Jones, M. R. et al. Adaptive introgression underlies polymorphic seasonal camouflage in snowshoe hares. Science 1358, 1355–1358 (2018).
Zimova, M. et al. Lack of phenological shift leads to increased camouflage mismatch in mountain hares: increased camouflage mismatch in hares. Proc. R. Soc. B 287, 20201786 (2020).
Cook, L. M. The rise and fall of the carbonaria form of the peppered moth. Q. Rev. Biol. 78, 399–417 (2003).
Niu, Y. et al. Grey leaves in an alpine plant: a cryptic colouration to avoid attack? New Phytol. 203, 953–963 (2014).
Ferreira, M. S. et al. The evolution of white-tailed jackrabbit camouflage in response to past and future seasonal climates. Rev. Sci. 1242, 1238–1242 (2023).
Hof, A. E. V. T. et al. The industrial melanism mutation in British peppered moths is a transposable element. Nature 534, 102–105 (2016).
Renner, S. S. & Zohner, C. M. Climate change and phenological mismatch in trophic interactions among plants, insects, and vertebrates. Annu. Rev. Ecol. Evol. Syst. 49, 165–182 (2018).
Barrett, R. D. H. et al. Linking a mutation to survival in wild mice. Science 363, 499–504 (2019).
Condamine, F. et al. Anthropogenic threats to high-altitude parnassian diversity. News Lepid. Soc. 60, 94–99 (2019).
Berenbaum, M. R. & Feeny, P. P. in The Evolutionary Biology of Herbivorous Insects (ed. Tilmon, K.) 3–19 (Univ. California Press, 2010).
Boitier, E., Descimon, H., Petit, D. P. & Bachelard, P. in Insectes d’Altitude, Insectes en Altitude (eds Boitier, E. et al.) 15–25 (Parc naturel régional Livradois-Forez et Société d’Histoire naturelle Alcide-d’Orbigny, 2008).
Rödder, D., Schmitt, T., Gros, P., Ulrich, W. & Habel, J. C. Climate change drives mountain butterflies towards the summits. Sci. Rep. 11, 14382 (2021).
Huang, T., Chen, Z., Xu, B., Sun, H. & Niu, Y. Camouflaged plants are shorter than non-camouflaged plants in the alpine zone. Biol. Lett. 19, 20220560 (2023).
Berardi, A. E. et al. Complex evolution of novel red floral color in Petunia. Plant Cell 33, 2273–2295 (2021).
Shi, M. Z. & Xie, D. Y. Biosynthesis and metabolic engineering of anthocyanins in Arabidopsis thaliana. Recent Pat. Biotechnol. 8, 47–60 (2014).
Liang, M., Foster, C. E. & Yuan, Y. W. Lost in translation: molecular basis of reduced flower coloration in a self-pollinated monkeyflower (Mimulus) species. Sci. Adv. 8, eabo1113 (2022).
Heim, M. A. et al. The basic helix-loop-helix transcription factor family in plants: a genome-wide study of protein structure and functional diversity. Mol. Biol. Evol. 20, 735–747 (2003).
Wells, J. N. & Feschotte, C. A field guide to eukaryotic transposable elements. Annu. Rev. Genet. 54, 539–561 (2020).
Bureau, T. E. & Wessler, S. R. Stowaway: a new family of inverted repeat elements associated with the genes of both monocotyledonous and dicotyledonous plants. Plant Cell 6, 907–916 (1994).
Nora, E. P. et al. Spatial partitioning of the regulatory landscape of the X-inactivation centre. Nature 485, 381–385 (2012).
Xu, W., Dubos, C. & Lepiniec, L. Transcriptional control of flavonoid biosynthesis by MYB-bHLH-WDR complexes. Trends Plant Sci. 20, 176–185 (2015).
Schiffels, S. & Wang, K. MSMC and MSMC2: the multiple sequentially Markovian coalescent. Methods Mol. Biol. 2090, 147–166 (2021).
Liu, X. & Fu, Y. X. Stairway Plot 2: demographic history inference with folded SNP frequency spectra. Genome Biol. 21, 280 (2020).
Excoffier, L. et al. Fastsimcoal2: demographic inference under complex evolutionary scenarios. Bioinformatics 37, 4882–4885 (2021).
Santiago, E. et al. Recent demographic history inferred by high-resolution analysis of linkage disequilibrium. Mol. Biol. Evol. 37, 3642–3653 (2020).
Niu, Y., Chen, Z., Stevens, M. & Sun, H. Divergence in cryptic leaf colour provides local camouflage in an alpine plant. Proc. R. Soc. B 284, 20171654 (2017).
Hughes, N. M. et al. Photosynthetic costs and benefits of abaxial versus adaxial anthocyanins in Colocasia esculenta ‘Mojito’. Planta 240, 971–981 (2014).
Gould, K. S. Nature’s Swiss army knife: the diverse protective roles of anthocyanins in leaves. J. Biomed. Biotechnol. 5, 314–320 (2004).
Mcclintock, B. The significance of responses of the genome to challenge. Science 226, 792–801 (1984).
Agati, G., Guidi, L., Landi, M. & Tattini, M. Anthocyanins in photoprotection: knowing the actors in play to solve this complex ecophysiological issue. New Phytol. 232, 2228–2235 (2021).
