Ali, J. R. (2012). Colonizing the Caribbean: is the GAARlandia land-bridge hypothesis gaining a foothold? J. Biogeogr. 39, 431-433. doi: 10.1111/j.1365-2699.2011.02674.x.
Alonso, R., Crawford, A. J., and Bermingham, E. (2012). Molecular phylogeny of an endemic radiation of Cuban toads (Bufonidae: Peltophryne) based on mitochondrial and nuclear genes. J. Biogeogr. 39, 434-451. doi: 10.1111/j.1365-2699.2011.02594.x.
Antonelli, A. (2008). Spatiotemporal Evolution of Neotropical Organisms: New Insights into an Old Riddle, Doctoral Thesis. Department of Plant and Environmental Sciences, University of Gothenburg, Göteborg.
Antonelli, A., and Sanmartín, I. (2011). Why are there so many plant species in the Neotropics? Taxon 60, 403-414.
Barthlott, W., Hostert, A., Kier, G., Koper, W., Kreft, H., Mutke, J., et al. (2007). Geographic patterns of vascular plant diversity at continental to global scales. Erdkunde 61, 305-315. doi: 10.3112/erdkunde.2007.04.01.
Boakes, E. H., Mcgowan, P. J., Fuller, R. A., Chang-Qing, D., Clark, N. E., O'connor, K., et al. (2010). Distorted views of biodiversity: spatial and temporal bias in species occurrence data. PLoS Biol. 8:e1000385. doi: 10.1371/journal.pbio.1000385.
Bossuyt, F., and Milinkovitch, M. C. (2001). Amphibians as indicators of early tertiary" Out-of-India" dispersal of vertebrates. Science 292, 93-95. doi: 10.1126/science.1058875.
Bremer, B., Bremer, K., Chase, M., Fay, M., Reveal, J., Soltis, D., et al. (2009). An update of the Angiosperm Phylogeny Group classification for the orders and families of flowering plants: APG III. Bot. J. Linn. Soc. 161, 105-121. doi: 10.1111/j.1095-8339.2009.00996.x.
Brown, J. H. (2014). Why are there so many species in the tropics? J. Biogeogr. 41, 8-22. doi: 10.1111/jbi.12228.
Chapman, A. D. (2009). Numbers of Living Species in Australia and the World. Canberra: Australian Government.
Clark, J. R., Ree, R. H., Alfaro, M. E., King, M. G., Wagner, W. L., and Roalson, E. H. (2008). A comparative study in ancestral range reconstruction methods: retracing the uncertain histories of insular lineages. Syst. Biol. 57, 693-707. doi: 10.1080/10635150802426473.
Conti, E., Eriksson, T., Schönenberger, J., Sytsma, K. J., and Baum, D. A. (2002). Early tertiary out-of-India dispersal of Crypteroniaceae: evidence from phylogeny and molecular dating. Evolution 56, 1931-1942. doi: 10.1111/j.0014-3820.2002.tb00119.x.
Crane, P. R. (2004). Documenting plant diversity: unfinished business. Philos. Trans. R. Soc.Lond. B Biol. Sci. 359, 735-737. doi: 10.1098/rstb.2003.1441.
Crews, S. C., and Gillespie, R. G. (2010). Molecular systematics of Selenops spiders (Araneae: Selenopidae) from North and Central America: implications for Caribbean biogeography. Biol. J. Linn. Soc. 101, 288-322. doi: 10.1111/j.1095-8312.2010.01494.x.
Cusimano, N., and Renner, S. S. (2010). Slowdowns in diversification rates from real phylogenies may not be real. Syst. Biol. 59, 458-464. doi: 10.1093/sysbio/syq032.
Cusimano, N., Stadler, T., and Renner, S. S. (2012). A new method for handling missing species in diversification analysis applicable to randomly or nonrandomly sampled phylogenies. Syst. Biol. 61, 785-792. doi: 10.1093/sysbio/sys031.
Drummond, C. S., Eastwood, R. J., Miotto, S. T., and Hughes, C. E. (2012). Multiple continental radiations and correlates of diversification in Lupinus (Leguminosae): testing for key innovation with incomplete taxon sampling. Syst. Biol. 61, 443-460. doi: 10.1093/sysbio/syr126.
