A palaeobiogeographic model for biotic diversification within Amazonia over the past three million years

Proceedings of the Royal Society B: Biological Sciences

Volumn 279, Issue 1729, 2012, Pages 681-689

  Ribas, Camila C ^a,b   Aleixo, Alexandre ^c   Nogueira, Afonso C R ^d   Miyaki, Cristina Y ^e   Cracraft, Joel ^b  

^a INSTITUTO NACIONAL DE PESQUISAS DA AMAZÔNIA   (Brazil)

^b DIVISION OF INVERTEBRATE ZOOLOGY   (United States)

^c Museu Paraense Emi lio Goeldi   (Brazil)

^d FEDERAL UNIVERSITY OF PARÁ   (Brazil)

^e UNIVERSITY OF SÃO PAULO   (Brazil)

Author keywords

Amazonia; Diversification; Palaeobiogeography; Speciation; Species diversity

Indexed keywords

BIRD; ENDEMISM; PALEOBIOGEOGRAPHY; PALEOGEOGRAPHY; PHYLOGENETICS; PHYLOGENY; PLEISTOCENE; PLIOCENE; SPATIOTEMPORAL ANALYSIS; SPECIATION (BIOLOGY); SPECIES DIVERSITY;

AMAZONIA;

AVES; PSOPHIA; PSOPHIIDAE; VERTEBRATA;

EID: 84855645516     PISSN: 09628452     EISSN: 14712970     Source Type: Journal    
DOI: 10.1098/rspb.2011.1120     Document Type: Article

References (61)

