Sequences from 14 mitochondrial genes provide a well-supported phylogeny of the Charadriiform birds congruent with the nuclear RAG-1 tree

Molecular Phylogenetics and Evolution

Volumn 39, Issue 3, 2006, Pages 657-667

  Paton, Tara A ^a,b   Baker, Allan J ^a,b  

^a DEPARTMENT OF NATURAL HISTORY   (Canada)

^b UNIVERSITY OF TORONTO   (Canada)

Author keywords

Charadriiformes; Genomes; Mitochondrial genes; Molecular phylogeny; Shorebirds

Indexed keywords

CYTOCHROME B; MITOCHONDRIAL DNA;

ANIMAL; ARTICLE; BIRD; CLASSIFICATION; GENE; GENETICS; NUCLEIC ACID HYBRIDIZATION; PHYLOGENY;

ANIMALS; BIRDS; CYTOCHROMES B; DNA, MITOCHONDRIAL; GENES, RAG-1; NUCLEIC ACID HYBRIDIZATION; PHYLOGENY;

AVES; CHARADRII; CHARADRIIFORMES;

EID: 33646393242     PISSN: 10557903     EISSN: 10959513     Source Type: Journal    
DOI: 10.1016/j.ympev.2006.01.011     Document Type: Article

References (60)

1. Barker F.K., Barrowclough G.F., and Groth J.G. A phylogenetic hypothesis for passerine birds: taxonomic and biogeographic implications of an analysis of nuclear DNA sequence data. Proc. R. Soc. Lond. B. Biol. Sci. 269 (2002) 295-308
2. Birks S.M., and Edwards S.V. A phylogeny of the megapodes (Aves: Megapodiidae) based on nuclear and mitochondrial DNA sequences. Mol. Phylogenet. Evol. 23 (2002) 408-421
3. Björklund M. Phylogenetic relationships among Charadriiformes: reanalysis of previous data. Auk 111 (1994) 825-832
4. Braun E.L., and Kimball R.T. Examining basal avian divergences with mitochondrial sequences: model complexity, taxon sampling, and sequence length. Syst. Biol. 51 (2002) 614-625
5. Cao Y., Adachi J., Janke A., Paabo S., and Hasegawa M. Phylogenetic relationships among eutherian orders estimated from inferred sequences of mitochondrial proteins: instability of a tree based on a single gene. J. Mol. Evol. 39 (1994) 519-527
6. Christian P.D., Christidis L., and Schodde R. Biochemical systematics of the Charadriiformes (Shorebirds): relationships between the Charadrii, Scolopaci and Lari. Aust. J. Zool. 40 (1992) 291-302
7. Chu P.C. Phylogenetic reanalysis of Strauch's osteological data set for the Charadriiformes. Condor 97 (1995) 174-196
8. Clements J.F. Birds of the World: A Checklist. 5th ed. (2000), Ibis Publishing Company, Temecula, California
9. Corneli P.S., and Ward R.H. Mitochondrial genes and mammalian phylogenies: increasing the reliability of branch length estimation. Mol. Biol. Evol. 17 (2000) 224-234
10. Cummings M.P., Otto S.P., and Wakeley J. Sampling properties of DNA sequence data in phylogenetic analysis. Mol. Biol. Evol. 12 (1995) 814-822
11. Debus S.J.S. Family Turnicidae (Buttonquails). Handbook of the Birds of the World. In: del Hoyo J., Elliott A., and Sargatal J. (Eds). Hoatzin to Auks Vol. 3 (1996), Lynx Edicions, Barcelona 44-59
12. DeFilippis V.R., and Moore W.S. Resolution of phylogenetic relationships among recently evolved species as a function of amount of DNA sequence: an empirical study based on woodpeckers (Aves: Picidae). Mol. Phylogenet. Evol. 16 (2000) 143-160
13. Desjardins P., and Morais R. Sequence and gene organization of the chicken mitochondrial genome. A novel gene order in higher vertebrates. J. Mol. Biol. 212 (1990) 599-634
14. Edwards S.V., and Arctander P. Re: congruence and phylogenetic reanalysis of perching bird cytochrome b sequences. Mol. Phylogenet. Evol. 7 (1997) 266-271
15. Ericson P.G.P., Christidis L., Cooper A., Irestedt M., Jackson J., Johansson U.S., and Norman J.A. A Gondwanan origin of passerine birds supported by DNA sequences of the endemic New Zealand wrens. Proc. R. Soc. Lond. B. Biol. Sci. 269 (2002) 235-241
16. Ericson P.G.P., Envall I., Irestedt M., and Norman J.A. Inter-familial relationships of the shorebirds (Aves: Charadriiformes) based on nuclear DNA sequence data. BMC Evol. Biol. 3 (2003) 16
