Phylogenetic relationships and historical biogeography of neotropical parrots (Psittaciformes: Psittacidae: Arini) inferred from mitochondrial and nuclear DNA sequences

Systematic Biology

Volumn 55, Issue 3, 2006, Pages 454-470

  Tavares, Erika Sendra ^a   Baker, Allan J ^b,c   Pereira, Sérgio Luiz ^b   Miyaki, Cristina Yumi ^a  

^a UNIVERSITY OF SÃO PAULO   (Brazil)

^b DEPARTMENT OF NATURAL HISTORY   (Canada)

^c UNIVERSITY OF TORONTO   (Canada)

Author keywords

Biogeography; Divergence times; Mitochondrial DNA; Molecular clock; Molecular phylogeny; Neotropical parrots; Nuclear DNA; Tribe arini

Indexed keywords

MITOCHONDRIAL DNA;

ANIMAL; ARTICLE; CELL NUCLEUS; CLASSIFICATION; GENETICS; GEOGRAPHY; NUCLEOTIDE SEQUENCE; PARROT; PHYLOGENY; SPECIES DIFFERENTIATION; TROPIC CLIMATE;

ANIMALS; BASE SEQUENCE; CELL NUCLEUS; DNA, MITOCHONDRIAL; GENETIC SPECIATION; GEOGRAPHY; PARROTS; PHYLOGENY; TROPICAL CLIMATE;

EID: 33747334924     PISSN: 10635157     EISSN: 1076836X     Source Type: Journal    
DOI: 10.1080/10635150600697390     Document Type: Article

References (92)

