Data from: The phylogeny of Rickettsia using different evolutionary signatures: how tree-like is bacterial evolution?

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.立克次体属（Rickettsia）是一类胞内细菌，其宿主范围与传播策略均极为多样，这一点在其高度动态的基因组中得到了充分体现。既往部分研究认为，立克次体的进化历史并非树形结构，这是因为基于基因组不同区域开展的系统发育重建结果存在不一致性。本研究利用全基因组数据重建立克次体的系统发育关系，其中包含两份来自此前未采样宿主类群的全新基因组序列。我们发现，一种被多种系统发育信号支持的单一拓扑结构，可以很好地阐释核心基因组（core genome）的进化历史。尽管确实观察到大量单个基因树之间存在不一致性，但基于单一拓扑结构的模拟分析以及位点间隔分区分析结果表明，这种不一致更可能源于系统误差，而非水平基因转移（horizontal gene transfer）。附属基因组（accessory genome）内容（即基因有无状态）的系统发育分析也得到了一些冲突的分支位置，但我们认为这些结果同样源于系统误差，具体为趋同基因组缩减，而现有系统发育方法无法对此进行有效校正。本研究结果表明，即便在同一属内，基于系统发育不一致性开展的基因交流检测也可能出现假阳性结果。