Including RNA secondary structures improves accuracy and robustness in reconstruction of phylogenetic trees

Biology Direct

Volumn 5, Issue , 2010, Pages

  Keller, Alexander ^a   Förster, Frank ^a   Müller, Tobias ^a   Dandekar, Thomas ^a   Schultz, Jörg ^a   Wolf, Matthias ^a  

^a UNIVERSITY OF WÜRZBURG   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

PLANT RNA;

ARTICLE; CHEMISTRY; COMPUTER SIMULATION; CONFORMATION; GENETICS; PHYLOGENY; PLANT;

COMPUTER SIMULATION; NUCLEIC ACID CONFORMATION; PHYLOGENY; PLANTS; RNA, PLANT;

EID: 76749097624     PISSN: None     EISSN: 17456150     Source Type: Journal    
DOI: 10.1186/1745-6150-5-4     Document Type: Article

References (40)

1. Woese C, Kandler O, Wheelis M. Towards a natural system of organisms: proposal for the domains Archaea, Bacteria, and Eucarya. Proc Natl Acad Sci USA 1990, 87(12):4576-4579. 10.1073/pnas.87.12.4576, 54159, 2112744.
2. Bremer B, Jansen R, Oxelman B, Backlund M, Lantz H, Kim KJ. More characters or more taxa for a robust phylogeny-case study from the Coffee family (Rubiaceae). Syst Biol 1999, 48(3):413-435. 10.1080/106351599260085, 12066290.
3. van Oppen M, McDonald B, Willis B, Miller D. The evolutionary history of the coral genus Acropora (Scleractinia, Cnidaria) based on a mitochondrial and a nuclear marker: reticulation, incomplete lineage sorting, or morphological convergence?. Mol Biol Evol 2001, 18(7):1315-1329.
4. Slowinski J, Lawson R. Snake phylogeny: evidence from nuclear and mitochondrial genes. Mol Phylogenet Evol 2002, 24(2):194-202. 10.1016/S1055-7903(02)00239-7, 12144756.
5. Erixon P, Svennblad B, Britton T, Oxelman B. Reliability of Bayesian posterior probabilities and bootstrap frequencies in phylogenetics. Syst Biol 2003, 52(5):665-73. 10.1080/10635150390235485, 14530133.
6. Whelan S, Liò P, Goldman N. Molecular phylogenetics: state-of-the-art methods for looking into the past. Trends Genet 2001, 17(5):262-72. 10.1016/S0168-9525(01)02272-7, 11335036.
7. Posada D, Crandall KA. The effect of recombination on the accuracy of phylogeny estimation. J Mol Evol 2002, 54(3):396-402.
8. Egger B, Koblmüller S, Sturmbauer C, Sefc K. Nuclear and mitochondrial data reveal different evolutionary processes in the Lake Tanganyika cichlid genus Tropheus. BMC Evol Biol 2007, 7:137. 10.1186/1471-2148-7-137, 2000897, 17697335.
9. Coleman AW. ITS2 is a double-edged tool for eukaryote evolutionary comparisons. TIG 2003, 19(7):370-375.
10. Coleman AW. Pan-eukaryote ITS2 homologies revealed by RNA secondary structure. Nucleic Acids Res 2007, 35(10):3322-3329. 10.1093/nar/gkm233, 1904279, 17459886.
11. Schöniger M, von Haeseler A. A stochastic model for the evolution of autocorrelated DNA sequences. Mol Phylogenet Evol 1994, 3(3):240-7. 10.1006/mpev.1994.1026, 7529616.
12. Tillier ERM, Collins RA. High apparent rate of simultaneous compensatory base-pair substitutions in ribosomal RNA. Genetics 1998, 148(4):1993-2002. 1460107, 9560412.
13. Young I, Coleman AW. The advantages of the ITS2 region of the nuclear rDNA cistron for analysis of phylogenetic relationships of insects: a Drosophila example. Mol Phylogenet Evol 2004, 30:236-242. 10.1016/S1055-7903(03)00178-7, 15022773.
14. Biffin E, Harrington M, Crisp M, Craven L, Gadek P. Structural partitioning, paired-sites models and evolution of the ITS transcript in Syzygium and Myrtaceae. Mol Phylogenet Evol 2007, 43:124-139. 10.1016/j.ympev.2006.08.013, 17070713.
15. Grajales A, Aguilar C, Sanchez J. Phylogenetic reconstruction using secondary structures of Internal Transcribed Spacer 2 (ITS2, rDNA): finding the molecular and morphological gap in Caribbean gorgonian corals. BMC Evol Biol 2007, 7:90. 10.1186/1471-2148-7-90, 1913914, 17562014.
16. Keller A, Schleicher T, Förster F, Ruderisch B, Dandekar T, Müller T, Wolf M. ITS2 data corroborate a monophyletic chlorophycean DO-group (Sphaeropleales). BMC Evol Biol 2008, 8:218. 10.1186/1471-2148-8-218, 2519086, 18655698.
17. Felsenstein J. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 1985, 39(4):1993-2002.
18. Hillis D, Bull J. An empirical test of bootstrapping as a method for assessing confidence in phylogenetic analysis. Syst Biol 1993, 42(2):182-192.
