Let them fall where they may: Congruence analysis in massive phylogenetically messy data sets

Molecular Biology and Evolution

Volumn 28, Issue 10, 2011, Pages 2773-2785

  Leigh, Jessica W ^a   Schliep, Klaus ^b   Lopez, Philippe ^b   Bapteste, Eric ^b  

^a UNIVERSITY OF OTAGO   (New Zealand)

^b Université Pierre et Marie Curie ^*  (France)

Author keywords

lateral gene transfer; phylogenetic congruence; phylogenetic networks; prokaryote phylogeny; spectral clustering

Indexed keywords

ARTICLE; CLUSTER ANALYSIS; GENE IDENTIFICATION; GENETIC DATABASE; NONHUMAN; PHYLOGENY; PROKARYOTE; SEQUENCE ALIGNMENT;

ALGORITHMS; ARCHAEA; BACTERIA; BAYES THEOREM; CLUSTER ANALYSIS; COMPUTATIONAL BIOLOGY; COMPUTER SIMULATION; DATABASES, GENETIC; EVOLUTION, MOLECULAR; FUNGI; GENETIC MARKERS; GENETIC VARIATION; PHYLOGENY; SEQUENCE ALIGNMENT;

ANIMALIA; PROKARYOTA;

EID: 80051792622     PISSN: 07374038     EISSN: 15371719     Source Type: Journal    
DOI: 10.1093/molbev/msr110     Document Type: Article

References (61)

