate that recurrent mutation (i.e., multiple mutations at some sites) can increase Theta by up to 39%. Significant evidence of molecular adaptation was detected in 28 loci from 13 pathogens. Three of these loci showed concordant patterns of adaptive selection in two to four different species.
authors.affiliation: Department of Integrative Biology, Brigham Young University, Provo, UT 84602, USA. mp323@email.byu.edu
authors.forename: Marcos
authors.initials: M
authors.lastname: Pérez-Losada
authors.forename: Emily B
authors.initials: EB
authors.lastname: Browne
authors.forename: Aaron
authors.initials: A
authors.lastname: Madsen
authors.forename: Thierry
authors.initials: T
authors.lastname: Wirth
authors.forename: Raphael P
authors.initials: RP
authors.lastname: Viscidi
authors.forename: Keith A
authors.initials: KA
authors.lastname: Crandall
mesh_terms: D000483:Alleles; D015373:Bacterial Typing Techniques; D004269:DNA, Bacterial / Q000032:analysis / Q000235:genetics; D030541:Databases, Genetic; D019143:Evolution, Molecular; D014644:Genetic Variation; D005828:Genetics, Population; D006090:Gram-Negative Bacteria / Q000235:genetics* / Q000472:pathogenicity*; D006094:Gram-Positive Bacteria / Q000235:genetics* / Q000472:pathogenicity*; D015233:Models, Statistical; D009154:Mutation; D016533:Mycological Typing Techniques; D010802:Phylogeny; D011995:Recombination, Genetic; D012641:Selection, Genetic; D017422:Sequence Analysis, DNA
chemical_list: D004269:DNA, Bacterial