Mitochondrial and nuclear DNA sequences support a cretaceous origin of columbiformes and a dispersal-driven radiation in the paleogene

Systematic Biology

Volumn 56, Issue 4, 2007, Pages 656-672

  Pereira, Sergio L ^a   Johnson, Kevin P ^b   Clayton, Dale H ^c   Baker, Allan J ^a,d  

^a DEPARTMENT OF NATURAL HISTORY   (Canada)

^b UNIVERSITY OF ILLINOIS   (United States)

^c UNIVERSITY OF UTAH   (United States)

^d UNIVERSITY OF TORONTO   (Canada)

Author keywords

Columbiformes; Dispersal; Divergence times; Doves; Fossil; K T boundary; Molecular phylogeny; Pigeons

Indexed keywords

APODIFORMES; AVES; CAPRIMULGIFORMES; COLUMBA; COLUMBIDAE; COLUMBIFORMES; COLUMBINA; GALLIFORMES; MYADESTES; PALAEOGNATHAE; PASSERIFORMES; PSITTACIDAE; RAPHIDAE; RAPHUS CUCULLATUS; SPHENISCIDAE; TINAMIFORMES;

MITOCHONDRIAL DNA;

ANIMAL; ARTICLE; CELL NUCLEUS; CLASSIFICATION; GENETICS; GEOLOGY; MOLECULAR EVOLUTION; PIGEONS AND DOVES; POPULATION DYNAMICS; TIME;

ANIMALS; CELL NUCLEUS; COLUMBIFORMES; DNA, MITOCHONDRIAL; EVOLUTION, MOLECULAR; GEOLOGY; POPULATION DYNAMICS; TIME FACTORS;

EID: 34948817510     PISSN: 10635157     EISSN: 1076836X     Source Type: Journal    
DOI: 10.1080/10635150701549672     Document Type: Article

References (83)

