Citing references in text
Allen, A.P., Gillooly, J.F., Savage, V.M. & Brown, J.H. (2006). Kinetic effects of temperature on rates of genetic divergence and speciation.Proc. Natl. Acad. Sci. , 103, 9130–9135.
Antoine, P.O., Roddaz, M., Brichau, S., Tejada-Lara, J., Salas-Gismondi, R., Altamirano, A., et al. (2013). Middle Miocene vertebrates from the Amazonian Madre de Dios Subandean Zone, Perú. J. South Am. Earth Sci. , 42, 91–102.
Antonelli, A., Ariza, M., Albert, J., Andermann, T., Azevedo, J., Bacon, C., et al. (2018a). Conceptual and empirical advances in Neotropical biodiversity research. PeerJ , 6, e5644.
Antonelli, A., Kissling, W.D., Flantua, S.G.A., Bermúdez, M.A., Mulch, A., Muellner-Riehl, A.N., et al. (2018b). Geological and climatic influences on mountain biodiversity. Nat. Geosci. , 11, 718.
Antonelli, A., Nylander, J. a a, Persson, C. & Sanmartín, I. (2009). Tracing the impact of the Andean uplift on Neotropical plant evolution.Proc. Natl. Acad. Sci. U. S. A. , 106, 9749–9754.
Antonelli, A. & Sanmartín, I. (2011). Why are there so many plant species in the Neotropics? Taxon , 60, 403–414.
Antonelli, A., Zizka, A., Carvalho, F.A., Scharn, R., Bacon, C.D., Silvestro, D., et al. (2018c). Amazonia is the primary source of Neotropical biodiversity. Proc. Natl. Acad. Sci. U. S. A. , 115, 6034–6039.
Armijo, R., Lacassin, R., Coudurier-Curveur, A. & Carrizo, D. (2015). Coupled tectonic evolution of Andean orogeny and global climate.Earth-Science Rev. , 143, 1–35.
Bacon, C.D., Velásquez-Puentes, F.J., Hoorn, C. & Antonelli, A. (2018). Iriarteeae palms tracked the uplift of Andean Cordilleras. J. Biogeogr. , 45, 1653–1663.
Bininda-Emonds, O.R.P., Cardillo, M., Jones, K.E., MacPhee, R.D.E., Beck, R.M.D., Grenyer, R., et al. (2007). The delayed rise of present-day mammals. Nature , 446, 507–512.
Blisniuk, P.M., Stern, L.A., Chamberlain, C.P., Idleman, B. & Zeitler, P.K. (2005). Climatic and ecologic changes during Miocene surface uplift in the Southern Patagonian Andes. Earth Planet. Sci. Lett. , 230, 125–142.
Chazot, N., Willmott, K.R., Lamas, G., Freitas, A.V.L., Piron-Prunier, F., Arias, C.F., et al. (2019). Renewed diversification following Miocene landscape turnover in a Neotropical butterfly radiation.Glob. Ecol. Biogeogr. , DOI: 10.11.
Chen, Y.-W., Wu, J. & Suppe, J. (2019). Southward propagation of Nazca subduction along the Andes. Nature , 565, 441–447.
Chomicki, G., Weber, M., Antonelli, A., Bascompte, J. & Kiers, E.T. (2019). The Impact of Mutualisms on Species Richness. Trends Ecol. Evol.
Condamine, F.L. (2018). Limited by the roof of the world: mountain radiations of Apollo swallowtails controlled by diversity-dependence processes. Biol. Lett. , 14, 20170622.
Condamine, F.L., Rolland, J. & Morlon, H. (2013). Macroevolutionary perspectives to environmental change. Ecol. Lett. , 16, 72–85.
Condamine, F.L., Rolland, J. & Morlon, H. (2019). Assessing the causes of diversification slowdowns: temperature-dependent and diversity-dependent models receive equivalent support. Ecol. Lett. , 0.
Davis, M.P., Midford, P.E. & Maddison, W. (2013). Exploring power and parameter estimation of the BiSSE method for analyzing species diversification. BMC Evol. Biol. , 13, 38.
