The use and validity of composite taxa in phylogenetic analysis

Systematic Biology

Volumn 58, Issue 6, 2009, Pages 560-572

  Campbell, Véronique ^a   Lapointe, François Joseph ^a  

^a UNIVERSITÉ DE MONTRÉAL   (Canada)

Author keywords

Composite sequences; Computer simulations; DNA sequences; Missing data; Phylogenetic accuracy; Phylogenomics; Supermatrices

Indexed keywords

ARTICLE; BIOLOGICAL MODEL; CLASSIFICATION; CLUSTER ANALYSIS; COMPARATIVE STUDY; COMPUTER SIMULATION; DNA SEQUENCE; EVALUATION; METHODOLOGY; NUCLEOTIDE SEQUENCE; PHYLOGENY; SPECIES DIFFERENCE; STATISTICAL MODEL; EVALUATION STUDY; PROCEDURES;

BASE SEQUENCE; CLASSIFICATION; CLUSTER ANALYSIS; COMPUTER SIMULATION; LIKELIHOOD FUNCTIONS; MODELS, GENETIC; PHYLOGENY; RESEARCH DESIGN; SEQUENCE ANALYSIS, DNA; SPECIES SPECIFICITY;

EID: 72849151958     PISSN: 10635157     EISSN: 1076836X     Source Type: Journal    
DOI: 10.1093/sysbio/syp056     Document Type: Article

References (98)

