Does elision account for molecular saturation: Case study based on mitochondrial ribosomal DNA among Characiform fishes (Teleostei: Ostariophysii)

Molecular Phylogenetics and Evolution

Volumn 35, Issue 1, 2005, Pages 300-308

  Hubert, Nicolas ^a   Bonillo, Céline ^a   Paugy, Didier ^a,b  

^a MUSÉUM NATIONAL D'HISTOIRE NATURELLE   (France)

^b INSTITUT DE RECHERCHE POUR LE DÉVELOPPEMENT   (France)

Author keywords

[No Author keywords available]

Indexed keywords

CHARACIFORMES; PISCES; TELEOSTEI;

EID: 14144255879     PISSN: 10557903     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.ympev.2005.01.010     Document Type: Article

References (42)

1. Barriel, V., 1994. Phylogénies moléculaires et insertions-délétions de nucléotides. Comptes Rendus de l' Académie des Sciences, Paris, Série III (Sciences de la Vie). 317, 693-701
2. Buckup, P.A., 1991. The Characidiinae: A phylogenetic study of the South American darters and their relationships with other characiform fishes. Ph. D. Dissertation, University Michigan, Ann Arbor
3. S. Cerchio, and P. Tucker Influence of alignment on the mtDNA Phylogeny of Cetacea: Questionable support for a Mysticeti/Physeteroidea clade Syst. Biol. 47 1998 336 344
4. G.C. Conant, and P.O. Lewis Effects of nucleotide composition bias on the success of the parsimony criterion in phylogenetic inference Mol. Biol. Evol. 18 2001 1024 1033
5. N. Galtier, and M. Gouy Inferring phylogenies from DNA sequences of unequal base compositions Proc. Natl. Acad. Sci. USA 92 1995 11317 11321
6. O. Gascuel BIONJ: An improved version of the NJ algorithm based on a simple model of sequence data Mol. Biol. Evol. 14 1997 685 695
7. J. Gatesy, R. DeSalle, and W. Wheeler Alignment ambiguous nucleotide sites and the exclusion of systematic data Mol. Phylogenet. Evol. 2 1994 152 157
8. D.L. Geiger Stretch coding and block coding: two new strategies to represent questionably aligned sequences J. Mol. Evol. 54 2002 191 199
9. G. Giribet, W.C. Wheeler, and J. Muona DNA multiple sequence alignments R. DeSalle G. Giribet W. Wheeler Molecular Systematics and Evolution: Theory and Practice 2001 Birkhäuser Verlag Switzerland
10. A. Hassanin, G. Lecointre, and S. Tillier The "evolutionary signal" of homoplasy in protein-coding gene sequences and its consequence for a priori weighting in phylogeny C. R. Acad. S., Série D 321 1998 611 620
11. A.J. Kluge A concern for evidence and a phylogenetic hypothesis of relationships among Epicrates (Boidae, Serpentes) Syst. Zool. 38 1989 7 25
12. M.K. Kuhner, and J. Felsenstein A simulation comparison of phylogeny algorithms under equal and unequal evolutionary rates Mol. Biol. Evol. 11 1994 459 468
13. Labarre, L., Billoud, B., Barriel, V., Viari, A., 1998. Barcod: Traitement automatique des insertions/délétions dans les alignements multiples. 7iéme Journées des Sciences de la Vie. Jussieu, Paris
14. M. Lee Unalignable sequences and molecular evolution Trends Ecol. Evol. 16 2001 681 685
15. D.G. Lloyd, and V.L. Calder Multi-residue gaps, a class of molecular characters with exceptional reliability for phylogenetic analysis J. Evol. Biol. 4 1991 9 21
16. Lucena, C.A.S.D.E., 1993. Estudo filogenético de famì lia Characidae com uma discussão dos grupos naturais propostos (Teleostei, Ostariophysi, Characiformes). Ph.D. Dissertation, University São Paulo, Brasil
17. J.G. Lundberg African South American freshwater fish clades and continental drift: Problems with a paradigm P. Goldblatt Biological Relationships Between Africa and South America 1993 Yales University Press New Haven, Connecticut 156 199
18. F. Lutzoni, P. Wagner, V. Reeb, and S. Zoller Integrating ambiguously aligned regions of DNA sequences in phylogenetic analyses without violating positional homology Syst. Biol. 49 2000 628 651