1. Baker, A. J., S. L. Pereira, O. P. Haddrath, and E. K.-A. 2006. Multiple gene evidence for expansion of extant penguins out of Antarctica due to global cooling. Proc. R. Soc. Lond. B 273:11-17. (Pubitemid 46768038)
2. Baker, A. J., S. L. Pereira, and T. A. Paton. 2007. Phylogenetic relationships and divergence times of Charadriiformes genera: Multigene evidence for the Cretaceous origin of at least 14 clades of shorebirds. Biol. Lett. 3:205-209. (Pubitemid 351878154)
3. Banks, R. C, C. Cicero, J. L. Dunn, A. W. Kratter, P. C. Rasmussen, J. V. Remsen Jr., J. D. Rising, and D. F. Stotz. 2003. Forty-fourth supplement to the American Ornithologists' Union check-list of North American birds. Auk 120:923-931. (Pubitemid 37029543)
4. Barker, F. K., A. Cibois, P. Schikler, J. Feinstein, and J. Cracraft. 2004. Phylogeny and diversification of the largest avian radiation. Proc. Natl. Acad. Sci. USA 101:11040-11045. (Pubitemid 38992336)
5. Bollback, J. P. 2006. SIMMAP: Stochastic character mapping of discrete traits on phylogenies. BMC Bioinformatics 7:88.
6. Brodkorb, P. 1964. Catalogue of fossil birds, part 2 (Anseriformes through Galliformes). Bull Florida State Mus. Biol. Sci 8:195-335.
7. Bumby, A. J., and R. Guiraud. 2005. The geodynamic setting of the Phanerozoic basins of Africa. J. Afr. Earth Sci. 43:1-12. (Pubitemid 43024639)
8. Chiappe, L. M., and G. J. Dyke. 2002. The Mesozoic radiation of birds. Annu. Rev. Ecol. Syst. 33:91-124. (Pubitemid 36035137)
9. Clarke, J. A., C. P. Tambussi, J. I. Noriega, G. M. Erickson, and R. A. Ketcham. 2005. Definitive fossil evidence for the extant avian radiation in the Cretaceous. Nature 433:305-308.
10. Cooper, A., and D. Penny. 1997. Mass survival of birds across the Cretaceous-Tertiary boundary: Molecular evidence. Science 275:1109-1113.
11. Cracraft, J. 2001. Avian evolution, Gondwana biogeography and the Cretaceous-Tertiary mass extinction event. Proc. R. Soc. Lond. B 268:459-469. (Pubitemid 32257889)
12. Crowe, T. M., R. C. Bowie, P. Bloomer, T. G. Mandiwana, T. A. J. Hedderson, E. Randi, S. L. Pereira, and J. Wakeling. 2006. Phylogenetics, biogeography and classification of, and character evolution in, gamebirds (Aves: Galliformes): Effects of character exclusion, data partitioning and missing data. Cladistics 22:495-532. (Pubitemid 44915871)
13. Darwin, C. 1859. On the origin of species by means of natural selection or the preservation of favoured races on the struggle for life. John Murray, London.
14. Dyke, G. J. 2001. The evolutionary radiation of modern birds: Systematics and patterns of diversification. Geol. J. 36:305-315. (Pubitemid 32956530)
15. Dyke, G. J., and M. Van Tuinen. 2004. The evolutionary radiation of modern birds (Neornithes): Reconciling molecules, morphology and the fossil record. Zool. J. Linn. Soc. 141:153-177. (Pubitemid 38847565)
16. Ericson, P. G., C. L. Anderson, T. Britton, A. Elzanowski, U. S. Johansson, M. Kallersjo, J. I. Ohlson, T. J. Parsons, D. Zuccon, and G. Mayr. 2006. Diversification of Neoaves: Integration of molecular sequence data and fossils. Biol. Lett. 2:543-547. (Pubitemid 44935427)
17. Gibbs, D., E. Barnes, and J. Cox. 2001. Pigeons and Doves. A guide to the pigeons and doves of the world. Pica Press, East Sussex, UK.
18. Goodwin, D. 1983. Pigeons and doves of the world, 3rd. edition. Cornstock Publishing Associates, Ithaca, NY.
19. Gradstein, F. M., J. G. Ogg, A. G. Smith, F. P. Agterberg, W. Bleeker, R. A. Cooper, V. Davydov, P. Gibbard, L. A. Hinnov, M. R. House, L. Lourens, H. P. Luterbacher, J. McArthur, M. J. Melchin, L. J. Robb, J. Shergold, M. Villeneuve, B. R. Wardlaw, J. Ali, H. Brinkhuis, F. J. Hilgen, J. Hooker, R. J. Howarth, A. H. Knoll, J. Laskar, S. Monechi, K. A. Plumb, J. Powell, I. Raffi, U. Rohl, P. Sadler, A. Sanfilippo, B. Schmitz, N. J. Shackleton, G. A. Shields, H. Strauss, J. Van Dam, T. van Kolfschoten, J. Veizer, and D. Wilson. 2004. A geologic time scale 2004. Cambridge University Press, Cambridge, UK.
