Phylogenetics of the common raven complex (Corvus: Corvidae) and the utility of ND4, COI and intron 7 of the β-fibrinogen gene in avian molecular systematics

Zoologica Scripta

Volumn 34, Issue 2, 2005, Pages 145-156

  Feldman, Chris R ^a   Omland, Kevin E ^b  

^a UTAH STATE UNIVERSITY   (United States)

^b UNIVERSITY OF MARYLAND BALTIMORE COUNTY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 14844286493     PISSN: 03003256     EISSN: None     Source Type: Journal    
DOI: 10.1111/j.1463-6409.2005.00182.x     Document Type: Article

References (98)

1. Alamargot, J. (1987). Pied crows Corvus albus with atypical plumage. Walia, 10, 7-12.
2. Allen, E. S. & Omland, K. E. (2003). Novel intron phylogeny supports plumage convergence in orioles (Icterus). Auk, 120, 961-969.
3. Arevalo, E., Davis, S. K. & Sites, J. W. (1994). Mitochondrial DNA sequence divergence and phylogenetic relationships among eight chromosome races of the Sceloporus grammicus complex (Phrynosomatidae) in central Mexico. Systematic Biology, 43, 387-418.
4. Ash, J. S. (1983). Over fifty additions of birds to the Somalia list including two hybrids, together with notes from Ethiopia and Kenya. Scopus, 7, 54-79.
5. Ashton, K. G. (2002). Patterns of within-species body size variation of birds: strong evidence for Bergmann's rule. Global Ecology and Biogeography, 11, 505-523.
6. Avise, J. C. (2004). Molecular Markers, Natural History and Evolution. Sunderland, MA: Sinauer Associates.
7. Avise, J. C., Ankney, C. D. & Nelson, W. S. (1990). Mitochondrial gene trees and the evolutionary relationship between mallard and black ducks. Evolution, 44, 1109-1119.
8. Blair, C. M. G. (1961). Hybridization of Corvus albus and Corvus edithae in Ethiopia. Ibis, 103, 499-502.
9. Boarman, W. I. & Heinrich, B. (1999). Common raven (Corvus corax). In A. Poole & F. Gill (Eds) The Birds of North America. Washington, DC and Philadelphia: The American Ornithologists' Union and the Academy of Natural Sciences.
10. Bremer, K. (1994). Branch support and tree stability. Cladistics, 10, 295-304.
11. Cibois, A. & Pasquet, E. (1999). Molecular analysis of the phylogeny of 11 genera of the Corvidae. Ibis, 141, 297-306.
12. Cicero, C. & Johnson, N. K. (2001). Higher-level phylogeny of New World vireos (Aves: Vireonidae) based on sequences of multiple mitochondrial DNA genes. Molecular Phylogenetics and Evolution, 20, 27-40.
13. Cicero, C. & Johnson, N. K. (2002). Phylogeny and character evolution in the Empidonax group of tyrant flycatchers (Aves: Tyranidae): a test of W. E. Lanyon's hypothesis using mtDNA sequences. Molecular Phylogenetics and Evolution, 22, 289-302.
14. Cracraft, J. (1983). Species concepts and speciation analysis. In R. F. Johnston (Ed.) Current Ornithology (pp. 159-187). New York: Plenum Press.
15. Edwards, S. V., Arctander, P. & Wilson, A. C. (1991). Mitochondrial resolution of a deep branch in the genealogical tree for perching birds. Proceedings of the Royal Society, Biological Sciences, Series B, 243, 99-107.
16. Engstrom, T. N., Shaffer, H. B. & McCord, W. P. (2002). Phylogenetic diversity of endangered and critically endangered southeast Asian softshell turtles (Trionychidae: Chitra). Biological Conservation, 104, 173-179.
17. Farris, J. S. (1983). The logical basis of phylogenetic analysis. In N. Platnick & V. A. Funk (Eds) Advances in Cladistics (pp. 7-36). New York: Columbia University Press.
