Topology testing of phylogenies using least squares methods

BMC Evolutionary Biology

Volumn 6, Issue , 2006, Pages

  Czarna, Aleksandra ^a   Sanjuán, Rafael ^b   González Candelas, Fernando ^c   Wróbel, Borys ^a,c  

^a INSTITUTE OF OCEANOLOGY   (Poland)

^b Ciudad Politécnica de la Innovación   (Spain)

^c UNIVERSITY OF VALENCIA   (Spain)

Author keywords

[No Author keywords available]

Indexed keywords

ACCURACY; AMINO ACID SEQUENCE; ARTICLE; CALCULATION; DATA ANALYSIS; DNA DNA HYBRIDIZATION; HUMAN; NONHUMAN; PHYLOGENY; RELIABILITY; STATISTICAL ANALYSIS; TAXONOMY; ANIMAL; CLASSIFICATION; GENETICS; HEPACIVIRUS; HEPATITIS C; MOLECULAR EVOLUTION; PROCEDURES; REGRESSION ANALYSIS; SEA URCHIN; VIROLOGY;

MITOCHONDRIAL DNA;

ANIMALS; CLASSIFICATION; DNA, MITOCHONDRIAL; EVOLUTION, MOLECULAR; HEPACIVIRUS; HEPATITIS C; HUMANS; LEAST-SQUARES ANALYSIS; PHYLOGENY; SEA URCHINS;

EID: 33845546228     PISSN: None     EISSN: 14712148     Source Type: Journal    
DOI: 10.1186/1471-2148-6-105     Document Type: Article

References (43)