1. Barrowclough, G. F, J. G. Groth, and L. A. Mertz. 2004. Phylogenetic relationships among parrots. One Hundred and Twenty-Second Stated Meeting of the American Ornithologist's Union. 16-21 August, Laval, Quebec.
2. Brereton, J. L. 1963. Evolution within the Psittaciformes. Proc. Int. Ornitol. Congr. 13:499-517.
3. Brereton, J. L., and K. Immelmann. 1962. Head-scratching in the Psittaciformes. Ibis 104:169-174.
4. Bruford, M. W., O. Hanotte, J. F. Y. Brookfield, and T. Burke. 1992. Single-locus and multilocus DNA fingerprinting. Pages 225-269 in Molecular genetic analysis of populations - A practical approach (A. R. Hoelzel, ed.). IRL Press, Oxford University Press, New York.
5. Chang, B. S. W., and D. L. Campbell. 2000. Bias in phylogenetic reconstruction of vertebrate rhodopsin sequences. Mol. Biol. Evol. 17:1220-1231. (Pubitemid 30617148)
6. Clarke, J. A., C. P. Tambussi, J. I. Noriega, G. M. Erickson, and R. A. Ketcham. 2005. Definitive fossil evidence for the exant avian radiation in the Cretaceous. Nature 433:305-308.
7. Collar, N. J. 1997. Family Psittacidae (parrots). Pages 280-477 in Handbook of the birds of the world, vol. 4: Sandgrouse to Coockos (J. del Hoyo, A. E. Elliot, and J. Sargatal, eds.). Lynx Editions, Barcelona.
8. Cooper, A., and D. Penny. 1997. Mass survival of birds across the Cretaceous-Tertiary boundary: Molecular evidence. Science 275:1109-1113.
9. Cooper, R. A., and P. Millener. 1993. The New Zealand biota: Historical background and new research. Trends. Ecol. Evol. 8:429-433.
10. Cracraft, J. 1973. Continental drift, paleoclimatology and the evolution and biogeography of birds. J. Zool. 169:455-545.
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. de Kloet, R. S., and S. R. de Kloet. 2005. The evolution of splindlin gene in birds: Sequencing analysis of an intron of the spindling W and Z gene reveals four major divisions of the Psittaciformes. Mol. Phylogenet. Evol. 36:706-721.
13. Desjardins, P., and R. Morais. 1990. Sequence and gene organization of the chicken mitochondrial genome: A novel gene order in higher vertebrates. J. Mol. Biol. 212:599-634.
14. Dingle, R. V., and M. Lavelle. 1998. Late Cretaceous-Cenozoic climatic variations of the northern Antarctica Peninsula: New geochemical evidence and review. Paleogeogr. Paleoclimat. Paleoecol. 141:215-232. (Pubitemid 28320365)
15. Eberhard, J. R., and E. Bermingham. 2004. Phylogeny and biogeography of the Amazona ochrocephala (Aves: Psittacidae) complex. Auk 121:318-332. (Pubitemid 38729925)
16. Eberhard, J. R., and E. Bermingham. 2005. Phylogeny and comparative biogeography of Pionopsitta parrots and Ptewglossus toucans. Mol. Phylogenet. Evol. 36:288-304. (Pubitemid 40801825)
17. Effron, B. 1979. Bootstrap methods: Another look at the jackknife. Ann. Stat. 7:1-26.
18. Felsenstein, J. 1985. Confidence limits on phylogenies: An approach using the bootstrap. Evolution 39:783-791.
19. Flynn, J. J., and A. R. Wyss. 1998. Recent advances in South American mammalian paleontology. TREE 13:449-454. (Pubitemid 28487316)
20. Forshaw, J. 1989. Parrots of the world, third ed. Landsdowne Editions, Melbourne, Australia.
21. Foster, P. G., and D. A. Hickey. 1999. Compositional bias may affect both DNA-based and protein-based phylogenetic reconstructions. J. Mol. Evol. 48:284-290.
22. Galtier, N., and M. Gouy. 1998. Inferring pattern and process: Maximum likelihood implementation of a nonhomogenous model of DNA sequence evolution for phylogenetic analysis. Mol. Biol. Evol. 15:871-879. (Pubitemid 28321885)
23. Garcia-Moreno, J., M. D. Sorenson, and D. P. Mindell. 2003. Congruent avian phylogenies inferred from mitochondrial and nuclear DNA sequences. J. Mol. Evol. 57:27-37. (Pubitemid 36920447)
