Beiko Robert G, Doolittle W Ford, Charlebois Robert L
Faculty of Computer Science, Dalhousie University, Institute for Molecular Bioscience/ARC Centre for Bioinformatics, Brisbane, Australia.
Syst Biol. 2008 Dec;57(6):844-56. doi: 10.1080/10635150802559265.
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.
基因组系统发育学用于构建基因组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单一的树时，这些方法通常没有明确考虑由于横向基因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既不反映任何一种历史类型的折衷树，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。通过对基因组进化的重复模拟，我们表明，即使使用了对系统发育不一致信号的校正，不同的横向基因转移场景对恢复基因组“真实”树的能力仍有显著影响。