1. Silva, J. M. C., Rylands, A. B. & Fonseca, G. A. B. 2005 The fate of Amazonian areas of endemism. Conserv. Biol. 19, 689-694. (doi:10.1111/j.1523-1739.2005.00705.x)
2. Bermingham, E. & Dick, C. W. 2005 Overview: the history and ecology of tropical rainforest communities. In Tropical rainforests: past, present, and future (eds E. Bermingham, C. W. Dick & C. Moritz), pp. 7-15. Chicago, IL: University of Chicago Press.
3. Haffer, J. 1969 Speciation inAmazonian forest birds. Science 165, 131-137. (doi:10.1126/science.165.3889.131)
4. Wallace, A. R. 1852 On the monkeys of the Amazon. Proc. Zool. Soc. Lond. 20, 107-110.
5. Ayres, J. M. C. & Clutton-Brock, T. H. 1992 River boundaries and species range size in Amazonian primates. Am. Nat. 140, 531-537. (doi:10.1086/285427)
6. Moritz, C., Patton, C. J., Schneider, C. J. & Smith, T. B. 2000 Diversification of rainforest faunas: an integrated molecular approach. Annu. Rev. Ecol. Syst. 31, 533-563. (doi:10.1146/annurev.ecolsys.31.1.533)
7. Bush, M. B. 1994 Amazonian speciation: a necessarily complex model. J. Biogeogr. 21, 5-17. (doi:10.2307/2845600)
8. Hoorn, C. et al. 2010 Amazonia through time: Andean uplift, climate change, landscape evolution, and biodiversity. Science 330, 927-931. (doi:10.1126/science.1194585)
9. Hoorn, C., Guerrero, J., Sarmiento, G. A. & Lorente, M. A. 1995 Andean tectonics as a cause for changing drainage patterns in Miocene northern South America. Geology 23, 237-240. (doi:10.1130/0091-7613(1995)023,0237:ATAACF.2.3.CO;2)
10. Rossetti, D. F., Toledo, P. M. & Góes, A. M. 2005 New geological framework for Western Amazonia (Brazil) and implications for biogeography and evolution. Quat. Res. 63, 78-89. (doi:10.1016/j.yqres.2004.10.001)
11. Campbell Jr, K. E., Frailey, C. D. & Romero-Pittman, L. 2006 The Pan-Amazonian Ucayali Peneplain, lateNeogene sedimentation in Amazonia, and the birth of the modern Amazon River system. Palaeogeogr. Palaeoclimatol. Palaeoecol. 239, 166-219. (doi:10.1016/j.palaeo.2006.01.020)
12. Figueiredo, J., Hoorn, C., van der Ven, P. & Soares, E. 2009 Late Miocene onset of the Amazon River and the Amazon deep-sea fan: evidence from the Foz do Amazonas Basin. Geology 37, 619-622. (doi:10.1130/G25567A.1)
13. Latrubesse, E. M., Cozzuol, M., Silva-Caminha, S. A. F., Rigsby, C. A., Absy, M. A. & Jaramillo, C. 2010 The late Miocene paleogeography of the Amazon Basin and the evolution of the Amazon River system. Earth Sci. Rev. 99, 99-124. (doi:10.1016/j.earscirev.2010.02.005)
14. Hoorn, C. 1994 An environmental reconstruction of the palaeo-Amazon river system (Middle-Late Miocene, NW Amazonia). Palaeogeogr. Palaeoclimatol. Palaeoecol. 112, 187-238. (doi:10.1016/0031-0182(94)90074-4)
15. Wesselingh, F. P., Räsänen, M. E., Irion, G., Vonhof, H. B., Kaandorp, R., Renema, W., Romero Pittman, L. & Gingras, M. 2002 Lake Pebas: a palaeoecological reconstruction of a Miocene, long-lived lake complex in western Amazonia. Cainozoic Res. 1, 35-81.
16. Hackett, S. J. et al. 2008 A phylogenomic study of birds reveals their evolutionary history. Science 320, 1763-1768. (doi:10.1126/science.1157704)
17. Haffer, J. 1974 Avian speciation in tropical America. Cambridge, UK: Nuttall Ornithological Club.
18. Cracraft, J. 1985 Historical biogeography and patterns of differentiation within the South American avifauna: areas of endemism. Am. Ornithol. Union Ornithol. Monogr. 36, 49-84.
19. Borges, S. H. 2007 Análise biogeográfica da avifauna da região oeste do baixo Rio Negro, Amazônia brasileira. Rev. Bras. Zool. 24, 919-940. (doi:10.1590/S0101-81752007000400008)
20. Swofford, D. L. 2002 PAUP*. Phylogenetic analysis using parsimony (*and other methods). Sunderland, MA: Sinauer Associates.
21. Ronquist, F. & Huelsenbeck, J. P. 2003 MrBayes 3:Bayesian phylogenetic inference under mixed models. Bioinformatics 19, 1572-1574. (doi:10.1093/bioinformatics/btg180)
