Untangling hybrid phylogenetic signals: horizontal gene transfer and artifacts of phylogenetic reconstruction.

Phylogenomic methods can be used to investigate the tangled evolutionary relationships among genomes. Building 'all the trees of all the genes' can potentially identify common pathways of horizontal gene transfer (HGT) among taxa at varying levels of phylogenetic depth. Phylogenetic affinities can be aggregated and merged with the information about genetic linkage and biochemical function to examine hypotheses of adaptive evolution via HGT. Additionally, the use of many genetic data sets increases the power of statistical tests for phylogenetic artifacts. However, large-scale phylogenetic analyses pose several challenges, including the necessary abandonment of manual validation techniques, the need to translate inferred phylogenetic discordance into inferred HGT events, and the challenges involved in aggregating results from search-based inference methods. In this chapter we describe a tree search procedure to recover the most parsimonious pathways of HGT, and examine some of the assumptions that are made by this method.

[1]  Timothy J. Harlow,et al.  Highways of gene sharing in prokaryotes. , 2005, Proceedings of the National Academy of Sciences of the United States of America.

[2]  Robert G. Beiko,et al.  A simulation test bed for hypotheses of genome evolution , 2007, Bioinform..

[3]  W. Doolittle,et al.  Phylogenetic analyses of cyanobacterial genomes: quantification of horizontal gene transfer events. , 2006, Genome research.

[4]  N. Galtier.  A model of horizontal gene transfer and the bacterial phylogeny problem. , 2007, Systematic biology.

[5]  Tandy J. Warnow,et al.  Reconstructing Reticulate Evolution in SpeciesTheory and Practice , 2005, J. Comput. Biol..

[6]  M. Steel,et al.  Recovering evolutionary trees under a more realistic model of sequence evolution. , 1994, Molecular biology and evolution.

[7]  Peer Bork,et al.  Genome-Wide Experimental Determination of Barriers to Horizontal Gene Transfer , 2007, Science.

[8]  C. Kurland,et al.  Horizontal gene transfer: A critical view , 2003 .

[9]  V. Moulton,et al.  Neighbor-net: an agglomerative method for the construction of phylogenetic networks. , 2002, Molecular biology and evolution.

[10]  W. Li,et al.  Evidence for higher rates of nucleotide substitution in rodents than in man. , 1985, Proceedings of the National Academy of Sciences of the United States of America.

[11]  M. Ragan.  Phylogenetic inference based on matrix representation of trees. , 1992, Molecular phylogenetics and evolution.

[12]  Timothy J. Harlow,et al.  Do different surrogate methods detect lateral genetic transfer events of different relative ages? , 2006, Trends in microbiology.

[13]  Mark A Ragan,et al.  Detecting lateral genetic transfer : a phylogenetic approach. , 2008, Methods in molecular biology.

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

[15]  W. Maddison.  Gene Trees in Species Trees , 1997 .

[16]  Y. Inagaki,et al.  Recombination between elongation factor 1alpha genes from distantly related archaeal lineages. , 2006, Proceedings of the National Academy of Sciences of the United States of America.

[17]  J. Peter Gogarten,et al.  Whole-Genome Analysis of Photosynthetic Prokaryotes , 2002, Science.

[18]  G. Singer,et al.  Nucleotide bias causes a genomewide bias in the amino acid composition of proteins. , 2000, Molecular biology and evolution.

[19]  S. Ho,et al.  Tracing the decay of the historical signal in biological sequence data. , 2004, Systematic biology.

[20]  J. S. Rogers,et al.  Bias in phylogenetic estimation and its relevance to the choice between parsimony and likelihood methods. , 2001, Systematic biology.

[21]  J. Hein.  A heuristic method to reconstruct the history of sequences subject to recombination , 1993, Journal of Molecular Evolution.

[22]  Adam Godzik,et al.  Clustering of highly homologous sequences to reduce the size of large protein databases , 2001, Bioinform..

[23]  W. Doolittle,et al.  Lateral gene transfer and the origins of prokaryotic groups. , 2003, Annual review of genetics.

