Abstract
BackgroundTo understand the evolutionary role of Lateral Gene Transfer (LGT), accurate methods are needed to identify transferred genes and infer their timing of acquisition. Phylogenetic methods are particularly promising for this purpose, but the reconciliation of a gene tree with a reference (species) tree is computationally hard. In addition, the application of these methods to real data raises the problem of sorting out real and artifactual phylogenetic conflict.ResultsWe present Prunier, a new method for phylogenetic detection of LGT based on the search for a maximum statistical agreement forest (MSAF) between a gene tree and a reference tree. The program is flexible as it can use any definition of "agreement" among trees. We evaluate the performance of Prunier and two other programs (EEEP and RIATA-HGT) for their ability to detect transferred genes in realistic simulations where gene trees are reconstructed from sequences. Prunier proposes a single scenario that compares to the other methods in terms of sensitivity, but shows higher specificity. We show that LGT scenarios carry a strong signal about the position of the root of the species tree and could be used to identify the direction of evolutionary time on the species tree. We use Prunier on a biological dataset of 23 universal proteins and discuss their suitability for inferring the tree of life.ConclusionsThe ability of Prunier to take into account branch support in the process of reconciliation allows a gain in complexity, in comparison to EEEP, and in accuracy in comparison to RIATA-HGT. Prunier's greedy algorithm proposes a single scenario of LGT for a gene family, but its quality always compares to the best solutions provided by the other algorithms. When the root position is uncertain in the species tree, Prunier is able to infer a scenario per root at a limited additional computational cost and can easily run on large datasets.Prunier is implemented in C++, using the Bio++ library and the phylogeny program Treefinder. It is available at: http://pbil.univ-lyon1.fr/software/prunier
Highlights
To understand the evolutionary role of Lateral Gene Transfer (LGT), accurate methods are needed to identify transferred genes and infer their timing of acquisition
Prunier Algorithm Objectives The phylogenetic detection of lateral gene transfers relies on differences between a gene tree TG, with branch lengths and support values, and a reference species tree TS on the same set of species S
We will suppose that the species tree is rooted, though the method offers the possibility of using an unrooted reference tree as input, with a reasonable increase in complexity
Summary
To understand the evolutionary role of Lateral Gene Transfer (LGT), accurate methods are needed to identify transferred genes and infer their timing of acquisition. In the case of a rooted species tree, both approaches are equivalent to minimizing the number of LGTs that occurred in the gene family. These problems are known to be computationally difficult, but several algorithms have been proposed, notably to efficiently address the SPR problem. Than and Nakhleh have proposed a decomposition approach, implemented in the RIATA-HGT program [10,11], which identifies regions of the tree where the conflict can be resolved independently, and significantly reduces the complexity of the SPR reconciliation in many cases. EEEP implements such a decomposition [12], and adds the possibility to restrict the type of SPR moves to those that immediately reduce the discordance among trees
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