22. Posada, D. & Crandall, A. 1998 MODELTEST: testing the model of DNA substitution. Bioinformatics 14, 817-818. (doi:10.1093/bioinformatics/14.9.817)
23. Nylander, J. A. A. 2004 MRMODELTEST (version 2). Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden. Program distributed by the author at http://www.csit.fsu.edu/nylander/.
24. Kass, R. E. & Raftery, A. E. 1995 Bayes factors. J. Am. Stat. Assoc. 90, 773-795. (doi:10.2307/2291091)
25. Rambaut, A. & Drummond, A. J. 2007. TRACER v. 1.4. See http://beast.bio.ed.ac.uk/Tracer.
26. Wilgenbusch, J. C., Warren, D. L. & Swofford, D. L. 2004 AWTY: a system for graphical exploration of MCMC convergence in Bayesian phylogenetic inference. See http://ceb.csit.fsu.edu/awty.
27. Drummond, A. J. & Rambaut, A. 2007 BEAST: Bayesian evolutionary analysis by sampling trees. BMC Evol. Biol. 7, 214. (doi:10.1186/1471-2148-7-214)
28. 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. Mol. Ecol. 7, 533-545. (doi:10.1046/j.1365-294x.1998.00364.x)
29. Weir, J. & Schluter, D. 2008 Calibrating the avian molecular clock. Mol. Ecol. 17, 2321-2328. (doi:10.1111/j.1365-294X.2008.03742.x)
30. 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. (doi:10.1093/bioinformatics/19.2.301)
31. van Tuinen, M. & Hedges, S. B. 2001 Calibration of avian molecular clocks. Mol. Biol. Evol. 18, 206-213.
32. Barker, F. K., Cibois, A., Schikler, P., Feinstein, J. & Cracraft, J. 2004 Phylogeny and diversification of the largest avian radiation. Proc. Natl Acad. Sci. USA 101, 11040-11045. (doi:10.1073/pnas.0401892101)
33. Tavares, E. S., Baker, A. J., Pereira, S. L. & Miyaki, C. Y. 2006 Phylogenetic relationships and historical biogeography of Neotropical parrots (Psittaciformes: Psittacidae: Arini) inferred from mitochondrial and nuclear DNA sequences. Syst. Biol. 55, 454-470. (doi:10.1080/10635150600697390)
34. Clement, M., Posada, D. & Crandall, K. A. 2000 TCS: a computer program to estimate gene genealogies. Mol. Ecol. 9, 1657-1660. (doi:10.1046/j.1365-294x.2000.01020.x)
35. Stephens, M.N. J., Smith, N. J. & Donnelly, P. 2001 A new statistical method for haplotype reconstruction from population data. Am. J. Hum. Genet. 68, 978-989. (doi:10.1086/319501)
36. Ramos-Onsins, S. & Rozas, J. 2002 Statistical properties of new neutrality test against population growth. Mol. Biol. Evol. 19, 2092-2100.
37. Rozas, J., Sanchez-DelBarrio, J. C., Messeguer, X. & Rozas, R. 2003 DNAsp, DNA polymorphism analyses by the coalescent and other methods. Bioinformatics 19, 2496-2497. (doi:10.1093/bioinformatics/btg359)
38. Schneider, S. D., Roesli, D. & Excoffier, L. 2000 Arlequin, Version 2.000: a software for population genetic data analysis. Geneva, Switzerland: University of Geneva.
39. Heled, J. & Drummond, A. J. 2008 Bayesian inference of population size history from multiple loci. BMC Evol. Biol. 8, 289. (doi:10.1186/1471-2148-8-289)
40. Sherman, P. T. 1996 Family Psophiidae (trumpeters). In Handbook of the birds of the world. Vol. 3. Hoatzin to auks (ed. J. del Hoyo), pp. 96-107. Barcelona, Spain: Lynx Edicions.
41. Cracraft, J. 1989 Speciation and its ontology: the empirical consequences of alternative species concepts for understanding patterns and processes of differentiation. In Speciation and its consequences (eds D. Otte & J. Endler), pp. 28-59. Sunderland, MA: Sinauer Associates.
42. Mayle, F. E., Beerling, D. J., Gosling, W. D. & Bush, M. B. 2004 Responses of Amazonian ecosystems to climatic and atmospheric carbon dioxide changes since the last glacial maximum. Phil. Trans. R. Soc. Lond. B 359, 499-514. (doi:10.1098/rstb.2003.1434)
43. Bonaccorso, E., Koch, I. & Peterson, A. T. 2006 Pleistocene fragmentation of Amazon species' ranges. Divers. Distrib. 12, 157-164. (doi:10.1111/j.1366-9516.2005.00212.x)