[24]  Glenn Hickey,et al.  SPR Distance Computation for Unrooted Trees , 2008, Evolutionary bioinformatics online.

[25]  Michael T. Hallett,et al.  Efficient algorithms for lateral gene transfer problems , 2001, RECOMB.

[26]  Mark A. Ragan,et al.  A word-oriented approach to alignment validation , 2005, Bioinform..

[27]  C R Woese,et al.  Archaeal phylogeny: reexamination of the phylogenetic position of Archaeoglobus fulgidus in light of certain composition-induced artifacts. , 1991, Systematic and applied microbiology.

[28]  D. Penny,et al.  Comment on "Hexapod Origins: Monophyletic or Paraphyletic?" , 2003, Science.

[29]  Faisal Ababneh,et al.  The biasing effect of compositional heterogeneity on phylogenetic estimates may be underestimated. , 2004, Systematic biology.

[30]  Distributional profiles of homologous open reading frames among bacterial phyla: implications for vertical and lateral transmission. , 2002 .

[31]  Simon A. A. Travers,et al.  Does a tree–like phylogeny only exist at the tips in the prokaryotes? , 2004, Proceedings of the Royal Society of London. Series B: Biological Sciences.

[32]  Eric Bapteste,et al.  Deduction of probable events of lateral gene transfer through comparison of phylogenetic trees by recursive consolidation and rearrangement , 2005, BMC Evolutionary Biology.

[33]  H. Ochman,et al.  Amelioration of Bacterial Genomes: Rates of Change and Exchange , 1997, Journal of Molecular Evolution.

[34]  Dirk Husmeier,et al.  Detecting recombination with MCMC , 2002, ISMB.

[35]  N. Moran,et al.  From Gene Trees to Organismal Phylogeny in Prokaryotes:The Case of the γ-Proteobacteria , 2003, PLoS biology.

[36]  Nicholas Hamilton,et al.  Phylogenetic identification of lateral genetic transfer events , 2006, BMC Evolutionary Biology.

[37]  Satoshi Fukuchi,et al.  Unique amino acid composition of proteins in halophilic bacteria. , 2003, Journal of molecular biology.

[38]  David L. Swofford,et al.  Are Guinea Pigs Rodents? The Importance of Adequate Models in Molecular Phylogenetics , 1997, Journal of Mammalian Evolution.

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

[40]  Mark A. Ragan,et al.  A two-phase strategy for detecting recombination in nucleotide sequences , 2007, South Afr. Comput. J..

[41]  M. Ragan.  On surrogate methods for detecting lateral gene transfer. , 2001, FEMS microbiology letters.

[42]  J. Lake,et al.  Horizontal gene transfer among genomes: the complexity hypothesis. , 1999, Proceedings of the National Academy of Sciences of the United States of America.

[43]  W. Martin,et al.  Ancestral genome sizes specify the minimum rate of lateral gene transfer during prokaryote evolution , 2007, Proceedings of the National Academy of Sciences.

[44]  Timothy J. Harlow,et al.  A hybrid clustering approach to recognition of protein families in 114 microbial genomes , 2004, BMC Bioinformatics.

[45]  M. Ragan,et al.  Inferring Genome Trees by Using a Filter To Eliminate Phylogenetically Discordant Sequences and a Distance Matrix Based on Mean Normalized BLASTP Scores , 2002, Journal of bacteriology.

[46]  Charles Semple,et al.  Computing the minimum number of hybridization events for a consistent evolutionary history , 2007, Discret. Appl. Math..

[47]  Edward Susko,et al.  Testing congruence in phylogenomic analysis. , 2008, Systematic biology.

[48]  Junhyong Kim,et al.  The Cobweb of Life Revealed by Genome-Scale Estimates of Horizontal Gene Transfer , 2005, PLoS biology.

[49]  J. Peter Gogarten,et al.  BranchClust: a phylogenetic algorithm for selecting gene families , 2007, BMC Bioinformatics.