Drummond, C.S., Eastwood, R.J., Miotto, S.T.S. & Hughes, C.E. (2012). Multiple continental radiations and correlates of diversification inLupinus (Leguminosae): testing for key innovation with incomplete taxon sampling. Syst. Biol. , 61, 443–460.
Elsen, P.R. & Tingley, M.W. (2015). Global mountain topography and the fate of montane species under climate change. Nat. Clim. Chang. , 5, 772.
Esquerré, D., Brennan, I.G., Catullo, R.A., Torres-Pérez, F. & Keogh, J.S. (2019). How mountains shape biodiversity: The role of the Andes in biogeography, diversification, and reproductive biology in South America’s most species-rich lizard radiation (Squamata: Liolaemidae).Evolution, https://do.
Etienne, R.S., Haegeman, B., Stadler, T., Aze, T., Pearson, P.N., Purvis, A., et al. (2012). Diversity-dependence brings molecular phylogenies closer to agreement with the fossil record. Proc. R. Soc. London B , 279, 1300–1309.
Etienne, R.S., Pigot, A.L. & Phillimore, A.B. (2016). How reliably can we infer diversity‐dependent diversification from phylogenies?Methods Ecol. Evol. , 7, 1092–1099.
Fjeldså, J., Bowie, R.C.K. & Rahbek, C. (2012). The role of mountain ranges in the diversification of birds. Annu. Rev. Ecol. Evol. Syst. , 43, 249–265.
Flantua, S.G.A., O’dea, A., Onstein, R.E., Giraldo, C. & Hooghiemstra, H. (2019). The flickering connectivity system of the north Andean páramos. J. Biogeogr.
Fouquet, A., Santana Cassini, C., Fernando Baptista Haddad, C., Pech, N. & Trefaut Rodrigues, M. (2014). Species delimitation, patterns of diversification and historical biogeography of the Neotropical frog genus Adenomera (Anura, Leptodactylidae). J. Biogeogr. , 41, 855–870.
Garzione, C.N., Hoke, G.D., Libarkin, J.C., Withers, S., MacFadden, B., Eiler, J., et al. (2008). Rise of the Andes. Science , 320, 1304–1307.
Gentry, A.H. (1982). Neotropical floristic diversity: phytogeographical connections between Central and South America, Pleistocene climatic fluctuations, or an accident of the Andean orogeny? Ann. - Missouri Bot. Gard. , 69, 557–593.
Gillooly, J.F., Brown, J.H., West, G.B., Savage, V.M. & Charnov, E.L. (2001). Effects of Size and Temperature on Metabolic Rate.Science , 293, 2248 LP – 2251.
Haffer, J. (1969). Speciation in Amazon forest birds. Science , 165, 131–137.
Hoorn, C., Bogotá-A, G.R., Romero-Baez, M., Lammertsma, E.I., Flantua, S.G.A., Dantas, E.L., et al. (2017). The Amazon at sea: Onset and stages of the Amazon River from a marine record, with special reference to Neogene plant turnover in the drainage basin. Glob. Planet. Change , 153, 51–65.
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.
Hoorn, C., Wesselingh, F.P., Ter Steege, H., Bermudez, M.A., Mora, A., Sevink, J., et al. (2010). Amazonia through time: Andean uplift, climate change, landscape evolution, and biodiversity. Science , 330, 927–931.
Hughes, C. & Eastwood, R. (2006). Island radiation on a continental scale: Exceptional rates of plant diversification after uplift of the Andes. Proc. Natl. Acad. Sci. U. S. A. , 103, 10334–10339.
Hutter, C.R., Guayasamin, J.M. & Wiens, J.J. (2013). Explaining Andean megadiversity: the evolutionary and ecological causes of glassfrog elevational richness patterns. Ecol. Lett. , 16, 1135–1144.
Hutter, C.R., Lambert, S.M. & Wiens, J.J. (2017). Rapid diversification and time explain Amphibian richness at different scales in the tropical Andes, Earth’s most biodiverse Hotspot. Am. Nat. , 190, 828–843.
