Temporal and spatial diversification of Pteroglossus araçaris (AVES: Ramphastidae) in the neotropics: Constant rate of diversification does not support an increase in radiation during the Pleistocene

Molecular Phylogenetics and Evolution

Volumn 58, Issue 1, 2011, Pages 105-115

  Patel, Swati ^a,b,d   Weckstein, Jason D ^b   Patané, José S L ^c   Bates, John M ^b   Aleixo, Alexandre ^d  

^a NORTHWESTERN UNIVERSITY   (United States)

^b FIELD MUSEUM OF NATURAL HISTORY   (United States)

^c INSTITUTO BUTANTAN   (Brazil)

^d MUSEU PARAENSE EMÍLIO GOELDI   (Brazil)

Author keywords

Amazon; Neotropics; Pleistocene; Pteroglossus; Rates of diversification

Indexed keywords

MITOCHONDRIAL DNA;

ANIMAL; ARTICLE; BIRD; CLASSIFICATION; GENETICS; MOLECULAR GENETICS; NUCLEOTIDE SEQUENCE; PHYLOGENY; TROPIC CLIMATE;

ANIMALS; BIRDS; DNA, MITOCHONDRIAL; MOLECULAR SEQUENCE DATA; PHYLOGENY; TROPICAL CLIMATE;

AVES; PTEROGLOSSUS; RAMPHASTIDAE;

EID: 78650986340     PISSN: 10557903     EISSN: 10959513     Source Type: Journal    
DOI: 10.1016/j.ympev.2010.10.016     Document Type: Article

References (80)