44. Ravelo, A., Andreasen, D., Lyle, M., Lyle, A. & Wara, M. 2004 Regional climate shifts caused by gradual global cooling in the Pliocene epoch. Nature 429, 263-267. (doi:10.1038/nature02567)
45. Carnaval, A. C., Hickerson, M. J., Haddad, C. F. B., Rodrigues, M. T. & Moritz, C. 2009 Stability predicts genetic diversity in the Brazilian Atlantic Forest hotspot. Science 323, 785-789. (doi:10.1126/science.1166955)
46. Borges, S. H. 2004 Species poor but distinct: bird assemblages in white sand vegetation in Jaú National Park, Brazilian Amazon. Ibis 146, 114-124. (doi:10.1111/j.1474-919X.2004.00230.x)
47. Soares, E. A., Tatumi, S. H. & Riccomini, C. 2010 OSL age determinations of Pleistocene fluvial deposits in Central Amazonia. Anais Acad. Bras. Ciências 82, 1-9. (doi:10.1590/S0001-37652010000100001)
48. Almeida-Filho, R. & Miranda, F. P. 2007 Mega capture of the Rio Negro and formation of the Anavilhanas Archipelago, Central Amazô nia, Brazil: evidences in an SRTM digital elevation model. Remote Sens. Environ. 110, 387-392. (doi:10.1016/j.rse.2007.03.005)
49. Rossetti, D. F. & Valeriano, M. M. 2007 Evolution of the lowest Amazon basin modeled from the integration of geological and SRTM topographic data. Catena 70, 253-265. (doi:10.1016/j.catena.2006.08.009)
50. Gascon, C., Malcolm, J. R., Patton, J. L., da Silva, M. N. F., Bogart, J. P., Loughreed, S. C., Peres, C., Neckel, S. & Boag, P. 2000 Riverine barriers and the geographic distribution of Amazonian species. Proc. Natl Acad. Sci. USA 97, 13672-13677. (doi:10.1073/pnas.230136397)
51. Aleixo, A. 2004 Historical diversification of a terra-firme forest bird superspecies: a phylogeographic perspective of the role of different hypotheses of Amazonian diversification. Evolution 58, 1303-1317.
52. 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 Amazonia, landscape and species evolution: a look into the past (eds C. Hoorn & E. P. Wesselingh), pp. 386-404. London, UK: Wiley-Blackwell.
53. Ayres, M. & Clutton-Brock, T. H. 1992 River boundaries and species range size in Amazonian primates. Am. Nat. 140, 531-537. (doi:10.1086/285427)
54. Marks, B. D., Hackett, S. & Capparella, A. 2002 Historical relationships among neotropical lowland forest areas of endemism as determined by mitochondrial DNA sequence variation within the wedge-billed woodcreeper (Aves: Dendrocolaptidae: Glyphorhynchus spirurus). Mol. Phylogenet. Evol. 24, 153-167. (doi:10.1016/S1055-7903(02)00233-6)
55. Cortés-Ortiz, L., Bermingham, E., Rico, C., Rodríguez-Luna, E., Sampaio, I. & Ruiz-Garcia, M. 2003 Molecular systematics and biogeography of the Neotropical monkey genus Alouatta. Mol. Phylogenet. Evol. 26, 64-81. (doi:10.1016/S1055-7903(02)00308-1)
56. Ribas, C. C., Gaban-Lima, R., Miyaki, C. Y. & Cracraft, J. 2005 Historical biogeography and diversification within the Neotropical parrot genus Pionopsitta (Aves: Psittacidae). J. Biogeogr. 32, 1409-1427. (doi:10.1111/j.1365-2699.2005.01289.x)
57. Weckstein, J. D. 2005 Molecular phylogenetics of the Ramphastos toucans: implications for the evolution of morphology, Vocalizations, and coloration. Auk 122, 1191-1209. (doi:10.1642/0004-8038(2005)122[1191:MPOTRT]2.0.CO;2)
58. Patel, S., Weckstein, J. D. & Bates, J. M. 2010 Molecular systematics and evolution of Pteroglossus araçaris: implications for Neotropical diversification. Mol. Phylogenet. Evol. 58, 105-115.
59. Armenta, J. K., Weckstein, J. D. & Lane, D. F. 2005 Geographic variation in mitochondrial DNA sequences of an Amazonian non-passerine: the Black-spotted Barbet complex. Condor 107, 527-536. (doi:10.1650/0010-5422(2005)107[0527:GVIMDS]2.0.CO;2)
60. Rull, V. 2011 Origins of biodiversity. Science 331, 398-399. (doi:10.1126/science.331.6016.398-c)
61. Maslin, M. A. & Burns, S. J. 2000 Reconstruction of the Amazon Basin effective moisture availability over the past 14,000 years. Science 290, 2285-2287. (doi:10.1126/science.290.5500.2285)