Engemann, K., Enquist, B. J., Sandel, B., Boyle, B., Jørgensen, P. M., Morueta-Holme, N., et al. (2015). Limited sampling hampers "big data" estimation of species richness in a tropical biodiversity hotspot. Ecol. Evol. 5, 807-820. doi: 10.1002/ece3.1405.
Erkens, R. H. J., Chatrou, L. W., Maas, J. W., Van Der Niet, T., and Savolainen, V. (2007). A rapid diversification of rainforest trees (Guatteria; Annonaceae) following dispersal from Central into South America. Mol. Phylogenet. Evol. 44, 399-411. doi: 10.1016/j.ympev.2007.02.017.
Favre, A., Päckert, M., Pauls, S. U., Jähnig, S. C., Uhl, D., Michalak, I., et al. (2014). The role of the uplift of the Qinghai-Tibetan Plateau for the evolution of Tibetan biotas. Biol. Rev. 90, 236-253. doi: 10.1111/brv.12107.
Fernández-Mendoza, F., and Printzen, C. (2013). Pleistocene expansion of the bipolar lichen Cetraria aculeata into the Southern hemisphere. Mol. Ecol. 22, 1961-1983. doi: 10.1111/mec.12210.
Fitzjohn, R. G. (2012). Diversitree: comparative phylogenetic analyses of diversification in R. Methods Ecol. Evol. 3, 1084-1092. doi: 10.1111/j.2041-210X.2012.00234.x.
Fritz, S. A., Schnitzler, J., Eronen, J. T., Hof, C., Böhning-Gaese, K., and Graham, C. H. (2013). Diversity in time and space: wanted dead and alive. Trends Ecol. Evol. 28, 509-516. doi: 10.1016/j.tree.2013.05.004.
Govaerts, R. (2001). How many species of seed plants are there? Taxon 50, 1085-1090. doi: 10.2307/1224723.
Gradstein, F. M., Ogg, J. G., Schmitz, M., and Ogg, G. (2012). The Geologic Time Scale. Oxford: Elsevier.
Hansen, J., Sato, M., Kharecha, P., Beerling, D., Berner, R., Masson-Delmotte, V., et al. (2008). Target atmospheric CO2: where should humanity aim? Open Atmos. Sci. J. 2, 217-231. doi: 10.2174/1874282300802010217.
Hillebrand, H. (2004). On the generality of the latitudinal diversity gradient. Am. Nat. 163, 192-211. doi: 10.1086/381004.
Hjarding, A., Tolley, K. A., and Burgess, N. D. (2014). Red list assessments of East African chameleons: a case study of why we need experts. Oryx 48, 1-7. doi: 10.1017/S0030605313001427.
Hohna, S., Stadler, T., Ronquist, F., and Britton, T. (2011). Inferring speciation and extinction rates under different sampling schemes. Mol. Biol. Evol. 28, 2577-2589. doi: 10.1093/molbev/msr095.
Holt, B. G., Lessard, J.-P., Borregaard, M. K., Fritz, S. A., Araújo, M. B., Dimitrov, D., et al. (2013). An update of Wallace's zoogeographic regions of the world. Science 339, 74-78. doi: 10.1126/science.1228282.
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. doi: 10.1126/science.1194585.
Huang, S., Roy, K., and Jablonski, D. (2014). Do past climate states influence diversity dynamics and the present-day latitudinal diversity gradient? Global Ecol. Biogeogr. 23, 530-540. doi: 10.1111/geb.12153.
Huelsenbeck, J. P., Nielsen, R., and Bollback, J. P. (2003). Stochastic mapping of morphological characters. Syst. Biol. 52, 131-158. doi: 10.1080/10635150390192780.
Hughes, C., and 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. doi: 10.1073/pnas.0601928103.
Iturralde-Vinent, M. A., and Macphee, R. D. E. (1999). Paleogeography of the Caribbean region: implications for Cenozoic biogeography. Bull. Am. Mus. Nat. History 238, 1-95.