1. Abratis M., Worner G. Ridge collision, slab-window formation, and the flux of Pacific asthenosphere into the Caribbean realm. Geology 2001, 29:127-130.
2. Aleixo A., Rossetti D.F. Avian gene trees, landscape evolution, and geology: towards a modern synthesis of Amazonian historical biogeography?. J. Ornithol. 2007, 148:443-453.
3. American Ornithologists' Union, 1998. Check-list of North American Birds, seventh ed. American Ornithologists' Union, Washington, DC.
4. Antonelli, A., Quijada-Mascareñas, A., Crawford, A. J., Bates, J. M., Velazco, P. M., Wüster, W., 2010. Molecular studies and phylogeography of Amazonian tetrapods and their relation to geological and climatic models. In Hoorn, C., Vonhof, H., Wesselingh, F. (Eds.), Neogene History of Western Amazonia and its Significance for Modern Biodiversity, pp. 388-404.
5. Arbogast B.S., Edwards S.V., Wakeley J., Beerli P., Slowinski J.B. Estimating divergence times from molecular data on phylogenetic and population genetic timescales. Annu. Rev. Ecol. Syst. 2002, 33:707-740.
6. Barker F.K., Lanyon S.M. The impacts of parsimony weighting schemes on inferred relationships among toucans and barbets (Aves: Piciformes). Mol. Phylogenet. Evol. 2000, 15:215-234.
7. Bates J.M. Avian diversification in Amazonia: evidence for historical complexity and a vicariance model for a basic diversification pattern. Diversidade Biológica e Cultural da Amazônia 2001, 11-9138. Museu Paraense Emílio Goeldi, Belém, Pará, Brazil. I. Viera, M.A. D'Incao, J.M. Cardoso da Silva, D. Oren (Eds.).
8. Bates J.M., Hackett S.J., Cracraft J. Area-relationships in the Neotropical lowlands: an hypothesis based on raw distributions of Passerine birds. J. Biogeogr. 1998, 25:783-793.
9. Bermingham E., Avise J.C. Molecular zoogeography of freshwater fishes in the southeastern United States. Genetics 1986, 113:939-965.
10. Burney C.W., Brumfield R.T. Ecology predicts levels of genetic differentiation in Neotropical birds. Am. Nat. 2009, 174:358-368.
11. Campbell K.E., Frailey C.D., Romero-Pittman L. The Pan-Amazonian Ucayali Peneplain, late Neogene sedimentation in Amazonia, and the birth of the modern Amazon River system. Palaeogeo. Palaeoclim. Palaeoecol. 2006, 239:166-219.
12. Cabanne G.S., d'Horta F.M., Sari E.H.R., Santos F.R., Miyaki C.Y. Nuclear and mitochondrial phylogeography of the Atlantic forest endemic Xiphorhynchus fuscus (Aves: Dendrocolaptidae): biogeography and systematics implications. Mol. Phylogenet. Evol. 2008, 49:760-773.
13. CBRO, Comitê Brasileiro de Registros Ornitológicos. Lista das aves do Brasil, 2009. 8a ed. (accessed 7.09.09). http://www.cbro.org.br/CBRO/listabr.htm.
14. Cracraft J., Prum R.O. Patterns and processes of diversification: speciation and historical congruence in some Neotropical birds. Evolution 1988, 42:603-620.
15. Cusimano N., Renner S.S. Slowdowns in diversification rates from real phylogenies may not be real. Syst. Biol. 2010, 49:458-464.
16. DeOliveira P.E., Barreto A.M.F., Suguio K. Late Pliocene/Holocene climatic and vegetational history of the Brazilian caatinga: the fossil dunes of the middle São Francisco River. Paleogeogr. Paleoclimatol. Paleoecol. 1999, 512:319-337.
17. Drummond A.J., Rambaut A. BEAST: Bayesian evolutionary analysis by sampling trees. BMC Evol. Biol. 2007, 7:214.
18. Eberhard J.R., Bermingham E. Phylogeny and comparative biogeography of Pionopsitta parrots and Pteroglossus toucans. Mol. Phylogenet. Evol. 2005, 36:288-304.
19. Endler J.A. Pleistocene forest refuges: fact or fancy?. Biological Diversification in the Tropics 1982, 641-657. Columbia University Press, New York. G.T. Prance (Ed.).
20. Figueiredo J., Hoorn C., der Ven P.V., Soares E. Late Miocene onset of the Amazon River and the Amazon deep-sea fan: evidence from the Foz do Amazonas Basin. Geology 2009, 37:619-622.
21. García-Moreno J. Is there a universal mtDNA clock for birds?. J. Avian Biol. 2004, 35:465-468.
22. Gascon C., Malcolm J.R., Patton J.L., Silva M.N.F., Bogart J.P., Lougheed S.C., Peres C.A., Neckel S., Boag P.T. Riverine barriers and the geographic distribution of Amazonian species. Proc. Natl. Acad. Sci. USA 2000, 97:13672-13677.
23. Gernhard T. The conditioned reconstructed process. J. Theor. Biol. 2008, 253:769-778.
