Phylogenetic support values are not necessarily informative: The case of the Serialia hypothesis (a mollusk phylogeny)

Frontiers in Zoology

Volumn 6, Issue 1, 2009, Pages

  Wägele, J Wolfgang ^a   Letsch, Harald ^a   Klussmann Kolb, Annette ^b   Mayer, Christoph ^c   Misof, Bernhard ^a   Wägele, Heike ^a  

^a ZOOLOGISCHES FORSCHUNGSMUSEUM ALEXANDER KOENIG   (Germany)

^b GOETHE UNIVERSITY   (Germany)

^c RUHR UNIVERSITY BOCHUM   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

MOLLUSCA; POLYPLACOPHORA;

EID: 67749142243     PISSN: None     EISSN: 17429994     Source Type: Journal    
DOI: 10.1186/1742-9994-6-12     Document Type: Article

References (76)

1. Use of Spectral Analysis to Test Hypotheses on the Origin of Pinnipeds. GM Lento E Hickson GK Chambers D Penny, Mol Biol Evol 1995 12 28 52 7877495
2. Genome-scale phylogeny and the detection of systematic biases. MJ Philipps F Delsuc D Penny, Mol Biol Evol 2004 21 1455 1458 15084674
3. Visualizing differences in phylogenetic information content of alignments and distinction of three classes of long-branch effects. JW Wägele C Mayer, BMC Evol Biol. 2007 7 147 17725833
4. Evidence for a clade composed of molluscs with serially repeated structures: monoplacophorans are related to chitons. G Giribet A Okusu AR Lindgren SW Huff M Schrödl MK Nishiguchi, Proc Natl Acad Sci USA 2006 103 7723 7728 16675549
5. Optimization alignment: the end of multiple sequence alignment in phylogenetics? W Wheeler, Cladistics 1996 12 1 9
6. Synapomorphies and plesiomorphies in higher classification of Mollusca. vL Salvini-Plawen G Steiner, Origin and evolutionary radiation of the Mollusca Oxford: Oxford University Press, Taylor J, 1996 29 51
7. A new look at early bivalve phylogeny. JCW Cope, The Evolutionary Biology of the Bivalvia London: Geological Society, Harper EM, Taylor JD, Crame JA, 2000 81 95
8. Bivalve phylogeny and molecular data. G Giribet DL Distel, Molecular Systematics and Phylogeography of Mollusks Washington D.C.: Smithsonian Books, Lydeard C, Lindberg DR, 2003 45 90
9. Relationship of higher molluscan taxa. G Haszprunar C Schander KM Halanych, Phylogeny and Evolution of the Mollusca Berkeley and Los Angeles: University of California Press, Ponder WF, Lindberg DR, 2007 19 32
10. Bivalvia. in Phylogeny and Evolution of the Mollusca. G Giribet, Phylogeny and Evolution of the Mollusca Berkeley and Los Angeles: University of California Press, Ponder WF, Lindberg DR, 2007 105 141
11. On the origin and evolution of major gastropod groups, with special reference to the Streptoneura. G Haszprunar, J Moll Stud 1988 54 367 441
12. Towards a phylogeny of gastropod molluscs: an analysis using morphological characters. WF Ponder DR Lindberg, Zool J Linn Soc 1997 119 83 265
13. Gastropoda: An overview and analysis. SW Aktipis G Giribet DR Lindberg WF Ponder, Phylogeny and Evolution of the Mollusca Berkeley and Los Angeles: University of California Press, Ponder WF, Lindberg DR, 2007 201 237
14. Heuristic reconstruction of hypothetical-ancestral DNA sequences: sequence alignment vs direct optimization. W Wheeler, Homology and Systematics London: Taylor and Francis, Scotland RW, Pennington T, 2000 106 113
15. A Monte Carlo approach successfully identifies randomness in multiple sequence alignments. B Misof K Misof, Syst Biol
16. MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform. K Katoh K Misawa K Kuma T Miyata, Nucl Acids Res 2002 30 3059 3066 12136088
17. MAFFT version 5: improvement in accuracy of multiple sequence alignment. K Katoh K Kuma H Toh T Miyata, Nucl Acids Res 2005 33 511 518 15661851
18. Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis. J Castresana, Mol Biol Evol. 2000 Apr;17(4):540-52 2000 17 4 40 552
19. Analyzing and Visualizing Sequence and Distance Data Using SplitsTree. A Dress D Huson V Moulton, Discrete Appl Mathem 1996 71 95 109
20. Application of phylogenetic networks in evolutionary studies. DH Huson D Bryant, Mol Biol Evol 2006 23 2 254 267 16221896
21. NeighborNet: An agglomerative method for the construction of planar phylogenetic networks. D Bryant V Moulton, Workshop in algorithms for bioinformatics Berlin, Heidelberg: Springer Verlag, Guigo R, Gusfield D, 2002 375 391
