Hoorn, C. et al. Amazonia through time: Andean uplift, climate change, landscape evolution, and biodiversity. Science 330, 927–931 (2010).
Feijó, A. et al. Mammalian diversification bursts and biotic turnovers are synchronous with cenozoic geoclimatic events in asia. Proc. Natl Acad. Sci. USA 119, e2207845119 (2022).
Antonelli, A. et al. Geological and climatic influences on mountain biodiversity. Nat. Geosci. 11, 718–725 (2018).
Sklenár, P., Hedberg, I. & Cleef, A. M. Island biogeography of tropical alpine floras. J. Biogeogr. 41, 287–297 (2014).
McCormack, J. E., Huang, H. & Knowles, L. L. in Encyclopedia of Islands (eds Gillespie, R. G. & Clague, D.) 839–843 (Univ. Chicago Press, 2009).
Ebersbach, J., Schnitzler, J., Favre, A. & Muellner-Riehl, A. Evolutionary radiations in the species-rich mountain genus Saxifraga L. BMC Evol. Biol. 17, 119 (2017).
Ding, W.-N., Ree, R. H., Spicer, R. A. & Xing, Y.-W. Ancient orogenic and monsoon-driven assembly of the world’s richest temperate alpine flora. Science 369, 578–581 (2020).
Boschman, L. M. & Condamine, F. L. Mountain radiations are not only rapid and recent: ancient diversification of South American frog and lizard families related to Paleogene Andean orogeny and Cenozoic climate variations. Glob. Planet. Change 208, 103704 (2022).
Sedano, R. E. & Burns, K. J. Are the Northern Andes a species pump for neotropical birds? Phylogenetics and biogeography of a clade of Neotropical tanagers (Aves: Thraupini). J. Biogeogr. 37, 325–343 (2010).
Lagomarsino, L. P., Condamine, F. L., Antonelli, A., Mulch, A. & Davis, C. C. The abiotic and biotic drivers of rapid diversification in Andean bellflowers (Campanulaceae). New Phytol. 210, 1430–1442 (2016).
Kandziora, M. et al. The enigmatic tropical alpine flora on the african sky islands is young, disturbed, and unsaturated. Proc. Natl Acad. Sci. USA 119, e2112737119 (2022).
Nevado, B., Contreras-Ortiz, N., Hughes, C. & Filatov, D. A. Pleistocene glacial cycles drive isolation, gene flow and speciation in the high-elevation Andes. New Phytol. 219, 779–793 (2018).
Zhang, J. et al. Evolutionary history of the Arctic flora. Nat. Commun. 14, 4021 (2023).
Vasconcelos, T. N. C. et al. Fast diversification through a mosaic of evolutionary histories characterizes the endemic flora of ancient neotropical mountains. Proc. R. Soc. B Biol. Sci. 287, 20192933 (2020).
Kadereit, J. W. The role of in situ species diversification for the evolution of high vascular plant species diversity in the European Alps—a review and interpretation of phylogenetic studies of the endemic flora of the Alps. Perspect. Plant Ecol. Evol. Syst. 26, 28–38 (2017).
Ball, J. On the origin of the flora of the European Alps. Proc. R. Geogr. Soc. 1, 564–589 (1879).
Ozenda, P. La végétation de la chai^ne alpine dans l’espace montagnard européen (Masson, 1985).
Ozenda, P. On the genesis of the plant population in the Alps: new or critical aspects. C. R. Biol. 332, 1092–1103 (2009).
Kadereit, J. W., Licht, W. & Uhink, C. H. Asian relationships of the flora of the European Alps. Plant Ecol. Divers. 1, 171–179 (2008).
Favre, A. et al. Out of Tibet: the spatio-temporal evolution of Gentiana (Gentianaceae). J. Biogeogr. 43, 1967–1978 (2016).
Comes, H. P. & Kadereit, J. W. Spatial and temporal patterns in the evolution of the flora of the European Alpine system. TAXON 52, 451–462 (2003).
Hughes, C. E. & Atchison, G. W. The ubiquity of alpine plant radiations: from the Andes to the Hengduan mountains. New Phytol. 207, 275–282 (2015).
Boucher, F. C., Zimmermann, N. E. & Conti, E. Allopatric speciation with little niche divergence is common among Alpine Primulaceae. J. Biogeogr. 43, 591–602 (2016).
Smyčka, J. et al. Tempo and drivers of plant diversification in the European mountain system. Nat. Commun. 13, 2750 (2022).
Fauquette, S. et al. Quantifying the Eocene to Pleistocene topographic evolution of the southwestern Alps, France and Italy. Earth Planet. Sci. Lett. 412, 220–234 (2015).
Gradwohl, G., Stüwe, K., ROBL, J. & Liebl, M. in Geodynamics of the Alps Vol. 1 (Rosenberg, C. L. & Bellahsen, N.) 115–160 (ISTE, 2023).