24. Gradstein F.M., Ogg J.G., Smith A.G., Bleeker W., Lourens L.J. A new geologic time scale, with special reference to Precambrian and Neogene. Episodes 2004, 27:83-100.
25. Grafe K., Frisch W., Villa I.M., Meschede M. Geodynamic evolution of southern Costa Rica related to low-angle subduction of the Cocos Ridge: constraints from thermochronology. Tectonophysics 2002, 348:187-204.
26. Gregory-Wodzicki K.M. Uplift history of the Central and Northern Andes: a review. Geol. Soc. Am. Bull. 2000, 112:1091-1105.
27. Hackett S.J. Molecular phylogenetics and biogeography of tanagers in the genus Ramphocelus (Aves). Mol. Phylogenet. Evol. 1996, 5:368-382.
28. 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. 1997, 48:267-279.
29. Haffer J. Speciation in Amazonian forest birds. Science 1969, 165:131-137.
30. Haffer J. Avian Speciation in Tropical South America 1974, Nuttall Ornithological Club, Cambridge, MA.
31. Haffer J. Alternative models of vertebrate speciation in Amazonia: an overview. Biodivers. Conserv. 1997, 6:451-476.
32. Hafner M.S., Sudman P.D., Villablanca F.X., Spradling T.A., Demastes J.W., Nadler S.A. Disparate rates of molecular evolution in cospeciating hosts and parasites. Science 1994, 265:1087-1090.
33. Helm-Bychowski K., Cracraft J. Recovering phylogenetic signal from DNA sequences: relationships within the Corvine assemblage (class Aves) as inferred from complete sequences of mitochondrial cytochrome-b gene. Mol. Biol. Evol. 1993, 10:1196-1214.
34. Hilty S.L., Brown W.L. A guide to the Birds of Colombia 1986, Princeton University Press, Princeton, New Jersey.
35. Huelsenbeck J.P., Bollback J.P. Empirical and hierarchichal Bayesian estimation of ancestral states. Syst. Biol. 2001, 50:351-366.
36. Kass R.E., Raftery A.E. Bayes factor. J. Am. Stat. Assoc. 1995, 90:773-795.
37. Kendall D.G. On the generalized ''birth-and-death'' process. Ann. Math. Stat. 1948, 19:1-15.
38. Kimura R.K., Pereira S.L., Grau E.T., Höfling E., Wajntal A. Genetic distances and phylogenetic analysis suggest that Baillonius Cassin, 1867 is a Pteroglossus Illiger, 1811. Ornitol. Neotrop. 2004, 15:527-537.
39. Kocher T.D., Thomas W.K., Meyer A., Edwards S.V., Pääbo 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 1989, 86:6196-6200.
40. Lovejoy N.R., Albert J.S., Crampton W.G.R. Miocene marine incursions and marine/freshwater transitions: evidence from Neotropical fishes. J South Am. Earth Sci. 2006, 21:5-13.
41. Lovette I.J. Mitochondrial dating and mixed support for the ''2% rule" in birds. Auk 2004, 121:1-6.
42. Maddison, W.P., Maddison, D.R., 2002. MacClade 4: Analysis of phylogeny and character evolution, version 4.05. Sinauer. Sunderland, Massachusetts.
43. Marks B.D., Hackett S.J., Capparella A.P. Historical relation-ships among Neotropical lowland forest areas of endemism as determined by mitochondrial DNA sequence variation within the wedge-billed woodcreeper (Aves: Dendrocolaptidae: Glyphorynchus spirurus). Mol. Phylogenet. Evol. 2002, 24:153-167.
44. Meyer de Schauensee R. A Guide to the Birds of South America 1970, Livingston Publishing Co., Wynnewood, Pennsylvania.
45. Miller M.J., Bermingham E., Klicka J., Escalante P., Raposo do Amaral F.S., Weir J.T., Winker K. Out of Amazonia again and again: episodic crossing of the Andes promotes diversification in a lowland forest flycatcher. Proc. Roy. Soc. B 2008, 275:1133-1142.
46. Moyle R.G. Phylogenetics of barbets (Aves: Piciformes) based on nuclear and mitochondrial DNA sequence data. Mol. Phylogenet. Evol. 2004, 30:187-200.
47. Moyle R.G., Filardi C.E., Smith C.E., Diamond J. Explosive Pleistocene diversification and hemispheric expansion of a " great speciator" Proc. Natl. Acad. Sci. USA 2009, 106:1863-1868.
48. Nelson D.L., Cox M.M. Lehninger Principles of Biochemistry 2004, W.H. Freeman and Co, New York. forth ed.
49. Nores M. The implications of Tertiary and Quaternary sea level rise events for avian distribution patterns in the lowlands of northern South America. Global Ecol. Biogeogr. 2004, 13:149-161.
50. Nylander J.A.A. MrModeltest v2. Program Distributed by the Author 2004, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden.
51. Patané J.S.L., Weckstein J.D., Aleixo A., Bates J.M. Evolutionary history of Ramphastos toucans: molecular phylogenetics, temporal diversification, and biogeography. Mol. Phylogenet. Evol. 2009, 53:923-934.
