title: The Phylogeny of Rickettsia Using Different Evolutionary Signatures: How Tree-Like is Bacterial Evolution?
abstract: Rickettsia is a genus of intracellular bacteria whose hosts and transmission strategies are both impressively diverse, and this is reflected in a highly dynamic genome. Some previous studies have described the evolutionary history of Rickettsia as non-tree-like, due to incongruity between phylogenetic reconstructions using different portions of the genome. Here, we reconstruct the Rickettsia phylogeny using whole-genome data, including two new genomes from previously unsampled host groups. We find that a single topology, which is supported by multiple sources of phylogenetic signal, well describes the evolutionary history of the core genome. We do observe extensive incongruence between individual gene trees, but analyses of simulations over a single topology and interspersed partitions of sites show that this is more plausibly attributed to systematic error than to horizontal gene transfer. Some conflicting placements also result from phylogenetic analyses of accessory genome content (i.e., gene presence/absence), but we argue that these are also due to systematic error, stemming from convergent genome reduction, which cannot be accommodated by existing phylogenetic methods. Our results show that, even within a single genus, tests for gene exchange based on phylogenetic incongruence may be susceptible to false positives.
authors.affiliation: Department of Genetics, University of Cambridge, Downing Street, Cambridge CB2 3EH, UK; and ggrm2@cam.ac.uk.
authors.forename: Gemma G R
authors.initials: GG
authors.lastname: Murray
authors.affiliation: Department of Veterinary Medicine, University of Cambridge, Madingley Road, Cambridge CB3 0ES, UK.
authors.forename: Lucy A
authors.initials: LA
authors.lastname: Weinert
authors.affiliation: Department of Genetics, University of Cambridge, Downing Street, Cambridge CB2 3EH, UK; and.
authors.forename: Emma L
authors.initials: EL
authors.lastname: Rhule
authors.affiliation: Department of Genetics, University of Cambridge, Downing Street, Cambridge CB2 3EH, UK; and.
authors.forename: John J
authors.initials: JJ
authors.lastname: Welch
mesh_terms: D005075:Biological Evolution; D002965:Classification; D003198:Computer Simulation / Q000592:standards*; D016680:Genome, Bacterial / Q000235:genetics*; D010802:Phylogeny; D012281:Rickettsia / Q000145:classification* / Q000235:genetics*
keywords: Gene tree discordance; genome reduction; horizontal gene transfer; reticulate evolution; systematic error