Collins, M. et al. In Climate Change 2013—The Physical Science Basis (ed. Intergovernmental Panel on Climate Change) 1029–1136 (Cambridge University Press, Cambridge, 2013).
Ackerly, D. D. et al. The geography of climate change: implications for conservation biogeography. Divers. Distrib. 16, 476–487 (2010).
Bradshaw, W. E. & Holzapfel, C. M. Evolutionary response to rapid climate change. Science 312, 1477–1478 (2006).
Chu, C., Mandrak, N. E. & Minns, C. K. Potential impacts of climate change on the distributions of several common and rare freshwater fishes in Canada. Divers. Distrib. 11, 299–310 (2005).
Princé, K. & Zuckerberg, B. Climate change in our backyards: the reshuffling of North America’s winter bird communities. Glob. Change Biol. 21, 572–585 (2015).
Scheffers, B. R. et al. The broad footprint of climate change from genes to biomes to people. Science 354, aaf7671 (2016).
Lisiecki, L. E. & Raymo, M. E. A Pliocene-Pleistocene stack of 57 globally distributed benthic δ 18 O records. Paleoceanography 20, PA1003 (2005).
Dyke, A. S. An outline of the deglaciation of North America with emphasis on central and northern Canada. Quat. Glaciat. Chronol. Part II 2b, 373–424 (2004).
Thompson, L. G. et al. Late glacial stage and Holocene tropical ice core records from Huascaran, Peru. Science 269, 46–50 (1995).
Johnsen, S. J. et al. Oxygen isotope and palaeotemperature records from six Greenland ice-core stations: camp century, dye-3, GRIP, GISP2, Renland and NorthGRIP. J. Quat. Sci. 16, 299–307 (2001).
Kawamura, K. et al. Northern Hemisphere forcing of climatic cycles in Antarctica over the past 360,000 years. Nature 448, 912–916 (2007).
Dyke, A. S. Late quaternary vegetation history of Northern North America based on pollen, macrofossil, and faunal remains. Géogr. Phys. Quat. 59, 211–262 (2005).
Froese, D. et al. Fossil and genomic evidence constrains the timing of bison arrival in North America. Proc. Natl Acad. Sci. USA 114, 3457–3462 (2017).
Palkopoulou, E. et al. Holarctic genetic structure and range dynamics in the woolly mammoth. Proc. R. Soc. B Biol. Sci. 280, 20131910 (2013).
Debruyne, R. et al. Out of America: ancient DNA evidence for a new world origin of late quaternary woolly mammoths. Curr. Biol. 18, 1320–1326 (2008).
Shapiro, B. et al. Rise and fall of the Beringian Steppe Bison. Science 306, 1561–1565 (2004).
Campos, P. F. et al. Ancient DNA analyses exclude humans as the driving force behind late Pleistocene musk ox (Ovibos moschatus) population dynamics. Proc. Natl Acad. Sci. USA 107, 5675–5680 (2010).
Chang, D. et al. The evolutionary and phylogeographic history of woolly mammoths: a comprehensive mitogenomic analysis. Sci. Rep. 7, 44585 (2017).
Heintzman, P. D. et al. Bison phylogeography constrains dispersal and viability of the ice free corridor in western Canada. Proc. Natl Acad. Sci. USA 113, 8057–8063 (2016).
Zazula, G. D. et al. American mastodon extirpation in the Arctic and Subarctic predates human colonization and terminal Pleistocene climate change. Proc. Natl Acad. Sci. USA 2014, 6–11 (2014).
Zazula, G. D. et al. A case of early Wisconsinan “over-chill”: New radiocarbon evidence for early extirpation of western camel (Camelops hesternus) in eastern Beringia. Quat. Sci. Rev. 171, 48–57 (2017).
Saunders, J. J. et al. Paradigms and proboscideans in the southern Great Lakes region, USA. Quat. Int. 217, 175–187 (2010).
Oltz, D. F. & Kapp, R. O. Plant remains associated with Mastodon and Mammoth remains in central Michigan. Am. Midl. Nat. 70, 339–346 (1963).
