The impact of parsimony weighting schemes on inferred relationships among toucans and Neotropical barbets (Aves: Piciformes)

Molecular Phylogenetics and Evolution

Volumn 15, Issue 2, 2000, Pages 215-234

  Barker, F Keith ^a,b   Lanyon, Scott M ^c  

^a UNIVERSITY OF CHICAGO   (United States)

^b FIELD MUSEUM OF NATURAL HISTORY   (United States)

^c UNIVERSITY OF MINNESOTA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ANDIGENA; ANIMALIA; ARIA; AULACORHYNCHUS; AVES; BAILLONIUS; CAPITONIDAE; PICIFORMES; PTEROGLOSSUS; RAMPHASTIDAE; RAMPHASTOS; SELENIDERA; SEMNORNIS;

EID: 0034079418     PISSN: 10557903     EISSN: None     Source Type: Journal    
DOI: 10.1006/mpev.2000.0752     Document Type: Article

References (81)

1. Albert V. A., Mishler B. D. On the rationale and utility of weighting nucleotide sequence data. Cladistics. 8:1992;73-83.
2. Albert V. A., Chase M. W., Mishler B. D. Character-state weighting for cladistic analysis of protein-coding DNA sequences. Ann. Missouri Bot. Gard. 80:1993;752-766.
3. Aquadro C. F., Kaplan N., Risko K. J. An analysis of the dynamics of mammalian mitochondrial DNA sequence evolution. Mol. Biol. Evol. 1:1984;423-434.
4. Bremer K. Combinable component consensus. Cladistics. 6:1990;369-372.
5. Bremer K. Branch support and tree stability. Cladistics. 10:1994;295-304.
6. Brown W. M., George M. Jr., Wilson A. C. Rapid evolution of animal mitochondrial DNA. Proc. Natl. Acad. Sci. USA. 76:1979;1967-1971.
7. Brown W. M., Prager E. M., Wang A., Wilson A. C. Mitochondrial DNA sequences of primates: Tempo and mode of evolution. J. Mol. Evol. 18:1982;225-239.
8. Bull J. J., Huelsenbeck J. P., Cunningham C. W., Swofford D. L., Waddell P. J. Partitioning and combining data in phylogenetic analysis. Syst. Biol. 42:1993;384-397.
9. Burton P. J. K. Anatomy and evolution of the feeding apparatus in the avian orders Coraciiformes and Piciformes. Bull. Br. Mus. (Nat. Hist.) Zool. 47:1984;331-443.
10. Collins T. M., Kraus F., Estabrook G. Compositional effects and weighting of nucleotide sequences for phylogenetic analysis. Syst. Biol. 43:1994;449-459.
11. Collins T. M., Wimberger P. H., Naylor G. J. P. Compositional bias, character-state bias, and character-state reconstruction using parsimony. Syst. Biol. 43:1994;482-496.
12. Cracraft J. Continental drift, paleoclimatology, and the evolution and biogeography of birds. J. Zool. 169:1973a;455-545.
13. Cracraft J. Vertebrate evolution and biogeography in the Old World Tropics: Implications of continental drift and palaeoclimatology. Tarling D. H., Runcorn S. K. Implications of Continental Drift to the Earth Sciences. 1973b;373-393 Academic Press, New York.
14. Cracraft J., Prum R. O. Patterns and processes of diversification: Speciation and historical congruence in some neotropical birds. Evolution. 42:1988;603-620.
15. Cunningham C. W. Is congruence between data partitions a reliable predictor of phylogenetic accuracy? Empirically testing an iterative procedure for choosing among phylogenetic methods. Syst. Biol. 46:1997;464-478.
16. Desjardins P., 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.
17. Edwards S. V., Arctander P., Wilson A. C. Mitochondrial resolution of a deep branch in the genealogical tree for perching birds. Proc. R. Soc. London B. 243:1991;99-107.
18. Espinosa de los Monteros A. Phylogenetic relationships among the trogons. Auk. 115:1998;937-954.
19. Eyre-Walker A. Problems with parsimony in sequences of biased base composition. J. Mol. Evol. 47:1998;686-690.
20. Faith D. P. Cladistic permutation tests for monophyly and nonmonophyly. Syst. Zool. 40:1991;366-375.
21. Farris J. S. A successive approximations approach to character weighting. Syst. Zool. 18:1969;374-385.
22. Felsenstein J. Evolutionary trees from DNA sequences: A maximum likelihood approach. J. Mol. Evol. 17:1981;368-376.
23. Felsenstein J. Confidence limits on phylogenies: An approach using the bootstrap. Evolution. 39:1985;783-791.
24. Frati F., Simon C., Sullivan J., Swofford D. L. Evolution of the mitochondrial cytochrome oxidase II gene in Collembola. J. Mol. Evol. 44:1997;145-158.
25. Friesen V. L., Baker A. J., Piatt J. F. Phylogenetic relationships within the Alcidae (Charadriiformes: Aves) inferred from total molecular evidence. Mol. Biol. Evol. 13:1996;359-367.
