Shackleton, N. J., Sánchez-Goñi, M. F., Pailler, D. & Lancelot, Y. Marine isotope substage 5e and the eemian interglacial. Glob. Planet. Change 36, 151–155 (2003).
Google Scholar
Shackleton, N. J., Chapman, M., Sánchez-Goñi, M. F., Pailler, D. & Lancelot, Y. The classic marine isotope substage 5e. Quat. Res. 58, 14–16 (2002).
Google Scholar
Hofreiter, M. & Stewart, J. Ecological change, range fluctuations and population dynamics during the pleistocene. Curr. Biol. 19, R584–R594 (2009).
Google Scholar
Hewitt, G. M. Post-glacial re-colonization of European biota. Biol. J. Linn. Soc. 68, 87–112 (1999).
Petit, R. J. et al. Glacial refugia: hotspots but not melting pots of genetic diversity. Science 300, 1563–1565 (2003).
Google Scholar
Magri, D., Di Rita, F., Aranbarri, J., Fletcher, W. & González-Sampériz, P. Quaternary disappearance of tree taxa from Southern Europe: timing and trends. Quat. Sci. Rev. 163, 23–55 (2017).
Google Scholar
Calatayud, J. et al. Pleistocene climate change and the formation of regional species pools. Proc. R. Soc. B Biol. Sci. 286, 20190291 (2019).
Ebdon, S. et al. The Pleistocene species pump past its prime: evidence from European butterfly sister species. Mol. Ecol. 30, 3575–3589 (2021).
Záveská, E. et al. Multiple auto- and allopolyploidisations marked the Pleistocene history of the widespread Eurasian steppe plant Astragalus onobrychis (Fabaceae). Mol. Phylogenet. Evol. 139, 106572 (2019).
Wesche, K. et al. The Palaearctic steppe biome: a new synthesis. Biodivers. Conserv. 25, 2197–2231 (2016).
Walter, H. & Breckle, S. Ökologie der Erde, Band 1. (Spektrum Akademischer Verlag, 1991).
Braun-Blanquet, J. Die inneralpine Trockenvegetation: von der Provence bis zur Steiermark. (Gustav Fischer, 1961).
Hurka, H. et al. The Eurasian steppe belt: Status quo, origin and evolutionary history. Turczaninowia 22, 5–71 (2019).
Jännicke, W. Die Sandflora von Mainz, ein Relict aus der Steppenzeit. (Gebrueder Knauer, 1892).
Allen, J. R. M. et al. Rapid environmental changes in southern Europe during the last glacial period. Nature 400, 740–743 (1999).
Google Scholar
Reille, M. & de Beaulieu, J. L. Pollen analysis of a long upper Pleistocene continental sequence in a Velay maar (Massif Central, France). Palaeogeogr. Palaeoclimatol. Palaeoecol. 80, 35–48 (1990).
Sadori, L. et al. Pollen-based paleoenvironmental and paleoclimatic change at Lake Ohrid (south-eastern Europe) during the past 500 ka. Biogeosciences 13, 1423–1437 (2016).
Google Scholar
Ellenberg, H. & Leuschner, C. Vegetation Mitteleuropas mit den Alpen: in ökologischer, dynamischer und historischer Sicht. (Stuttgart: Verlag Eugen Ulmer, 2010).
Kirschner, P. et al. Long-term isolation of European steppe outposts boosts the biomes conservation value. Nat. Commun. 11, 1968 (2020).
Google Scholar
Fonseca, E. M., Colli, G. R., Werneck, F. P. & Carstens, B. C. Phylogeographic model selection using convolutional neural networks. Mol. Ecol. Resour. 21, 2661–2675 (2021).
Beaumont, M. A., Zhang, W. & Balding, D. J. Approximate Bayesian computation in population genetics. Genetics 162, 2025–2035 (2002).
Google Scholar
Csilléry, K., Blum, M. G. B., Gaggiotti, O. E. & François, O. Approximate Bayesian computation (ABC) in practice. Trends Ecol. Evol. 25, 410–418 (2010).