18. Feldman, C. R. & Spicer, G. S. (2002). Mitochondrial variation in sharp-tailed snakes (Contia tenuis): evidence of a cryptic species. Journal of Herpetology, 36, 648-655.
19. Felsenstein, J. (1978). Cases in which parsimony and compatibility methods will be positively misleading. Systematic Zoology, 27, 401-410.
20. Felsenstein, J. (1981). Evolutionary trees from DNA sequences: a maximum likelihood approach. Journal of Molecular Evolution, 17, 368-376.
21. Felsenstein, J. (1985). Confidence limits on phylogenies: an approach using the bootstrap. Evolution, 39, 783-791.
22. Felsenstein, J. (1993). Phylip (Phylogentic Inference Package). Seattle: Department of Genetics, University of Washington.
23. Fleischer, R. C. & McIntosh, C. E. (2001). Molecular systematics and biogeography of the Hawiian avifauna. Studies in Avian Biology, 22, 51-60.
24. Fleischer, R. C., McIntosh, C. E. & Tarr, C. L. (1998). Evolution on a volcanic conveyor belt: using phylogeographic reconstructions and K-Ar-based ages of the Hawaiian Islands to estimate molecular evolutionary rates. Molecular Ecology, 7, 533-545.
25. Folmer, O., Black, M., Hoeh, W., Lutz, R. & Vrijenhoek, R. (1994). DNA primers for amplification of mitochondrial cytochrome c oxidase subunit I from diverse metazoan invertebrates. Molecular Marine Biology and Biotechnology, 3, 294-299.
26. Funk, D. J. & Omland, K. E. (2003). Species-level paraphyly and polyphyly: frequency, causes, and consequences, with insights from animal mitochondrial DNA. Annual Review of Ecology and Systematics, 34, 397-423.
27. Gill, F. B., Slikas, B. & Argo, D. (1999). Speciation in North American chickadees: II. Geography of mtDNA haplotypes in Poecile carolinensis. Auk, 116, 274-277.
28. Goldman, N. (1993). Statistical tests of models of DNA substitution. Journal of Molecular Evolution, 63, 182-198.
29. Goodwin, D. (1986). Crows of the World. Seattle: University of Washington Press.
30. Graur, D. & Martin, W. (2004). Reading the entrails of chickens: molecular timescales of evolution and the illusion of precision. Trends in Genetics, 20, 80-86.
31. Graybeal, A. (1993). The phylogenetic utility of cytochrome b: lessons from bufonid frogs. Molecular Phylogenetics and Evolution, 2, 256-269.
32. Graybeal, A. (1994). Evaluating the phylogenetic utility of genes: a search for genes informative about deep divergences among vertebrates. Systematic Biology, 43, 174-193.
33. Griffiths, C. S. (1997). Correlation of functional domains and rates of nucleotide substitution in cytochrome b. Molecular Phylogenetics and Evolution, 7, 352-365.
34. Gu, X., Fu, Y. & Li, W.-H. (1995). Maximum likelihood estimation of the heterogeneity of substitution rate among nucleotide sites. Molecular Biology and Evolution, 12, 546-557.
35. Hackett, J. J. (1996). Molecular phylogenetics and biogeography of tanagers in the genus Ramphocelus (Aves). Molecular Phylogenetics and Evolution, 5, 368-382.
36. Härlid, A. & Arnason, U. (1999). Analyses of mitochondrial DNA nest ratite birds within the Neognathae: supporting a neotenous origin of ratite morphological characters. Proceedings of the Royal Society, Biological Sciences, Series B, 266, 305-309.
37. Hasegawa, M., Kishino, K. & Yano, T. (1985). Dating of the human-ape splitting by a molecular clock of mitochondrial DNA. Journal of Molecular Evolution, 21, 160-174.
38. Heinrich, B. (1989). Ravens in Winter. New York: Simon & Schuster.
39. Heinrich, B. (1999). Mind of the Ravens: Investigations and Adventures with Wolf-Birds. New York: Cliff Street Books.