26. Galtier N., Gouy M. Inferring pattern and process: Maximum-likelihood implementation of a nonhomogeneous model of DNA sequence evolution for phylogenetic analysis. Mol. Biol. Evol. 15:1998;871-879.
27. Griffiths C. S. Correlation of functional domains and rates of nucleotide substitution in cytochrome b. Mol. Phylogenet. Evol. 7:1997;352-365.
28. Grimes L. G. Co-operative breeding in African birds. Frith H. J., Calaby J. H. Proceedings of the 16th International Ornithological Congress. 1976;667-673 Australian Academy of Sciences, Canberra.
29. Gu X., Fu Y., Li W.-H. Maximum likelihood estimation of the heterogeneity of substitution rate among nucleotide sites. Mol. Biol. Evol. 12:1995;546-557.
30. Hackett S. J. Molecular phylogenetics and biogeography of tanagers in the genus Ramphocelus (Aves). Mol. Phylogenet. Evol. 5:1996;368-382.
31. Hackett S. J., Lehn C. A. Lack of genetic divergence in a genus (Pteroglossus) of Neotropical birds: The connection between life-history characteristics and levels of genetic divergence. Ornithol. Monogr. 48:1997;267-279.
32. Haffer J. Avian speciation in South America. Publ. Nuttall Ornithol. Club. 14:1974.
33. Harshman J. Reweaving the tapestry: What can we learn from Sibley and Ahlquist (1990). Auk. 111:1994;377-388.
34. Harshman J. Phylogeny, Evolutionary Rates, and Ducks. 1996;Univ. of Chicago.
35. Hasegawa M., Kishino M., Yano T. Dating the human-ape split by a molecular clock of mitochondrial DNA. J. Mol. Evol. 22:1985;160-174.
36. Helm-Bychowski K., Cracraft J. Recovering phylogenetic signal from DNA sequences: Relationships within the corvine assemblage (Class Aves) as inferred from complete sequences of the mitochondrial DNA cytochrome-b gene. Mol. Biol. Evol. 10:1993;1196-1214.
37. Hillis D. M. Approaches for assessing phylogenetic accuracy. Syst. Biol. 44:1995;3-16.
38. Hillis D. M., Bull J. J. An empirical test of bootstrapping as a method for assessing confidence in phylogenetic analysis. Syst. Biol. 42:1993;182-192.
39. Hillis D. M., Huelsenbeck J. P., Cunningham C. W. Application and accuracy of molecular phylogenies. Science. 264:1994;671-677.
40. Huelsenbeck J. P. The robustness of two phylogenetic methods: Four-taxon simulations reveal a slight superiority of maximum likelihood over neighbor joining. Mol. Biol. Evol. 12:1995;843-849.
41. Huelsenbeck J. P., Hillis D. M. Success of phylogenetic methods in the four-taxon case. Syst. Biol. 42:1993;247-264.
42. Huelsenbeck J. P., Rannala B. Phylogenetic methods come of age: Testing hypotheses in an evolutionary context. Science. 276:1997;227-232.
43. Irwin D. M., Kocher T. D., Wilson A. C. Evolution of the cytochrome b gene of mammals. J. Mol. Evol. 32:1991;128-144.
44. Kimura M. A simple method for estimating evolutionary rate of base substitution through comparative studies of nucleotide sequences. J. Mol. Evol. 16:1980;111-120.
45. Kishino H., Hasegawa M. Evaluation of the maximum likelihood estimate of the evolutionary tree topologies from DNA sequence data, and the branching order in Hominoidea. J. Mol. Evol. 29:1989;170-179.
46. Knight A., Mindell D. P. Substitution bias, weighting of DNA sequence evolution, and the phylogenetic position of Fea's viper. Syst. Biol. 42:1993;18-31.
47. Kocher T. D., Thomas W. K., Meyer A., Edwards S. V., Paabo S., Villablanca F. X., 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.
48. Kornegay J. R., Kocher T. D., Williams L. A., Wilson A. C. Pathways of lysozyme evolution inferred from the sequences of cytochrome b in birds. J. Mol. Evol. 37:1993;367-379.
49. Kuhner M. K., Felsenstein J. A simulation comparison of phylogeny algorithms under equal and unequal evolutionary rates. Mol. Biol. Evol. 11:1994;459-468.
50. Lanyon S. M. Phylogenetic frameworks: Towards a firmer foundation for the comparative approach. Biol. J. Linn. Soc. 49:1993;45-61.
51. Lanyon S. M., Hall J. G. Reexamination of barbet monophyly using mitochondrial-DNA sequence data. Auk. 111:1994;389-397.
52. Lanyon S. M., Zink R. M. Genetic variation in Piciform birds: Monophyly and generic and familial relationships. Auk. 104:1987;724-732.
