Unringing a bell: Metazoan phylogenomics and the partition bootstrap

Cladistics

Volumn 26, Issue 4, 2010, Pages 444-452

  Siddall, Mark E ^a  

^a DIVISION OF INVERTEBRATE ZOOLOGY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

AUTOCORRELATION; BAYESIAN ANALYSIS; DATA SET; GENOMICS; METAZOAN; PARSIMONY ANALYSIS; PHYLOGENETICS;

METAZOA;

EID: 77954501352     PISSN: 07483007     EISSN: 10960031     Source Type: Journal    
DOI: 10.1111/j.1096-0031.2009.00295.x     Document Type: Article

References (38)

1. Brown WM, Prager EM, Wang A, Wilson AC. Mitochondrial DNA sequences of primates: tempo and mode of evolution. J. Mol. Evol. 1982, 18:225-239.
2. Caira JN, Scholz T, Georgiev BB. Cestode systematics and phylogeny move forward. Syst. Parasitol. 2006, 65:171-174.
3. Chiu JC, Lee EK, Egan MG, Sarkar IN, Coruzzi GM, DeSalle R. OrthologID: automation of genome-scale ortholog identification within a parsimony framework. Bioinformatics 2006, 22:699-707.
4. Davis J. Character removal as a means to assessing stability of clades. Cladistics 1993, 9:201-210.
5. Davis JI, Stevenson DW, Petersen G, Seberg O, Campbell LM, Freudenstein JV, Goldman DH, Hardy CR, Michelangi FA, Simmons MP, Specht CD, Vergara-Silva F, Gandolfo M. A phylogeny of the monocots, as inferred from rbcL and atpA sequence variation, and a comparison of methods for calculating jackknife and bootstrap values. Syst. Bot. 2004, 29:467-510.
6. Douady CJ, Delsuc F, Boucher Y, Doolittle WF, Douzery EJP. Comparison of Bayesian and maximum likelihood bootstrap measures of phylogenetic reliability. Mol. Biol. Evol. 2003, 20:248-254.
7. Dunn CW, Hejnol A, Matus DQ, Pang K, Browne WE, Smith SA, Seaver E, Rouse GW, Obst M, Edgecombe GD, Sørensen MV, Haddock SH, 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.
8. Eernisse DJ, Albert JS, Anderson FE. Annelida and Arthropoda are not sister taxa: a phylogenetic analysis of spiralian metazoan phylogeny. Syst. Biol. 1992, 41:305-330.
9. Efron B, Halloran E, Holmes S. Bootstrap confidence levels for phylogenetic trees. Proc. Natl Acad. Sci. USA 1996, 93:7085-7090.
10. Erixon P, Svennblad B, Britton T, Oxelman B. Reliability of Bayesian posterior probabilities and bootstrap frequencies in phylogenetics. Syst. Biol. 2003, 52:665-673.
11. Felsenstein J. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 1985, 39:783-791.
12. Gatesy J, O'Grady PO, Baker RH. Corroboration among data sets in simultaneous analysis: hidden support for phylogenetic relationships among higher level artiodactyl taxa. Cladistics 1999, 15:271-313.
13. Goloboff PA, Catalano SA, Mirande JM, Szumik CA, Arias JS, Källersjö M, Farris JS. Phylogenetic analysis of 73 060 taxa corroborates major eukaryotic groups. Cladistics 2009, 25:211-230.
14. Goloboff P, Farris J, Nixon K. TNT: a free program for phylogenetic analysis. Cladistics 2008, 24:774-786.
15. Gray MW, Sankoff D, Cedergren RJ. On the evolutionary descent of organisms and organelles: a global phylogeny based on a highly conserved structural core in small subunit ribosomal RNA. Nucleic Acids Res. 1984, 12:5837-5852.
16. Hadzi J. An attempt to reconstruct the system of animal classification. Syst. Zool. 1953, 2:145-154.
17. 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.
18. Hillis DM, Dixon MT. Ribosomal DNA: molecular evolution and phylogenetic inference. Q. Rev. Biol. 1991, 66:411-453.