1. Asher R.J., Horovitz I., Sanchez-Villagra M.R. 2004. First combined cladistic analysis of marsupial mammal interrelationships. Mol. Phylogenet. Evol. 33:240-250.
2. Beck R.M.D. 2008.A dated phylogeny of marsupials usinga molecular supermatrix and multiple fossil constraints. J. Mammal. 89:175-189.
3. Bininda-Emonds O.R.P. 2004a. The evolution of supertrees. Trends Ecol. Evol. 19:315-322.
4. Bininda-Emonds O.R.P. 2004b. Trees versus characters and the supertree/supermatrix "paradox." Syst. Biol. 53:356-359.
5. Bininda-Emonds O.R.P., Gittleman J.L., Steel M.A. 2002. The (super) tree of life: procedures, problems, and prospects. Annu. Rev. Ecol. Syst. 33:265-289.
6. Bourlat S.J., Nielsen C., Economou A.D., Telford M.J. 2008. Testing the new animal phylogeny: a phylum level molecular analysis of the animal kingdom. Mol. Phylogenet. Evol. 49:23-31.
7. Crandall K.A., Buhay J.E. 2004. Genomic databases and the tree of life. Science. 306:1144-1145.
8. Delsuc F., Brinkmann H., Chourrout D., Philippe H. 2006. Tunicates and not cephalochordates are the closest living relatives of vertebrates. Nature. 439:965-968.
9. Delsuc F., Brinkmann H., Philippe H. 2005. Phylogenomics and the reconstruction of the tree of life. Nature. 6:361-375.
10. de Queiroz A. 1993. For consensus (sometimes). Syst. Biol. 42:368-372. (Pubitemid 23971845)
11. de Queiroz A., Donoghue M.J., Kim J. 1995. Separate versus combined analysis of phylogenetic evidence. Annu. Rev. Ecol. Syst. 26:657-681.
12. de Queiroz A., Gatesy J. 2007. The supermatrix approach to systemat-ics. Trends Ecol. Evol. 22:34-41.
13. Doolittle W.F. 1999. Phylogenetic classifcation and the universal tree. Science. 284:2124-2128.
14. Driskell A.C., Ané C., Burleigh J.G., McMahon M.M., O'Meara B.C., Sanderson M.J. 2004. Prospects for building the tree of life from large sequence databases. Science. 306:1172-1174.
15. Dunn C.W., Hejnol A., Matus D.Q., Pang K., Browne W.E., Smith S.A., Seaver E., Rouse G.W., Obst M., Edgecombe G.D., Sorensen M.V., Haddock S.H.D., Schmidt-Rhaesa A., Okusu A., Kristensen R.M., Wheeler W.C., Martindale M.Q., Giribet G. 2008. Broad phyloge-nomic sampling improves resolution of the animal tree of life. Nature. 452:745-749.
16. Duvall M.R., Robinson J.W., Mattson J.G., Moore A. 2008. Phylogenetic analyses of two mitochondrial metabolic genes sampled in parallel from angiosperms fnd fundamental interlocus incongruence. Am. J. Bot. 95:871-884.
17. Eernisse D.J., Kluge A.G. 1993. Taxonomic congruence versus total evidence, and amniote phylogeny inferred from fossils, molecules, and morphology. Mol. Biol. Evol. 10:1170-1195.
18. Eisen J.A., Fraser C.M. 2003. Phylogenomics: intersection of evolution and genomics. Science. 300:1706-1707.
19. Farris J.S., Källersjö M., Kluge A.G., Bult C. 1995. Constructing a signifcance test for incongruence. Syst. Biol. 44:570-572.
20. Felsenstein J. 1978. Cases in which parsimony or compatibility methods will be positively misleading. Syst. Zool. 27:401-410.
21. Fiala K.L., Sokal R.R. 1985. Factors determining the accuracy of clado-gram estimation: evaluation using computer simulation. Evolution. 39:609-622.
22. Fitzpatrick D.A., Logue M.E., Stajich J.E., Butler G. 2006. A fungal phy-logeny based on 42 complete genomes derived from supertree and combined gene analysis. BMC Evol. Biol. 6:1-15.
23. Flynn J.J., Finarelli J.A., Zehr S., Hsu J., Nedbal M.A. 2005. Molecular phylogeny of the Carnivora (Mammalia): assessing the impact of increased sampling on resolving enigmatic relationships. Syst. Biol. 54:317-337.
24. Gadagkar S.R., Rosenberg M.S., Kumar S. 2005. Inferring species phy-logenies from multiple genes: concatenated sequence tree versus consensus gene tree. J. Exp. Zool. B Mol. Dev. Evol. 304B:64-74.