53. Lockhart P. J., Steel M. A., Hendy M. D., Penny D. Recovering evolutionary trees under a more realistic model of sequence evolution. Mol. Biol. Evol. 12:1994;605-612.
54. Maddison, W. P, and, Maddison, D. R. 1993, MacClade: Analysis of phylogeny and character evolution, Version 3.05, Sinauer, Sunderland, MA.
55. Meyer A. Shortcomings of the cytochrome b gene as a molecular marker. Trends Ecol. Evol. 9:1994;278-280.
56. Milinkovitch M. C., LeDuc R. G., Adachi J., Farnir F., Georges M., Hasegawa M. Effects of character weighting and species sampling on phylogeny reconstruction: A case study based on DNA sequence data in Cetaceans. Genetics. 144:1996;1817-1833.
57. Miyaki C. Y., Matioli S. R., Burke T., Wajntal A. Parrot evolution and paleogeographical events: Mitochondrial DNA evidence. Mol. Biol. Evol. 15:1998;544-551.
58. Miyamoto M. M., Allard M. W., Adkins R. M., Janacek L. L., Honeycutt R. L. A congruence test of reliability using linked mitochondrial DNA sequences. Syst. Biol. 43:1994;236-249.
59. Moore W. S., DeFilippis D. R. The window of taxonomic resolution for phylogenies based on mitochondrial cytochrome b. Mindell D. P. Avian Molecular Evolution and Systematics. 1997;83-119 Academic Press, San Diego.
60. Neff N. A. A rational basis for a priori character weighting. Syst. Zool. 35:1986;110-123.
61. Nunn G. B., Cracraft J. Phylogenetic relationships among the major lineages of the birds-of-paradise (Paradisaeidae) using mitochondrial DNA gene sequences. Mol. Phylogenet. Evol. 5:1996;445-459.
62. Peters J. L. Check-List of Birds of the World. 1948;Harvard Univ. Press, Cambridge.
63. Prum R. O. Phylogenetic interrelationships of the barbets (Aves: Capitonidae) and toucans (Aves: Ramphastidae) based on morphology with comparisons to DNA-DNA hybridization. Zool. J. Linn. Soc. 92:1988;313-343.
64. Reeder T. W. Phylogenetic relationships among Phrynosomatid lizards as inferred from mitochondrial ribosomal DNA sequences: Substitutional bias and information content of transitions relative to transversions. Mol. Phylogenet. Evol. 4:1995;203-222.
65. Restrepo C., Mondragón M. L. Cooperative breeding in the frugivorous toucan barbet (Semnornis ramphastinus). Auk. 115:1998;4-15.
66. Rodrigo A. G. A modification to Wheeler's combinatorial weights calculations. Cladistics. 8:1992;165-170.
67. Saitou N., Nei M. The neighbor-joining method: A new method for reconstructing phylogenetic trees. Mol. Biol. Evol. 4:1987;406-425.
68. Sanderson M. Confidence limits on phylogenies: The bootstrap revisited. Cladistics. 5:1989;113-130.
69. Schöniger M., von Haeseler A. Performance of the maximum likelihood, neighbor joining, and maximum parsimony methods when sequence sites are not independent. Syst. Biol. 44:1995;533-547.
70. Sibley C. G., Ahlquist J. E. Phylogeny and Classification of Birds. 1990;Yale Univ. Press, New Haven.
71. Simpson S. F., Cracraft J. The phylogenetic relationships of the Piciformes (Class Aves). Auk. 98:1981;481-494.
72. Skutch A. F. Roosting and nesting of araçari toucans. Condor. 60:1958;201-219.
73. Smith A. B. Rooting molecular trees: Problems and strategies. Biol. J. Linn. Soc. 51:1994;279-292.
74. Swierczewski E. V., Raikow R. J. Hind limb morphology, phylogeny, and classification of the Piciformes. Auk. 98:1981;466-480.
75. Templeton A. R. Phylogenetic inference from restriction endonuclease cleavage site maps with particular reference to the evolution of humans and apes. Evolution. 37:1983;221-244.
76. Vuilleumier F., Andors A. V. Avian biological relationships between Africa and South America. Goldblatt P. Biological Relationships between Africa and South America. 1993;289-328 Yale Univ. Press, New Haven.
77. Wheeler Q. D. Character weighting and cladistic analysis. Syst. Zool. 35:1986;102-109.
78. Wheeler W. C. Combinatorial weights in phylogenetic analysis: A statistical parsimony procedure. Cladistics. 6:1990;269-275.
79. Williams P. L., Fitch W. M. Finding the minimal change in a given tree. Fernholm B. The Hierarchy of Life. 1989;453-470 Elsevier Press, Amsterdam.
80. Yang Z. Estimating the pattern of nucleotide substitution. J. Mol. Evol. 39:1994;105-111.
81. Yang Z., Roberts D. On the use of nucleic acid sequences to infer early branchings in the tree of life. Mol. Biol. Evol. 12:1995;451-458.