40. Heinrich, B. & Marzluff, J. M. (1995). Why ravens share. American Scientist, 83, 342-349.
41. Heinrich, B. & Smolker, M. (1998). Raven play. In M. Bekoff & J. A. Byers (Eds) Animal Play: Evolutionary, Comparative, and Ecological Aspects. Cambridge: Cambridge University Press.
42. Hendy, M. D. & Penny, D. (1982). Branch and bound algorithms to determine minimal evolutionary trees. Mathematical Biosciences, 59, 277-290.
43. Hillis, D. M., Mable, B. K. & Moritz, C. (1996). Applications of molecular systematics: the state of the field and a look to the future. In D. M. Hillis, C. Moritz & B. K. Mable (Eds) Molecular Systematics (pp. 515-543). Sunderland, MA: Sinauer Associates.
44. Huelsenbeck, J. P. & Hillis, D. M. (1993). Success of phylogenetic methods in the four-taxon case. Systematic Biology, 42, 247-264.
45. Huelsenbeck, J. P. & Ronquist, F. (2001). MrBayes: Bayesian inference of phylogenetic trees. Bioinformatics, 17, 754-755
46. Hunt, G. R. & Gray, R. D. (2003). Diversification and cumulative evolution in New Caledonian crow tool manufacture. Proceedings of the Royal Society, Biological Sciences, Series B, 270, 867-874.
47. Johnson, K. P. & Clayton, D. H. (2000). A molecular phylogeny of the dove genus Zenaida. Condor, 102, 864-870.
48. Jollie, M. (1978). Phylogeny of the species of Corvus. Biologist, 60, 73-108.
49. Klicka, J. & Zink, R. M. (1997). The importance of recent ice ages in speciation: a failed paradigm. Science, 227, 1666-1669.
50. Kocher, T. D., Thomas, W. K., Meyer, A., Edwards, S. V., Paabo, S., Villablanca, F. X. & Wilson, A. C. (1989). Dynamics of mitochondrial DNA evolution in mammals: amplification and sequencing with conserved primers. Proceedings of the National Academy of Sciences of the USA, 86, 6196-6200.
51. Kryukov, A. P. & Suzuki, H. (2000). Phylogeography of carrion, hooded, and jungle crows (Aves, Corvidae) inferred from partial sequencing of the mitochondrial DNA cytochrome b gene. Genetika, 36, 1111-1118.
52. Kumazawa, Y. & Nishida, M. (1993). Sequence evolution of mitochondrial tRNA genes and deep-branch animal phylogenetics. Journal of Molecular Evolution, 37, 380-398.
53. Kumazawa, Y. & Nishida, M. (1995). Variations in mitochondrial tRNA gene organization of reptiles as phylogenetic markers. Molecular Biology and Evolution, 12, 759-772.
54. Larget, B. & Simon, D. L. (1999). Markov chain Monte Carlo algorithms for the Bayesian analysis of phylogenetic trees. Molecular Biology and Evolution, 16, 750-759.
55. Leaché, A. D. & Reeder, T. W. (2002). Molecular systematics of the eastern fence lizard (Sceloporus undulatus): a comparison of parsimony, likelihood, and Bayesian approaches. Systematic Biology, 51, 44-68.
56. Macey, J. R. & Vernia, A. (1997). Homology in phylogenetic analysis: alignment of transfer RNA genes and the phylogenetic position of snakes. Molecular Phylogenetics and Evolution, 7, 272-279.
57. Maddison, D. R. & Maddison, W. P. (2000). Matclade: Analysis of Phylogeny and Character Evolution. Sunderland, MA: Sinauer Associates.
58. Madge, S. & Burn, H. (1994). Crows and Ravens. Boston: Houghton Mifflin Company.
59. Martin, A. P., Kessing, B. D. & Palumbi, S. R. (1990). Accuracy of estimating genetic distance between species from short sequences of mitochondrial DNA. Molecular Biology and Evolution, 7, 485-488.