20. Groth, J. G., and G. F. Barrowclough. 1999. Basal divergences in birds and the phylogenetic utility of the nuclear RAG-1 gene. Mol. Phylogenet. Evol. 12:115-123. (Pubitemid 129499294)
21. Guindon, S., and O. Gascuel. 2003. A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. Syst. Biol. 52:696-704. (Pubitemid 37365050)
22. Haddrath, O., and A. J. Baker. 2001. Complete mitochondrial DNA genome sequences of extinct birds: Ratite phylogenetics and the vicariance biogeography hypothesis. Proc. R. Soc. Lond. B 268:939- 945. (Pubitemid 32453384)
23. Hall, R. 1998. The plate tectonics of Cenozoic SE Asia and the distribution of land and sea. Pages 99-131 in Biogeography and geological evolution of SE Asia (R. Hall and J. D. Holloway, eds.). Backhuys Publishers, Leiden, The Netherlands.
24. Hall, R. 2001. Cenozoic reconstructions of SE Asia and the SW Pacific: Changing patterns of land and sea. Pages 35-56 in Faunal and floral migrations and evolution in SE Asia-Australasia (I. Metcalfe, J. M. B. Smith, M. Morwood, and I. D. Davidson, eds.). Swets & Zeitlinger Publishers, Lisse.
25. Haq, B. U., J. Hardenbol, and P. R. Vail. 1987. Chronology of fluctuating sea levels since the Triassic. Science 235:1156-1167. (Pubitemid 17263665)
26. Hasegawa, M., H. Kishino, and T. Yano. 1985. Dating of the human-ape splitting by a molecular clock of mitochondrial DNA. J. Mol. Evol. 22:160-174. (Pubitemid 16227864)
27. Hedges, S. B., P. H. Parker, C. G. Sibley, and S. Kumar. 1996. Continental breakup and the ordinal diversification of birds and mammals. Nature 381:226-9.
28. Huelsenbeck, J. P., R. Nielsen, and J. P. Bollback. 2003. Stochastic mapping of morphological characters. Syst. Biol. 52:131-158. (Pubitemid 36599273)
29. Johnson, K. P. 2004. Deletion bias in avian introns over evolutionary timescales. Mol. Biol. Evol. 21:599-602. (Pubitemid 38339675)
30. Johnson, K. P., and D. H. Clayton. 2000. Nuclear and mitochondrial genes contain similar phylogenetic signal for pigeons and doves (Aves: Columbiformes). Mol. Phylogenet. Evol. 14:141-51. (Pubitemid 30457820)
31. Johnson, K. P., S. de Kort, K. Dinwoodey, A. C. Mateman, C. ten Cate, C. M. Lessells, and D. H. Clayton. 2001. A molecular phylogeny of the dove genera Streptopelia and Columba. Auk 118:874-887. (Pubitemid 33132827)
32. Kishino, H., J. L. Thorne, and W. J. Bruno. 2001. Performance of a divergence time estimation method under a probabilistic model of rate evolution. Mol. Biol. Evol. 18:352-361. (Pubitemid 32225084)
33. Kroepelin, S. 2006. Revisiting the age of the Sahara Desert (letters). Science 312:1138. (Pubitemid 43801121)
34. Ksepka, D. T, S. Bertelli, and N. P. Giannini. 2006. The phylogeny of the living and fossil Sphenisciformes (penguins). Cladistics 22:412- 441. (Pubitemid 44423504)
35. Lewis, P. O. 2001. A likelihood approach to estimating phylogeny from discrete morphological character data. Syst. Biol. 50:913- 925.
36. Li, Z. X., and C. M. Powell. 2001. An outline of the palaeogeographic evolution of the Australasian region since the beginning of the Neoproterozoic. Earth-Sci. Rev. 53:237-277. (Pubitemid 32477750)
37. Livezey, B. C. 1997. A phylogenetic analysis of basal Anseriformes, the fossil Prcsbyomis, and the interordinal relationships of waterfowl. Zool. J. Linn. Soc. 121:361-428.
38. Livezey, B. C, and R. L. Zusi. 2007. Higher-order phylogeny of modern birds (Theropoda, Aves: Neornithes) based on comparative anatomy. II. Analysis and discussion. Zool. J. Linn. Soc. 149:1-95. (Pubitemid 46084798)
39. Lundberg, J. G., L. G. Marshall, J. Guerrero, B. Horton, M. C. S. L. Malabarba, and F. Wesselingh. 1998. The stage for Neotropical fish diversification: A history of tropical South American rivers. Pages 13-48 in Phylogeny and classification of neotropical fishes (L. R. Malabarba, R. E. Reis, R. P. Vari, Z. M. S. Lucena, and C. A. S. Lucena, eds.). Editora Universitaria PUCRS, Porto Alegre, Brazil.