1. Bapteste E, O'Malley MA, Beiko RG, et al. (11 co-authors). 2009. Prokaryotic evolution and the tree of life are two different things. Biol Direct. 4:34.
2. Bapteste E, Susko E, Leigh J, Ruiz-Trillo I, Bucknam J, Doolittle WF. 2008. Alternative methods for concatenation of core genes indicate a lack of resolution in deep nodes of the prokaryotic phylogeny. Mol Biol Evol. 25:83-91.
3. Beiko RG, Keith JM, Harlow TJ, Ragan MA. 2006. Searching for convergence in phylogenetic Markov chain Monte Carlo. Syst Biol. 55:553-565.
4. Bordewich M, Semple C. 2004.Onthe computational complexityof the rooted subtree prune and regraft distance. Ann Combin. 8:409-423.
5. Brochier C, Bapteste E, Moreira D, Philippe H. 2002. Eubacterial phylogeny based on translational apparatus proteins. Trends Genet. 18:1-5. (Pubitemid 34031845)
6. Bryant D, MacKenzie A, Steel M. 2003. The size of maximum agreement subtree for random binary trees. In: Janowitz M, Lapointe F-J, McMorris FR, Mirkin B, Roberts FS, editors. Bioconsensus. Vol. 61. DIMACS series in discrete mathematics and theoretical computer science. Providence (RI): American Mathematical Society. p. 55-66.
7. Caliński T, Harabasz J. 1974. A dendrite method for cluster analysis. Commun Stat Simul Comp. 3:1-27.
8. Campbell V, Legendre P, Lapointe FJ. 2009. Assessing congruence among ultrametric distance matrices. J Classif. 26:103-117.
9. Campbell V, Legendre P, Lapointe FJ. 2011. The performance of the Congruence Among Distance Matrices (CADM) test in phylogenetic analysis. BMC Evol Biol. 11:64.
10. de Vienne DM, Giraud T, Martin OC. 2007. A congruence index for testing topological similarity between trees. Bioinformatics 23:3119-3124. (Pubitemid 350187512)
11. Deusch O, Landan G, Roettger M, Gruenheit N, Kowallik KV, Allen JF, Martin W, Dagan T. 2008. Genes of cyanobacterial origin in plant nuclear genomes point to a heterocyst-forming plastid ancestor. Mol Biol Evol. 25:748-761. (Pubitemid 351398331)
12. Edwards J, Oman P. 2003. Dimensional reduction for data mapping. R News. 3:2-7.
13. Estabrook GF, McMorris FR, Meacham CA. 1985. Comparison of undirected phylogenetic trees based on subtrees of four evolutionary units. Syst Zool. 34:193-200.
14. Farris JS, Källersjö M, Kluge AG, Bult C. 1994. Testing significance of incongruence. Cladistics 10:315-319.
15. Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. Mol Biol Evol. 14:685-695. (Pubitemid 27287289)
16. Gribaldo S, Philippe H. 2002. Ancient phylogenetic relationships. Theor Popul Biol. 61:391-408. (Pubitemid 38051044)
17. Hobolth A, Dutheil JY, Hawks J, Schierup MH, Mailund T. 2011. Incomplete lineage sorting patterns among human, chimpanzee, and orangutan suggest recent orangutan speciation and widespread selection. Genome Res. 21:349-356.
18. Hudson RR. 1983. Testing the constant-rate neutral allele model with protein sequence data. Evolution 37:203-217.
19. Huelsenbeck JP, Bull JJ. 1996. A likelihood ratio test to detect conflicting phylogenetic signal. Syst Biol. 45:92-98.
20. Huson DH, Bryant D. 2006. Application of phylogenetic networks in evolutionary studies. Mol Biol Evol. 23:254-267. (Pubitemid 43100040)
21. Huson DH, Dezulian T, Klopper T, Steel MA. 2004. Phylogenetic super-networks from partial trees. IEEE Trans Comput Biol Bioinform. 1:151-158. (Pubitemid 40325592)
22. Jain R, Rivera MC, Lake JA. 1999. Horizontal gene transfer among genomes: the complexity hypothesis. Proc Natl Acad Sci USA. 96:3801-3806. (Pubitemid 29168991)
23. Kishino H, Miyata T, Hasegawa M. 1990. Maximum likelihood inference of protein phylogeny and the origin of chloroplasts. J Mol Evol. 30:151-160. (Pubitemid 20261943)
24. Koblmüller S, Duftner N, Sefc KM, Aibara M, Stipacek M, Blanc M, Egger B, Sturmbauer C. 2007. Reticulate phylogeny of gastropod-shell-breeding cichlids from Lake Tanganyika-the result of repeated introgressive hybridization. BMC Evol Biol. 7:7.
25. Krivánek M. 1986. Computing the nearest neighbor interchange metric for unlabeled binary trees is NP-complete. J Classif. 3:55-60.
26. Lapointe FJ, Rissler LJ. 2005. Consensus, congruence, and the comparative phylogeography of codistributed species in California. Am Nat. 166:290-299. (Pubitemid 41076651)
27. Lartillot N, Philippe H. 2004. A Bayesian mixture model for across-site heterogeneities in the amino-acid replacement process. Mol Biol Evol. 21:1095-1109. (Pubitemid 38658218)
28. Leigh JW, Susko E, Baumgartner M, Roger AJ. 2008. Testing congruence in phylogenomic analysis. Syst Biol. 57:104-115.
29. Lento GM, Hickson RE, Chambers GK, Penny D. 1995. Use of spectral analysis to test hypotheses on the origin of pinnipeds. Mol Biol Evol. 12:28-52.