17. Galtier N., and Gouy M. Inferring pattern and process: maximum likelihood implementation of a nonhomogenous model of DNA sequence evolution for phylogenetic analysis. Mol. Biol. Evol. 15 (1998) 871-879
18. Garcia-Moreno J., Sorenson M.D., and Mindell D.P. Congruent avian phylogenies inferred from mitochondrial and nuclear DNA sequences. J. Mol. Evol. 57 (2003) 27-37
19. Groth J.G., and Barrowclough G.F. Basal divergences in birds and the phylogenetic utility of the nuclear RAG-1 gene. Mol. Phylogenet. Evol. 12 (1999) 115-123
20. Haddrath O.P., and Baker A.J. Complete mitochondrial DNA genome sequences of extinct birds: ratite phylogenetics and the vicariance biogeography hypothesis. Proc. R. Soc. Lond. B. Biol. Sci. 268 (2001) 939-945
21. Huelsenbeck J.P., and Ronquist F. MRBAYES: Bayesian inference of phylogenetic trees. Bioinformatics 17 (2001) 754-755
22. Irestedt M., Johansson U.S., Parsons T.J., and Ericson P.G.P. Phylogeny of major lineages of suboscines (Passeriformes) analysed by nuclear DNA sequence data. J. Avian Biol. 32 (2001) 15-25
23. Johansson U.S., Parsons T.J., Irestedt M., and Ericson P.G.P. Clades within the 'higher land birds,' evaluated by nuclear DNA sequences. J. Zool. Syst. Evol. Res. 39 (2001) 37-51
24. Johnson K.P. Taxon sampling and the phylogenetic position of Passeriformes: evidence from 916 avian cytochrome b sequences. Syst. Biol. 50 (2001) 128-136
25. Johnson K.P., and Clayton D.H. Nuclear and mitochondrial genes contain similar phylogenetic signal for pigeons and doves (Aves: Columbiformes). Mol. Phylogenet. Evol. 14 (2000) 141-151
26. Kumar S., Tamura K., Jakobsen I.B., and Nei M. MEGA2: molecular evolutionary genetics analysis software. Bioinformatics 17 (2001) 1244-1245
27. Mayr G. Charadriiform birds from the early Oligocene of Céreste (France) and the Middle Eocene of Messel (Hessen, Germany). Geobios 33 (2000) 625-636
28. Mickevitch M.F., and Parenti L.R. Review of, "The phylogeny of the Charadriiformes (Aves): a new estimate using the method of character compatibility analysis". Syst. Zool. 29 (1980) 108-113
29. Mindell D.P., Sorenson M.D., and Dimcheff D.E. An extra nucleotide is not translated in mitochondrial ND3 of some birds and turtles. Mol. Biol. Evol. 15 (1998) 1568-1571
30. Mindell D.P., Sorenson M.D., Dimcheff D.E., Hasegawa M., Ast J.C., and Yuri T. Interordinal relationships of birds and other reptiles based on whole mitochondrial genomes. Syst. Biol. 48 (1999) 138-152
31. Moore W.S., and DeFilippis V.R. The window of taxonomic resolution for phylogenies based on mitochondrial cytochrome b. In: Mindell D.P. (Ed). Avian Molecular Evolution and Systematics (1997), Academic Press, New York 83-119
32. Olson S.L., and Steadman D.W. The relationships of the Pedionomidae (Aves: Charadriiformes). Smithsonian Contrib. Zool. 337 (1981)
33. Paton T., Haddrath O., and Baker A.J. Complete mitochondrial DNA genome sequences show that modern birds are not descended from transitional shorebirds. Proc. R. Soc. Lond. B. Biol. Sci. 269 (2002) 839-846
34. Paton T., Baker A.J., Groth J.G., and Barrowclough G.F. RAG-1 sequences resolve phylogenetic relationships within Charadriiform birds. Mol. Phylogenet. Evol. 29 (2003) 268-278
35. Pereira S.L., Baker A.J., and Wajntal A. Combined nuclear and mitochondrial DNA sequences resolve generic relationships within the Cracidae (Galliformes, Aves). Syst. Biol. 51 (2002) 946-958
36. Pitra C., Lieckfeldt D., Frahnert S., and Fickel J. Phylogenetic relationships and ancestral areas of the bustards (Gruiformes: Otididae), inferred from mitochondrial DNA and nuclear intron sequences. Mol. Phylogenet. Evol. 23 (2002) 63-74
37. Pollock D.D., Zwickl D.J., McGuire J.A., and Hillis D.M. Increased taxon sampling is advantageous for phylogenetic inference. Syst. Biol. 51 (2002) 664-671