25. Gatesy J., Baker R.H., Hayashi C. 2004. Inconsistencies in arguments for the supertree approach: supermatrices versus supertrees of Crocodylia. Syst. Biol. 53:342-355.
26. Graybeal A. 1998. Is it better to add taxa or characters to a diffcult phylogenetic problem? Syst. Biol. 47:9-17.
27. Guindon S., Gascuel O. 2003. A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. Syst. Biol. 52:696-704.
28. Hedtke S.M., Townsend T.M., Hillis D.M. 2006. Resolution of phyloge-netic confict in large data sets by increasing taxon sampling. Syst. Biol. 55:522-529.
29. Hendy M.D., Penny D. 1989. A framework for the quantitative study of evolutionary trees. Syst. Zool. 38:297-309.
30. Hillis D.M. 1995. Approaches for assessing phylogenetic accuracy. Syst. Biol. 44:3-16.
31. Hillis D.M. 1998. Taxonomic sampling, phylogenetic accuracy, and investigator bias. Syst. Biol. 47:3-8.
32. Hillis D.M., Allard M.W., Miyamoto M.M. 1993. Analysis of DNA sequence data: phylogenetic inference. Methods Enzymol. 224: 456-487.
33. Hillis D.M., Bull J.J., White M.E., Badgett M.R., Molineux I.J. 1992. Experimental phylogenetics: generation of a known phylogeny. Science. 255:589-592.
34. Hillis D.M., Huelsenbeck J.P., Swofford D.L. 1994. Hobgoblin of phy-logenetics. Nature. 369:363-364.
35. Hillis D.M., Moritz C., Mable B.K. 1996. Molecular systematics. 2nd edition. Sunderland (MA): Sinauer Associates.
36. Huelsenbeck J.P. 1991. When are fossils better than extant taxa in phy-logenetic analysis. Syst. Zool. 40:458-469.
37. Huelsenbeck J.P. 1995. Performance of phylogenetic methods in simulation. Syst. Biol. 44:17-48.
38. Huelsenbeck J.P., Bull J.J. 1996. A likelihood ratio test to detect confict-ing phylogenetic signal. Syst. Biol. 45:92-98.
39. Huelsenbeck J.P., Bull J.J., Cunningham C.W. 1996a. Combining data in phylogenetic analysis. Trends Ecol. Evol. 11:152-158.
40. Huelsenbeck J.P., Bull J.J., Cunningham C.W. 1996b. Combining data in phylogenetic analysis-Reply. Trends Ecol. Evol. 11:335.
41. Huelsenbeck J.P., Hillis D.M. 1993. Success of phylogenetic methods in the 4-taxon case. Syst. Biol. 42:247-264.
42. Jukes T.H., Cantor C.R. 1969. Evolution of protein molecules. In: Munro H.N., editor. Mammalian protein metabolism. New York: Academic Press. p. 21-132.
43. Kearney M. 2002. Fragmentary taxa, missing data, and ambiguity: mistaken assumptions and conclusions. Syst. Biol. 51:369-381.
44. Kluge A.G., Wolf A.J. 1993. Cladistics: what's in a word? Cladistics. 9:183-199.
45. Lecointre G., Philippe H., Van Le H.L., Le Guyader H. 1993. Species sampling has a major impact on phylogenetic inference. Mol. Phy-logenet. Evol. 2:205-224.
46. Leebens-Mack J., Raubeson L.A., Cui L.Y., Kuehl J.V., Fourcade M.H., Chumley T.W., Boore J.L., Jansen R.K., dePamphilis C.W. 2005. Identifying the basal angiosperm node in chloroplast genome phy-logenies: sampling one's way out of the Felsenstein zone. Mol. Biol. Evol. 22:1948-1962.
47. Lerat E., Daubin V., Moran N.A. 2003. From gene trees to organismal phylogeny in prokaryotes: the case of the γ-proteobacteria. PLoS Biol. 1:101-109.
48. Madsen O., Scally M., Douady C.J., Kao D.J., DeBry R.W., Adkins R., Amrine H.M., Stanhope M.J., de Jong W.W., Springer M.S. 2001. Parallel adaptive radiations in two major clades of placental mammals. Nature. 409:610-614. (Pubitemid 32154811)
49. Malia M.J., Lipscomb D.L., Allard M.W. 2003. The misleading effects of composite taxa in supermatrices. Mol. Phylogenet. Evol. 27:522-527.
