Selecting informative subsets of sparse supermatrices increases the chance to find correct trees

BMC Bioinformatics

Volumn 14, Issue 1, 2013, Pages

  Misof, Bernhard ^a   Meyer, Benjamin ^b   von Reumont, Björn M ^c   Kück, Patrick ^a   Misof, Katharina ^a   Meusemann, Karen ^a,d  

^a ZOOLOGISCHES FORSCHUNGSMUSEUM ALEXANDER KOENIG   (Germany)

^b UNIVERSITY MEDICAL CENTER HAMBURG EPPENDORF   (Germany)

^c DEPARTMENT OF LIFE SCIENCES   (United Kingdom)

^d CSIRO   (Australia)

Author keywords

[No Author keywords available]

Indexed keywords

DATA COVERAGE; EMPIRICAL DATA; INFORMATION CONTENTS; PARTIAL TREES; POTENTIAL SIGNAL; PRESENCE/ABSENCE; SIMULATION STUDIES; TREE RECONSTRUCTION;

FORESTRY; GENES; MATRIX ALGEBRA; SET THEORY;

TREES (MATHEMATICS);

ALGORITHMS; FORESTRY; GENES; INFORMATION RETRIEVAL;

VERTEBRATA;

ALGORITHM; ANIMAL; ARTICLE; CATTLE; CLASSIFICATION; COMPARATIVE STUDY; COMPUTER PROGRAM; COMPUTER SIMULATION; DNA REPAIR; GENETICS; HUMAN; METHODOLOGY; MOLECULAR EVOLUTION; MOUSE; PHYLOGENY; PROBABILITY; RANDOMIZATION; RAT; SIGNAL TRANSDUCTION; STATISTICAL MODEL; SUPPORT VECTOR MACHINE; SWINE;

ALGORITHMS; ANIMALS; CATTLE; CLASSIFICATION; COMPUTER SIMULATION; DNA REPAIR; EVOLUTION, MOLECULAR; HUMANS; LIKELIHOOD FUNCTIONS; MICE; PHYLOGENY; PROBABILITY; RANDOM ALLOCATION; RATS; SIGNAL TRANSDUCTION; SOFTWARE; SUPPORT VECTOR MACHINES; SUS SCROFA;

EID: 84888788505     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-14-348     Document Type: Article

References (62)