24. Griffiths, C. S., G. F. Barrowclough, J. G. Groth, and L. Mertz. 2004. Phylogeny of the Falconidae (Aves): A comparison of the efficacy of morphological, mitochondrial, and nuclear data. Mol. Phylogenet. Evol. 32:101-109. (Pubitemid 38851933)
25. Groth, J. G., and G. F. Barrowclough. 1999. Basal divergence in birds and the phylogenetic utility of the nuclear RAG-1 gene. Mol. Phylogenet. Evol. 12:115-123. (Pubitemid 129499294)
26. 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)
27. 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. Ser. B 268:939-945. (Pubitemid 32453384)
28. Hagelberg, E. 1994. Mitochondrial DNA from ancient bones. Pages 195-204 in Ancient DNA (B. Herrmann and S. Hummel, eds.). Springer, New York.
29. Haq, B. U., J. Hardenbol, and P. R. Vail. 1987. Chronology of fluctuating sea levels since the Triassic. Science 235:1156-1167. (Pubitemid 17263665)
30. Harlid, A., A. Janke, and U. Arnason. 1998. The complete mitochondrial genome of Rhea americana and early avian divergences. J. Mol. Evol. 46:669-679. (Pubitemid 28270224)
31. Harrison, G. L., P. A. McLenachan, M. J. Phillips, K. E. Slack, A. Cooper, and D. Penny. 2004. Four new avian mitochondrial genomes help get to basic evolutionary questions in the Late Cretaceous. Mol. Biol. Evol. 21:974-983. (Pubitemid 38658205)
32. Hooghiemstra, H., and T. van der Hammen. 1998. Neogene and Quaternary development of the Neotropical rain forest: The forest refugia hypothesis, and a literature overview. Earth Sci. Rev. 44:147-183. (Pubitemid 29097041)
33. Jermiin, L. S., P. G. Foster, D. Graur, R. M. Lowe, and R. H. Crazier. 1996. Unbiased estimation of symmetrical directional mutation pressure from protein-coding DNA. J. Mol. Evol. 42:476-480. (Pubitemid 26154326)
34. Johnson, K. P., and M. D. Sorenson. 1998. Comparing molecular evolution in two mitochondrial protein coding genes (cytochrome b and ND2) in the dabbling ducks (Tribe: Anatini). Mol. Phylogenet. Evol. 10:82-94. (Pubitemid 128350708)
35. Kishino, H., J. L. Thorne, and W. J. Bruno. 2001. Performance of a divergence time method under a probabilistic model of rate evolution. Mol. Biol. Evol. 18:352-361. (Pubitemid 32225084)
36. Kocher, T. D., W. K. Thomas, A. Meyer, S. V. Edwards, S. Paabo, F. X. Villablanca, and A. C. Wilson. 1989. Dynamics of mitochondrial DNA evolution in animals: Amplification and sequencing with conserved primers. Proc. Natl. Acad. Sci. USA 86:6196-6200. (Pubitemid 19210622)
37. Lawver, L. A., and Gahagan, L. M. 2003. Evolution of Cenozoic seaways in the circum-Antarctic region. Paleogeogr. Paleoclimat. Paleoecol. 198:11-37. (Pubitemid 37134992)
38. Liu, H. T., Y. H. Hu, C. T. Wang, and L. Y. Lin. 1996. Sequences and comparisons of duck mitochondrial DNA control regions. Biochem. Mol. Biol. 115:209-214.
39. Livezey, B. C, and R. L. Zusi. 2001. Higher-order phylogenetics of modern aves based on comparative anatomy. Netherlands J. Zool. 51:179-205. (Pubitemid 33613736)
40. Lockhart, P. J., M. A. Steel, M. D. Hendy, and D. Penny. 1994. Recovering evolutionary trees under a more realistic model of sequence evolution. Mol. Biol. Evol. 11:605-612. (Pubitemid 24198536)
41. Lovette, I. J. 2004. Mitochondrial dating and mixed support for the "2% rule" in birds. Auk 121:1-6. (Pubitemid 38215551)
42. 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.
43. Maddison, W. P., and D. R. Maddison. 2000. MacClade 4: Analysis of phylogeny and character evolution. Sinauer Associates, Sunderland, Massachusetts.
44. Maddison, W. P., and D. R. Maddison. 2004. Mesquite: A modular system for evolutionary analysis. Version 1.05. http://mesquiteproject.org
45. Mindell, D. P., M. D. Sorenson, and D. E. Dimcheff. 1998. Multiple independent origins of mitochondrial gene order in birds. Proc. Nat. Acad. Sci. USA 95:10693-10697. (Pubitemid 28413130)
