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.