Reconstructing the shape of a tree from observed dissimilarity data
Advances in Applied Mathematics
Inferring evolutionary trees with strong combinatorial evidence
Theoretical Computer Science - computing and combinatorics
Maximum likelihood of phylogenetic networks
Bioinformatics
The gene evolution model and computing its associated probabilities
Journal of the ACM (JACM)
Parsimony Score of Phylogenetic Networks: Hardness Results and a Linear-Time Heuristic
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
Quartets MaxCut: A Divide and Conquer Quartets Algorithm
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
Phylogenetic Networks: Concepts, Algorithms and Applications
Phylogenetic Networks: Concepts, Algorithms and Applications
Alignment-Free phylogenetic reconstruction
RECOMB'10 Proceedings of the 14th Annual international conference on Research in Computational Molecular Biology
A probabilistic model for gene content evolution with duplication, loss, and horizontal transfer
RECOMB'06 Proceedings of the 10th annual international conference on Research in Computational Molecular Biology
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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.