Phylogenetics of Chondrichthyes and the problem of rooting phylogenies with distant outgroups

Molecular Phylogenetics and Evolution

Volumn 63, Issue 2, 2012, Pages 365-373

  Li, Chenhong ^a,c   Matthes Rosana, Kerri A ^b   Garcia, Michael ^b   Naylor, Gavin J P ^b  

^a UNIVERSITY OF NEBRASKA   (United States)

^b FLORIDA STATE UNIVERSITY   (United States)

^c School of Business   (United States)

Author keywords

Chondrichthyes; Compositional bias; Nuclear gene markers; Outgroup; Phylogenetics; Rooting

Indexed keywords

ANIMAL; ARTICLE; CLASSIFICATION; DNA SEQUENCE; ELASMOBRANCH; GENETIC MARKER; GENETICS; MOLECULAR EVOLUTION; NUCLEOTIDE SEQUENCE; PHYLOGENY; SEQUENCE ALIGNMENT;

ANIMALS; BASE SEQUENCE; ELASMOBRANCHII; EVOLUTION, MOLECULAR; GENETIC MARKERS; PHYLOGENY; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS, DNA;

CHONDRICHTHYES; ELASMOBRANCHII; PISCES;

EID: 84862794264     PISSN: 10557903     EISSN: 10959513     Source Type: Journal    
DOI: 10.1016/j.ympev.2012.01.013     Document Type: Article

References (54)