Jablonski, D., Belanger, C. L., Berke, S. K., Huang, S., Krug, A. Z., Roy, K., et al. (2013). Out of the tropics, but how? Fossils, bridge species, and thermal ranges in the dynamics of the marine latitudinal diversity gradient. Proc. Natl. Acad. Sci.U.S.A. 110, 10487-10494. doi: 10.1073/pnas.1308997110.
Jablonski, D., Roy, K., and Valentine, J. W. (2006). Out of the tropics: evolutionary dynamics of the latitudinal diversity gradient. Science 314, 102-106. doi: 10.1126/science.1130880.
Jansson, R., Rodríguez-Castañeda, G., and 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. doi: 10.1111/evo.12089.
Jaramillo, C., Ochoa, D., Contreras, L., Pagani, M., Carvajal-Ortiz, H., Pratt, L. M., et al. (2010). Effects of rapid global warming at the paleocene-eocene boundary on neotropical vegetation. Science 330, 957-961. doi: 10.1126/science.1193833.
Jetz, W., Thomas, G., Joy, J., Hartmann, K., and Mooers, A. (2012). The global diversity of birds in space and time. Nature 491, 444-448. doi: 10.1038/nature11631.
Karanth, P. K. (2006). Out-of-India Gondwanan origin of some tropical Asian biota. Curr. Sci. 90, 789-792.
Kerkhoff, A. J., Moriarty, P. E., and Weiser, M. D. (2014). The latitudinal species richness gradient in New World woody angiosperms is consistent with the tropical conservatism hypothesis. Proc. Natl. Acad. Sci. U.S.A. 111, 8125-8130. doi: 10.1073/pnas.1308932111.
Kier, G., Mutke, J., Dinerstein, E., Ricketts, T. H., Kuper, W., Kreft, H., et al. (2005). Global patterns of plant diversity and floristic knowledge. J. Biogeogr. 32, 1107-1116. doi: 10.1111/j.1365-2699.2005.01272.x.
Kottek, M., Grieser, J., Beck, C., Rudolf, B., and Rubel, F. (2006). World map of the Köppen-Geiger climate classification updated. Meteorologische Z. 15, 259-263. doi: 10.1127/0941-2948/2006/0130.
Kreft, H., and Jetz, W. (2007). Global patterns and determinants of vascular plant diversity. Proc. Natl. Acad. Sci. U.S.A. 104, 5925-5930. doi: 10.1073/pnas.0608361104.
Kreft, H., and Jetz, W. (2010). A framework for delineating biogeographical regions based on species distributions. J. Biogeogr. 37, 2029-2053. doi: 10.1111/j.1365-2699.2010.02375.x.
Kreft, H., Jetz, W., Mutke, J., and Barthlott, W. (2010). Contrasting environmental and regional effects on global pteridophyte and seed plant diversity. Ecography 33, 408-419. doi: 10.1111/j.1600-0587.2010.06434.x.
Lawing, A. M., and Matzke, N. J. (2014). Conservation paleobiology needs phylogenetic methods. Ecography 37, 001-014. doi: 10.1111/ecog.00783.
Madriñán, S., Cortes, A., and Richardson, J. (2013). Páramo is the world's fastest evolving and coolest biodiversity hotspot. Front. Genet. 4:192. doi: 10.3389/fgene.2013.00192.
Magallón, S., and Sanderson, M. J. (2001). Absolute diversification rates in angiosperm clades. Evolution 55, 1762-1780. doi: 10.1111/j.0014-3820.2001.tb00826.x.
Mannion, P. D., Upchurch, P., Benson, R. B., and Goswami, A. (2014). The latitudinal biodiversity gradient through deep time. Trends Ecol. Evol. 29, 42-50. doi: 10.1016/j.tree.2013.09.012.
Mcloughlin, S. (2001). The breakup history of Gondwana and its impact on pre-Cenozoic floristic provincialism. Aust. J. Bot. 49, 271-300. doi: 10.1071/BT00023.
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. doi: 10.1111/j.1461-0248.2007.01020.x.
Mora, C., Tittensor, D. P., Adl, S., Simpson, A. G. B., and Worm, B. (2011). How many species are there on Earth and in the Ocean? PLoS Biol. 9:e1001127. doi: 10.1371/journal.pbio.1001127.