52. Pereira S.L., Wajntal A. The historical biogeography of Pteroglossus Aracaris (Aves, Piciformes, Ramphastidae) based on Bayesian analysis of mitochondrial DNA sequences. Genet. Mol. Biol. 2008, 31:964-973.
53. Peterson A.T. Application of molecular clocks in ornithology revisited. J. Avian Biol. 2007, 37:541-544.
54. Posada D., Crandall K.A. Modeltest: testing the model of DNA substitution. Bioinformatics 1998, 14:817-818.
55. Prum, R.O., 1988. Historical relationships among avian forest areas of endemism in the Neotropics. In: Quellet, H. (Ed.), XIX International Ornithological Congress, Ottawa, Canada, pp. 2562-2572.
56. Prychitko T.M., Moore W.S. The utility of DNA sequences of an intron from the beta-fibrinogen gene in phylogenetic analysis of woodpeckers (Aves: Picidae). Mol. Phylogenet. Evol. 1997, 8:193-204.
57. Pybus O.G., Harvey P.H. Testing macroevolutionary models using incomplete molecular phylogenies. Proc. Roy. Soc. Lond. B 2000, 267:2267-2272.
58. Queiroz deK. Ernst Mayr and the modern concept of species. Proc. Natl. Acad. Sci. USA 2005, 102:6600-6607.
59. R Development Core Team. R: A Language and Environment for Statistical Computing, 2009. http://www.R-project.org.
60. Rabosky D.L. Likelihood methods for detecting temporal shifts in diversification rates. Evolution 2006, 60:1162-1164.
61. Rabosky D.L. LASER: a maximum likelihood toolkit for detecting temporal shifts in diversification rates from molecular phylogenies. Evol. Bioinform. Online 2007, 2:273-276.
62. Rabosky D.L., Lovette I. Explosive evolutionary radiations: decreasing speciation or increasing extinction through time?. Evolution 2008, 62:1866-1875.
63. Rambaut, A., Drummond, A.J., 2008. Tracer Version 1.4.
64. Remsen, J.V., Jr., Cadena, C.D, Jaramillo, A., Nores, M., Pacheco, J.F., Robbins, M.B., Schulenberg, T.S., Stiles, F.G., Stotz, D.F., Zimmer, K.J., 2010. A Classification of the Bird Species of South America. Amer. Ornithologists' Union. http://www.museum.lsu.edu/~Remsen/SACCBaseline.html.
65. Ribas C.C., Miyaki C.Y., Cracraft J. Phylogenetic relationships, diversification and biogeography in Neotropical Brotogeris parakeets. J. Biogeogr. 2009, 36:1712-1729.
66. Ribas C.C., Moyle R.G., Miyaki C.Y., Cracraft J. The assembly of montane biotas: linking Andean tectonics and climatic oscillations to independent regimes of diversification in Pionus parrots. Proc. Roy. Soc. B 2007, 274:2399-2408.
67. Ridgely R.S., Greenfield P.J. The Birds of Ecuador 2001, Cornell University Press, Ithaca, New York.
68. Ronquist F., Huelsenbeck J.P. MrBayes 3. Bayesian phylogenetic inference under mixed models. Bioinformatics 2003, 19:1572-1574.
69. Rossetti D.F., Toledo P.M., Góes A.M. New geological framework for Western Amazonia (Brazil) and implications for biogeography and evolution. Quat. Res. 2005, 63:78-89.
70. Shields G.F., Wilson A.C. Calibration of mitochondrial DNA evolution in geese. J. Mol. Evol. 1987, 24:212-217.
71. Short L.L., Horne J.F.M. Toucans, Barbets and Honeyguides 2001, Oxford University Press, Oxford.
72. Short L.L., Horne J.F.M. Family Ramphastidae. Handbook of Birds of the World 2002, vol. 7:220-273. Jacamars to woodepeckers, Lynx Edicions, Spain.
73. Sorenson M.D., Ast J.C., Dimcheff D.E., Yuri T., Mindell D.P. Primers for a PCR based approach to mitochondrial genome sequencing in birds and other vertebrates. Mol. Phylogenet. Evol. 1999, 12:105-114.
74. Swofford, D.L., 2002. PAUP* Phylogenetic Analysis Using Parsimony (*and other methods). Version 4. Sinauer Associates, Sunderland, MA.
75. Tobias J.A., Bates J.M., Hackett S.J., Seddon N. Comment on " Latitudinal gradient in recent speciation and extinction rates of birds and mammals" Science 2008, 319:901.
76. Weckstein J.D. Molecular phylogenetics of the Ramphastos toucans: implications for the evolution of morphology, vocalizations, and coloration. Auk 2005, 122:1191-1209.
77. Weir J.T. Divergent timing and patterns of species accumulation in lowland and highland Neotropical birds. Evolution 2006, 60:842-855.
78. Weir J.T., Schluter D. Calibrating the avian molecular clock. Mol. Ecol. 2008, 17:2321-2328.
79. Willis E.O. Zoogeographical origins of Eastern Brazilian birds. Ornitol. Neotrop. 1992, 3:1-15.
80. Yule G.U. A mathematical theory of evolution based on the conclusions of Dr. J.C. Willis. Philos. Trans. Roy. Soc. Lond. B 1924, 213:21-87.