Dreimanis, A. Extinction of Mastodons in Eastern North America: testing a new climatic-environmental hypothesis. Ohio J. Sci. 68, 257–272 (1968).
Shoshani, J. Understanding proboscidean evolution: a formidable task. Trends Ecol. Evol. 13, 480–487 (1998).
Teale, C. L. & Miller, N. G. Mastodon herbivory in mid-latitude late-Pleistocene boreal forests of eastern North America. Quat. Res. 78, 72–81 (2012).
Green, J. L., DeSantis, L. R. G. & Smith, G. J. Regional variation in the browsing diet of Pleistocene Mammut americanum (Mammalia, Proboscidea) as recorded by dental microwear textures. Palaeogeogr. Palaeoclimatol. Palaeoecol. 487, 59–70 (2017).
Birks, H. H. et al. Evidence for the diet and habitat of two late Pleistocene mastodons from the Midwest, USA. Quat. Res. 91, 792–812 (2019).
Owen-Smith, N. Pleistocene extinctions: the pivotal role of megaherbivores. Paleobiology 13, 351–362 (1987).
Barnosky, A. D. et al. Variable impact of late-quaternary megafaunal extinction in causing ecological state shifts in North and South America. Proc. Natl Acad. Sci. USA 113, 856–861 (2016).
Widga, C. et al. Late pleistocene proboscidean population dynamics in the North American midcontinent. Boreas 46, 772–782 (2017).
Godfrey-Smith, D., Grist, A. & Stea, R. Dosimetric and radiocarbon chronology of a pre-Wisconsinan mastodon fossil locality at East Milford, Nova Scotia, Canada. Quat. Sci. Rev. 22, 1353–1360 (2003).
Enk, J. et al. Mammuthus population dynamics in late pleistocene North America: divergence, phylogeogrpaphy and introgression. Front. Ecol. Evol. 4, 1–13 (2016).
Ishida, Y., Georgiadis, N. J., Hondo, T. & Roca, A. L. Triangulating the provenance of African elephants using mitochondrial DNA. Evol. Appl. 6, 253–265 (2013).
Fernando, P., Pfrender, M. E., Encalada, S. E. & Lande, R. Mitochondrial DNA variation, phylogeography and population structure of the Asian elephant. Heredity 84, 362–372 (2000).
Fisher, D. In The Proboscidea: Evolution and Paleoecology of Elephants andtheir Relatives (eds. Shoshani, J. & Tassy, P.) 296–315 (Oxford University Press, Oxford, 1996).
Fisher, D. C. Paleobiology of pleistocene proboscideans. Annu. Rev. Earth Planet. Sci. https://doi.org/10.1146/annurev-earth-060115-012437 (2018).
Rohland, N. et al. Genomic DNA sequences from mastodon and woolly mammoth reveal deep speciation of forest and savanna elephants. PLoS Biol. 8, e1000564 (2010).
Muhs, D. R., Ager, T. A. & Begét, J. E. Vegetation and paleoclimate of the last interglacial period, central Alaska. Quat. Sci. Rev. 20, 41–61 (2001).
Jass, C. N. & Barrón-Ortiz, C. I. A review of quaternary proboscideans from Alberta, Canada. Quat. Int. 443, 88–104 (2017).
Shapiro, B. et al. A Bayesian phylogenetic method to estimate unknown sequence ages. Mol. Biol. Evol. 28, 879–887 (2011).
Drummond, A. J. & Stadler, T. Bayesian phylogenetic estimation of fossil ages. Philos. Trans. R. Soc. B Biol. Sci. 371, 20150129 (2016).
Plint, T., Longstaffe, F. J. & Zazula, G. Giant beaver palaeoecology inferred from stable isotopes. Sci. Rep. 9, 7179 (2019).
Yalden, D. W. The history of British mammals 12–27 (T & A D Poyser Ltd, Berkhamsted, 1999).
