Some problems in the study of the origin of neotropical biodiversity using palaeoecological and molecular phylogenetic evidence

References

• Ab'Sáber, N. 1982. The paleoclimate and paleoecology of Brazilian Amazônia. In Prance, G.T., Ed., Biological Diversification in the Tropics. Columbia University Press, New York, USA, pp. 95–104.
   Google Scholar
• Arita, H.T. & Vásquez-Domínguez, E. 2008. The tropics, cradle, museum or casino? A dynamic null model for latitudinal gradients of species diversity. Ecology Letters 11, 653–663.
   PubMed Web of Science ®Google Scholar
• Blumberg, B.S. 2010. Astrobiology, space and the future age of discovery. Philosophical Transactions of the Royal Society A 369, 508–515.
   Web of Science ®Google Scholar
• Brook, B.W., Sodhi, N.S. & Bradshaw, J.A. 2008. Synergies among extinction drivers under global change. Trends in Ecology and Evolution 23, 453–460.
   PubMed Web of Science ®Google Scholar
• Brumfield, R.T. 2012. Inferring the origins of lowland neotropical birds. Auk 129, 367–376.
   Web of Science ®Google Scholar
• Bush, M.B. 1994. Amazonian speciation, a necessarily complex model. Journal of Biogeography 21, 5–17.
   Web of Science ®Google Scholar
• Bush, M.B. & De Oliveira, P.E. 2006. The rise and fall of the refugial hypothesis of Amazonian speciation: a paleoecological perspective. Biota Neotropica 6, 1–17.
   Google Scholar
• Chamberlin, T.C. 1890. The method of multiple working hypotheses. Science (old series) 15, 92–96 (reprinted 1965, 148, 754–759).
   PubMedGoogle Scholar
• Cheng, H., Sinha, A., Cruz, F.W., Wang, X., Edwards, R.L., d'Horta, F.M., Ribas, C.C., Vuille, M., Scott, L.D. & Auler, A.S. 2013. Climate change patterns in Amazonia and biodiversity. Nature Communications 4:1411. doi: 10.1038/ncomms2415.
   PubMed Web of Science ®Google Scholar
• Cody, S., Richardson, J.R., Rull, V., Ellis, C. & Pennington, R.T. 2010. The Great American Biotic Interchange revisited. Ecography 33, 326–332.
   Web of Science ®Google Scholar
• Colinvaux, P.A. & De Oliveira, P.E. 2001. Amazon plant diversity and climate through the Cenozoic. Palaeogeography, Palaeoclimatology, Palaeoecology 166, 51–63.
   Web of Science ®Google Scholar
• Colinvaux, P.A., De Oliveira, P.E. & Bush, M.B. 2000. Amazonian and neotropical plant communities on glacial time scales: The failure of the aridity and refuge hypothesis. Quaternary Science Reviews 19, 141–169.
   Web of Science ®Google Scholar
• Erwin, D.H. 2009. Climate as driver of evolutionary change. Current Biology 19, 575–583.
   Web of Science ®Google Scholar
• Haffer, J. 1969. Speciation in Amazonian forest birds. Science 165, 131–137.
   PubMed Web of Science ®Google Scholar
• Haffer, J. 2008. Hypotheses to explain the origin of species in Amazonia. Brazilian Journal of Biology 68, 917–947.
   PubMed Web of Science ®Google Scholar
• Harrison, A.A. 2011. Fear, pandemonium, equanimity and delight: human responses to extra-terrestrial life. Philosophilal Transactions of the Royal Society A 369, 656–668.
   Web of Science ®Google Scholar
• Hoorn, C. & Wesselingh, F.P. 2010. Amazonia, landscape and species evolution: a look into the past. Wiley-Blackwell, New York, USA.
   Google Scholar
• Hoorn, C., Wesselingh, F.P., ter Steege, H., Bermudez, M.A., Mora, A., Sevink, J., Sanmartín, I., Sanchez-Meseguer, A. Anderson, C.L., Figueiredo, J.P., Jaramillo, C., Riff, D., Negri, F.R., Hooghiemstra, H., Lundberg, J., Stadler, T., Sarkinen, T. & Antonelli, A. 2010. Amazonia through time: Andean uplift, climate change, landscape evolution, and biodiversity. Science 330, 927–931.
   PubMed Web of Science ®Google Scholar
• Hoorn, C., Wesselingh, F.P., ter Steege, H., Bermudez, M.A., Mora, A., Sevink, J., Sanmartín, I., Sanchez-Meseguer, A., Anderson, C.L., Figueiredo, J.P., Jaramillo, C., Riff, D., Negri, F.R., Hooghiemstra, H., Lundberg, J., Stadler, T., Sarkinen, T. & Antonelli, A. 2011. Origins of biodiversity-response. Science 331, 399–400.
   Web of Science ®Google Scholar
• Hubbell, S.P. 2001. The Unified Neutral Theory of Biodiversity and Biogeography. Princeton University Press, Princeton, NJ, USA.
   Google Scholar
• Hughes, C. & Eastwood, R. 2006. Island radiation on a continental scale: exceptional rates of plant diversification after uplift of the Andes. Proceedings of the National Academy of Sciences USA 103, 10334–10339.
   PubMed Web of Science ®Google Scholar
• Hughes, C.E., Pennington, R.T. & Antonelli, A. 2013. Neotropical plant evolution. Botanical Journal of the Linnean Society 171, 1–18.
   Web of Science ®Google Scholar
• Jansson, R., Rodríguez-Castaneda, G. & Harding, L.E. 2013. What can multiple phylogenies say about the latitudinal diversity gradient? A new look at the tropical conservatism, out of the tropics, and diversification rate hypthesis. Evolution 67, 1741–1755.