Morlon, H., Parsons, T. L., and Plotkin, J. B. (2011). Reconciling molecular phylogenies with the fossil record. Proc. Natl. Acad. Sci. U.S.A. 108, 16327-16332. doi: 10.1073/pnas.1102543108.
Mutke, J., Sommer, J. H., Kreft, H., Kier, G., and Barthlott, W. (2011). Vascular plant diversity in a changing world: global centres and biome-specific patterns. Biodivers. Hotspots 83-96. doi: 10.1007/978-3-642-20992-5_5.
Olson, D. M., Dinerstein, E., Wikramanayake, E. D., Burgess, N. D., Powell, G. V., Underwood, E. C., et al. (2001). Terrestrial ecoregions of the world: a new map of life on Earth. Bioscience 51, 933-938. doi: 10.1641/0006-3568(2001)051[0933:TEOTWA]2.0.CO;2.
Parker, J., Rambaut, A., and Pybus, O. G. (2008). Correlating viral phenotypes with phylogeny: accounting for phylogenetic uncertainty. Infect. Genet. Evol. 8, 239-246. doi: 10.1016/j.meegid.2007.08.001.
Pennington, R. T., and Dick, C. W. (2004). The role of immigrants in the assembly of the South American rainforest tree flora. Philos. Trans. R. Soc.B Biol. Sci. 359, 1611-1622. doi: 10.1098/rstb.2004.1532.
Pianka, E. R. (1966). Latitudinal gradients in species diversity: a review of concepts. Am. Nat. 100, 33-46. doi: 10.1086/282398.
Pyron, R. A. (2014). Temperate extinction in squamate reptiles and the roots of latitudinal diversity gradients. Global Ecol. Biogeog. 23, 1126-1134. doi: 10.1111/geb.12196.
Pyron, R. A., and Wiens, J. J. (2013). Large-scale phylogenetic analyses reveal the causes of high tropical amphibian diversity. Proc. R. Soc. B Biol. Sci. 280:20131622. doi: 10.1098/rspb.2013.1622.
Quental, T. B., and Marshall, C. R. (2010). Diversity dynamics: molecular phylogenies need the fossil record. Trends Ecol. Evol. 25, 434-441. doi: 10.1016/j.tree.2010.05.002.
Revell, L. J. (2012). phytools: an R package for phylogenetic comparative biology (and other things). Methods Ecol. Evol. 3, 217-223. doi: 10.1111/j.2041-210X.2011.00169.x.
Rícan, O., Piálek, L., Zardoya, R., Doadrio, I., and Zrzavỳ, J. (2013). Biogeography of the Mesoamerican Cichlidae (Teleostei: Heroini): colonization through the GAARlandia land bridge and early diversification. J. Biogeogr. 40, 579-593. doi: 10.1111/jbi.12023.
Richardson, J. E., Pennington, R. T., Pennington, T. D., and Hollingsworth, P. M. (2001). Rapid diversification of a species-rich genus of neotropical rain forest trees. Science 293, 2242-2245. doi: 10.1126/science.1061421.
Rolland, J., Condamine, F. L., Jiguet, F., and Morlon, H. (2014). Faster speciation and reduced extinction in the tropics contribute to the mammalian latitudinal diversity gradient. PLoS Biol. 12:e1001775. doi: 10.1371/journal.pbio.1001775.
Ronquist, F., Klopfstein, S., Vilhelmsen, L., Schulmeister, S., Murray, D. L., and Rasnitsyn, A. P. (2012). A totaly-evidence approach to dating with fossils, applied to the early radiation of the Hymenoptera. Syst. Biol. 61, 973-999. doi: 10.1093/sysbio/sys058.
Rull, V. (2011). Neotropical biodiversity: Timing and potential drivers. Trends Ecol. Evol. 26, 508-513. doi: 10.1016/j.tree.2011.05.011.
Silvestro, D. (2012). Diversification in Time and Space. Methodological Advancement and Case Studies from the Neotropical Plant Family Bromeliaceae. Doctoral Dissertation, Frankfurt am Main: Johann-Wolfgang-Goethe-University.