Google Scholar
Flagel, L., Brandvain, Y. & Schrider, D. R. The unreasonable effectiveness of convolutional neural networks in population genetic inference. Mol. Biol. Evol. 36, 220–238 (2019).
Google Scholar
Robert, C. P., Cornuet, J.-M., Marin, J.-M. & Pillai, N. S. Lack of confidence in approximate Bayesian computation model choice. Proc. Natl Acad. Sci. USA 108, 15112–15117 (2011).
Google Scholar
Sanchez, T., Cury, J., Charpiat, G. & Jay, F. Deep learning for population size history inference: design, comparison and combination with approximate Bayesian computation. Mol. Ecol. Resour. 21, 2645–2660 (2021).
Liu, X. & Fu, Y.-X. Stairway Plot 2: demographic history inference with folded SNP frequency spectra. Genome Biol. 21, 280 (2020).
Google Scholar
Liu, X. & Fu, Y.-X. Exploring population size changes using SNP frequency spectra. Nat. Genet. 47, 555–559 (2015).
Google Scholar
Magri, D. et al. A new scenario for the quaternary history of European beech populations: palaeobotanical evidence and genetic consequences. New Phytol. 171, 199–221 (2006).
Google Scholar
Pironon, S. et al. Geographic variation in genetic and demographic performance: new insights from an old biogeographical paradigm. Biol. Rev. 92, 1877–1909 (2017).
Google Scholar
Arenas, M., Ray, N., Currat, M. & Excoffier, L. Consequences of range contractions and range shifts on molecular diversity. Mol. Biol. Evol. 29, 207–218 (2012).
Google Scholar
Excoffier, L., Foll, M. & Petit, R. J. Genetic consequences of range expansions. Annu. Rev. Ecol. Evol. Syst. 40, 481–501 (2008).
Mona, S., Ray, N., Arenas, M. & Excoffier, L. Genetic consequences of habitat fragmentation during a range expansion. Heredity 112, 291–299 (2014).
Google Scholar
Szűcs, M., Melbourne, B. A., Tuff, T. & Hufbauer, R. A. The roles of demography and genetics in the early stages of colonization. Proc. R. Soc. B Biol. Sci. 281, 20141073 (2014).
Loog, L. Sometimes hidden but always there: the assumptions underlying genetic inference of demographic histories. Philos. Trans. R. Soc. B Biol. Sci. 376, 20190719 (2021).
Narbona, E., Arista, M. & Ortiz, P. L. Explosive seed dispersal in two perennial Mediterranean Euphorbia species (Euphorbiaceae). Am. J. Bot. 92, 510–516 (2005).
Google Scholar
Stevens, V. M. et al. A comparative analysis of dispersal syndromes in terrestrial and semi-terrestrial animals. Ecol. Lett. 17, 1039–1052 (2014).
Google Scholar
Flouri, T., Jiao, X., Rannala, B. & Yang, Z. Species tree inference with BPP using genomic sequences and the multispecies coalescent. Mol. Biol. Evol. 35, 2585–2593 (2018).
Google Scholar
Willeit, M., Ganopolski, A., Calov, R. & Brovkin, V. Mid-Pleistocene transition in glacial cycles explained by declining CO2 and regolith removal. Sci. Adv. 5, eaav7337 (2019).
Google Scholar
Hansen, J., Sato, M., Russell, G. & Kharecha, P. Climate sensitivity, sea level and atmospheric carbon dioxide. Philos. Trans. R. Soc. Math. Phys. Eng. Sci. 371, 20120294 (2013).
Google Scholar
Martinson, D. G. et al. Age dating and the orbital theory of the ice ages: Development of a high-resolution 0 to 300,000-year chronostratigraphy. Quat. Res. 27, 1–29 (1987).
Google Scholar
OConnell, K. A. et al. Impacts of the Toba eruption and montane forest expansion on diversification in Sumatran parachuting frogs (Rhacophorus). Mol. Ecol. 29, 2994–3009 (2020).
Theodoridis, S. et al. How do cold-adapted plants respond to climatic cycles? Interglacial expansion explains current distribution and genomic diversity in Primula farinosa L. Syst. Biol. 66, 715–736 (2017).