Jansson, R., Rodríguez-Castañeda, 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 hypotheses. Evolution, 67, 1741–1755.
Jaramillo, C. (2019). 140 million years of tropical biome evolution. In:The Geology of Colombia (ed. Gomez, J.). Colombian Geological Survey, Bogota, Colombia.
Jaramillo, C. & Cárdenas, A. (2013). Global warming and neotropical rainforests: a historical perspective. Annu. Rev. Earth Planet. Sci. , 41, 741–766.
Jaramillo, C., Rueda, M.J. & Mora, G. (2006). Cenozoic plant diversity in the Neotropics. Science , 311, 1893–1896.
Jaramillo, C.A. (2018). Evolution of the Isthmus of Panama: biological, paleoceanographic and paleoclimatological implications. Mt. Clim. biodiversity. Oxford Wiley Blackwell , 323–338.
Jetz, W., Thomas, G.H., Joy, J.B., Hartmann, K. & Mooers, A.O. (2012). The global diversity of birds in space and time. Nature , 491, 444–448.
Kozak, K.H. & Wiens, J.J. (2010). Accelerated rates of climatic-niche evolution underlie rapid species diversification. Ecol. Lett. , 13, 1378–1389.
Kuhn, T.S., Mooers, A. & Thomas, G.H. (2011). A simple polytomy resolver for dated phylogenies. Methods Ecol. Evol. , 2, 427–436.
Kursar, T.A., Dexter, K.G., Lokvam, J., Pennington, R.T., Richardson, J.E., Weber, M.G., et al. (2009). The evolution of antiherbivore defenses and their contribution to species coexistence in the tropical tree genus Inga . Proc. Natl. Acad. Sci. , 106, 18073–18078.
Lagomarsino, L.P., Condamine, F.L., Antonelli, A., Mulch, A. & Davis, C.C. (2016). The abiotic and biotic drivers of rapid diversification in Andean bellflowers (Campanulaceae). New Phytol. , 210, 1430–1442.
Lambert, A. (2017). The genealogy of a sample from a binary branching process. arXiv Prepr. arXiv1710.02220 .
Leigh Jr, E.G., Davidar, P., Dick, C.W., Terborgh, J., Puyravaud, J., ter Steege, H., et al. (2004). Why do some tropical forests have so many species of trees? Biotropica , 36, 447–473.
Luebert, F. & Weigend, M. (2014). Phylogenetic insights into Andean plant diversification. Front. Ecol. Evol. , doi:10.338.
Luzuriaga-Aveiga, V.E. & Weir, J.T. (2019). Elevational differentiation accelerates trait evolution but not speciation rates in Amazonian birds.Ecol. Lett. , 22, 624–633.
Madriñán, S., Cortés, A. & Richardson, J. (2013). Páramo is the world’s fastest evolving and coolest biodiversity hotspot. Front. Genet.
Mayhew, P.J., Bell, M.A., Benton, T.G. & McGowan, A.J. (2012). Biodiversity tracks temperature over time. Proc. Natl. Acad. Sci. , 109, 15141–15145.
McPeek, M.A. (2008). The ecological dynamics of clade diversification and community assembly. Am. Nat. , 172, E270–E284.
Meseguer, A.S., Lobo, J.M., Cornuault, J., Beerling, D., Ruhfel, B.R., Davis, C.C., et al. (2018). Reconstructing deep-time paleoclimate legacies in the clusioid Malpighiales unveils their role in the evolution and extinction of the boreotropical flora. Glob. Ecol. Biogeogr. , 27, 616–628.
Mittelbach, G.G., Schemske, D.W., Cornell, H. V, Allen, A.P., Brown, J.M., Bush, M.B., et al. (2007). Evolution and the latitudinal diversity gradient: speciation, extinction and biogeography. Ecol. Lett. , 10, 315–331.
