On Tree-Based Phylogenetic Networks

A large class of phylogenetic networks can be obtained from trees by the addition of horizontal edges between the tree edges. These networks are called tree-based networks. We present a simple necessary and sufficient condition for tree-based networks and prove that a universal tree-based network exists for any number of taxa that contains as its base every phylogenetic tree on the same set of taxa. This answers two problems posted by Francis and Steel recently. A byproduct is a computer program for generating random binary phylogenetic networks under the uniform distribution model.

[1]  Yi Pan,et al.  A Fast Hierarchical Clustering Algorithm for Functional Modules Discovery in Protein Interaction Networks , 2011, IEEE/ACM Transactions on Computational Biology and Bioinformatics.

[2]  D. Posada,et al.  Characterization of Reticulate Networks Based on the Coalescent with Recombination , 2008, Molecular biology and evolution.

[3]  L. Orgel,et al.  Phylogenetic Classification and the Universal Tree , 1999 .

[4]  Barth F. Smets,et al.  Horizontal gene transfer: perspectives at a crossroads of scientific disciplines , 2005, Nature Reviews Microbiology.

[5]  Leo van Iersel,et al.  Locating a tree in a phylogenetic network , 2010, Inf. Process. Lett..

[6]  Ignazio Carbone,et al.  Phylogenetic relatedness of the M2 double-stranded RNA in Rhizoctonia fungi , 2008, Mycologia.

[7]  Kaizhong Zhang,et al.  Perfect phylogenetic networks with recombination , 2001, J. Comput. Biol..

[8]  David Posada,et al.  Recodon: Coalescent simulation of coding DNA sequences with recombination, migration and demography , 2007, BMC Bioinformatics.

[9]  Mark Stoneking,et al.  Denisovan Ancestry in East Eurasian and Native American Populations , 2015, bioRxiv.

[10]  Doolittle Wf.  Phylogenetic Classification and the Universal Tree , 1999 .

[11]  Mike A. Steel,et al.  Which Phylogenetic Networks are Merely Trees with Additional Arcs? , 2015, Systematic biology.

[12]  Andrew G. Clark,et al.  Conundrum of jumbled mosquito genomes , 2015, Science.

[13]  L. Nakhleh,et al.  Computational approaches to species phylogeny inference and gene tree reconciliation. , 2013, Trends in ecology & evolution.

[14]  R. Pendavingh,et al.  Reconstructing a Phylogenetic Level-1 Network from Quartets , 2013, Bulletin of Mathematical Biology.

[15]  Daniel H. Huson,et al.  Computing galled networks from real data , 2009, Bioinform..

[16]  W. Martin,et al.  The tree of one percent , 2006, Genome Biology.

[17]  Daniel H. Huson,et al.  Beyond Galled Trees - Decomposition and Computation of Galled Networks , 2007, RECOMB.

[18]  K. McBreen,et al.  Reconstructing reticulate evolutionary histories of plants. , 2006, Trends in plant science.

[19]  Xiaofang Jiang,et al.  Extensive introgression in a malaria vector species complex revealed by phylogenomics , 2015, Science.

[20]  Gabriel Cardona,et al.  A distance metric for a class of tree-sibling phylogenetic networks , 2008, Bioinform..

[21]  F. Leighton,et al.  Introduction to Parallel Algorithms and Architectures: Arrays, Trees, Hypercubes , 1991 .

[22]  E. Rocha,et al.  Horizontal Transfer, Not Duplication, Drives the Expansion of Protein Families in Prokaryotes , 2011, PLoS genetics.

[23]  Louxin Zhang,et al.  Locating a Tree in a Phylogenetic Network in Quadratic Time , 2015, RECOMB.

[24]  Eric Bapteste,et al.  INAUGURAL ARTICLE by a Recently Elected Academy Member:Pattern pluralism and the Tree of Life hypothesis , 2007 .