Resolving the root of the avian mitogenomic tree by breaking up long branches

Molecular Phylogenetics and Evolution

Volumn 42, Issue 1, 2007, Pages 1-13

  Slack, Kerryn E ^a,b   Delsuc, Frédéric ^a   Mclenachan, Patricia A ^a   Arnason, Ulfur ^b   Penny, David ^a  

^a MASSEY UNIVERSITY   (New Zealand)

^b LUND UNIVERSITY   (Sweden)

Author keywords

Avian evolution; Cracrafti; Galloanseres; Long branches; Neoaves; Passeriformes

Indexed keywords

MITOCHONDRIAL DNA;

ANIMAL; ARTICLE; BIRD; CHEMISTRY; CLASSIFICATION; DNA SEQUENCE; GENETICS; MOLECULAR EVOLUTION; MOLECULAR GENETICS; NUCLEOTIDE SEQUENCE; PHYLOGENY;

ANIMALS; BIRDS; DNA, MITOCHONDRIAL; EVOLUTION, MOLECULAR; MOLECULAR SEQUENCE DATA; PHYLOGENY; SEQUENCE ANALYSIS, DNA;

AVES; CATHARTES AURA; GALLIFORMES; MELEAGRIS GALLOPAVO; PASSERI; PASSERIFORMES; REPTILIA;

EID: 33750983626     PISSN: 10557903     EISSN: 10959513     Source Type: Journal    
DOI: 10.1016/j.ympev.2006.06.002     Document Type: Article

References (68)