1. Huelsenbeck JP, Rannala B, Masly JP: Accommodating phylogenetic uncertainty in evolutionary studies. Science 2000, 288:2349-2350.
2. Felsenstein J: Confidence limits on phylogenies: an approach using the bootstrap. Evolution 1985, 39:783-791.
3. Shimodaira H: An approximately unbiased test of phylogenetic tree selection. Systematic Biology 2002, 51:492-508.
4. Hillis DM, Bull JJ: An empirical test of bootstrapping as a method for assessing confidence in phylogenetic analysis. Syst Biol 1993, 42:182-192.
5. Newton MA: Bootstrapping phylogenies: Large deviations and dispersion effects. Biometrika 1996, 83:315-328.
6. Sanjuan R, Wróbel B: Weighted least-squares likelihood ratio test for branch testing in phylogenies reconstructed from distance measures. Systematic Biology 2005, 54:218-229.
7. Kishino H, Hasegawa M: Evaluation of the maximum likelihood estimate of the evolutionary tree topologies from DNA sequence data, and the branching order in Hominoidea. J Mol Evol 1989, 29:170-179.
8. Shimodaira H, Hasegawa M: Multiple comparisons of log-likelihoods with applications to phylogenetic inference. Mol Biol Evol 1999, 16:1114-1116.
9. Swofford DL, Olsen GJ, Waddell PJ, Hillis DM: Phylogenetic inference. In Molecular Systematics Volume 11. 2nd edition. Edited by: Hillis DM, Moritz C and Mable BK. Sunderland, MA, Sinauer; 1996:407-514.
10. Goldman N, Anderson JP, Rodrigo AG: Likelihood-based tests of topologies in phylogenetics. Systematic Biology 2000, 49:652-670.
11. Strimmer K, Rambaut A: Inferring confidence sets of possibly misspecified gene trees. Proc R Soc Lond Ser B 2002, 269:137-142.
12. Bulmer MG: Use of the method of generalized least squares in reconstructing phylogenies from sequence data. Mol Biol Evol 1991, 8:868-883.
13. Susko E: Confidence regions and hypothesis tests for topologies using generalized least squares. Mol Biol Evol 2003, 20:862-868.
14. Cavalli-Sforza LL, Edwards AWF: Phylogenetic analysis: Models and estimation procedures. Am J Hum Genet 1967, 19:233-257.
15. Fitch WM, Margoliash E: Construction of phylogenetic trees. A method based on mutation distances as estimated from cytochrome c sequences is of general applicability. Science 1967, 155:279-284.
16. Marshall CR: Statistical tests and bootstrapping: assessing the reliability of phylogenies based on distance data. Mol Biol Evol 1991, 8:386-391.
17. Lapointe FJ, Kirsch JA, Bleiweiss R: Jackknifing of weighted trees: validation of phylogenies reconstructed from distance matrices. Mol Phylogenet Evol 1994, 3:256-267.
18. Susko E: Software for confidence regions and hypothesis tests for topologies using generalized least squares. 2005 [http://www.mathstat.dal.ca/ ~tsusko/doc/gls_soft.pdf].
19. Dayhoff MO, Schwartz RM, Orcutt BC: A model of evolutionary change in proteins. In Atlas of Protein Sequence and Structure Edited by: Dayhoff MP. Washington,DC, National Biomedical Foundation; 1978:345-352.
20. Adachi J, Hasegawa M: Model of amino acid substitution in proteins encoded by mitochondrial DNA. Journal of Molecular Evolution 1996, 42:459-468.
21. EMBL-ALIGN 2006 [ftp://ftp.ebi.ac.uk/pub/databases/embl/align/].
22. Castresana J: Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis. Mol Biol Evol 2000, 17:540-552.
23. Felsenstein J: Distance methods for inferring phylogenies: A justification. Evolution 1984, 38:16-24.
24. Posada D, Crandall KA: Modeltest: testing the model of DNA substitution. Bioinformatics 1998, 14:917-918.
25. Schmidt HA, Strimmer K, Vingron M, von Haeseler A: TREE-PUZZLE: maximum likelihood phylogenetic analysis using quartets and parallel computing. Bioinformatics 2002, 18:502-504.
26. Shi X, Gu H, Susko E, Field C: The comparison of the confidence regions in phylogeny. Mol Biol Evol 2005, 22:2285-2296.
27. Murphy WJ, Elzirik E, Johnson WE, Zhang YP, Ryder OA, O'Brien SJ: Molecular phylogenetics and the origins of placental animals. Nature 2001, 409:614-618.
28. Yang Z: PAML: a program package for phylogenetic analysis by maximum likelihood. Computer Applications in the Biosciences 1997, 13:555-556.
29. Swofford DL: PAUP*. Phylogenetic Analysis Using Parsimony (* and Other Methods). Sunderland, MA, Sinauer Associates; 2002.
30. Akaike H: A new look at the statistical model identification. Ieee Transactions on Automatic Control 1974, 19:716-723.
31. Gonzalez-Candelas F, Bracho MA, Moya A: Molecular epidemiology and forensic genetics: application to a hepatitis C virus transmission event at a hemodialysis unit. Journal of Infectious Diseases 2003, 187:352-358.
32. Bracho MA, Gosalbes MJ, Blasco D, Moya A, Gonzalez-Candelas F: Molecular epidemiology of a hepatitis C virus outbreak in a hemodialysis unit. J Clin Microbiol 2005, 43:2750-2755.
33. Marshall CR, Swift H: DNA-DNA hybridization phylogeny of sand dollars and highly reproducible extent of hybridization values. J Mol Evol 1992, 34:31-44.
34. Jukes TH, Cantor CR: Evolution of protein molecules. In Mammalian protein metabolism Edited by: Munro HN. New York, Academic Press; 1969:21-132.
35. Kuhner MK, Felsenstein J: A simulation comparison of phylogeny algorithms under equal and unequal evolutionary rates. Mol Biol Evol 1994, 11 :459-468.
36. Felsenstein J: An alternating least squares approach to inferring phylogenies from pairwise distances. Syst Biol 1997, 46:101-111.
37. Swofford DL, Waddell PJ, Huelsenbeck JP, Foster PG, Lewis PO, Rogers JS: Bias in phylogenetic estimation and its relevance to the choice between parsimony and likelihood methods. Systematic Biology 2001, 50:525-539.
38. Desper R, Gascuel O: Theoretical foundation of the balanced minimum evolution method of phylogenetic inference and its relationship to weighted least-squares tree fitting. Mol Biol Evol 2004, 21:587-598.
39. Takahata N, Kimura M: A model of evolutionary base substitutions and its application with special reference to rapid change of pseudogenes. Genetics 1981, 98:641-657.
40. Waddell PJ, Kishino H, Ota R: A Phylogenetic Foundation for Comparative Mammalian Genomics. Genome Informatics 2001, 1:141-154.
41. Berkson J: Some difficulties of interpretation encountered in the application of the chi-square test. Journal of the American Statistical Association 1938, 33:526-536.
42. Lindley DV: A statistical paradox. Biometrika 1957, 44:187-192.
43. Wróbel B: WeightLESS: a program for branch testing in phylogenies reconstructed from distance measures using weighted least-squares likelihood ratio test. 2006 [http://www.iopan.gda.pl/~wrobel].