40. MacFadden, B. J. 2000. Cenozoic mammalian herbivores from the Americas: Reconstructing ancient diets and terrestrial communities. Annu. Rev. Ecol. Syst. 31:33-59. (Pubitemid 32122394)
41. Maddison, D. R., and W. P. Maddison. 2000. MacClade 4.0. Sinauer Associates, Sunderland, Massachusetts.
42. Maddison, W. P., and D. R. Maddison. 2005a. Mesquite: A modular system for evolutionary analysis, version 1.06. http://mesquiteproject.org.
43. Maddison, W. P., and D. R. Maddison. 2005b. Stochar: A package of Mesquite modules for stochastic models of character evolution, version 1.06. http://mesquiteproject.org.
44. McDougall, I., and F. H. Chamalaun. 1969. Isotopic dating and geomagnetic polarity studies on volcanic rocks from Mauritius, Indian Ocean. Geol. Soc. Am. Bull. 80:419-442.
45. Moss, S. J., and M. E. J. Wilson. 1998. Biogeographic implications of the Tertiary palaeoeographic evolution of Sulawesi and Borneo. Pages 133-163 in Biogeography and geological evolution of SE Asia (R. Hall and J. D. Holloway, eds.). Backhuys Publishers, Leiden, The Netherlands.
46. Moyle, R. 2005. Phylogeny and biogeographical history of Trogoniformes, a pantropical bird order. Biol. J. Linn. Soc. 84:725- 738.
47. Nahum, L. A., S. L. Pereira, F. M. D. Fernandes, S. R. Matioli, and A. Wajntal. 2003. Diversification of Ramphastinae (Aves, Ramphastidae) prior to the Cretaceous/Tertiary boundary as shown by molecular clock of mtDNA sequences. Genet. Mol. Biol. 26:411- 418. (Pubitemid 38054859)
48. Nores, M. 2004. The implications of Tertiary and Quaternary sea level rise events for avian distribution patterns in the lowlands of northern South America. Global Ecol. Biogeogr. 13:149-161.
49. Nylander, J. A. 2004. MrModelTest 2.0. Program distributed by the author. Evolutionary Biology Centre, Uppsala University.
50. Olson, S. L. (ed.) 1985. The fossil record of birds. Academic Press, New York.
51. Padian, K., and L. M. Chiappe. 1998. The origin and early evolution of birds. Biol. Rev. 73:1-42. (Pubitemid 28140311)
52. Paton, T. A., A. J. Baker, J. G. Groth, and G. F. Barrowclough. 2003. RAG- 1 sequences resolve phylogenetic relationships within Charadriiform birds. Mol. Phylogenet. Evol. 29:268-278. (Pubitemid 38370215)
53. Pereira, S. L., and A. J. Baker. 2004. Vicariant speciation of curassows (Aves, Cracidae): A hypothesis based on mitochondrial DNA phylogeny. Auk 121:682-694. (Pubitemid 38946453)
54. Pereira, S. L., and A. J. Baker. 2005. Multiple gene evidence for parallel evolution and retention of ancestral morphological states in the shanks (Charadriiformes: Scolopacidae). Condor 107:514-526. (Pubitemid 41130000)
55. Pereira, S. L., and A. J. Baker. 2006a. A mitogenomics timescale for birds detects variable phylogenetic rates of molecular evolution and refutes the standard molecular clock. Mol. Biol. Evol. 23:1731- 1740. (Pubitemid 44309767)
56. Pereira, S. L., and A. J. Baker. 2006b. A molecular timescale for galliform birds accounting for uncertainty in time estimates and heterogeneity of rates of DNA substitutions across lineages and sites. Mol. Phylogenet. Evol. 38:499-509. (Pubitemid 43069392)
57. Pereira, S. L., A. J. Baker, and A. Wajntal. 2002. Combined nuclear and mitochondrial DNA sequences resolve generic relationships within the Cracidae (Galliformes, Aves). Syst. Biol. 51:946-958. (Pubitemid 36111107)
58. Peters, J. L. 1937. Check-list of birds of the world. Harvard University Press, Cambridge, Massachusetts.
59. Poe, S., and D. L. Swofford. 1999. Taxon sampling revisited. Nature 398:299-300. (Pubitemid 129522963)
60. Prychitko, T. M., and W. S. Moore. 1997. The utility of DNA sequences of an intron from the beta-fibrinogen gene in phylogenetic analysis of woodpeckers (Aves: Picidae). Mol. Phylogenet. Evol. 8:193-204. (Pubitemid 127347514)
61. Pubellier, M., J. Ali, and C. Monnier. 2003. Cenozoic plate interaction of the Australia and Philippine sea plates: "Hit-and-run" tectonics. Tectonophysics 363:181-199. (Pubitemid 36435059)
