Data from: The phylogeny of Rickettsia using different evolutionary signatures: how tree-like is bacterial evolution?
Data files
Nov 12, 2015 version files 32.37 MB
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16S rRNA alignment.fasta
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accessory genes alignment- presence absence with truncated genes as absent.nex
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accessory genes alignment- presence absence with truncated genes as present.nex
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core genome alignment - 1st & 2nd codon positions.nex
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core genome alignment - 3rd codon positions.nex
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core genome alignment - indels.nex
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Representatives of orthology groups.fasta
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Rickettsia gene orthology groups.csv
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Rickettsia symbiont of Adalia bipunctata scaffolds.fasta
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Supplementary Figures.pdf
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Supplementary Tables.xlsx
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.