1. Sanderson MJ, Driskell AC. The challenge of constructing large phylogenetic trees. Trends Plant Sci 2003, 8:374-379. 10.1016/S1360-1385(03)00165-1, 12927970.
2. Driskell AC, Ané C, Burleigh JG, McMahon MM, O'Meara BC, Sanderson MJ. Prospects for building the tree of life from large sequence databases. Science 2004, 306:1172-1174. 10.1126/science.1102036, 15539599.
3. Philippe H, Delsuc F, Brinkmann H, Lartillot N. Phylogenomics. Annu Rev Ecol Evol Syst 2005, 36:541-562.
4. Dunn CW, Hejnol A, Matus DQ, Pang K, Browne WE, Smith SA, Seaver E, Rouse GW, Obst M, Edgecombe GD, Sorensen MV, Haddock SHD, Schmidt-Rhaesa A, Okusu A, Kristensen RM, Wheeler WC, Martindale MQ, Giribet G. Broad phylogenomic sampling improves resolution of the animal tree of life. Nature 2008, 452:745-749. 10.1038/nature06614, 18322464.
5. Bourlat SJ, Nielsen C, Economou AD, Telford MJ. Testing the new animal phylogeny: a phylum level molecular analysis of the animal kingdom. Mol Phylogenet Evol 2008, 49:23-31. 10.1016/j.ympev.2008.07.008, 18692145.
6. de Queiroz A, Gatesy J. The supermatrix approach to systematics. Trends Ecol Evol (Amst) 2006, 22:34-41.
7. Delsuc F, Brinkmann H, Philippe H. Phylogenomics and the reconstruction of the tree of life. Nat Rev Genet 2005, 6:361-375.
8. Galtier N, Daubin V. Dealing with incongruence in phylogenomic analyses. Philos Trans R Soc Lond, B, Biol Sci 2008, 363:4023-4029. [http://dx.doi.org/10.1098/rstb.2008.0144], 10.1098/rstb.2008.0144, 2607408, 18852109.
9. Hausdorf B, Helmkampf M, Meyer A, Witek A, Herlyn H, Bruchhaus I, Hankeln T, Struck TH, Lieb B. Spiralian phylogenomics supports the resurrection of Bryozoa comprising Ectoprocta and Entoprocta. Mol Biol Evol 2007, 24:2723-2729. 10.1093/molbev/msm214, 17921486.
10. Murphy WJ, Pevzner PA, O'Brien SJ. Mammalian phylogenomics comes of age. Trends Genet 2004, 20:631-639. 10.1016/j.tig.2004.09.005, 15522459.
11. Philippe H, Derelle R, Lopez P, Pick K, Borchiellini C, Boury-Esnault N, Vacelet J, Renard E, Houliston E, Quéinnec E, Da Silva C, Wincker P, Le Guyader H, Leys S, Jackson DJ, Schreiber F, Erpenbeck D, Morgenstern B, Wörheide G, Manuël M. Phylogenomics revives traditional views on deep animal relationships. Curr Biol 2009, 19:706-712. 10.1016/j.cub.2009.02.052, 19345102.
12. Regier JC, Shultz JW, Ganley ARD, Hussey A, Shi D, Ball B, Zwick A, Stajich JE, Cummings MP, Martin JW, Cunningham CW. Resolving arthropod phylogeny: exploring phylogenetic signal within 41 kb of protein-coding nuclear gene sequence. Syst Biol 2008, 57:920-938. 10.1080/10635150802570791, 19085333.
13. Shedlock AM, Botka CW, Zhao S, Shetty J, Zhang T, Liu JS, Deschavanne PJ, Edwards SV. Phylogenomics of nonavian reptiles and the structure of the ancestral amniote genome. Proc Natl Acad Sci USA 2007, 104:2767-2772. 10.1073/pnas.0606204104, 1815256, 17307883.
14. Smith SA, Beaulieu JM, Donoghue MJ. Mega-phylogeny approach for comparative biology: an alternative to supertree and supermatrix approaches. BMC Evol Biol 2009, 9:37. 10.1186/1471-2148-9-37, 2645364, 19210768.
15. Roeding F, Hagner-Holler S, Ruhberg H, Ebersberger I, von Haeseler A, Kube M, Reinhardt R, Burmester T. EST sequencing of Onychophora and phylogenomic analysis of Metazoa. Mol Phylogenet Evol 2007, 45:942-951. 10.1016/j.ympev.2007.09.002, 17933557.
16. Simon S, Strauss S, von Haeseler A, Hadrys H. A phylogenomic approach to resolve the basal pterygote divergence. Mol Biol Evol 2009, 12:2719-2730.
17. Struck T, Paul C, Hill N, et al. Phylogenomic analyses unravel annelid evolution. Nature 2011, 471:452-456. 10.1038/471452a, 21430766.
18. Kocot K, Cannon J, Todt C, et al. Phylogenomics reveals deep molluscan relationships. Nature 2011, 477:452-456. 10.1038/nature10382, 21892190.
19. Sanderson MJ. Construction and annotation of large phylogenetic trees. Aust Syst Bot 2007, 20:287-301.
20. Wiens JJ. Missing data, incomplete taxa, and phylogenetic accuracy. Syst Biol 2003, 52:528-538. 10.1080/10635150390218330, 12857643.