22. Neighbor-Net: An Agglomerative Method for the Construction of Phylogenetic Networks. D Bryant V Moulton, Mol Biol Evol 2004 21 255 265 14660700
23. Dating of the Human Ape Splitting by a Molecular Clock of Mitochondrial-DNA. M Hasegawa H Kishino TA Yano, J Mol Evol 1985 22 160 174 3934395
24. Maximum-Likelihood phylogenetic estimation from DNA-sequences with variable rates over sites approximate methods. ZH Yang, J Mol Evol 1994 39 306 314 7932792
25. Origin and phylogeny of metazoans as reconstructed with rDNA sequences. JW Wägele F Rödding, Progr Mol Subcell Biol 1998 21 45 70
26. A priori estimation of phylogenetic information conserved in aligned sequences. JW Wägele F Rödding, Mol Phylog Evol 1998 9 358 365
27. Quartet-mapping, a generalization of the likelihood-mapping procedure. K Nieselt-Struwe A von Haeseler, Mol Biol Evol 2001 18 1204 121 11420361
28. Evidence for independent Hox gene duplications in the hagfish lineage: a PCR-based gene inventory of Eptatretus stoutii. PF Stadler C Fried SJ Prohaska WJ Bailey B Misof FH Ruddle GP Wagner, Mol Phylogenet Evol 2004 32 686 694 15288047
29. MRBAYES: Bayesian inference of phylogenetic trees. JP Huelsenbeck F Ronquist, Bioinformatics 2001 17 754 755 11524383
30. MrBayes 3: Bayesian phylogenetic inference under mixed models. F Ronquist JP Huelsenbeck, Bioinformatics 2003 19 1572 1574 12912839
31. Maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models. A Stamatakis, Bioinformatics 2006 22 2688 2690 16928733
32. A molecular phylogeny of the bivalve mollusks. SL Adamkewicz MG Harasewych J Blake D Saudek CJ Bult, Mol Biol Evol 1997 14 619 629 9190063
33. Investigation of molluscan phylogeny using large-subunit and small-subunit nuclear rRNA sequences. YJ Passamaneck C Schander KM Halanych, Mol Phylogenet Evol. 2004 32 1 25 38 15186794
34. Mitochondrial genomes suggest that hexapods and crustaceans are mutually paraphyletic. CE Cook Q Yue M Akam, Proc R Soc B 2005 272 1295 1304 16024395
35. Further use of nearly complete 28S and 18S rRNA genes to classify Ecdysozoa: 37 more arthropods and a kinorhynch. J Mallatt G Giribet, Mol Phylog Evol 2006 40 772 794
36. EST sequencing of Onychophora and phylogenomic analysis of Metazoa. F Roeding S Hagner-Holler H Ruhberg I Ebersberger A von Haeseler M Kube R Reinhardt T Burmester, Mol Phylog Evol 2007 45 942 951
37. Broad phylogenomic sampling improves resolution of the animal tree of life. CW Dunn A Hejnol DQ Matus K Pang W Browne SA Smith E Seaver GW Rouse M Obst GD Edgecombe MV Sørensen SH Haddock A Schmidt-Rhaesa A Okusu R Kristensen WC Wheeler MQ Martindale G Giribet, Nature 2008 452 745 749 18322464
38. Exploring the relationship between sequence similarity and accurate phylogenetic trees. BL Cantarel HG Morrison W Pearson, Mol Biol Evol 2006 23 2090 2100 16891377
39. The Bayesian "Star Paradox" persists for long finite sequences. M Steel FA Matsen, Mol Biol Evol 2007 24 1075 1079 17299027
40. Using ESTs for phylogenomics: Can one accurately infer a phylogenetic tree from a gappy alignment? S Hartmann TJ Vision, BMC Evol Biol 2008 8 95 18366758
41. Generating implied alignments under direct optimization using POY. G Giribet, Cladistics 2005 21 396 402
42. Treeness triangles: Visualizing the loss of phylogenetic signal. WT White SF Hills R Gaddam BR Holland D Penny, Mol Biol Evol 2007 24 2029 2039 17630280
43. An analysis of the taxonomist's judgment of affinity. AJ Cain, Proc Zool Soc Lond 1958 131 85 98
44. Structures and functions, their general significance for phylogenetic reconstruction in recent and fossil taxa. D Schlee, Zool Scripta 1976 5 181 183
45. The homology concept: its philosophical foundation and practical methodology. WJ Bock, Zool Beitr 1989 32 327 353
46. Three steps of homology assessment. AVZ Brower V Schawaroch, Cladistics 1996 12 265 272
47. Moore J, Willmer P: Convergent evolution in invertebrates. Biol Rev 1997 72 1 60 9116163
48. O Rieppel M: Kearney, Similarity. Biol J Linn Soc 2002 75 59 82