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 269 (2002) 295-308
2. Barker F.K., Cibois A., Schikler P., Feinstein J., and Cracraft J. Phylogeny and diversification of the largest avian radiation. Proc. Natl. Acad. Sci. USA 101 (2004) 11040-11045
3. Bensch S., and Härlid A. Mitochondrial genomic rearrangements in songbirds. Mol. Biol. Evol. 17 (2000) 107-113
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. Buckley T.R. Model misspecification and probabilistic tests of topology: evidence from empirical data sets. Syst. Biol. 51 (2002) 509-523
6. Chang J.T. Inconsistency of evolutionary tree topology reconstruction methods when substitution rates vary across characters. Math. Biosci. 134 (1996) 189-215
7. Chubb A.L. New nuclear evidence for the oldest divergence among neognath birds: the phylogenetic utility of ZENK (i). Mol. Phylogenet. Evol. 30 (2004) 140-151
8. Cooper A., and Penny D. Mass survival of birds across the Cretaceous-Tertiary boundary: molecular evidence. Science 275 (1997) 1109-1113
9. Cooper A., Lalueza-Fox C., Anderson S., Rambaut A., Austin J., and Ward R. Complete mitochondrial genome sequences of two extinct moas clarify ratite evolution. Nature 409 (2001) 704-707
10. Cracraft J. Avian evolution, Gondwana biogeography and the Cretaceous-Tertiary mass extinction event. Proc. R. Soc. Lond. B 268 (2001) 459-469
11. Cracraft, J., Barker, F.K., Braun, M. et al., 2004. Phylogenetic relationships among modern birds (Neornithes). In: J. Cracraft, M.J. Donoghue (Eds.), Assembling the Tree of Life. Oxford University Press, pp. 468-489.
12. Delsuc F., Phillips M.J., and Penny D. Comment on "Hexapod origins: monophyletic or paraphyletic?". Science 301 (2003) 1482d
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 Boles W.E. Out of Gondwana: the origin of passerine birds. Trends Ecol. Evol. 17 (2002) 340-347
15. Edwards S.V., Fertil B., Giron A., and Deschavanne P.J. A genomic schism in birds revealed by phylogenetic analysis of DNA strings. Syst. Biol. 51 (2002) 599-613
16. Ericson P.G.P., and Johansson U.S. Phylogeny of Passerida (Aves: Passeriformes) based on nuclear and mitochondrial sequence data. Mol. Phylogenet. Evol. 29 (2003) 126-138
17. Ericson P.G.P., Christidis P.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 269 (2002) 235-241
18. Ericson P.G.P., Christidis P.L., Irestedt M., and Norman J.A. Systematic affinities of the lyrebirds (Passeriformes: Menura), with a novel classification of the major groups of passerine birds. Mol. Phylogenet. Evol. 25 (2002) 53-62
19. 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
20. Fain M.G., and Houde P. Parallel radiations in the primary clades of birds. Evolution 58 (2004) 2558-2573
21. Feduccia A. Mesozoic aviary takes form. Proc. Natl. Acad. Sci. USA 103 (2006) 5-6
22. Fuchs J., Fjeldsa J., Bowie R.C.K., Voelker G., and Pasquet E. The African warbler genus Hyliota as a lost lineage in the oscine songbird tree. Mol. Phylogenet. Evol. 39 (2006) 186-197
23. Garcia-Moreno J., and Mindell D.P. Rooting a phylogeny with homologous genes on opposite sex chromosomes (gametologs): a case study using avian CHD. Mol. Biol. Evol. 17 (2000) 1826-1832
24. Garcia-Moreno J., Sorenson M.D., and Mindell D.P. Congruent avian phylogenies inferred from mitochondrial and nuclear DNA sequences. J. Mol. Evol. 56 (2003) 1-11
25. Haddrath O., and Baker A.J. Complete mitochondrial DNA genome sequences of extinct birds: ratite phylogenetics and the vicariance biogeography hypothesis. Proc. R. Soc. Lond. B 268 (2001) 939-945
26. Haring E., Kruckenhauser L., Gamauf A., Riesing M.J., and Pinsker W. The complete sequence of the mitochondrial genome of Buteo buteo (Aves, Accipitridae) indicates an early split in the phylogeny of raptors. Mol. Biol. Evol. 18 (2001) 1892-1904
27. Härlid A., and Arnason U. Analyses of mitochondrial DNA nest ratite birds within the "Neognathae" supporting a neotenous origin of ratite morphological characters. Mol. Phylogenet. Evol. 12 (1999) 115-123
28. Härlid A., Janke A., and Arnason U. The complete mitochondrial sequence of Rhea americana and early avian divergences. J. Mol. Evol. 46 (1999) 669-679
29. Harrison G.L., McLenachan P.A., Phillips M.J., Slack K.E., Cooper A., and Penny D. Four new avian mitochondrial genomes help get to basic evolutionary questions in the Late Cretaceous. Mol. Biol. Evol. 21 (2004) 974-983
30. Helbig A.J., and Seibold I. Are storks and New World vultures paraphyletic?. Mol. Phylogenet. Evol. 6 (1996) 315-319
31. Hendy M.D., and Penny D. A framework for the quantitative study of evolutionary trees. Syst. Zool. 38 (1989) 297-309
32. Holland B.R., Penny D., and Hendy M.D. Outgroup misplacement and phylogenetic inaccuracy under a molecular clock: a simulation study. Syst. Biol. 52 (2003) 229-238
33. Huson D.H., and Bryant D. Application of phylogenetic networks in evolutionary studies. Mol. Biol. Evol. 23 (2006) 254-267