1. Bapteste E., Brinkmann H., Lee J.A., Moore D.V., Sensen C.W., Gordon P., Durufle L., Gaasterland T., Lopez P., Muller M., Philippe H. The analysis of 100 genes supports the grouping of three highly divergent amoebae: Dictyostelium, Entamoeba, and Mastigamoeba. Proc. Natl. Acad. Sci. USA 2002, 99:1414-1419.
2. Berg L.S. Classification of fishes, both recent and fossil. Trav. Inst. Zool. Acad. Sci. URSS 1940, 5:87-517.
3. Blair J.E., Shah P., Hedges S.B. Evolutionary sequence analysis of complete eukaryote genomes. BMC Bioinform. 2005, 6:53.
4. Collins T.M., Fedrigo O., Naylor G.J. Choosing the best genes for the job: the case for stationary genes in genome-scale phylogenetics. Syst. Biol. 2005, 54:493-500.
5. Compagno L.J.V. Interrelationships of living elasmobranchs. Interrelationships of Fishes 1973, Academic Press, London. P.H. Greenwood, R.S. Miles, C. Patterson (Eds.).
6. Compagno L.J.V. Phyletic relationships of living sharks and rays. Am. Zool. 1977, 17:303-322.
7. Compagno, L.J.V., 2005. Global checklist of living chondrichthyan fishes. In Fowler, S.L., Cavanagh, R.D., Camhi, M., Burgess, G.H., Cailliet, G.M., Fordham, S.V., Simpfendorfer, C.A., Musick, J.A. (Eds.), Sharks, Rays and Chimaeras: The Status of Chondrichthyan Fishes. International Union for the Conservation of Nature and Natural Resources, Gland and Cambridge, pp. 401-423.
8. de Carvalho M.R. Higher-level elasmobranch phylogeny, basal squaleans, and paraphyly. Interrelationships of Fishes 1996, Academic Press, San Diego. M.L.J. Stiassny, L.R. Parenti, G.D. Johnson (Eds.).
9. Douady C.J., Dosay M., Shivji M.S., Stanhope M.J. Molecular phylogenetic evidence refuting the hypothesis of Batoidea (rays and skates) as derived sharks. Mol. Phylogen. Evol. 2003, 26:215-221.
10. 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., Schmidt-Rhaesa A., Okusu A., Kristensen R.M., Wheeler W.C., Martindale M.Q., Giribet G. Broad phylogenomic sampling improves resolution of the animal tree of life. Nature 2008, 452:745-749.
11. Felsenstein J. Cases in which parsimony or compatibility methods will be positively misleading. Syst. Zool. 1978, 27:401-410.
12. Gatesy J., DeSalle R., Wahlberg N. How many genes should a systematist sample? Conflicting insights from a phylogenomic matrix characterized by replicated incongruence. Syst. Biol. 2007, 56:355-363.
13. Gowri-Shankar V., Rattray M. A reversible jump method for Bayesian phylogenetic inference with a nonhomogeneous substitution model. Mol. Biol. Evol. 2007, 24:1286-1299.
14. Graham S.W., Olmstead R.G., Barrett S.C. Rooting phylogenetic trees with distant outgroups: a case study from the commelinoid monocots. Mol. Biol. Evol. 2002, 19:1769-1781.
15. Grogan E.D., Lund R., Didier D. Description of the chimaerid jaw and its phylogenetic origins. J. Morphol. 1999, 239:45-59.
16. Huelsenbeck J.P., Bollback J.P., Levine A.M. Inferring the root of a phylogenetic tree. Syst. Biol. 2002, 51:32-43.
17. Human B.A., Owen E.P., Compagno L.J., Harley E.H. Testing morphologically based phylogenetic theories within the cartilaginous fishes with molecular data, with special reference to the catshark family (Chondrichthyes; Scyliorhinidae) and the interrelationships within them. Mol. Phylogen. Evol. 2006, 39:384-391.
18. Inoue J.G., Miya M., Lam K., Tay B.H., Danks J.A., Bell J., Walker T.I., Venkatesh B. Evolutionary origin and phylogeny of the modern holocephalans (Chondrichthyes: Chimaeriformes): a mitogenomic perspective. Mol. Biol. Evol. 2010.
19. Jeffroy O., Brinkmann H., Delsuc F., Philippe H. Phylogenomics: the beginning of incongruence?. Trends Genet. 2006, 22:225-231.
20. Jobb, G., 2008. TreeFinder, Munich, Germany. Distributed by the author at http://www.treefinder.de.
21. Katoh K., Toh H. Recent developments in the MAFFT multiple sequence alignment program. Brief. Bioinform. 2008, 9:286-298.
22. Li C., Ortí G., Zhang G., Lu G. A practical approach to phylogenomics: the phylogeny of ray-finned fish (Actinopterygii) as a case study. BMC Evol. Biol. 2007, 7:44.
23. Li C., Riethoven J.J., Ma L. Exon-primed intron-crossing (EPIC) markers for non-model teleost fishes. BMC Evol. Biol. 2010, 10:90.
24. Lim D.D., Motta P., Mara K., Martin A.P. Phylogeny of hammerhead sharks (Family Sphyrnidae) inferred from mitochondrial and nuclear genes. Mol. Phylogen. Evol. 2010, 55:572-579.
25. Lopez J.A., Ryburn J.A., Fedrigo O., Naylor G.J. Phylogeny of sharks of the family Triakidae (Carcharhiniformes) and its implications for the evolution of carcharhiniform placental viviparity. Mol. Phylogen. Evol. 2006, 40:50-60.
26. Maisey J.G., Naylor G.J.P., Ward D.J. Mesozoic elasmobranchs, neoselachian phylogeny, and the rise of modern neoselachian diversity. Mesozoic Fishes 3-Systematics, Paleoenvironments and Biodiversity 2004, 17-56. Verlag Dr. Friedrich Pfeil, München. G. Arratia, A. Tintori (Eds.).
