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，其宿主类群与传播策略均极为多样，这一特征在其高度动态的基因组中得到了充分体现。此前已有多项研究将立克次体的演化历史描述为非树形结构，其依据为基于基因组不同区域构建的系统发育重建结果之间存在不一致性。本研究采用全基因组数据重建立克次体的系统发育关系，纳入了两个来自此前未被采样的宿主类群的全新基因组。研究结果表明，一种获得多种系统发育信号支持的单一系统发育拓扑结构（topology），能够很好地阐释核心基因组（core genome）的演化历史。尽管我们确实观察到单个基因树之间存在广泛的不一致性，但基于单一拓扑结构的模拟分析与位点间隔分区分析显示，该不一致性更可能源于系统误差，而非水平基因转移（horizontal gene transfer）。针对附属基因组（accessory genome）内容（即基因的有无状态）开展的系统发育分析，同样得到了部分冲突的拓扑位置，但我们认为这些冲突同样源于系统误差，其根源为趋同基因组缩减，而现有系统发育方法无法对该过程进行有效适配。本研究结果显示，即便在同一属内，基于系统发育不一致性检测基因交流的方法也可能产生假阳性结果。