Schreve, D. C. A new record of Pleistocene hippopotamus from River Severn terrace deposits, Gloucester, UK—palaeoenvironmental setting and stratigraphical significance. Proc. Geol. Assoc. 120, 58–64 (2009).
Stoffel, C. et al. Genetic consequences of population expansions and contractions in the common hippopotamus (Hippopotamus amphibius) since the late Pleistocene. Mol. Ecol. 24, 2507–2520 (2015).
Tape, K. D., Gustine, D. D., Ruess, R. W., Adams, L. G. & Clark, J. A. Range expansion of moose in Arctic Alaska linked to warming and increased shrub habitat. PLoS ONE 11, e0152636 (2016).
Tape, K. D., Jones, B. M., Arp, C. D., Nitze, I. & Grosse, G. Tundra be dammed: beaver colonization of the Arctic. Glob. Change Biol. 24, 4478–4488 (2018).
Dabney, J. et al. Complete mitochondrial genome sequence of a Middle Pleistocene cave bear reconstructed from ultrashort DNA fragments. Proc. Natl Acad. Sci. USA 110, 15758–15763 (2013).
Glocke, I. & Meyer, M. Extending the spectrum of DNA sequences retrieved from ancient bones and teeth. Genome Res. 27, 1–8 (2017).
Kircher, M., Sawyer, S. & Meyer, M. Double indexing overcomes inaccuracies in multiplex sequencing on the Illumina platform. Nucleic Acids Res. 40, 1–8 (2012).
Meyer, M. & Kircher, M. Illumina sequencing library preparation for highly multiplexed target capture and sequencing. Cold Spring Harb. Protoc. 2010, 1–10 (2010).
Gansauge, M.-T. & Meyer, M. Single-stranded DNA library preparation for the sequencing of ancient or damaged DNA. Nat. Protoc. 8, 737–748 (2013).
Gansauge, M.-T. et al. Single-stranded DNA library preparation from highly degraded DNA using T4 DNA ligase. Nucleic Acids Res. 45, 1–10 (2017).
Renaud, G., Stenzel, U. & Kelso, J. leeHom: adaptor trimming and merging for Illumina sequencing reads. Nucleic Acids Res. https://doi.org/10.1093/nar/gku699 (2014).
Li, H. & Durbin, R. Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics 25, 1754–1760 (2009).
Edgar, R. C. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res. 32, 1792–1797 (2004).
Darriba, D., Taboada, G. L., Doallo, R. & Posada, D. jModelTest 2: more models, new heuristics and parallel computing. Nat. Methods 9, 772–772 (2012).
Nguyen, L. T., Schmidt, H. A., Von Haeseler, A. & Minh, B. Q. IQ-TREE: a fast and effective stochastic algorithm for estimating maximum-likelihood phylogenies. Mol. Biol. Evol. 32, 268–274 (2015).
Drummond, A. J., Suchard, M. A., Xie, D. & Rambaut, A. Bayesian phylogenetics with BEAUti and the BEAST 1.7. Mol. Biol. Evol. 29, 1969–1973 (2012).
Baele, G., Lemey, P. & Suchard, M. A. Genealogical working distributions for Bayesian model testing with phylogenetic uncertainty. Syst. Biol. 65, 250–264 (2016).
Suchard, M. A. et al. Bayesian phylogenetic and phylodynamic data integration using BEAST 1.10. Virus Evol. 4, vey016 (2018).
Stuiver, M. & Reimer, P. J. Extended 14C database and revised CALIB radiocarbon calibration program. Radiocarbon 35, 215–230 (1993).
Paradis, E., Claude, J. & Strimmer, K. APE: analyses of phylogenetics and evolution in R language. Bioinformatics 20, 289–290 (2004).
Colleoni, F., Wekerle, C., Näslund, J.-O., Brandefelt, J. & Masina, S. Constraint on the penultimate glacial maximum Northern Hemisphere ice topography (≈140 kyrs BP). Quat. Sci. Rev. 137, 97–112 (2016).
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