46. Mindell, D. P., M. D. Sorenson, D. E. Dimcheff, M. Hasegawa, J. C. Ast, and T. Yuri. 1999. Interordinal relationships of birds and other reptiles based on whole mitochondrial genomes. Syst. Biol. 48:138-152. (Pubitemid 129481129)
47. Miyaki, C. Y, M. B. Duarte, R. Caparroz, A. L. Nunes, and A. Wajntal. 1997. Sex identification of South American parrots (Psittacidae, Aves) using the human minisatellite probe 33.15. Auk 114:516-520. (Pubitemid 27309121)
48. Miyaki, C. Y, S. R. Matioli, T. Burke, and A. Wajntal. 1998. Parrot evolution and paleogeographical events: Mitochondrial DNA evidence. Mol. Biol. Evol. 15:544-551. (Pubitemid 28194618)
49. Nahum, L. A., S. L. Pereira, F. M. C. 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. Gen. Mol. Biol. 26:411-418. (Pubitemid 38054859)
50. 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. Biogeog. 13:149-161.
51. Paton, T., O. Haddrath, and A. J. Baker. 2002. Complete mitochondrial DNA genome sequences show that modern birds are not descended from transitional shorebirds. Proc. R. Soc. Lond. Ser. B 269:839-846. (Pubitemid 34495421)
52. Penhallurick, J. 2001. Primolius Bonaparte, 1857 has priority over Propyrrhura Ribeiro, 1920. Bull. B. Orn. C 121:38-39.
53. Pennington, R. T., M. Lavin, D. E. Prado, C. A. Pendry, S. K. Pell, and C. A. Butterworth. 2004. Historical climate change and speciation: Neotropical seasonally dry forest plants show patterns of both Tertiary and Quaternary diversification. Phil. Trans. R. Soc. Lond. B 359:515-537. (Pubitemid 38370781)
54. Penny, D., M. D. Hendy, E. A. Zimmer, and R. K. Hamby. 1990. Trees from sequences: Panacea or Pandora's box? Aust. Syst. Bot. 3:21-38.
55. Pereira, S. L., and A. J. Baker. 2004. Low number of mitochondrial pseudogenes in the chicken (Gallus gallus) nuclear genome: Implications for molecular inference of population history and phylogenetics. BMC Evol. Biol. 4:17.
56. Pereira, S. L., and A. J. Baker. 2006. 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. Poe, S., and D. L. Swofford. 1999. Taxon sampling revisited. Nature 398:299-300. (Pubitemid 129522963)
59. Poole, I., D. J. Cantrill, and T. Utescher. 2005. A multi-proxy approach to determine Antarctic terrestrial palaeoclimate during the Late Cretaceous and Early Tertiary. Palaeogeogr. Palaeoclimat. Palaeoecol. 222:95-121 (Pubitemid 40793471)
60. Poole, I., R. J. Hunt, and D. J. Cantrill. 2001. A fossil wood flora from King George Island: Ecological implications for an Antarctic Eocene vegetation. Ann. Bot. 88:33-54. (Pubitemid 32632386)
61. Posada, D., and K. A. Crandall. 1998. ModelTest: Testing the model of DNA substitution. Bioinformatics 14:817-818. (Pubitemid 28552116)
62. Ramirez, V., P. Savoie, and R. Morais. 1993. Molecular characterization and evolution of a duck mitochondrial genome. J. Mol. Evol. 37:296-310. (Pubitemid 23249707)
63. Ribas, C. C., R. Gaban-Lima, C. Y. Miyaki, and J. Cracraft. 2005. Historical biogeography and diversification within the Neotropical parrot genus "Pionopsitta" (Aves; Psittacidae). J. Biogeogr. 32:1409-1427. (Pubitemid 41615370)
64. Ribas, C. C., and C. Y. Miyaki. 2004. Molecular systematics in Aratinga parakeets: Species limits and historical biogeography in the solstitialis group, and the systematic position of Nandayus nenday. Mol. Phylogenet. Evol. 30:663-675. (Pubitemid 38260967)
65. Ronquist, F. R., and J. P. H. Huelsenbeck. 2003. MrBayes: Bayesian inference of phylogeny. Bioinformatics 19:1572-1574.
66. Rowley, I. 1997. Family Cacatuidae (cockatoos). Pages 246-279 in Handbook of the birds of the world, volume 4 (del Hoyo, J., A. E. Elliot, and J. Sargatal, eds.). Lynx Editions, Barcelona.