50. Marek P.E., Bond J.E. 2006. Phylogenetic systematics of the colorful, cyanide-producing millipedes of Appalachia (Polydesmida, Xys-todesmidae, Apheloriini) using a total evidence Bayesian approach. Mol. Phylogenet. Evol. 41:704-729.
51. Murphy W.J., Eizirik E., Johnson W.E., Zhang Y.P., Ryderk O.A., O'Brien S.J. 2001. Molecular phylogenetics and the origins of pla-cental mammals. Nature. 409:614-618.
52. Murphy W.J., Eizirik E., O'Brien S.J., Madsen O., Scally M., Douady C.J., Teeling E., Ryder O.A., Stanhope M.J., de Jong W.W., Springer M.S. 2001. Resolution of the early placental mammal radiation using Bayesian phylogenetics. Science. 294:2348-2351. (Pubitemid 33140557)
53. Nishihara H., Okada N., Hasegawa M. 2007. Rooting the eutherian tree: the power and pitfalls of phylogenomics. Genome Biol. 8:R199.
54. Nixon K.C., Davis J.I. 1991. Polymorphic taxa, missing values, and cladistic analysis. Cladistics. 7:233-241.
55. Page R.D. 2000. Extracting species trees from complex gene trees: reconciled trees and vertebrate phylogeny. Mol. Phylogenet. Evol. 14:89-106.
56. Philippe H., Brinkmann H., Martinez P., Riutort M., Baguñà J. 2007. Acoel fatworms are not Platyhelminthes: evidence from phyloge-nomics. PLoS ONE. 2:e717.
57. Philippe H., Delsuc F., Brinkmann H., Lartillot N. 2005. Phyloge-nomics. Annu. Rev. Ecol. Evol. Syst. 36:541-562.
58. Philippe H., Lartillot N., Brinkmann H. 2005. Multigene analyses of bilaterian animals corroborate the monophyly of Ecdysozoa, Lophotrochozoa, and Protostomia. Mol. Biol. Evol. 22:1246-1253.
59. Philippe H., Snell E.A., Bapteste E., Lopez P., Holland P.W.H., Casane D. 2004. Phylogenomics of eukaryotes: impact of missing data on large alignments. Mol. Biol. Evol. 21:1740-1752.
60. Phillips M.J., Delsuc F., Penny D. 2004. Genome-scale phylogeny and the detection of systematic biases. Mol. Biol. Evol. 21:1455-1458.
61. Poe S., Swofford D.L. 1999. Taxon sampling revisited. Nature. 398:299-300.
62. Pollock D.D., Bruno W.J. 2000. Assessing an unknown evolutionary process: effect of increasing site-specifc knowledge through taxon addition. Mol. Biol. Evol. 17:1854-1858.
63. Pollock D.D., Zwickl D.J., McGuire J.A., Hillis D.M. 2002. Increased taxon sampling is advantageous for phylogenetic inference. Syst. Biol. 51:664-671.
64. Posada D., Crandall K.A. 1998. ModelTest: testing the model of DNA substitution. Bioinformatics. 9:817-818.
65. Posada D., Crandall K.A. 2001. Selecting the best-ft model of substitution. Syst. Biol. 50:580-601.
66. Poux C., Chevret P., Huchon D., deJong W.W., Douzery E.J.P. 2006. Arrival and diversifcation of caviomorph rodents and platyrrhine primates in South America. Syst. Biol. 55:228-244.
67. Prendini L. 2001. Species or supraspecies taxa as terminals in cladis-tic analysis? Groundplans versus exemplars revisited. Syst. Biol. 50:290-300.
68. R Development Core Team. 2007. R: a language and environment for statistical computing. Vienna (Austria): R Foundation for Statistical Computing.
69. Rambaut A., Grassly N.C. 1997. Seq-Gen: an application for the Monte Carlo simulation of DNA sequence evolution along phylogenetic frees. Comput. Appl. Biosci. 13:235-238. (Pubitemid 27249927)
70. Rannala B., Huelsenbeck J.P., Yang Z.H., Nielsen R. 1998. Taxon sampling and the accuracy of large phylogenies. Syst. Biol. 47: 702-710.
71. Rice W.E. 1989. Analyzing tables of statistical tests. Evolution. 43: 223-225.
72. Rokas A., Carroll S.B. 2005. More genes or more taxa? The relative contribution of gene number and taxon number to phylogenetic accuracy. Mol. Biol. Evol. 22:1337-1344.
73. Rokas A., Krüger D., Carroll S.B. 2005. Animal evolution and the molecular signature of radiations compressed in time. Science. 310:1933-1938.