21. Wiens JJ. Missing data and the design of phylogenetic analyses. J Biomed Inform 2006, 39:34-42. 10.1016/j.jbi.2005.04.001, 15922672.
22. Philippe H, Snell EA, Bapteste E, Lopez P, Holland PWH, Casane D. Phylogenomics of eukaryotes: impact of missing data on large alignments. Mol Biol Evol 2004, 21:1740-1752. 10.1093/molbev/msh182, 15175415.
23. Sanderson MJ, Driskell AC, Ree RH, Eulenstein O, Langley S. Obtaining maximal concatenated phylogenetic data sets from large sequence databases. Mol Biol Evol 2003, 20:1036-1042. 10.1093/molbev/msg115, 12777519.
24. Hartmann S, Vision TJ. Using ESTs for phylogenomics: can one accurately infer a phylogenetic tree from a gappy alignment?. BMC Evol Biol 2008, 8:95. 10.1186/1471-2148-8-95, 2359737, 18366758.
25. Poe S. Sensitivity of phylogeny estimation to taxonomic sampling. Syst Biol 1998, 47:18-31. 10.1080/106351598261003, 12064237.
26. Kearny M, Clark JM. Problems due to missing data in phylogenetic analyses including fossils: a critical review. J Vertebr Paleontology 2003, 23:263-274.
27. Wiens JJ. Can incomplete taxa rescue phylogenetic analyses from long-branch attraction?. Syst Biol 2005, 54:731-742. 10.1080/10635150500234583, 16243761.
28. Wiens JJ, Moen DS. Missing data and the accuracy of Bayesian phylogenetics. J Syst Evol 2008, 46:307-314.
29. Phillips MJ, Delsuc F, Penny D. Genome-scale phylogeny and the detection of systematic biases. Mol Biol Evol 2004, 21:1455-1458. 10.1093/molbev/msh137, 15084674.
30. Jeffroy O, Brinkmann H, Delsuc F, Philippe H. Phylogenomics: the beginning of incongruence?. Trends Genet 2006, 22:225-231. 10.1016/j.tig.2006.02.003, 16490279.
31. Rodríguez-Ezpeleta N, Brinkmann H, Roure B, Lartillot N, Lang BF, Philippe H. Detecting and overcoming systematic errors in genome-scale phylogenies. Syst Biol 2007, 56:389-399. 10.1080/10635150701397643, 17520503.
32. Ho SYW, Jermiin LS. Tracing the decay of the historical signal in biological sequence data. Syst Biol 2004, 53:623-637. 10.1080/10635150490503035, 15371250.
33. Inagaki Y, Nakajima Y, Sato M, Sakaguchi M, Hashimoto T. Gene sampling can bias multi-gene phylogenetic inferences: the relationship between red algae and green plants as a case study. Mol Biol Evol 2009, 26:1171-1178. 10.1093/molbev/msp036, 19246622.
34. Jermiin LS, Ho SYW, Ababneh F, Robinson J, Larkum AWD. The biasing effect of compositional heterogeneity on phylogenetic estimates may be underestimated. Syst Biol 2004, 53:638-643. 10.1080/10635150490468648, 15371251.
35. Rosenberg MS, Kumar S. Taxon sampling, bioinformatics, and phylogenomics. Syst Biol 2003, 52:119-124. 10.1080/10635150390132894, 2796430, 12554445.
36. Leigh JW, Susko E, Baumgartner M, Roger AJ. Testing congruence in phylogenomic analysis. Syst Biol 2008, 57:104-115. 10.1080/10635150801910436, 18288620.
37. Nieselt-Struwe K, von Haeseler A. Quartet-Mapping, a generalization of the likelihood-mapping procedure. Mol Biol Evol 2001, 18:1204-1219. 10.1093/oxfordjournals.molbev.a003907, 11420361.
38. Grünewald S, Forslund K, Dress A, Moulton V. QNet: An agglomerative method for the construction of phylogenetic networks from weighted quartets. Mol Biol Evol 2007, 24:532-538.
39. Eigen M, Winkler-Oswatitsch R, Dress A. Statistical geometry in sequence space: a method of quantitative comparative sequence analysis. Proc Natl Acad Sci USA 1988, 85:5913-5917. 10.1073/pnas.85.16.5913, 281875, 3413065.
40. Nieselt-Struwe K. Graphs in sequence spaces: a review of statistical geometry. Biophys Chem 1997, 66:111-131. 10.1016/S0301-4622(97)00064-1, 9362556.
41. Alexe G, Alexe S, Crama Y, Foldes S, Hammer PL, Simeone B. Consensus algorithms for the generation of all maximal bicliques. DIMACS Technical Reports 2002-52, Rutgers University, Piscataway, NJ, USA 2002. [http://dimacs.rutgers.edu/TechnicalReports/2002.html].
42. Dias VM, de Figueiredob CM, Szwarcfiter JL. On the generation of bicliques of a graph. Discrete Appl Math 2007, 155:1826-1832.