62. Ronquist, F., and J. P. Huelsenbeck. 2003. MrBayes 3: Bayesian phylogenetic inference under mixed models. Bioinformatics 19:1572-4. (Pubitemid 37038874)
63. Sclater, P. L. 1858. On the general geographic distribution of the members of the class Aves. J. Proc. Linn. Soc. Zool. 2:130-145.
64. Shapiro, B., D. Sibthorpe, A. Rambaut, J. Austin, G. M. Wragg, O. R. Bininda-Emonds, P. L. Lee, and A. Cooper. 2002. Flight of the dodo. Science 295:1683. (Pubitemid 34202897)
65. Shevenell, A. E., J. P. Kennett, and D. W. Lea. 2004. Middle Miocene Southern Ocean cooling and Antarctic cryosphere expansion. Science 305:1766-1770. (Pubitemid 39249642)
66. Shimodaira, H. 2002. An approximately unbiased test of phylogenetic tree selection. Syst. Biol. 51:492-508. (Pubitemid 35180700)
67. Shimodaira, H., and M. Hasegawa. 2001. CONSEL: For assessing the confidence of phylogenetic tree selection. Bioinformatics 17:1246- 1247. (Pubitemid 33735360)
68. Sibley, C. G., and J. E. Ahlquist. 1990. Phylogeny and classification of Birds: A study in molecular evolution. Yale University Press, New Haven, Connecticut.
69. Slack, K. E., C. M. Jones, T. Ando, G. L. Harrison, R. E. Fordyce, U. Arnason, and D. Penny. 2006. Early penguin fossils, plus mitochondrial genomes, calibrate avian evolution. Mol. Biol. Evol. 23:1144- 1155. (Pubitemid 43781590)
70. Strimmer, K., and A. von Haeseler. 1996. Quartet puzzling: A quartet maximum likelihood method for reconstructing tree topologies. Mol. Biol. Evol. 13:964-969. (Pubitemid 26284912)
71. Swofford, D. L. 2001. PAUP*: Phylogenetic analysis using parsimony (*and other methods), version 4.0. Sinauer Associates, Sunderland, Massachussets.
72. Tavares, E. S., A. J. Baker, S. L. Pereira, and C. Y. Miyaki. 2006. Phylogenetic relationships and historical biogeography of neotropical parrots (Psittaciformes: Psittacidae: Arini) inferred from mitochondrial and nuclear DNA sequences. Syst. Biol. 55:454-70.
73. Thorne, J. L., and H. Kishino. 2002. Divergence time and evolutionary rate estimation with multilocus data. Syst. Biol. 51:689-702. (Pubitemid 35294802)
74. Thome, J. Lv H. Kishino, and I. S. Painter. 1998. Estimating the rate of evolution of the rate of molecular evolution. Mol. Biol. Evol. 15:1647- 57. (Pubitemid 28550989)
75. van Tuinen, M., and S. B. Hedges. 2001. Calibration of avian molecular clocks. Mol. Biol. Evol. 18:206-13. (Pubitemid 32118865)
76. Wallace, A. R. 1876. The geographic distribution of animals. Macmillan, London.
77. Wiegmann, B. M., D. K. Yeates, J. L. Thorne, and H. Kishino. 2003. Time flies, a new molecular time-scale for brachyceran fly evolution without a clock. Syst. Biol. 52:745-56. (Pubitemid 38106045)
78. Wiens, J. J. 2005. Can incomplete taxa rescue phylogenetic analyses from long-branch attraction? Syst. Biol. 54:731-742. (Pubitemid 43142293)
79. Yang, Z. 1997. PAML: A program package for phylogenetic analysis by maximum likelihood. Comput. Appl. Biosci. 13:555-556. (Pubitemid 27480216)
80. Yang, Z., and A. D. Yoder. 2003. Comparison of likelihood and Bayesian methods for estimating divergence times using multiple gene loci and calibration points, with application to a radiation of cute-looking mouse lemur species. Syst. Biol. 52:705-716. (Pubitemid 37365051)
81. Zachos, J., M. Pagani, L. Sloan, E. Thomas, and K. Billups. 2001. Trends, rhythms, and aberrations in global climate 65 Ma to present. Science 292:686-693. (Pubitemid 32385533)
82. Zhu, B., W. S. F. Kidd, D. B. Rowley, B. S. Currie, and N. Shafique. 2005. Age of initiation of the India-Asia collision in the East-Central Himalaya. J. Geol. 113:265-285. (Pubitemid 40815644)
83. Zwickl, D= J. 2006: Genetic algorithm approaches for the phylogenetic analysis of large biological sequence datasets under the maximum likelihood criterion. PhD Dissertation, The University of Texas at Austin.