19. Hughes J, Longhorn SJ, Papadopoulou A, Theodorides K, de Riva A, Mejia-Chang M, Foster PG, Vogler AP. Dense taxonomic EST sampling and its applications for molecular systematics of the Coleoptera (beetles). Mol. Biol. Evol. 2006, 23:268-278.
20. Lartillot N, Philippe H. A Bayesian mixture model for across-site heterogeneities in the amino-acid replacement process. Mol. Biol. Evol. 2004, 21:1095-1109.
21. Lemmon AR, Brown JM, Stanger-Hall K, Moriarty Lemmon E. The effect of ambiguous data on phylogenetic estimates obtained by maximum likelihood and Bayesian inference. Syst. Biol. 2009, 58:130-145.
22. Nixon KC. The Parsimony Ratchet, a new method for rapid parsimony analysis. Cladistics 1999, 15:407-414.
23. Pace NR, Olsen GJ, Woese CR. Ribosomal RNA phylogeny and the primary lines of evolutionary descent. Cell 1986, 45:325-326.
24. Page RD, Charleston MA. From gene to organismal phylogeny: reconciled trees and the gene tree/species tree problem. Mol. Phylogenet. Evol. 1997, 7:231-240.
25. Perkins SL, Schall JJ. A molecular phylogeny of malarial parasites recovered from cytochrome b gene sequences. J. Parasitol. 2002, 88:972-978.
26. 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, Manuel M. Phylogenomics revives traditional views on deep animal relationships. Curr. Biol. 2009, 19:706-712.
27. Schierwater B, Eitel M, Jakob W, Osigus HJ, Hadrys H, Dellaporta SL, Kolokotronis SO, Desalle R. Concatenated analysis sheds light on early metazoan evolution and fuels a modern 'urmetazoon' hypothesis. PLoS Biol. 2009, 7:e20.
28. Siddall ME. Success of parsimony in the four-taxon case: long-branch repulsion by likelihood in the Farris Zone. Cladistics 1998, 14:209-220.
29. Siddall ME. Philosophy and phylogenetic inference: a comparison of likelihood and parsimony methods in the context of Karl Popper's writings on corroboration. Cladistics 2001, 17:395-399.
30. Siddall ME, Kluge AG. Letter to the editor. Cladistics 1999, 15:439-440.
31. Stamatakis A, Hoover P, Rougemont J. A rapid bootstrap algorithm for the RAxML Web servers. Syst. Biol. 2008, 57:758-71.
32. Struck TH, Purschke G, Halanych KM. Phylogeny of Eunicida (Annelida) and exploring data congruence using a partition addition bootstrap alteration (PABA) approach. Syst. Biol. 2006, 55:1-20.
33. Suzuki Y, Glazko GV, Nei M. Overcredibility of molecular phylogenetics obtained by Bayesian phylogenetics. Proc. Natl Acad. Sci. USA 2002, 99:16138-16143.
34. Theodorides K, De Riva A, Gómez-Zurita J, Foster PG, Vogler AP. Comparison of EST libraries from seven beetle species: towards a framework for phylogenomics of the Coleoptera. Insect Mol. Biol. 2002, 11:467-475.
35. de la Torre JE, Egan MG, Katari M, Brenner ED, Stevenson DW, Coruzzi GM, DeSalle R. ESTimating plant phylogeny: lessons from partitioning. BMC Evol. Biol. 2006, 6:48.
36. Wiens JJ, Moen DS. Missing data and the accuracy of Bayesian phylogenetics. J. Syst. Evol. 2008, 46:307-314.
37. Zrzavy J, Mihulka S, Kepka P, Bezdek A, Tietz D. Phylogeny of the metazoa based on morphological and 18S ribosomal DNA evidence. Cladistics 1998, 14:249-285.
38. Zwickl DJ. Genetic Algorithm Approaches for the Phylogenetic Analysis of Large Biological Sequence Datasets under the Maximum Likelihood Criterion 2006, PhD thesis, The University of Texas, Austin, TX