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Lateral gene transfer (LGT) is a common mechanism of non-vertical evolutionwhere genetic material is transferred between two more or less distantlyrelated organisms. It is particularly common in bacteria where it contributesto adaptive evolution with important medical implications. In evolutionarystudies, LGT has been shown to create widespread discordance between gene treesas genomes become mosaics of gene histories. In particular, the Tree of Lifehas been questioned as an appropriate representation of bacterial evolutionaryhistory. Nevertheless a common hypothesis is that prokaryotic evolution isprimarily tree-like, but that the underlying trend is obscured by LGT.Extensive empirical work has sought to extract a common tree-like signal fromconflicting gene trees. Here we give a probabilistic perspective on the problemof recovering the tree-like trend despite LGT. Under a model of randomlydistributed LGT, we show that the species phylogeny can be reconstructed evenin the presence of surprisingly many (almost linear number of) LGT events pergene tree. Our results, which are optimal up to logarithmic factors, are basedon the analysis of a robust, computationally efficient reconstruction methodand provides insight into the design of such methods. Finally we show that ourresults have implications for the discovery of highways of gene sharing.

Recovering the tree-like trend of evolution despite extensive lateral genetic transfer: A probabilistic analysis