TreeOfTrees Method to Evaluate the Congruence Between Gene Trees

A new method, TreeOfTrees, is proposed to compare X-tree structures obtained from several sets of aligned gene sequences of the same taxa. Its aim is to detect genes or sets of genes having different evolutionary histories. The comparison between sets of trees is based on several tree metrics, leading to a unique tree labelled by the gene trees. The robustness values of its edges are estimated by bootstrapping and consensus procedures that allow detecting subsets of genes having differently evolved. Simulations are performed under various evolutionary conditions to test the efficiency of the method and an application on real data is described. Tests of arboricity and various consensus algorithms are also discussed. A corresponding software package is available.

[1]  Alain Guénoche Ordinal properties of tree distances , 1998, Discret. Math..

[2]  Fred R. McMorris,et al.  COMPARISON OF UNDIRECTED PHYLOGENETIC TREES BASED ON SUBTREES OF FOUR EVOLUTIONARY UNITS , 1985 .

[3]  S. Graham,et al.  Phylogenetic congruence and discordance among one morphological and three molecular data sets from Pontederiaceae. , 1998, Systematic biology.

[4]  C. Bult,et al.  TESTING SIGNIFICANCE OF INCONGRUENCE , 1994 .

[5]  N. Saitou,et al.  The neighbor-joining method: a new method for reconstructing phylogenetic trees. , 1987, Molecular biology and evolution.

[6]  Tandy J. Warnow,et al.  Kaikoura Tree Theorems: Computing the Maximum Agreement Subtree , 1993, Inf. Process. Lett..

[7]  M. Steel,et al.  Trees from Languages and Genes are Very Similar , 1993 .

[8]  S. Carroll,et al.  Genome-scale approaches to resolving incongruence in molecular phylogenies , 2003, Nature.

[9]  Jeffrey C. Oliver AUGIST: inferring species trees while accommodating gene tree uncertainty , 2008, Bioinform..

[10]  François-Joseph Lapointe,et al.  ASSESSING CONGRUENCEAMONG DISTANCE MATRICES: SINGLE‐MALT SCOTCH WHISKIES REVISITED , 2004 .

[11]  James O. McInerney,et al.  TOPD/FMTS: a new software to compare phylogenetic trees , 2007, Bioinform..

[12]  Alain Guénoche,et al.  Can We Have Confidence in a Tree Representation? , 2000, JOBIM.

[13]  D. Pearl,et al.  High-resolution species trees without concatenation , 2007, Proceedings of the National Academy of Sciences.

[14]  M. Steel,et al.  Subtree Transfer Operations and Their Induced Metrics on Evolutionary Trees , 2001 .

[15]  T. M. Nye Trees of trees: an approach to comparing multiple alternative phylogenies. , 2008, Systematic biology.

[16]  Hidetoshi Shimodaira,et al.  Multiple Comparisons of Log-Likelihoods with Applications to Phylogenetic Inference , 1999, Molecular Biology and Evolution.

[17]  Luay Nakhleh,et al.  Confounding Factors in HGT Detection: Statistical Error, Coalescent Effects, and Multiple Solutions , 2007, J. Comput. Biol..

[18]  Alain Guénoche,et al.  Trees and proximity representations , 1991, Wiley-Interscience series in discrete mathematics and optimization.

[19]  Andrew Rambaut,et al.  Seq-Gen: an application for the Monte Carlo simulation of DNA sequence evolution along phylogenetic trees , 1997, Comput. Appl. Biosci..

[20]  A. D. Gordon,et al.  Obtaining common pruned trees , 1985 .

[21]  Fred R. McMorris,et al.  Consensusn-trees , 1981 .

[22]  Olivier C. Martin,et al.  A congruence index for testing topological similarity between trees , 2007, Bioinform..

[23]  O. Gascuel,et al.  A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. , 2003, Systematic biology.

[24]  I. Matic,et al.  Role of Intraspecies Recombination in the Spread of Pathogenicity Islands within the Escherichia coli Species , 2009, PLoS pathogens.

[25]  Temple F. Smith,et al.  On the similarity of dendrograms. , 1978, Journal of theoretical biology.

[26]  D. Robinson,et al.  Comparison of phylogenetic trees , 1981 .

[27]  D. Penny Inferring Phylogenies.—Joseph Felsenstein. 2003. Sinauer Associates, Sunderland, Massachusetts. , 2004 .