Google Scholar
Williams, M. The <73 ka Toba super-eruption and its impact: history of a debate. Quat. Int. 258, 19–29 (2012).
Marquer, L. et al. Quantifying the effects of land use and climate on Holocene vegetation in Europe. Quat. Sci. Rev. 171, 20–37 (2017).
Google Scholar
Jackson, N. D., Morales, A. E., Carstens, B. C. & OMeara, B. C. PHRAPL: phylogeographic inference using approximate likelihoods. Syst. Biol. 66, 1045–1053 (2017).
Google Scholar
Oaks, J. R. Full Bayesian comparative phylogeography from genomic data. Syst. Biol. 68, 371–395 (2019).
Google Scholar
Perez, M. F. et al. Coalescent-based species delimitation meets deep learning: Insights from a highly fragmented cactus system. Mol. Ecol. Resour. 22, 1016–1028 (2022).
Baird, N. A. et al. Rapid SNP discovery and genetic mapping using sequenced RAD markers. PLoS ONE 3, 1–7 (2008).
Paun, O. et al. Processes driving the adaptive radiation of a tropical tree (Diospyros, Ebenaceae) in New Caledonia, a biodiversity hotspot. Syst. Biol. 65, 212–227 (2016).
Google Scholar
Catchen, J., Hohenlohe, P. A., Bassham, S., Amores, A. & Cresko, W. A. Stacks: an analysis tool set for population genomics. Mol. Ecol. 22, 3124–3140 (2013).
Google Scholar
Paris, J. R., Stevens, J. R. & Catchen, J. M. Lost in parameter space: a road map for stacks. Methods Ecol. Evol. 8, 1360–1373 (2017).
Pritchard, J. K., Stephens, M. & Donnelly, P. Inference of population structure using multilocus genotype data. Genetics 155, 945–959 (2000).
Google Scholar
O’Leary, S. J., Puritz, J. B., Willis, S. C., Hollenbeck, C. M. & Portnoy, D. S. These aren’t the loci you’re looking for: principles of effective SNP filtering for molecular ecologists. Mol. Ecol. 27, 3193–3206 (2018).
Evanno, G., Regnaut, S. & Goudet, J. Detecting the number of clusters of individuals using the software STRUCTURE: a simulation study. Mol. Ecol. 14, 2611–2620 (2005).
Google Scholar
Maier, P. A., Vandergast, A. G., Ostoja, S. M., Aguilar, A. & Bohonak, A. J. Pleistocene glacial cycles drove lineage diversification and fusion in the Yosemite toad (Anaxyrus canorus). Evolution 73, 2476–2496 (2019).
Google Scholar
Ortiz, D., Pekár, S., Bilat, J. & Alvarez, N. Poor performance of DNA barcoding and the impact of RAD loci filtering on the species delimitation of an Iberian ant-eating spider. Mol. Phylogenet. Evol. 154, 106997 (2021).
Google Scholar
Tiley, G. P., Poelstra, J. W., dos Reis, M., Yang, Z. & Yoder, A. D. Molecular clocks without rocks: new solutions for old problems. Trends Genet. 36, 845–856 (2020).
Rambaut, A., Drummond, A. J., Xie, D., Baele, G. & Suchard, M. A. Posterior summarization in Bayesian phylogenetics using tracer 1.7. Syst. Biol. 67, 901–904 (2018).
Google Scholar
Angelis, K. & Dos Reis, M. The impact of ancestral population size and incomplete lineage sorting on Bayesian estimation of species divergence times. Curr. Zool. 61, 874–885 (2015).
Yoder, A. D. et al. Geogenetic patterns in mouse lemurs (genus Microcebus) reveal the ghosts of Madagascar’s forests past. Proc. Natl Acad. Sci. USA 113, 8049–8056 (2016).
Google Scholar
Ossowski, S. et al. The rate and molecular spectrum of spontaneous mutations in Arabidopsis thaliana. Science 327, 92–94 (2010).