60. Mayr, E. (1963). Animal Species and Evolution. Cambridge: Belknap Press.
61. Meyer, A. (1994). The shortcomings of the cytochrome b gene as a molecular marker. Trends in Ecology and Evolution, 9, 278-280.
62. Moore, W. S. & DeFilippis, V. R. (1997). The window of taxonomic resolution for phylogenies based on mitochondria cytochrome b. In D. P. Mindell (Ed.) Avian Molecular Evolution and Systematics (pp. 84-120). San Diego: Academic Press.
63. Omland, K. E. (1997). Examining two standard assumptions of ancestral reconstructions: repeated loss of dimorphism in dabbling ducks (Anatini). Evolution, 51, 1636-1646.
64. Omland, K. E., Lanyon, S. M. & Fritz, S. J. (1999). A molecular phylogeny of the New World orioles (Icterus): the importance of dense taxon sampling. Molecular Phylogenetics and Evolution, 12, 224-239.
65. Omland, K. E., Tarr, C. L., Boarman, W. I., Marzluff, J. M. & Fleischer, R. C. (2000). Cryptic genetic variation and paraphyly in ravens. Proceedings of the Royal Society, Biological Sciences, Series B, 267, 2475-2482.
66. Parham, J. F., Simison, W. B., Kozak, K. H., Feldman, C. R. & Shi, H. (2001). New Chinese turtles: endangered or invalid? A reassessment of two species using mitochondrial DNA, allozyme electrophoresis, and known locality specimens. Animal Conservation, 4, 357-367.
67. Patton, J. L. & Smith, M. F. (1994). Paraphyly, polyphyly, and the nature of species boundaries in pocket gophers (genus Thomomys). Systematic Biology, 43, 11-26.
68. Paxinos, E. E., James, H. F., Olson, S. L., Sorenson, M. D., Jackson, J. & Fleischer, R. C. (2002). mtDNA from fossils reveals a radiation of Hawaiian geese recently derived from the Canada goose (Branta canadensis). Proceedings of the National Academy of Sciences of the USA, 99, 1399-1404.
69. Posada, D. & Crandall, K. A. (1998). Modeltest: testing the model of DNA substitution. Bioinformatics, 14, 817-818.
70. Prychitko, T. M. & Moore, W. S. (1997). The utility of DNA sequences of an intron from the β-fibrinogen gene in phylogenetic analysis of woodpeckers (Aves: Picidae). Molecular Phylogenetics and Evolution, 8, 193-204.
71. Prychitko, T. M. & Moore, W. S. (2000). Comparative evolution of the mitochondrial cytochrome b gene and nuclear β-fibrinogen intron 7 in woodpeckers. Molecular Biology and Evolution, 17, 1101-1111.
72. Prychitko, T. M. & Moore, W. S. (2003). Alignment and phylogenetic analysis of β-fibrinogen intron 7 sequences among avian orders reveal conserved regions within the intron. Molecular Biology and Evolution, 20, 762-771.
73. de Queiroz, K. (1998). The general lineage concept of species, species criteria, and the process of speciation: a conceptual unification and terminological recommendations. In D. J. Howard & S. H. Berlocher (Eds) Endless Forms: Species and Speciation (pp. 57-75). New York: Oxford University Press.
74. Rambaut, A. & Drummond, A. (2003). Tracer: MCMC Trace Analysis Tool. Oxford: University of Oxford.
75. Rand, D. M. (1994). Thermal habit, metabolic rate and the evolution of mitochondrial DNA. Trends in Ecology and Evolution, 9, 125-131.
76. Raxworthy, C. J., Forstner, M. R. J. & Nussbaum, R. A. (2002). Chameleon radiation by oceanic dispersal. Nature, 415, 784-787.
77. Rodriguez, F., Oliver, J. L., Marin, A. & Medina, J. R. (1990). The general stochastic model of nucleotide substitution. Journal of Theoretical Biology, 142, 485-501.