27. Mallatt J., Winchell C.J. Ribosomal RNA genes and deuterostome phylogeny revisited: more cyclostomes, elasmobranchs, reptiles, and a brittle star. Mol. Phylogen. Evol. 2007, 43:1005-1022.
28. Naylor G.J.P., Ryburn J.A., Fedrigo O., Lopez J.A. Phylogenetic relationships among the major lineages of modern elasmobranchs. Reproductive Biology and Phylogeny of Chondrichthyes: Sharks, Batoids and Chimaeras 2005, 1-25. Science Publishers, Enfield, New Hampshire. W.C. Hamlett (Ed.).
29. Naylor, G.J.P., Caira, J.N., Jensen, K., Rosana, K.A.M., White, W.T., Last, P.R., in press. A sequence based approach to the identification of shark and ray species and its implications for global elasmobranch diversity and parasitology. Bull. Am. Mus. Nat. Hist.
30. Nelson J.S. Fishes of the World 1976, Wiley, New York.
31. Nelson J.S. Fishes of the World 1984, Wiley, New York.
32. Nelson J.S. Fishes of the World 2006, John Wiley and Sons, Inc., New York.
33. Nylander J.A., Ronquist F., Huelsenbeck J.P., Nieves-Aldrey J.L. Bayesian phylogenetic analysis of combined data. Syst. Biol. 2004, 53:47-67.
34. Nylander J.A.A., Wilgenbusch J.C., Warren D.L., Swofford D.L. AWTY (are we there yet?): a system for graphical exploration of MCMC convergence in Bayesian phylogenetics. Bioinformatics 2008, 24:581-583.
35. Philippe H., Delsuc F., Brinkmann H., Lartillot N. Phylogenomics. Annu. Rev. Ecol. Evol. Syst. 2005, 36:541-562.
36. Philippe H., Lartillot N., Brinkmann H. Multigene analyses of bilaterian animals corroborate the monophyly of Ecdysozoa, Lophotrochozoa, and Protostomia. Mol. Biol. Evol. 2005, 22:1246-1253.
37. Phillips M.J., Penny D. The root of the mammalian tree inferred from whole mitochondrial genomes. Mol. Phylogen. Evol. 2003, 28:171-185.
38. Phillips M.J., Delsuc F., Penny D. Genome-scale phylogeny and the detection of systematic biases. Mol. Biol. Evol. 2004, 21:1455-1458.
39. Posada D., Crandall K.A. MODELTEST: testing the model of DNA substitution. Bioinformatics 1998, 14:817-818.
40. Qiu Y.L., Li L., Wang B., Chen Z., Knoop V., Groth-Malonek M., Dombrovska O., Lee J., Kent L., Rest J., Estabrook G.F., Hendry T.A., Taylor D.W., Testa C.M., Ambros M., Crandall-Stotler B., Duff R.J., Stech M., Frey W., Quandt D., Davis C.C. The deepest divergences in land plants inferred from phylogenomic evidence. Proc. Natl. Acad. Sci. USA 2006, 103:15511-15516.
41. Regier J.C., Shultz J.W., Zwick A., Hussey A., Ball B., Wetzer R., Martin J.W., Cunningham C.W. Arthropod relationships revealed by phylogenomic analysis of nuclear protein-coding sequences. Nature 2010, 463:1079-1083.
42. Rokas A., Williams B.L., King N., Carroll S.B. Genome-scale approaches to resolving incongruence in molecular phylogenies. Nature 2003, 425:798-804.
43. Rosenberg M.S. MySSP: non-stationary evolutionary sequence simulation, including indels. Evol. Bioinform. Online 2005, 1:81-83.
44. Shimodaira H., Hasegawa M. Multiple comparisons of log-likelihoods with applications to phylogenetic inference. Mol. Biol. Evol. 1999, 16:1114-1116.
45. Shirai S. Squalean Phylogeny, a New Framework of "Squaloid" Sharks and Related Taxa 1992, Hokkaido University Press, Sapporo.
46. Shirai S. Phylogenetic interrelationships of neoselachians (Chondrichthyes: Euselachii). Interrelationships of Fishes 1996, 9-34. Academic Press, San Diego. M.L.J. Stiassny, L.R. Parenti, G.D. Johnson (Eds.).
47. Stamatakis A., Ludwig T., Meier H. RAxML-III: a fast program for maximum likelihood-based inference of large phylogenetic trees. Bioinformatics 2005, 21:456-463.
48. Swofford, D.L., 2003. PAUP*. Phylogenetic Analysis Using Parsimony (* and Other Methods). Version 4 Sinauer Associates, Sunderland, Massachusetts.
49. Tamura K., Dudley J., Nei M., Kumar S. MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) software version 4.0. Mol. Biol. Evol. 2007, 24:1596-1599.
50. Tarrio R., Rodriguez-Trelles F., Ayala F.J. Tree rooting with outgroups when they differ in their nucleotide composition from the ingroup: the Drosophila saltans and willistoni groups, a case study. Mol. Phylogen. Evol. 2000, 16:344-349.
51. Wheeler W.C. Nucleic acid sequence phylogeny and random outgroups. Cladistics 1990, 6:363-367.
52. Winchell C.J., Martin A.P., Mallatt J. Phylogeny of elasmobranchs based on LSU and SSU ribosomal RNA genes. Mol. Phylogen. Evol. 2004, 31:214-224.
53. Woese C.R., Achenbach L., Rouviere P., Mandelco L. Archaeal phylogeny: reexamination of the phylogenetic position of Archaeoglobus fulgidus in light of certain composition-induced artifacts. Syst. Appl. Microbiol. 1991, 14:364-371.
54. Wolf Y.I., Rogozin I.B., Koonin E.V. Coelomata and not Ecdysozoa: evidence from genome-wide phylogenetic analysis. Genome Res. 2004, 14:29-36.