43. Dawande M, Keskinocak P, Swaminathan J, Tayur S. On bipartite and multipartite clique problems. J Algorithms 2001, 41:388-403.
44. Yan C, Burleigh JG, Eulenstein O. Identifying optimal incomplete phylogenetic data sets from sequence databases. Mol Phylogenet Evol 2005, 30(3):528-535.
45. Li J, Sim K, Liu G, Wong L. Maximal quasi-bicliques with balanced noise tolerance: concepts and co-clustering applications. Proceedings of the SIAM International Conference on Data Mining SDM 2008, April 24-26, 2008 2008, Atlanta, Georgia, USA: SIAM.
46. Cheng F, Hartmann S, Gupta M, Ibrahim JG, Vision TJ. A hierarchical model for incomplete alignments in phylogenetic inference. Bioinformatics 2009, 25:592-598. [http://bioinformatics.oxfordjournals.org/cgi/content/abstract/25/5/592], 10.1093/bioinformatics/btp015, 2647833, 19147663.
47. Henikoff S, Henikoff JG. Amino acid substitution matrices from protein blocks. Proc Natl Acad Sci USA 1992, 89:10915-10919. 10.1073/pnas.89.22.10915, 50453, 1438297.
48. Rambaut A, Grassly NC. Seq-Gen: an application for the Monte Carlo simulation of DNA sequence evolution along phylogenetic trees. Comput Appl Biosci 1997, 13:235-238.
49. Li W, Liu Y. Modeling species-genes data for efficient phylogenetic inference. Proceedings LSS Computational Systems Bioinformatics Conference, August, 2007., Volume 6. 2007, 429-440. LSS - Life Sciences Society, [http://www.lifesciencessociety.org/CSB2007/toc/429.2007.html].
50. Stamatakis A. 20th International Parallel and Distributed Processing Symposium (IPDPS 2006), Proceedings, 25-29 April 2006. 2006, Rhodes Island, Greece: IEEE.
51. Ott M, Zola J, Aluru S, Stamatakis A. Large-scale Maximum Likelihood-based phylogenetic analysis on the IBM BlueGene/L. Proceedings of ACM/IEEE Supercomputing conference 2007 2007, New York, Reno, Nevada: ACM.
52. Mailund T, Pedersen CNS. QDist-quartet distance between evolutionary trees. Bioinformatics 2004, 20:1636-1637. 10.1093/bioinformatics/bth097, 14962942.
53. Christiansenm C, Mailund T, Pedersen CNS, Randers M. Algorithms for computing the quartet distance between trees of arbitrary degree. 2005, 77-88. Springer, Casadio R, Myers G.
54. Christiansen C, Mailund T, Pedersen CNS, Randers M, Stissing MS. Fast calculation of the quartet distance between trees of arbitrary degrees. Algorithms Mol Biol 2006, 1:16. 10.1186/1748-7188-1-16, 1592098, 16999860.
55. Stissing M, Mailund T, Pedersen CN, Brodal GS, Fagerberg R. Computing the all-pairs quartet distance on a set of evolutionary trees. J Bioinform Comput Biol 2008, 6:37-50. 10.1142/S0219720008003266, 18324744.
56. Whelan S, Goldman N. A general empirical model of protein evolution derived from multiple protein families using a maximum-likelihood approach. Mol Biol Evol 2001, 18:691-699. 10.1093/oxfordjournals.molbev.a003851, 11319253.
57. Pattengale N, Alipour M, Bininda-Emonds O, Moret B, Gottlieb E, Stamatakis A. How many bootstrap replicates are necessary?. J Comput Biol 2010, 17:337-354. 10.1089/cmb.2009.0179, 20377449.
58. Holland B, Clarke A, Meudt H. Optimizing Automated AFLP Scoring Parameters to Improve Phylogenetic Resolution. Syst Biol 2008, 57:347-366. 10.1080/10635150802044037, 18570031.
59. Thorley JL, Wilkinson M. Testing the phylogenetic stability of early tetrapods. J Theor Biol 1999, 200(3):343-344. 10.1006/jtbi.1999.0999, 10527723.
60. Thorley JL, Page RDM. RadCon: phylogenetic tree comparison and consensus. Bioinformatics 2000, 16:486-487. 10.1093/bioinformatics/16.5.486, 10871273.
61. Strimmer K, von Haeseler A. Likelihood-mapping: a simple method to visualize phylogenetic content of a sequence alignment. Proc Natl Acad Sci USA 1997, 94:6815-6819. [http://www.pnas.org/cgi/content/abstract/94/13/6815], 10.1073/pnas.94.13.6815, 21241, 9192648.
62. Steel M, Sanderson MJ. Characterizing phylogenetically decisive taxon coverage. Applied Mathematics Letters 2009,