Who is Who in Phylogenetic Networks

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1 Leo van Iersel, Steven Kelk, Regula Rupp and Daniel H. Huson. Phylogenetic Networks Do not Need to Be Complex: Using Fewer Reticulations to Represent Conflicting Clusters. In ISMB10, Vol. 26(12):i124-i131 of BIO, 2010.   Keywords: from clusters, level k phylogenetic network, Program Dendroscope, Program HybridInterleave, Program HybridNumber, reconstruction. Note: http://dx.doi.org/10.1093/bioinformatics/btq202, with proofs: http://arxiv.org/abs/0910.3082.         Toggle abstract "Phylogenetic trees are widely used to display estimates of how groups of species are evolved. Each phylogenetic tree can be seen as a collection of clusters, subgroups of the species that evolved from a common ancestor. When phylogenetic trees are obtained for several datasets (e.g. for different genes), then their clusters are often contradicting. Consequently, the set of all clusters of such a dataset cannot be combined into a single phylogenetic tree. Phylogenetic networks are a generalization of phylogenetic trees that can be used to display more complex evolutionary histories, including reticulate events, such as hybridizations, recombinations and horizontal gene transfers. Here, we present the new CASS algorithm that can combine any set of clusters into a phylogenetic network. We show that the networks constructed by CASS are usually simpler than networks constructed by other available methods. Moreover, we show that CASS is guaranteed to produce a network with at most two reticulations per biconnected component, whenever such a network exists. We have implemented CASS and integrated it into the freely available Dendroscope software. Contact: l.j.j.v.iersel@gmail.com. Supplementary information: Supplementary data are available at Bioinformatics online. © The Author(s) 2010. Published by Oxford University Press." 2 Yufeng Wu. Close Lower and Upper Bounds for the Minimum Reticulate Network of Multiple Phylogenetic Trees. In ISMB10, Vol. 26(12):i140-i148 of BIO, 2010.   Keywords: explicit network, from rooted trees, hybridization, minimum number, phylogenetic network, phylogeny, Program PIRN, software. Note: http://dx.doi.org/10.1093/bioinformatics/btq198.         Toggle abstract "Motivation: Reticulate network is a model for displaying and quantifying the effects of complex reticulate processes on the evolutionary history of species undergoing reticulate evolution. A central computational problem on reticulate networks is: given a set of phylogenetic trees (each for some region of the genomes), reconstruct the most parsimonious reticulate network (called the minimum reticulate network) that combines the topological information contained in the given trees. This problem is well-known to be NP-hard. Thus, existing approaches for this problem either work with only two input trees or make simplifying topological assumptions. Results: We present novel results on the minimum reticulate network problem. Unlike existing approaches, we address the fully general problem: there is no restriction on the number of trees that are input, and there is no restriction on the form of the allowed reticulate network. We present lower and upper bounds on the minimum number of reticulation events in the minimum reticulate network (and infer an approximately parsimonious reticulate network). A program called PIRN implements these methods, which also outputs a graphical representation of the inferred network. Empirical results on simulated and biological data show that our methods are practical for a wide range of data. More importantly, the lower and upper bounds match for many datasets (especially when the number of trees is small or reticulation level is low), and this allows us to solve the minimum reticulate network problem exactly for these datasets. Availability: A software tool, PIRN, is available for download from the web page: http://www.engr.uconn.edu/ywu. Contact: ywu@engr.uconn.edu. Supplementary information: Supplementary data is available at Bioinformatics online. © The Author(s) 2010. Published by Oxford University Press."