49. Homology and ontogeny: pattern and process in comparative developmental biology. G Scholtz, Theory Biosci 2005 124 121 143 17046352
50. JW Wägele, Foundations of Phylogenetic Systematics München: Verlag Dr. Friedrich Pfeil 2005
51. Size, frequency, and phylogenetic signal of multiple-residue indels in sequence alignment of introns. J Pons AP Vogler, Cladistics 2006 22 144 156
52. Opinions on multiple sequence alignment and an empirical comparison of repeatability and accuracy between POY and structural alignment. KM Kjer JJ Gillespie KA Ober, Syst Biol 2007 56 133 146 17366144
53. Alignment and topological accuracy of the direct optimization approach via POY and traditional phylogenetics via ClustalW + PAUP. TH Ogden MS Rosenberg, Syst Biol 2007 56 182 193 17454974
54. Split decomposition: a new and useful approach to phylogenetic analysis of distance data. HJ Bandelt AWM Dress, Mol Phylog Evol 1992 1 242 252
55. Network models for sequence evolution. A von Haeseler GA Churchill, J Mol Evol 1993 37 77 85 8395605
56. Spectral Analysis, Systematic Bias, and the Evolution of Chloroplasts. PJ Lockhart CJ Howe AC Barbrook AWD Larkum D Penny, Mol Biol Evol 1999 16 573 576
57. Split support and split conflict randomization tests in phylogenetic inference. M Wilkinson, Syst Biol 1998 47 673 695 12066310
58. Initial results on the molecular phylogeny of the Nudibranchia (Gastropoda, Opisthobranchia) based on 18S rDNA data. E Wollscheid H Wägele, Mol Phylog Evol 1999 13 215 226
59. Preliminary study on molecular phylogeny of Sacoglossa and a compilation of their food organisms. K Händeler H Wägele, Bonner Zool Beitr 2007 55 231 254
60. How meaningful are Bayesian support values? MP Simmons KM Pickett M Miya, Mol Biol Evol 2004 21 188 199 14595090
61. Phylogenomics and the number of characters required for obtaining an accurate phylogeny of eukaryote model species. H Dopazo J Santoyo J Dopazo, Bioinformatics 2004 20 116 121
62. How much can evolved characters tell us about the tree that generated them? E Mossel M Steel, Mathematical evolution and phylogeny Oxford: Oxford University Press, Gascuel O, 2005 384 412
63. The "inverse" relationship between evolutionary rate and age of mammalian genes" is an artifact of increased genetic distance with rate of evolution and time of divergence. E Elhaik N Sabath D Graur, Mol Biol Evol 2006 23 1 3 16151190
64. Haszprunar G: Monoplacophora (Tryblidia). In Phylogeny and Evolution of the Mollusca Berkeley and Los Angeles: University of California Press, Ponder WF, Lindberg DR, 2007 97 104
65. Erörterungen zur Stammesgeschichte der Mollusca, insbesondere der Conchifera. KE Lauterbach, Z zool Syst Evol-forsch 1983 21 201 216
66. Das phylogenetische System der Mollusca. KE Lauterbach, Mitt deutsch malakozool Ges 1984 37 66 81
67. An evolutionary tree for the Mollusca: branches or roots? DR Lindberg WF Ponder, Origin and evolutionary radiation of the Mollusca Oxford: Oxford University Press, Taylor J, 1996 67 75
68. Is the Aplacophora monophyletic? A cladistic point of view. G Haszprunar, Amer Malac Bull 2000 15 115 130
69. P Ax, Multicellular animals: a new approach to the phylogenetic order in nature Berlin-Heidelberg: Springer Verlag 1996
70. EF Ruppert RS Fox RD Barnes, Invertebrate Zoology: a functional evolutionary approach Belmont USA: Thomson, Brooks/Cole 7 2004
71. The palaeontology of rostroconch mollusks and the early history of the phylum Mollusca. J Pojeta B Runnegar, Geol Surv Prof Pap (U.S.) 1976 968 1 88
72. The earliest bivalves and their Ordovician descendants. B Runnegar J Pojeta, Amer Malac Bull 1992 9 117 122
73. A reconsideration of systematics in Mollusca (Phylogeny and higher classification). vL Salvini-Plawen, Malacologia 1980 19 247 278
74. On the anatomy and relationships of recent Monoplacophora. KG Wingstrand, Galathea Report 1985 16 7 94
75. Monoplacophora. G Haszprunar K Schäfer, Microscopic Anatomy of Invertebrates. Mollusca II New York: Wiley-Liss, Harrison FW, Kohn AJ, 1997 6B 415 457
76. La matrice organique de la coquille et position phyletique de Neopilina galatheae (Mollusques, Monoplacophores). M Poulicek C Jeuniaux, Ann Soc Roy Zool Belg 1981 111 143 150