19. Machado-Allison, A., 1982. Studies on the systematics of the subfamily Serrasalminae (Pisces-Characidae). Unpublished Ph. D. The George Washington University
20. A.M. Murray, and K.M. Stewart Phylogenetic relationships of the African genera Alestes and Brycinus (Teleostei, Characiformes, Alestidae) Can. J. Zool. 80 2002 1887 1899
21. G. Orti, and A. Meyer The radiation of characiform fishes and the limits of resolution of mitochondrial ribosomal DNA sequences Syst. Biol. 46 1997 75 100
22. G. Orti, P. Petry, J.I.R. Porto, M. Jégu, and A. Meyer Pattern of nucleotide change in mitochondrial ribosomal RNA genes and the phylogeny of piranhas J. Mol. Evol. 42 1996 169 182
23. H. Philippe, U. Sorhannus, A. Baroin, R. Perasso, F. Gasse, and A. Adoutte Comparison of molecular and paleontological data in diatoms suggests a major gap in the fossil record J. Evol. Biol. 8 1994 193 204
24. H. Philippe, and J. Laurent How good are deep phylogenetic trees? Curr. Opin. Genet. Dev. 8 1998 616 623
25. A. Phillips, D. Janies, and W. Wheeler Multiple sequence alignment in phylogenetic analysis Mol. Phylogenet. Evol. 16 2000 317 330
26. W.C.I. Pittman, S. Cande, J. Labrecque, and J. Pindell Fragmentation of Ganwana: Separation of Africa from South America P. Goldblatt Biological Relationships Between Africa and South America 1993 Yales University Press New Haven Connecticut 15 34
27. T.R. Roberts Osteology and Classification of the neotropical characoid families Hemiodontidae (including Anodontidae) and Parodontidae Bull. Mus. Comp. Zool. 146 1974 412 472
28. M.P. Simmons, H. Ochoterena, and T.G. Carr Incorporation, relative homoplasy, and effect of gap-characters in sequence-based phylogenetic analyses Syst. Biol. 50 2001 454 462
29. M.D. Sorenson Treerot second ed 1999 Boston University Boston MA
30. StatGraphic., 1999. Statistical Graphics Corp. 1998
31. D.L. Swofford PAUP*. Phylogenetic Analysis Using Parsimony (* and Other Methods) 1999 Sinaeur Associates Sunderland, MA
32. D.L. Swofford, and G.J. Olsen Phylogeny reconstruction D.M. Hillis C. Moritz Molecular Systematics 1990 Sinauer Ass. Sunderland, Massachussetts 411 501
33. K. Tamura, and S. Kumar Evolutionary distance estimation under heterogeneous substitution pattern among lineages Mol. Biol. Evol. 19 2002 1727 1736
34. Thioulouse, J., Chessel, D., Dolédec, S., Olivier, J.-M., Goreaud, F., Pelissier, R., 1997. ADE-4 Ecological Data Analysis: Exploratory and Euclidean methods in Environmental sciences. Version 2001. CNRS
35. J.D Thompson, D.G. Higgins, and T.J. Gibson CLUSTAL W: Improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice Nucleic Acids Res. 22 1993 4673 4680
36. Uj, A., 1990. Etude comparative de l'ostéologie cranienne des poisons de la famille des Characidae et son importance phylogéné tique. Ph.D. Dissertation, University Genève, Genève, Switzerland
37. R.P. Vari Phylogenetic relationships of the families Curimatidae, Prochilodontidae, Anostomidae, and Chilodontidae Smithsonian Contribution to Zoology 378 1983 1 60
38. R.P. Vari The Neotropical fish family Ctenoluciidae (Teleostei: Ostariophysi: Characiformes): Supra and intrafamilial phylogenetic relationships, with a revisionary study Smithsonian Contribution to Zoology 564 1995 1 97
39. J.W. Wenzel, and M.E. Siddall Noise Cladistics 15 1999 51 64
40. S.H. Weitzman The osteology and the relationships of the south American characid fishes of the subfamily Gasteropelecidae Stanf. Ichtyol. Bull. 4 1954 213 278
41. W.C. Wheeler, J. Gatesy, and R. DeSalle Elision: A method for accommodating multiple molecular sequence alignments with alignment-ambiguous sites Mol. Phylogenet. Evol. 4 1995 1 9
42. W.C. Wheeler Fixed character states and the optimization of molecular sequence data Cladistics 15 1999 379 385