Krsnik, E. et al. Miocene high elevation in the Central Alps. Solid Earth 12, 2615–2631 (2021).
Fox, M., Herman, F., Willett, S. D. & Schmid, S. M. The exhumation history of the European Alps inferred from linear inversion of thermochronometric data. Am. J. Sci. 316, 505–541 (2016).
Herwegh, M. et al. Late stages of continent–continent collision: timing, kinematic evolution, and exhumation of the Northern rim (Aar Massif) of the Alps. Earth Sci. Rev 200, 102959 (2020).
Winterberg, S. & Willett, S. D. Greater Alpine river network evolution, interpretations based on novel drainage analysis. Swiss J. Geosci. 112, 3–22 (2019).
Zachos, J., Pagani, M., Sloan, L., Thomas, E. & Billups, K. Trends, rhythms, and aberrations in global climate 65 Ma to present. Science 292, 686–693 (2001).
Favre, A. et al. The role of the uplift of the Qinghai Tibetan Plateau for the evolution of Tibetan biotas. Biol. Rev. 90, 236–253 (2015).
Hagen, O. et al. Mountain building, climate cooling and the richness of cold-adapted plants in the Northern Hemisphere. J. Biogeogr. 46, 1792–1807 (2019).
Sternai, P. et al. Present-day uplift of the European Alps: evaluating mechanisms and models of their relative contributions. Earth Sci. Rev. 190, 589–604 (2019).
Valla, P. G., Sternai, P. & Fox, M. How climate, uplift and erosion shaped the Alpine topography. Elements 17, 41–46 (2021).
Winkworth, R. Evolution of the New Zealand mountain flora: origins, diversification and dispersal. Org. Divers. Evol. 5, 237–247 (2005).
Flantua, S. G., O’Dea, A., Onstein, R. E., Giraldo, C. & Hooghiemstra, H. The flickering connectivity system of the North Andean páramos. J. Biogeogr. 46, 1808–1825 (2019).
Schonswetter, P., Stehlik, I., Holderegger, R. & Tribsch, A. Molecular evidence for glacial refugia of mountain plants in the European Alps. Mol. Ecol. 14, 3547–3555 (2005).
Alvarez, N. et al. History or ecology? Substrate type as a major driver of spatial genetic structure in Alpine plants. Ecol. Lett. 12, 632–640 (2009).
Thiel-Egenter, C. et al. Break zones in the distributions of alleles and species in alpine plants: break zones in allele and species distributions. J. Biogeogr. 38, 772–782 (2011).
Taberlet, P. et al. Genetic diversity in widespread species is not congruent with species richness in Alpine plant communities. Ecol. Lett. 15, 1439–1448 (2012).
Paun, O., Schönswetter, P., Winkler, M., Consortium, I. & Tribsch, A. Historical divergence vs. contemporary gene flow: evolutionary history of the calcicole Ranunculus alpestris group (Ranunculaceae) in the European Alps and the Carpathians. Mol. Ecol. 17, 4263–4275 (2008).
Zhang, L., Comes, H. P. & Kadereit, J. W. The temporal course of quaternary diversification in the European high mountain endemic Primula sect. Auricula (Primulaceae). Int. J. Plant Sci. 165, 191–207 (2004).
Parisod, C. Plant speciation in the face of recurrent climate changes in the Alps. Alp. Bot. 132, 21–28 (2022).
Boucher, F. C. et al. Discovery of cryptic plant diversity on the rooftops of the Alps. Sci. Rep. 11, 11128 (2021).
Alsos, I. G. et al. The treasure vault can be opened: large-scale genome skimming works well using herbarium and silica gel dried material. Plants 9, 432 (2020).
Wang, Y. et al. Late quaternary dynamics of Arctic biota from ancient environmental genomics. Nature 600, 86–92 (2021).
Lavergne, S. et al. Towards a comprehensive barcoding and phylogenomic reference for the European Arctic–alpine flora. Preprint at Research Square https://doi.org/10.21203/rs.3.rs-6136147/v1 (2025).
Aeschimann, D., Lauber, K., Moser, D. M. & Theurillat, J.-P. Flora Alpina Vols 1–3 (Haupt, 2004).
Smith, S. A. & O’Meara, B. C. treePL: divergence time estimation using penalized likelihood for large phylogenies. Bioinformatics 28, 2689–2690 (2012).
Ramírez-Barahona, S., Sauquet, H. & Magallón, S. The delayed and geographically heterogeneous diversification of flowering plant families. Nat. Ecol. Evol. 4, 1232–1238 (2020).
Hörandl, E. & Emadzade, K. The evolution and biogeography of alpine species in Ranunculus (Ranunculaceae): a global comparison. TAXON 60, 415–426 (2011).
Wagner, N. D., He, L. & Hörandl, E. The evolutionary history, diversity, and ecology of willows (Salix L.) in the European Alps. Diversity 13, 146 (2021).