38. Posada D., and Crandall K.A. Modeltest: testing the model of DNA substitution. Bioinformatics 14 (1998) 817-818
39. Rosenberg M.S., and Kumar S. Incomplete taxon sampling is not a problem for phylogenetic inference. Proc. Natl. Acad. Sci. USA 98 (2001) 10751-10756
40. Rosenberg M.S., and Kumar S. Taxon sampling, bioinformatics, and phylogenomics. Syst. Biol. 52 (2003) 119-124
41. Rotthowe K., and Starck J.M. Evidence for a phylogenetic position of buttonquails (Turnicidae, Aves) among the Gruiformes. J. Zool. Syst. Evol. Res. 36 (1998) 39-51
42. Russo C.A., Takezaki N., and Nei M. Efficiencies of different genes and different tree-building methods in recovering a known vertebrate phylogeny. Mol. Biol. Evol. 13 (1996) 525-536
43. Sambrook J. Molecular Cloning: A Laboratory Manual. 2nd ed. (1989), Cold Spring Harbor Laboratory, Cold Spring Harbor, New York
44. Schmidt H.A., Strimmer K., Vingron M., and von Haeseler A. TREE-PUZZLE: maximum likelihood phylogenetic analysis using quartets and parallel computing. Bioinformatics 18 (2002) 502-504
45. Sheldon F.H., Whittingham L.A., and Winkler D.W. A comparison of cytochrome b and DNA hybridization data bearing on the phylogeny of swallows (Aves: Hirundinidae). Mol. Phylogenet. Evol. 11 (1999) 320-331
46. Shimodaira H., and Hasegawa M. CONSEL: for assessing the confidence of phylogenetic tree selection. Bioinformatics 17 (2001) 1246-1247
47. Shimodaira H. An approximately unbiased test of phylogenetic tree selection. Syst. Biol. 51 (2002) 492-508
48. Sibley C.G., and Ahlquist J.E. Phylogeny and Classification of Birds: A Study in Molecular Evolution (1990), Yale University Press, New Haven
49. Slack K.E., Janke A., Penny D., and Arnason U. Two new avian mitochondrial genomes (penguin and goose) and a summary of bird and reptile mitogenomic features. Gene 302 (2003) 43-52
50. Slikas B. Phylogeny of the avian family Ciconiidae (storks) based on cytochrome b sequences and DNA-DNA hybridization distances. Mol. Phylogenet. Evol. 8 (1997) 275-300
51. Strauch J.G. The phylogeny of the Charadriiformes (Aves): a new estimate using the method of character compatibility analysis. Trans. Zool. Soc. Lond. 34 (1978) 263-345
52. *: Phylogenetic Analysis Using Parsimony (* and other methods), Version 4.0b10, Sinauer Associates, Sunderland, Massachusetts.
53. Thomas G.H., Wills M.A., and Székely T. Phylogeny of shorebirds, gulls, and alcids (Aves: Charadrii) from the cytochrome-b gene: parsimony, Bayesian inference, minimum evolution, and quartet puzzling. Mol. Phylogenet. Evol. 30 (2004) 516-526
54. Thomassen H.A., Wiersema A.T., de Bakker M.A., de Knijff P., Hetebrij E., and Povel G.D. A new phylogeny of swiftlets (Aves: Apodidae) based on cytochrome-b DNA. Mol. Phylogenet. Evol. 29 (2003) 86-93
55. Thompson J.D., Gibson T.J., Plewniak F., Jeanmougin J., and Higgins D.G. The Clustal X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res. 25 (1997) 4876-4882
56. van Tuinen M., Waterhouse D., and Dyke G.J. Avian molecular systematics on the rebound: a fresh look at modern shorebird phylogenetic relationships. J. Avian Biol. 35 (2004) 191-194
57. Weibel A.C., and Moore W.S. A test of a mitochondrial gene-based phylogeny of woodpeckers (genus Picoides) using an independent nuclear gene, beta-fibrinogen intron 7. Mol. Phylogenet. Evol. 22 (2002) 247-257
58. Weibel A.C., and Moore W.S. Molecular phylogeny of a cosmopolitan group of woodpeckers (genus Picoides) gased on COI and cyt b mitochondrial gene sequences. Mol. Phylogenet. Evol. 22 (2002) 65-75
59. Zardoya R., and Meyer A. Phylogenetic performance of mitochondrial protein-coding genes in resolving relationships among vertebrates. Mol. Biol. Evol. 13 (1996) 933-942
60. Zwickl D.J., and Hillis D.M. Increased taxon sampling greatly reduces phylogenetic error. Syst. Biol. 51 (2002) 588-598