Genome phylogenies are used to build tree-like representations of evolutionary relationships among genomes. However, in condensing the phylogenetic signals within a set of genomes down to a single tree, these methods generally do not explicitly take into account discordant signals arising due to lateral genetic transfer. Because conflicting vertical and horizontal signals can produce compromise trees that do not reflect either type of history, it is essential to understand the sensitivity of inferred genome phylogenies to these confounding effects. Using replicated simulations of genome evolution, we show that different scenarios of lateral genetic transfer have significant impacts on the ability to recover the "true" tree of genomes, even when corrections for phylogenetically discordant signals are used.

中文翻译：

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网状进化对基因组系统发育的影响

基因组系统发育用于构建基因组之间进化关系的树状表示。然而，在将一组基因组内的系统发育信号浓缩为一棵树时，这些方法通常不会明确考虑由于横向遗传转移而产生的不一致信号。由于相互冲突的垂直和水平信号会产生不反映任何类型历史的折衷树，因此了解推断的基因组系统发育对这些混杂效应的敏感性至关重要。使用基因组进化的复制模拟，我们表明横向遗传转移的不同场景对恢复“真实”基因组树的能力有显着影响，即使在使用系统发育不一致信号的校正时也是如此。