78. Saiki, R. K., Gelfand, D. H., Stoffel, S., Scharf, S. J., Higuchi, R. G., Horn, T. T., Mullis, K. B. & Erlich, H. A. (1988). Primer directed enzymatic amplification of DNA with a thermostable DNA polymerase. Science, 239, 487-491.
79. Sanger, F., Nicklen, S. & Coulson, A. R. (1977). DNA sequencing with chain-terminating inhibitors. Proceedings of the National Academy of Sciences of the USA, 74, 5463-5467.
80. Shimodaira, H. & Hasegawa, M. (1999). Multiple comparisons of log-likelihoods with applications to phylogenetic inference. Molecular Biology and Evolution, 16, 1114-1116.
81. Slowinski, J. B. & Arbogast, B. (1999). Is the rate of molecular evolution inversely related to body size? Systematic Biology, 48, 396-399.
82. Sokal, R. R. & Rohlf, F. J. (1995). Biometry, the Principles and Practice of Statistics in Biology Research, 3rd edn. New York: W.H. Freeman.
83. Sorenson, M. D. (1999). Treerot. Boston: Boston University.
84. Swofford, D. L. (2002). PAUP*: Phylogenetic Analysis Using Parsimony (*and Other Methods). Sunderland, MA: Sinauer Associates.
85. Tamura, K. & Nei, M. (1993). Estimation of the number of nucleotide substitutions in the control region of mitochondrial DNA in humans and chimpanzees. Molecular Biology and Evolution, 10, 512-526.
86. Tarr, C. L. (1995). Primers for amplification and determination of mitochondrial control-region sequences in oscine passerines. Molecular Ecology, 4, 527-529.
87. Tarr, C. L. & Fleischer, R. C. (1999). Population boundaries and genetic diversity in the endangered Mariana crow (Corvus kubaryi). Molecular Ecology, 8, 941-950.
88. Templeton, A. R. (1983). Phylogenetic inference from restriction endonuclease cleavage site maps with particular reference to the evolution of humans and the apes. Evolution, 37, 221-244.
89. van Tuinen, M. & Hedges, S. B. (2001). Calibration of avian molecular clocks. Molecular Biology and Evolution, 18, 206-213.
90. Vaurie, C. (1954). Systematic notes on Palearctic birds, 5. American Museum Novitates, 1668, 1-23.
91. Weibel, A. C. & Moore, W. S. (2002a). Molecular phylogeny of a cosmopolitan group of woodpeckers (genus Picoides) based on COI and cyt b mitochondrial gene sequences. Molecular Phylogenetics and Evolution, 22, 65-77.
92. Weibel, A. C. & Moore, W. S. (2002b). A test of mitochondrial gene-based phylogeny of woodpeckers (genus Picoides) using an independent nuclear gene, β-fibrinogen intron 7. Molecular Phylogenetics and Evolution, 22, 247-257.
93. Wilgenbusch, J. & de Queiroz, K. (2000). Phylogenetic relationships among the phrynosomatid sand lizards inferred from mitochondrial DNA sequences generated by heterogeneous evolutionary processes. Systematic Biology, 49, 592-612.
94. Willett, G. (1941). Variation in North American ravens. Auk, 58, 246-249.
95. Yang, Z. (1994a). Estimating patterns of nucleotide substitution. Journal of Molecular Evolution, 39, 105-111.
96. Yang, Z. (1994b). Maximum likelihood phylogenetic estimation from DNA sequences with variable rates over sites: approximate methods. Journal of Molecular Evolution, 39, 306-314.
97. Yang, Z. (1996). Maximum likelihood models for combined analyses of multiple sequence data. Journal of Molecular Evolution, 42, 587-596.
98. Zink, R. M. & Blackwell, R. C. (1998). Molecular systematics and biogeography of aridland gnatcatchers (genus Polioptila) and evidence supporting species status of the California gnatcatcher (Polioptila californica). Molecular Phylogenetics and Evolution, 9, 26-32.