Carruthers, T. et al. Repeated upslope biome shifts in Saxifraga during Late-Cenozoic climate cooling. Nat. Commun. 15, 1100 (2024).
Valente, L. M., Phillimore, A. B. & Etienne, R. S. Equilibrium and non equilibrium dynamics simultaneously operate in the Galápagos Islands. Ecol. Lett. 18, 844–852 (2015).
Mosbrugger, V., Favre, A., Muellner-Riehl, A. N., Päckert, M. & Mulch, A. in Mountains, Climate and Biodiversity (eds Hoorn, C. et al.) Ch. 28 (Wiley-Blackwell, 2018).
Muellner Riehl, A. N. et al. Origins of global mountain plant biodiversity: testing the ‘mountain geobiodiversity hypothesis’. J. Biogeogr. 46, 2826–2838 (2019).
MacArthur, R. H. & Wilson, E. O. The Theory of Island Biogeography (Princeton Univ. Press, 1967).
Legrain, N., Stüwe, K. & Wölfler, A. Incised relict landscapes in the Eastern Alps. Geomorphology 221, 124–138 (2014).
Muttoni, G. et al. Onset of major Pleistocene glaciations in the Alps. Geology 31, 989–992 (2003).
Steinbauer, M. J. et al. Topography-driven isolation, speciation and a global increase of endemism with elevation: topographic isolation and endemism. Glob. Ecol. Biogeogr. 25, 1097–1107 (2016).
Aguilée, R., Claessen, D. & Lambert, A. Adaptive radiation driven by the interplay of eco-evolutionary and landscape dynamics. Evolution 67, 1291–1306 (2013).
Thomas, A. et al. Multiple origins of mountain biodiversity in New Zealand’s largest plant radiation. J. Biogeogr. 50, 947–960 (2023).
Dullinger, S. et al. Post-glacial migration lag restricts range filling of plants in the European Alps: range filling of alpine plants. Glob. Ecol. Biogeogr. 21, 829–840 (2012).
Janzen, D. H. Why mountain passes are higher in the tropics. Am. Nat. 101, 233–249 (1967).
Qian, H. & Sandel, B. Phylogenetic structure of regional angiosperm assemblages across latitudinal and climatic gradients in North America. Glob. Ecol. Biogeogr. 26, 1258–1269 (2017).
Gehrke, B. Staying cool: preadaptation to temperate climates required for colonising tropical alpine-like environments. PhytoKeys 96, 111–125 (2018).
Qian, H., Ricklefs, R. E. & Thuiller, W. Evolutionary assembly of flowering plants into sky islands. Nat. Ecol. Evol. 5, 640–646 (2021).
Pouchon, C. et al. Orthoskim: in silico sequence capture from genomic and transcriptomic libraries for phylogenomic and barcoding applications. Mol. Ecol. Resour. 22, 2018–2037 (2022).
Katoh, K. & Standley, D. M. MAFFTmultiple sequence alignment software version 7: improvements in performance and usability. Mol. Biol. Evol. 30, 772–780 (2013).
Capella-Gutiérrez, S., Silla-Martínez, J. M. & Gabaldón, T. trimal: a tool for automated alignment trimming in large-scale phylogenetic analyses. Bioinformatics 25, 1972–1973 (2009).
Minh, B. Q. et al. Iq-tree 2: new models and efficient methods for phylogenetic inference in the genomic era. Mol. Biol. Evol. 37, 1530–1534 (2020).
Li, H.-T. et al. Origin of angiosperms and the puzzle of the Jurassic gap. Nat. Plants 5, 461–470 (2019).
Paradis, E. & Schliep, K. ape 5.0: an environment for modern phylogenetics and evolutionary analyses in R. Bioinformatics 35, 526–528 (2019).
Salisbury, B. A. & Kim, J. Ancestral state estimation and taxon sampling density. Syst. Biol. 50, 557–564 (2001).
Körner, C. Alpine Plant Life: Functional Plant Ecology of High Mountain Ecosystems 2nd edn (Springer, 2011).
Westerhold, T. et al. An astronomically dated record of Earth’s climate and its predictability over the last 66 million years. Science 369, 1383–1387 (2020).
Lindeløv, J. K. mcp: an R package for regression with multiple change points. OSF Preprints https://doi.org/10.31219/osf.io/fzqxv (2020).
Vehtari, A., Gelman, A. & Gabry, J. Practical Bayesian model evaluation using leave-one-out cross-validation and WAIC. Stat. Comput. 27, 1413–1432 (2017).
Wootton, L. M. et al. The late rise of sky-island vegetation in the European Alps: supplementary data. figshare https://doi.org/10.6084/m9.figshare.25459135 (2025).
PhyloAps & PhyloNorway. A Genome Skim Database for the Arctic-Alpine Flora (Arctic-Alpine PhyloSkims, accessed 1 February 2024); https://phyloalps.osug.fr/main/home