Mittermeier, R.A., Turner, W.R., Larsen, F.W., Brooks, T.M. & Gascon, C. (2011). Global biodiversity conservation: the critical role of hotspots. In: Biodiversity Hotspots (eds. Zachos, F.E. & Habel, J.C.). Springer-Verlag, Berlin Heidelberg, Germany, pp. 3–22.
Moen, D. & Morlon, H. (2014). Why does diversification slow down?Trends Ecol. Evol. , 29, 190–197.
Moen, D.S. & Wiens, J.J. (2017). Microhabitat and climatic niche change explain patterns of diversification among frog families. Am. Nat. , 190, 29–44.
Moritz, C., Patton, J.L., Schneider, C.J. & Smith, T.B. (2000). Diversification of rainforest faunas: An integrated molecular approach.Annu. Rev. Ecol. Syst. , 31, 533–563.
Morlon, H., Lewitus, E., Condamine, F.L., Manceau, M., Clavel, J. & Drury, J. (2016). RPANDA: an R package for macroevolutionary analyses on phylogenetic trees. Methods Ecol. Evol. , 7, 589–597.
Morlon, H., Parsons, T.L. & Plotkin, J.B. (2011). Reconciling molecular phylogenies with the fossil record. Proc. Natl. Acad. Sci. , 108, 16327–16332.
Morlon, H., Potts, M.D. & Plotkin, J.B. (2010). Inferring the dynamics of diversification: a coalescent approach. PLOS Biol. , 8, e1000493.
Olalla‐Tárraga, M.Á., McInnes, L., Bini, L.M., Diniz‐Filho, J.A.F., Fritz, S.A., Hawkins, B.A., et al. (2011). Climatic niche conservatism and the evolutionary dynamics in species range boundaries: global congruence across mammals and amphibians. J. Biogeogr. , 38, 2237–2247.
Pérez-Escobar, O.A., Chomicki, G., Condamine, F.L., Karremans, A.P., Bogarín, D., Matzke, N.J., et al. (2017). Recent origin and rapid speciation of Neotropical orchids in the world’s richest plant biodiversity hotspot. New Phytol. , 215, 891–905.
Phillimore, A.B. & Price, T.D. (2008). Density-dependent cladogenesis in birds. PLOS Biol. , 6, e71.
Pie, M.R., Campos, L.L.F., Meyer, A.L.S. & Duran, A. (2017). The evolution of climatic niches in squamate reptiles. Proc. R. Soc. B Biol. Sci. , 284, 1858.
Pinto‐Ledezma, J.N., Simon, L.M., Diniz‐Filho, J.A.F. & Villalobos, F. (2017). The geographical diversification of Furnariides: the role of forest versus open habitats in driving species richness gradients.J. Biogeogr. , 44, 1683–1693.
Pouchon, C., Boyer, F., Lavergne, S., Mavárez, J., Aubert, S., Fernández, A., et al. (2018). Phylogenomic analysis of the explosive adaptive radiation of the Espeletia Complex (Asteraceae) in the Tropical Andes. Syst. Biol. , 67, 1041–1060.
Prokoph, A., Shields, G.A. & Veizer, J. (2008). Compilation and time-series analysis of a marine carbonate δ18O, δ13C, 87Sr/86Sr and δ34S database through Earth history. Earth-Science Rev. , 87, 113–133.
Pyron, R.A. (2014). Biogeographic analysis reveals ancient continental vicariance and recent oceanic dispersal in amphibians. Syst. Biol. , 63, 779–797.
Pyron, R.A. & Burbrink, F.T. (2014). Early origin of viviparity and multiple reversions to oviparity in squamate reptiles. Ecol. Lett. , 17, 13–21.
Rabosky, D.L. (2009). Ecological limits and diversification rate: alternative paradigms to explain the variation in species richness among clades and regions. Ecol. Lett. , 12, 735–743.
Rabosky, D.L., Donnellan, S.C., Grundler, M. & Lovette, I.J. (2014). Analysis and visualization of complex macroevolutionary dynamics: an example from Australian scincid lizards. Syst. Biol. , 63, 610–627.