Google Scholar
Keightley, P. D., Ness, R. W., Halligan, D. L. & Haddrill, P. R. Estimation of the spontaneous mutation rate per nucleotide site in a Drosophila melanogasterfull-sib family. Genetics 196, 313–320 (2014).
Google Scholar
Charlesworth, B. Evolution in Age-Structured Populations. (Cambridge University Press, 1994). https://doi.org/10.1017/CBO9780511525711.
Ingram, K. K., Pilko, A., Heer, J. & Gordon, D. M. Colony life history and lifetime reproductive success of red harvester ant colonies. J. Anim. Ecol. 82, 540–550 (2013).
Google Scholar
Lauenroth, W. K. & Adler, P. B. Demography of perennial grassland plants: survival, life expectancy and life span. J. Ecol. 96, 1023–1032 (2008).
Golubeva, I. V. The age structure and numbers dynamics of feather grass (Stipa pennata L.) in the conditions of meadow steppe. Sci. Proc. Mosc. Reg. Pedagog. Inst. Nat. Geogr. Inst. 153, 283–303 (1964).
Danecek, P. et al. The variant call format and VCFtools. Bioinformatics 27, 2156–2158 (2011).
Google Scholar
Hudson, R. R. Generating samples under a Wright–Fisher neutral model of genetic variation. Bioinformatics 18, 337–338 (2002).
Google Scholar
Oliveira, E. A. et al. Historical demography and climate driven distributional changes in a widespread Neotropical freshwater species with high economic importance. Ecography 43, 1291–1304 (2020).
Guo, C., Pleiss, G., Sun, Y. & Weinberger, K. Q. On calibration of modern neural networks. Preprint at arXiv https://arxiv.org/abs/1706.04599 (2017).
Mondal, M., Bertranpetit, J. & Lao, O. Approximate Bayesian computation with deep learning supports a third archaic introgression in Asia and Oceania. Nat. Commun. 10, 246 (2019).
Google Scholar
Rosauer, D. F., Catullo, R. A., VanDerWal, J., Moussalli, A. & Moritz, C. Lineage range estimation method reveals fine-scale endemism linked to Pleistocene stability in Australian rainforest herpetofauna. PLoS ONE 10, e0126274 (2015).
Google Scholar
Watanabe, S. et al. MIROC-ESM 2010: model description and basic results of CMIP5-20c3m experiments. Geosci. Model Dev. 4, 845–872 (2011).
Google Scholar
Gent, P. R. et al. The Community Climate System Model Version 4. J. Clim. 24, 4973–4991 (2011).
Google Scholar
Richmond, O. M. W., McEntee, J. P., Hijmans, R. J. & Brashares, J. S. Is the climate right for Pleistocene rewilding? Using species distribution models to extrapolate climatic suitability for mammals across continents. PLoS ONE 5, e12899 (2010).
Google Scholar
Perez, M. F. Congruent evolutionary responses of European steppe biota to late Quaternary climate change: insights from convolutional neural network-based demographic modeling. CNN_ABCsteppe https://doi.org/10.5281/zenodo.5948567 (2022).
Anhuf, D., Bräuning, A., Burkhard, F. & Max, S. Die Vegetationsentwicklung seit dem Höhepunkt der letzten Eiszeit. In Nationalatlas Bundesrepublik Deutschland. Band 3. Klima, Pflanzen- und Tierwelt (ed. Kappas, M.) 88–91 (Spektrum, 2003).
Becker, D., Verheul, J., Zickel, M. & Willmes, C. LGM paleoenvironment of Europe—Map. CRC806-Database https://doi.org/10.5880/SFB806.15 (2015).
de Beaulieu, J.-L. & Reille, M. Long Pleistocene pollen sequences from the Velay Plateau (Massif Central, France). Veg. Hist. Archaeobotany 1, 233–242 (1992).
Tzedakis, P. C. C., Emerson, B. C. C. & Hewitt, G. M. M. Cryptic or mystic? Glacial tree refugia in northern Europe. Trends Ecol. Evol. 28, 696–704 (2013).
Google Scholar
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