19. Hillis DM, Huelsenbeck JP, Cunningham CW. Application and accuracy of molecular phylogenies. Science 1994, 264(5159):671-7. 10.1126/science.8171318, 8171318.
20. Graybeal A. Is it better to add taxa or characters to a difficult phylogenetic problem?. Syst Biol 1998, 47:9-17. 10.1080/106351598260996, 12064243.
21. Rokas A, Carroll SB. More genes or more taxa? The relative contribution of gene number and taxon number to phylogenetic accuracy. Mol Biol Evol 2005, 22(5):1337-44. 10.1093/molbev/msi121, 15746014.
22. Yang Z. On the best evolutionary rate for phylogenetic analysis. Syst Biol 1998, 47:125-33. 10.1080/106351598261067, 12064232.
23. Seibel PN, Müller T, Dandekar T, Schultz J, Wolf M. 4SALE - a tool for synchronous RNA sequence and secondary structure alignment and editing. BMC Bioinformatics 2006, 7:498. 10.1186/1471-2105-7-498, 1637121, 17101042.
24. Jow H, Hudelot C, Rattray M, Higgs P. Bayesian phylogenetics using an RNA substitution model applied to early mammalian evolution. Mol Biol Evol 2002, 19(9):1591-1601.
25. Schultz J, Wolf M. ITS2 sequence-structure analysis in phylogenetics: a how-to manual for molecular systematics. Mol Phylogenet Evol 2009, 52:520-523. 10.1016/j.ympev.2009.01.008, 19489124.
26. Gesell T, von Haeseler A. In silico sequence evolution with site-specific interactions along phylogenetic trees. Bioinformatics 2006, 22(6):716-722. 10.1093/bioinformatics/bti812, 16332711.
27. Meyer S, von Haeseler A. Identifying site-specific substitution rates. Mol Biol Evol 2003, 20(2):182-189. 10.1093/molbev/msg019, 12598684.
28. Müller T, Vingron M. Modeling amino acid replacement. J Comput Biol 2000, 37(6):761-776.
29. Schultz J, Müller T, Achtziger M, Seibel PN, Dandekar T, Wolf M. The internal transcribed spacer 2 database-a web server for (not only) low level phylogenetic analyses. Nucleic Acids Res 2006, 34(Supp 2):W704-707. 10.1093/nar/gkl129, 1538906, 16845103.
30. Selig C, Wolf M, Muller T, Dandekar T, Schultz J. The ITS2 Database II: homology modelling RNA structure for molecular systematics. Nucleic Acids Res 2008, (36 Database):D377-80. 2238964, 17933769.
31. Keller A, Schleicher T, Schultz J, Müller T, Dandekar T, Wolf M. 5.8S-28S rRNA interaction and HMM-based ITS2 annotation. Gene 2009, 430(1-2):50-7. 10.1016/j.gene.2008.10.012, 19026726.
32. Alfaro ME, Zoller S, Lutzoni F. Bayes or bootstrap? A simulation study comparing the performance of Bayesian Markov Chain Monte Carlo sampling and bootstrapping in assessing phylogenetic confidence. Mol Biol Evol 2003, 20(2):255-266. 10.1093/molbev/msg028, 12598693.
33. Wolf M, Achtziger M, Schultz J, Dandekar T, Müller T. Homology modeling revealed more than 20,000 rRNA internal transcribed spacer 2 (ITS2) secondary structures. RNA 2005, 11(11):1616-1623. 10.1261/rna.2144205, 1370847, 16244129.
34. Thompson J, Higgins D, Gibson T. ClustalW: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res 1994, 22(22):4673-4680. 10.1093/nar/22.22.4673, 308517, 7984417.
35. Seibel PN, Müller T, Dandekar T, Wolf M. Synchronous visual analysis and editing of RNA sequence and secondary structure alignments using 4SALE. BMC Res Notes 2008, 1:91. 10.1186/1756-0500-1-91, 2587473, 18854023.
36. Friedrich J, Dandekar T, Wolf M, Müller T. ProfDist: a tool for the construction of large phylogenetic trees based on profile distances. Bioinformatics 2005, 21(9):2108-2109. 10.1093/bioinformatics/bti289, 15677706.
37. Wolf M, Ruderisch B, Dandekar T, Schultz J, Müller T. ProfDistS: (profile-) distance based phylogeny on sequence - structure alignments. Bioinformatics 2008, 24:2401-2402. 10.1093/bioinformatics/btn453, 18723521.
38. Felsenstein J. PHYLIP - Phylogeny Inference Package (Version 3.2). Cladistics 1989, 5:164-166.
39. Mailund T, Pedersen CNS. QDist-quartet distance between evolutionary trees. Bioinformatics 2004, 20(10):1636-7. 10.1093/bioinformatics/bth097, 14962942.
40. R Development Core Team R: A Language and Environment for Statistical Computing 2009, R Foundation for Statistical Computing, Vienna, Austria, R Development Core Team., http://www.R-project.org