67. Russello, M. A., and G. Amato. 2004. A molecular phylogeny of Amazona: Implications for Neotropical parrot biogeography, taxonomy, and conservation. Mol. Phylogenet. Evol. 30:421-437. (Pubitemid 38162044)
68. Salvadori, T. 1891. Catalogue of Psittaci, or Parrots, in the Collection of the British Museum. Longman and Company, London.
69. Sanderson, M. J. 2002. Estimating absolute rates of molecular evolution and divergence times: A penalized likelihood approach. Mol. Biol. Evol. 19:101-109. (Pubitemid 34008052)
70. Sanderson, M. J. 2003. r8s: Inferring absolute rates of molecular evolution and divergence times in the absence of a molecular clock. Bioinformatics 19:301-302. (Pubitemid 36181923)
71. Schluter, D. 2000. The ecology of adaptive radiation. Oxford University Press, Oxford, UK.
72. Schmidt, H. A., K. Strimmer, M. Vingron, and A. von Haeseler. 2002. Maximum likelihood phylogenetic analysis using quartets and parallel computing. Bioinformatics 18:502-504. (Pubitemid 34284960)
73. Shevenall, A. E., J. P. Kennett, and D. W. Lea. 2004. Middle Miocene Southern ocean cooling and Antarctica cryosphere expansion. Science 305:1766-1770.
74. Shimodaira, H. 2002. An approximately unbiased test of phylogenetic tree selection. Syst. Biol. 51:492-508. (Pubitemid 35180700)
75. Shimodaira, H., and M. Hasegawa. 2001. CONSEL: For assessing the confidence of phylogenetic tree selection. Bioinformatics 17:1246-1247. (Pubitemid 33735360)
76. Sibley, C. G., and J. E. Alquist. 1990. Phylogeny classification of birds: A study in molecular evolution. Yale University Press, New Haven, Connecticut.
77. Sick, H. 1997. Ornitologia Brasileira, 2nd edition. Editora Nova Fronteira S. A., Rio de Janeiro, Brazil.
78. Slowinski, J. B. 2001. Molecular polytomies. Mol. Phylogenet Evol. 19:114-120. (Pubitemid 32996705)
79. Smith, A. G., D. G. Smith, and B. M. Funnell. 1994. Atlas of Mesozoic and Cenozoic coastlines. Cambridge, UK, Cambridge University Press.
80. Smith, G. A. 1975. Systematics of parrots. Ibis 117:18-68.
81. Swofford, D. L. 2002. PAUP*: Phylogenetic analysis using parsimony (*and related methods), version 4. Sinauer Associates, Sunderland, Massachusetts.
82. Takezaki, N., A. Rzhetsky, and M. Nei. 1995. Phylogenetic test of molecular clock and linearized trees. Mol. Biol. Evol. 12:823-833.
83. Tavares, E. S., C. Yamashita, and C. Y. Miyaki. 2004. Phylogenetic relationships among some Neotropical parrot genera (Psittacidae) based on mitochondrial sequences. Auk 121:230-242. (Pubitemid 38215575)
84. Thorne, J. L., and H. Kishino. 2002. Divergence time and evolutionary rate estimation with multilocus DNA data. Syst. Biol. 51:689-702. (Pubitemid 35294802)
85. Thorne, J. L., H. Kishino, and I. S. Painter. 1998. Estimating the rate of evolution of the rate of molecular evolution. Mol. Biol. Evol. 15:1647-1657. (Pubitemid 28550989)
86. Van Tuinen, M., and S. B. Hedges. 2001. Calibration of avian molecular clocks. Mol. Biol. Evol. 18:206-213. (Pubitemid 32118865)
87. Verheyen, R. 1956. Analyse du potentiel morphologique et projet d'une nouvelle classification des Psittaciformes. Bull. Inst. R. Sci. Nat. Belg. 32:54.
88. von Boetticher, H. 1943. Gedanken "uber die systematic Stellung einiger Papagaien. Zool. Anz. 143:191-200.
89. von Boetticher, H. 1959. Papagaien. Wittenberg Lutherstadt, A. Ziemsen.
90. Woodbourne, M. O., and J. A. Case. 1996. Dispersal, vicariance, and the Late Cretaceous to Early Tertiary land mammal biogeography from South America to Australia. J. Mamm. Evol. 3:121-161.
91. Yang, Z. 1997. Phylogenetic analysis by maximum likelihood (PAML), version 2.0. University of Carlifornia, Berkeley.
92. 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)