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具有显著多样性，这一点在其高度动态的基因组中得到了体现。以往部分研究因使用基因组不同区域进行系统发育重建时存在不一致性，将立克次体属的进化历史描述为非树状。本研究利用全基因组数据重建了立克次体属的系统发育关系，其中包含来自此前未取样宿主类群的两个新基因组。我们发现，一个得到多种系统发育信号来源支持的单一拓扑结构，能够很好地描述核心基因组的进化历史。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以及位点的分散分区分析表明，这种不一致性更可能源于系统误差而非水平基因转移（horizontal gene transfer）。附属基因组内容（即基因存在/缺失）的系统发育分析也导致了一些冲突性的分支位置，但我们认为这些冲突同样源于系统误差——具体是趋同基因组缩减所致，而现有系统发育方法无法对此进行处理。我们的结果表明，即使在单一属内，基于系统发育不一致性的基因交换检测也可能出现假阳性。