74. Rokas A., Williams B.L., King N., Carroll S.B. 2003. Genome-scale approaches to resolving incongruence in molecular phylogenies. Nature. 425:798-804.
75. Saitou N., Nei M. 1987. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol. Biol. Evol. 4:406-425.
76. Sanderson M.J., Purvis A., Henze C. 1998. Phylogenetic supertrees: assembling the trees of life. Trends Ecol. Evol. 13:105-109.
77. Sanson G.F.O., Kawashita S.Y., Brunstein A., Briones M.R.S. 2002. Experimental phylogeny of neutrally evolving DNA sequences generated by a bifurcate series of nested polymerase chain reactions. Mol. Biol. Evol. 19:170-178.
78. Scally M., Madsen O., Douady C.J., deJong W.W., Stanhope M.J., Springer M.S. 2001. Molecular evidence for the major clades of pla-cental mammals. J. Mammal. Evol. 8:239-277. (Pubitemid 34731206)
79. Shoshani J., McKenna M.C. 1998. Higher taxonomic relationships among extant mammals based on morphology, with selected comparisons of results from molecular data. Mol. Phylogenet. Evol. 9:572-584.
80. Springer M.S., Scally M., Madsen O., de Jong W.W., Douady C.J., Stanhope M.J. 2004. The use of composite taxa in supermatrices. Mol. Phylogenet. Evol. 30:883-884.
81. Swofford D.L. 1991. When are phylogeny estimates from molecular and morphological data incongruent? In: Miyamoto M.M., Cracraft J., editors. Phylogenetic analyses of DNA sequences. Oxford: Oxford University Press. p. 295-333.
82. Swofford D.L. 1998. PAUP*. Phylogenetic analysis using parsimony (*and other methods). Sunderland (MA): Sinauer Associates.
83. Telford M.J. 2007. Phylogenomics. Curr. Biol. 17:R945-R946.
84. Telford M.J. 2008. Resolving animal phylogeny: a sledgehammer for a though nut? Dev. Cell. 14:457-459.
85. Weisrock D.W., Harmon L.J., Larson A. 2005. Resolving deep phyloge-netic relationships in salamanders: analyses of mitochondrial and nuclear genomic data. Syst. Biol. 54:758-777.
86. Wiens J.J. 1998a. Combining data sets with different phylogenetic histories. Syst. Biol. 47:568-581.
87. Wiens J.J. 1998b. Does adding characters with missing data increase or decrease phylogenetic accuracy? Syst. Biol. 47:625-640.
88. Wiens J.J. 1998c. The accuracy of methods for coding and sampling higher-level taxa for phylogenetic analysis: a simulation study. Syst. Biol. 47:397-413.
89. Wiens J.J. 2003. Missing data, incomplete taxa, and phylogenetic accuracy. Syst. Biol. 52:528-538.
90. Wiens J.J. 2005. Can incomplete taxa rescue phylogenetic analyses from long-branch attraction? Syst. Biol. 54:731-742.
91. Wiens J.J. 2006. Missing data and the design of phylogenetic analyses. J. Biomed. Inform. 39:34-42.
92. Wiens J.J., Fetzner J.W., Parkinson C.L., Reeder T.W. 2005. Hylid frog phylogeny and sampling strategies for speciose clades. Syst. Biol. 54:719-748.
93. Wiens J.J., Reeder T.W. 1995. Combining data sets with different numbers of taxa for phylogenetic analysis. Syst. Biol. 44:548-558.
94. Wildman D.E., Uddin M., Opazo J.C., Liu G., Lefort V., Guindon S., Gascuel O., Grossman L.I., Romero R., Goodman M. 2007. Genomics, biogeography, and the diversifcation of placental mammals. Proc. Nat. Acad. Sci. USA. 104:14395-14400.
95. Yang Z. 1993. Maximum-likelihood estimation of phylogeny from DNA sequences when substitution rates differ over sites. Mol. Biol. Evol. 10:1396-1401.
96. Yang Z. 1996. Phylogenetic analysis using parsimony and likelihood methods. J. Mol. Evol. 42:294-307.
97. Zou X.-H., Zhang F.-M., Zhang J.-G., Zang L.-L., Tang L., Wang J., Sang T., Ge S. 2008. Analysis of 142 genes resolves the rapid di-versifcation of the rice genus. Genome Biol. 9:R49.
98. Zwickl D.J., Hillis D.M. 2002. Increased taxon sampling greatly reduces phylogenetic error. Syst. Biol. 51:588-598.