30. MacQueen J. 1967. Some methods for classification and analysis of multivariate observations. In: Le Cam LM, Neyman J, editors. Proceedings of the fifth Berkeley symposium on mathematical statistics and probability. Vol. 1. p. 281-297.
31. Matte-Tailliez O, Brochier C, Forterre P, Philippe H. 2002. Archaeal phylogeny based on ribosomal proteins. Mol Biol Evol. 19:631-639. (Pubitemid 34521295)
32. McBreen K, Lockhart PJ. 2006. Reconstructing reticulate evolutionary histories of plants. Trends Plant Sci. 11:398-404. (Pubitemid 44108708)
33. Newman ME. 2006. Finding community structure in networks using the eigenvectors of matrices. Phys Rev. 74:36104.
34. Ng AY, Jordan MI, Weiss Y. 2001. On spectral clustering: analysis and an algorithm. In: Dietterich TG, Becker S, Ghahramani Z, editors. Advances in neural information processing systems. Vol. 14. Cambridge (MA): MIT Press p. 849-856.
35. Nye TMW. 2008. Trees of trees: an approach to comparing multiple alternative phylogenies. Syst Biol. 57:785-794.
36. Penny D, Hendy MD, Henderson IM. 1987. Reliability of evolutionary trees. Cold Spring Harbor symposia on quantitative biology. Vol. 52. p. 857-862. (Pubitemid 18262394)
37. Planet PJ, Sarkar IN. 2005. mILD: a tool for constructing and analyzing matrices of pairwise phylogenetic character incongru-ence tests. Bioinformatics 21:4423-4424. (Pubitemid 41782937)
38. Puigbò P, Wolf YI, Koonin EV. 2009. Search for a 'Tree of Life' in the thicket of the phylogenetic forest. J Biol. 8:59.
39. Quang LS, Gascuel O, Lartillot N. 2008. Empirical profile mixture models for phylogenetic reconstruction. Bioinformatics 2317-2323.
40. Rambaut A, Grassly NC. 1997. Seq-Gen: an application for the Monte Carlo simulation of DNA sequence evolution along phylogenetic trees. Comput Appl Biosci. 13:235-238. (Pubitemid 27249927)
41. Roberts DL, Solow AR. 2003. Flightless birds: when did the dodo become extinct? Nature 426:245. (Pubitemid 37463134)
42. Robinson D, Foulds L. 1981. Comparison of phylogenetic trees. Math Biosci. 53:131-147. (Pubitemid 11129084)
43. Sammon JW. 1969. A nonlinear mapping for data structure analysis. IEEE Trans Comput. 18:401-409.
44. Schliep K, Lopez P, Lapointe F, Bapteste E. 2011. Harvesting evolutionary signals in a forest of prokaryotic gene trees. Mol Biol Evol. 28:1393-1405.
45. Schmidt HA, Strimmer K, Vingron M, von Haeseler A. 2002. TREE-PUZZLE: maximum likelihood phylogenetic analysis using quartets and parallel computing. Bioinformatics 18:502-504. (Pubitemid 34284960)
46. Shaffer JP. 1995. Multiple hypothesis testing. Annu Rev Psychol. 46:561-584.
47. Stamatakis A. 2006. RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models. Bioinformatics 22:2688-2690. (Pubitemid 44642609)
48. Stamatakis A, Hoover P, Rougemont J. 2008. A rapid bootstrap algorithm for the RAxML web servers. Syst Biol. 57:758-771.
49. Steel MA, Penny D. 1993. Distributions of tree comparison metrics: some new results. Syst Biol. 42:126-141.
50. Swofford DL. 2003. PAUP* 4.0 b10. Phylogenetic analysis using parsimony (* and other methods). Sunderland (MA): Sinauer Associates.
51. Tatusov RL, Koonin EV, Lipman DJ. 1997. A genomic perspective on protein families. Science 278:631-637. (Pubitemid 27464953)
52. Tibshirani R, Walther G, Hastie T. 2001. Estimating the number of clusters in a data set via the gap statistic. J R Stat Soc Ser B Biol Sci. 63:411-423.
53. Vinh le S, Von Haeseler A. 2004. IQPNNI: moving fast through tree space and stopping in time. Mol Biol Evol. 21:1565-1571. (Pubitemid 38971767)
54. Von Luxburg U. 2007. A tutorial on spectral clustering. Stat Comput. 17:395-416.
55. Waddell PJ, Kishino H, Ota R. 2000. Rapid evaluation of the phylogenetic congruence of sequence data using likelihood ratio tests. Mol Biol Evol. 17:1988-1992.
56. Waddell PJ, Kishino H, Ota R. 2007. Phylogenetic methodology for detecting protein interactions. Mol Biol Evol. 24:650-659. (Pubitemid 46355789)
57. Wellner A, Lurie MN, Gophna U. 2007. Complexity, connectivity, and duplicability as barriers to lateral gene transfer. Genome Biol. 8:R156.
58. Whelan S, Goldman N. 2001. A general empirical model of protein evolution derived from multiple protein families using a maximum-likelihood approach. Mol Biol Evol. 18:691-699. (Pubitemid 32372940)
59. White WT, Hills SF, Gaddam R, Holland BR, Penny D. 2007. Treeness triangles: visualizing the loss of phylogenetic signal. Mol Biol Evol. 24:2029-2039.
60. Wu Y. 2009. A practical method for exact computation of subtree prune and regraft distance. Bioinformatics 25:190-196.
61. Zelnik-Manor L, Perona P. 2004. Self-tuning spectral clustering. In: Saul LK, Weiss Y, Bottou L, editors. Advances in neural information processing systems. Vol. 17. Cambridge (MA): MIT Press. p. 1601-1608