   PubMed Web of Science ®Google Scholar
• Lötters, S., Meijden, A., Rödder, D., Köster, T.E., Kraus, T., La Marca, E., Haddad, C.F.B. & Veith, M. 2010. Reinforcing and expanding the predictions of the disturbance vicariance hypothesis in Amazonian harlequin frogs: a molecular phylogenetic and climate envelope modelling approach. Biodiversity and Conservation 19, 2125–2146.
   Web of Science ®Google Scholar
• Mittelbach, G.G., Schemske, D.W., Cornell, H.V., Allen, A.P., Brown, J.M., Bush, M.B., Harrison, S.P., Hurlbert, A.H., Knowlton, N., Lessios, H.A., McCain, C.M., McCune, A.R., McDade, L.A., McPeek, M.A., Near, T.J., Price, T.D., Ricklefs, R.E., Roy, K., Sax, D.F., Schluter, D., Sobel, J.M. & Turelli, M. 2007. Evolution and the latitudinal diversity gradient, speciation, extinction and biogeography. Ecology Letters 4, 315–331.
   Web of Science ®Google Scholar
• Moritz, C. 1994. Defining ‘evolutionarily significant units’ for conservation. Trends in Ecology and Evolution 9, 373–375.
   PubMed Web of Science ®Google Scholar
• Moritz, C., Patton, J.L., Schneider, C.J. & Smith, T. B. 2000. Diversification of rainforest faunas: an integrated molecular approach. Annual Reviews of Ecology and Systematics 31, 533–563.
   Google Scholar
• Nagalingum, N.S., Marshall, C.R., Quental, T.B., Rai, H.S., Little, D.P. & Mathews, S. 2011. Recent synchronous radiation of a living fossil. Science 334, 796–799.
   PubMed Web of Science ®Google Scholar
• Noonan, B.P. & Gaucher, P. 2005. Phylogeography and demography of Guianan harlequin toads (Atelopus): diversification within a refuge. Molecular Ecology 14, 3017–3031.
   PubMed Web of Science ®Google Scholar
• Nores, M. 1999. An alternative hypothesis for the origin of Amazonian bird diversity. Journal of Biogeography 26, 475–485.
   Web of Science ®Google Scholar
• Parenti, L.R. & Ebach, M.C. 2013. Evidence and hypothesis in biogeography. Journal of Biogeography 40, 813–820.
   Web of Science ®Google Scholar
• Pennington, R.T., Lavin M., Prado, D.E., Pendry, C.A., Pell, S.K. & Butterworth, C.A. 2004. Historical climate change and speciation: neotropical seasonally dry forest plants show patterns of both Tertiary and Quaternary diversification. Philosophical Transactions of the Royal Society B 359, 515–537.
   PubMed Web of Science ®Google Scholar
• Prance, G.T. 1982. Biological Diversification in the Tropics. Columbia University Press, New York, USA.
   Google Scholar
• Quental, T.B. & Marshall, C.R. 2010. Diversity dynamics, molecular phylogenies need the fossil record. Trends in Ecology and Evolution 25, 434–441.
   PubMed Web of Science ®Google Scholar
• Renner, S.S. 2011. Living fossil younger than thought. Science 334, 766–767.
   PubMed Web of Science ®Google Scholar
• Ribas, C.C., Aleixo, A., Nogueira, A.C.R., Miyaki, C.Y. & Cracraft, J. 2011. A palaeobiogeographic model for biotic diversification within Amazonia over the past three million years. Proceedings of the Royal Society B 279, 681–689.
   PubMed Web of Science ®Google Scholar
• Ricklefs, R.E. 2007. Estimating diversification rates from phylogenetic information. Trends in Ecology and Evolution 22: 601–610.
   PubMed Web of Science ®Google Scholar
• Rull, V. 2008. Speciation timing and neotropical biodiversity, the Tertiary-Quaternary debate in the light of molecular phylogenetic evidence. Molecular Ecology 17, 2722–2729.
   PubMed Web of Science ®Google Scholar
• Rull, V. 2011a. Origins of biodiversity. Science 331, 398–399.
   PubMed Web of Science ®Google Scholar
• Rull, V. 2011b. Neotropical biodiversity: timing and potential drivers. Trends in Ecology and Evolution 26, 508–513.
   PubMed Web of Science ®Google Scholar
• Rull, V. 2012a. Community ecology: diversity and dynamics over time. Community Ecology 13, 102–116.
   Web of Science ®Google Scholar
• Rull, V. 2012b. Palaeobiodiversity and taxonomic resolution: linking past trends with present patterns. Journal of Biogeography 39, 1005–1006.
   Web of Science ®Google Scholar
• Rutschmann, F. 2006. Molecular dating of phylogenetic trees: a brief review of current methods that estimate divergence times. Diversity and Distributions 12, 35–48.
   Web of Science ®Google Scholar
• Tattersall, I. & Schwartz, J.H. 2009. Evolution of the genus Homo. Annual Reviews of Earth and Planetary Sciences 37, 67–72.
   Web of Science ®Google Scholar
• Turchetto-Zolet, A.C., Pinheiro, F., Salgueiro, F. & Palma-Silva, C. 2013. Phylogeographical patterns shed light on evolutionary process in South America. Molecular Ecology 22, 1193–1213.
   PubMed Web of Science ®Google Scholar
• Whitmore, T.C. & Prance, G.T. 1987. Biogeography and Quaternary History in Tropical America. Oxford University Press, London, UK.
   Google Scholar
• Wiens, J.J. & Donoghue, M.J. 2004. Historical biogeography, ecology and species richness. Trends in Ecology and Evolution 19, 639–644.
   PubMed Web of Science ®Google Scholar