Richardson, J.-E., Pennington, T.-D. & Hollingsworth, P.-M. (2001). Rapid diversification of a species-rich genus of neotropical rain forest trees. Science , 293, 2242–2245.
Rowan, J., Beaudrot, L., Franklin, J., Reed, K.E., Smail, I.E., Zamora, A., et al. (2019). Geographically divergent evolutionary and ecological legacies shape mammal biodiversity in the global tropics and subtropics. Proc. Natl. Acad. Sci.
Rull, V. (2011a). Neotropical biodiversity: Timing and potential drivers. Trends Ecol. Evol. , 26, 508–513.
Rull, V. (2011b). Origins of biodiversity. Science , 331, 398–399.
Salas-Gismondi, R., Flynn, J.J., Baby, P., Tejada-Lara, J. V, Wesselingh, F.P. & Antoine, P.-O. (2015). A Miocene hyperdiverse crocodylian community reveals peculiar trophic dynamics in proto-Amazonian mega-wetlands. Proc. R. Soc. B Biol. Sci. , 282, 20142490.
Santos, J.C., Coloma, L.A. & Summers, K. (2009). Amazonian amphibian diversity is primarily derived from late Miocene Andean lineages.PLoS Biol. , 7, e1000056.
Silva, G.A.R., Antonelli, A., Lendel, A., Moraes, E. de M. & Manfrin, M.H. (2018). The impact of early Quaternary climate change on the diversification and population dynamics of a South American cactus species. J. Biogeogr. , 45, 76–88.
Silva, S.M., Peterson, A.T., Carneiro, L., Burlamaqui, T.C.T., Ribas, C.C., Sousa-Neves, T., et al. (2019). A dynamic continental moisture gradient drove Amazonian bird diversification. Sci. Adv. , 5, eaat5752.
Simon, M.F., Grether, R., de Queiroz, L.P., Skema, C., Pennington, R.T. & Hughes, C.E. (2009). Recent assembly of the Cerrado, a neotropical plant diversity hotspot, by in situ evolution of adaptations to fire.Proc. Natl. Acad. Sci. , 106, 20359–20364.
Simpson, G.G. (1980). Splendid isolation: the curious history of South American mammals . Yale University Press.
Smith, B.T., McCormack, J.E., Cuervo, A.M., Hickerson, M.J., Aleixo, A., Cadena, C.D., et al. (2014). The drivers of tropical speciation.Nature , 515, 406–409.
Springer, M.S., Meredith, R.W., Gatesy, J., Emerling, C.A., Park, J., Rabosky, D.L., et al. (2012). Macroevolutionary dynamics and historical biogeography of primate diversification inferred from a species supermatrix. PLoS One , 7, e49521.
Stadler, T. (2009). On incomplete sampling under birth–death models and connections to the sampling-based coalescent. J. Theor. Biol. , 261, 58–66.
Stebbins, G.L. (1974). Flowering plants: evolution above the species level . Harvard University Press, Cambridge, Massachusetts.
Veizer, J. & Prokoph, A. (2015). Temperatures and oxygen isotopic composition of Phanerozoic oceans. Earth-Science Rev. , 146, 92–104.
Wallace, A.R. (1878). Tropical nature, and other essays . Macmillan, London.
Weir, J.T. (2006). Divergent timing and patterns of species accumulation in lowland and highland neotropical birds. Evolution, 60, 842–855.
Wiens, J.J. (2017). What explains patterns of biodiversity across the Tree of Life? New research is revealing the causes of the dramatic variation in species numbers across branches of the Tree of Life.BioEssays , 39, 1600128.
Zachos, J.C., Dickens, G.R. & Zeebe, R.E. (2008). An early Cenozoic perspective on greenhouse warming and carbon-cycle dynamics.Nature , 451, 279–283.
Zanne, A.E., Tank, D.C., Cornwell, W.K., Eastman, J.M., Smith, S.A., FitzJohn, R.G., et al. (2014). Three keys to the radiation of angiosperms into freezing environments. Nature , 506, 89–92.