尽管存在广泛的横向遗传转移，但恢复树状进化趋势：概率分析
Recovering the tree-like trend of evolution despite extensive lateral genetic transfer: A probabilistic analysis
摘要：
横向基因转移（LGT）是非垂直进化的一种常见机制，其中遗传物质在两个或多或少的亲缘关系较远的生物之间转移。它在细菌中特别常见，有助于适应性进化，具有重要的医学意义。在进化研究中，LGT已被证明会在基因树之间产生广泛的不一致性，因为基因组成为基因历史的马赛克。特别是，生命之树被质疑为细菌进化史的适当代表。然而，一个常见的假设是，原核生物的进化主要是树状的，但潜在的趋势是模糊的LGT。大量的实证研究试图从相互冲突的基因树中提取一个共同的树状信号。在这里，我们给出了一个概率的角度来看，尽管LGT恢复的树状趋势的问题。随机分布的LGT模型下，我们表明，即使在存在令人惊讶的许多（几乎线性数量的）LGT事件每个基因树的物种遗传可以重建。我们的结果，这是最佳的对数因子，是基于一个强大的，计算效率高的重建方法的分析，并提供了深入了解这些方法的设计。最后，我们表明，我们的研究结果的发现公路的基因共享的影响。
英文摘要：
Lateral gene transfer (LGT) is a common mechanism of non-vertical evolution where genetic material is transferred between two more or less distantly related organisms. It is particularly common in bacteria where it contributes to adaptive evolution with important medical implications. In evolutionary studies, LGT has been shown to create widespread discordance between gene trees as genomes become mosaics of gene histories. In particular, the Tree of Life has been questioned as an appropriate representation of bacterial evolutionary history. Nevertheless a common hypothesis is that prokaryotic evolution is primarily tree-like, but that the underlying trend is obscured by LGT. Extensive empirical work has sought to extract a common tree-like signal from conflicting gene trees. Here we give a probabilistic perspective on the problem of recovering the tree-like trend despite LGT. Under a model of randomly distributed LGT, we show that the species phylogeny can be reconstructed even in the presence of surprisingly many (almost linear number of) LGT events per gene tree. Our results, which are optimal up to logarithmic factors, are based on the analysis of a robust, computationally efficient reconstruction method and provides insight into the design of such methods. Finally we show that our results have implications for the discovery of highways of gene sharing.
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