34. Huson D.H., Dezulian T., Kloepper T., and Steel M.A. Phylogenetic super-networks from partial trees. IEEE/ACM Trans. Comput. Biol. Bioinform. 1 (2004) 151-158
35. 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
36. Kocher T.D., Thomas W.K., Meyer A., Edwards S.V., Pääbo S., Villablanca F.X., and Wilson A.C. Dynamics of mitochondrial DNA evolution in animals: amplification and sequencing with conserved primers. Proc. Natl. Acad. Sci. USA 86 (1989) 6196-6200
37. Lanyon S.C. Detecting internal inconsistencies in distance data. Syst. Zool. 34 (1985) 397-403
38. Lin Y.-L., McLenachan P.A., Gore A.R., Phillips M.J., Ota R., Hendy M.D., and Penny D. Four new mitochondrial genomes, and the stability of evolutionary trees of mammals. Mol. Biol. Evol. 19 (2002) 2060-2070
39. Livezey B.C., and Zusi R.L. Higher-order phylogenetics of modern Aves based on comparative anatomy. Netherlands J. Zool. 51 (2001) 179-205
40. Mayr G., and Clarke J. The deep divergences of neornithine birds: a phylogenetic analysis of morphological characters. Cladistics 19 (2003) 527-553
41. Mindell D.P., Sorenson M.D., and Dimcheff D.E. Multiple independent origins of mitochondrial gene order in birds. Proc. Natl. Acad. Sci. USA 95 (1998) 10693-10697
42. 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
43. 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 269 (2002) 839-846
44. 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
45. Penny D. Our relative genetics. Nature 427 (2004) 208-209
46. Penny D., and Hendy M.D. The use of tree comparison metrics. Syst. Zool. 34 (1985) 75-82
47. Penny D., and Phillips M.J. The rise of birds and mammals: are microevolutionary processes sufficient for macroevolution. Trends Ecol. Evol. 19 (2004) 516-522
48. Penny D., Foulds L.R., and Hendy M.D. Testing the theory of evolution by comparing phylogenetic trees constructed from five different protein sequences. Nature 297 (1982) 197-200
49. Penny D., Hendy M.D., and Steel M.A. Testing the theory of descent. In: Miyamoto M.M., and Cracraft J. (Eds). "Phylogenetic Analysis of DNA Sequences" (1991), Oxford University Press 155-183
50. Phillips M.J., and Penny D. The root of the mammalian tree inferred from whole mitochondrial genomes. Mol. Phylogenet. Evol. 28 (2003) 171-185
51. Phillips M.J., Delsuc F., and Penny D. Genome-scale phylogeny: sampling and systematic errors are both important. Mol. Biol. Evol. 21 (2004) 1455-1458
52. Phillips M.J., McLenachan P.A., Gibb G.C., and Penny D. Combined nuclear and mitochondrial protein-coding DNA sequences resolve the interrelations of the major Australasian marsupial radiations. Syst. Biol. 55 (2006) 122-137
53. Poe S., and Chubb A.L. Birds in a bush: five genes indicate explosive evolution of avian orders. Evolution 58 (2004) 404-415
54. Posada D., and Crandall K.A. Modeltest: testing the model of DNA substitution. Bioinformatics 14 (1998) 817-818
55. Rambaut, A., 1996. Se-Al: Sequence Alignment Editor. Available at .
56. Rea A.M. Cathartid affinities: a brief overview. In: Wilbur S.R., and Jackson J.A. (Eds). Vulture Biology and Management (1983), University of California Press, Berkeley, California 26-54
57. Reyes A., Gissi C., Catzeflis F., Nevo E., Pesole G., and Saccone C. Congruent mammalian trees from mitochondrial and nuclear genes using Bayesian methods. Mol. Biol. Evol. 21 (2004) 397-403
58. Ronquist F., and Huelsenbeck J.P. MrBayes3: Bayesian phylogenetic inference under mixed models. Bioinformatics 19 (2003) 1572-1574
59. Seibold I., and Helbig A.J. Evolutionary history of New and Old World vultures inferred from nucleotide sequences of the mitochondrial cytochrome b gene. Phil. Trans. R. Soc. Lond. B 350 (1995) 163-178
60. Sibley C.G., and Ahlquist J.E. Phylogeny and classification of birds (1990), Yale University Press, New Haven, CT
61. 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
62. Slack K.E., Jones C.M., Tatsuro A., Harrison G.L., Fordyce R.E., Arnason U., and Penny D. Early penguin fossils, plus mitochondrial genomes, calibrate avian evolution. Mol. Biol. Evol. 23 (2006) 1144-1155
63. Sorenson M.D., Ast J.C., Dimcheff D.E., Yuri T., and Mindell D.P. Primers for a PCR-based approach to mitochondrial genome sequencing in birds and other vertebrates. Mol. Phylogenet. Evol. 12 (1999) 105-114
64. Steel M.A., and Penny D. Two further links between MP and ML under the Poisson model. Appl. Math Lett. 17 (2004) 785-790
65. * and other methods) (1998), Sinauer Associates Sunderland, Massachusetts
66. Thomas G.H., Wills M.A., and Székely T. Phylogeny of shorebirds, gulls, and alcids (Aves: Charadri) from the cytochrome c gene: parsimony, Bayesian inference, minimum evolution and quartet puzzling. Mol. Phylogenet. Evol. 30 (2004) 516-526
67. Van Tuinen M., Sibley C., and Hedges S.B. The early history of modern birds inferred from DNA sequences of nuclear and mitochondrial ribosomal genes. Mol. Biol. Evol. 17 (2000) 451-457
68. 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