Silvestro, D., Cascales-Miñana, B., Bacon, C. D., and Antonelli, A. (2015). Revisiting the origin and diversification of vascular plants through a comprehensive Bayesian analysis of the fossil record. New Phytol. doi: 10.1111/nph.13247. [Epub ahead of print].
Silvestro, D., Schnitzler, J., Liow, L. H., Antonelli, A., and Salamin, N. (2014). Bayesian estimation of speciation and extinction from incomplete fossil occurrence data. Syst. Biol. 63, 349-367. doi: 10.1093/sysbio/syu006.
Slater, G. J., and Harmon, L. J. (2013). Unifying fossils and phylogenies for comparative analyses of diversification and trait evolution. Methods Ecol. Evol. 4, 699-702. doi: 10.1111/2041-210X.12091.
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. doi: 10.1038/nature13687.
Stadler, T. (2011). Inferring speciation and extinction processes from extant species data. Proc. Natl. Acad. Sci. U.S.A. 108, 16145-16146. doi: 10.1073/pnas.1113242108.
Stadler, T., and Bokma, F. (2013). Estimating speciation and extinction rates for phylogenies of higher taxa. Syst. Biol. 62, 220-230. doi: 10.1093/sysbio/sys087.
Stebbins, G. L. (1974). Flowering Plants: Evolution Above the Species Level. Cambridge, MA: Belknap.
Team, R. C. (2014). R: A Language and Environment for Statistical Computing. Vienna: Foundation for Statistical Computing.
Ter Steege, H., Haripersaud, P. P., Bánki, O. S., and Schieving, F. (2011). A model of botanical collectors' behavior in the field: never the same species twice. Am. J. Bot. 98, 31-37. doi: 10.3732/ajb.1000215.
Töpel, M., Calió, M. F., Zizka, A., Scharn, R., Silvestro, D., and Antonelli, A. (2014). SpeciesGeoCoder: fast categorisation of species occurrences for analyses of biodiversity, biogeography, ecology and evolution. bioRxiv doi: 10.1101/009274.
Ungricht, S. (2004). How many plant species are there? And how many are threatened with extinction? Endemic species in global biodiversity and conservation assessments. Taxon 53, 481-484. doi: 10.2307/4135626.
Vilhena, D. A., and Antonelli, A. (2014). Beyond Similarity: a Network Approach for Identifying and Delimiting Biogeographical Regions.
Weir, J. T., and Schluter, D. (2007). The latitudinal gradient in recent speciation and extinction rates of birds and mammals. Science 315, 1574-1576. doi: 10.1126/science.1135590.
Wesselingh, F. P., Hoorn, C., Kroonenberg, S. B., Antonelli, A., Lundberg, J. G., Vonhof, H. B., et al. (2010). On the origin of Amazonian landscapes and biodiversity: a synthesis. in Amazonia, Landscape and Species Evolution, 1st Edn., eds C. Hoorn and F. P. Wesselingh (Oxford: Blackwell publishing), 421-431.
Wiens, J. J., Graham, C. H., Moen, D. S., Smith, S. A., and Reeder, T. W. (2006). Evolutionary and ecological causes of the latitudinal diversity gradient in hylid frogs: treefrog trees unearth the roots of high tropical diversity. Am. Nat. 168, 579-596. doi: 10.1086/507882.
Wood, H. M., Matzke, N. J., Gillespie, R. G., and Griswold, C. E. (2013). Treating fossils as terminal taxa in divergence time estimation reveals ancient vicariance patterns in the palpimanoid spiders. Syst. Biol. 62, 264-284. doi: 10.1093/sysbio/sys092.
Wortley, A. H., and Scotland, R. W. (2004). Synonymy, sampling and seed plant numbers. Taxon 478-480. doi: 10.2307/4135625.
Zachos, J. C., Dickens, G. R., and Zeebe, R. E. (2008). An early Cenozoic perspective on greenhouse warming and carbon-cycle dynamics. Nature 451, 279-283. doi: 10.1038/nature06588.
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. doi: 10.1038/nature12872.
Zhang, Z., Ramstein, G., Schuster, M., Li, C., Contoux, C., and Yan, Q. (2014). Aridification of the Sahara desert caused by Tethys Sea shrinkage during the Late Miocene. Nature 513, 401-404. doi: 10.1038/nature13705.