Feng, X. et al. Temperature fluctuations during the Common Era in subtropical southwestern China inferred from brGDGTs in a remote alpine lake. Earth Planet. Sci. Lett. 510, 26–36 (2019).
Wang, S., Che, Y., Pang, H., Du, J. & Zhang, Z. Accelerated changes of glaciers in the Yulong Snow Mountain, Southeast Qinghai-Tibetan Plateau. Reg. Environ. Change 20, 38 (2020).
Kelber, A. Ovipositing butterflies use a red receptor to see green. J. Exp. Biol. 202, 2619–2630 (1999).
Luo, P. et al. Disequilibrium of flavonol synthase and dihydroflavonol-4-reductase expression associated tightly to white vs. red color flower formation in plants. Front. Plant Sci. 6, 1257 (2016).
Inskeep, W. P. & Bloom, P. R. Extinction coefficients of chlorophyll a and b in N,N-dimethylformamide and 80% acetone. Plant Physiol. 77, 483–485 (1985).
Sawada, Y. et al. Widely targeted metabolomics based on large-scale MS/MS data for elucidating metabolite accumulation patterns in plants. Plant Cell Physiol. 50, 37–47 (2009).
Kim, D., Langmead, B. & Salzberg, S. L. HISAT: a fast spliced aligner with low memory requirements. Nat. Methods 12, 357–360 (2015).
Pertea, M., Kim, D., Pertea, G. M., Leek, J. T. & Salzberg, S. L. Transcript-level expression analysis of RNA-seq experiments with HISAT, StringTie and Ballgown. Nat. Protoc. 11, 1650–1667 (2016).
Ramírez, F. et al. DeepTools2: a next generation web server for deep-sequencing data analysis. Nucleic Acids Res. 44, 160–165 (2016).
Love, M. I., Huber, W. & Anders, S. Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biol. 15, 550 (2014).
Li, H. & Durbin, R. Fast and accurate short read alignment with Burrows–Wheeler transform. Bioinformatics 25, 1754–1760 (2009).
Li, H., Feng, X. & Chu, C. The design and construction of reference pangenome graphs with minigraph. Genome Biol. 21, 265 (2020).
Zheng, Z. et al. A sequence-aware merger of genomic structural variations at population scale. Nat. Commun. 15, 960 (2024).
Wang, K., Li, M. & Hakonarson, H. ANNOVAR: functional annotation of genetic variants from high-throughput sequencing data. Nucleic Acids Res. 38, e164 (2010).
Zhou, W. et al. Efficiently controlling for case-control imbalance and sample relatedness in large-scale genetic association studies. Nat. Genet. 50, 1335–1341 (2018).
Kurtz, S. et al. Versatile and open software for comparing large genomes. Genome Biol. 5, R12 (2004).
Khelik, K., Lagesen, K., Sandve, G. K., Rognes, T. & Nederbragt, A. J. NucDiff: in-depth characterization and annotation of differences between two sets of DNA sequences. BMC Bioinf. 18, 338 (2017).
Lee, T. I., Johnstone, S. E. & Young, R. A. Chromatin immunoprecipitation and microarray-based analysis of protein location. Nat. Protoc. 1, 729–748 (2010).
Langmead, B. & Salzberg, S. L. Fast gapped-read alignment with Bowtie 2. Nat. Methods 9, 357–359 (2012).
Pattanaik, S. et al. Isolation and functional characterization of a floral tissue-specific R2R3 MYB regulator from tobacco. Planta 231, 1061–1076 (2010).
Clough, S. J. & Bent, A. F. Floral dip: a simplified method for Agrobacterium-mediated transformation of Arabidopsis thaliana. Plant J. 16, 735–743 (1998).
Zhu, B., Zhang, W., Zhang, T., Liu, B. & Jiang, J. Genome-wide prediction and validation of intergenic enhancers in Arabidopsis using open chromatin signatures. Plant Cell 27, 2415–2426 (2015).
Zhou, H. et al. Molecular genetics of blood-fleshed peach reveals activation of anthocyanin biosynthesis by NAC transcription factors. Plant J. 82, 105–121 (2015).
Livak, K. J. & Schmittgen, T. D. Analysis of relative gene expression data using real-time quantitative PCR and the 2-ΔΔCT method. Methods 25, 402–408 (2001).
Cummings, M. P. PHYLIP (Phylogeny Inference Package). in Dictionary of Bioinformatics and Computational Biology (eds. Hancock, J. M. & Zvelebil, M. J.) (Wiley, 2004).
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).
Jin, J. et al. GetOrganelle: a fast and versatile toolkit for accurate de novo assembly of organelle genomes. Genome Biol. 21, 241 (2020).
Stamatakis, A. RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics 30, 1312–1313 (2014).
Alexander, D. H., Novembre, J. & Lange, K. Fast model-based estimation of ancestry in unrelated individuals. Genome Res. 19, 1655–1664 (2009).
Patterson, N., Price, A. L. & Reich, D. Population structure and eigenanalysis. PLoS Genet. 2, 2074–2093 (2006).
Li, Q. et al. Molecular phylogeography and evolutionary history of the endemic species Corydalis hendersonii (Papaveraceae) on the Tibetan Plateau inferred from chloroplast DNA and ITS sequence variation. Front. Plant Sci. 11, 436 (2020).
Ma, Y. P. et al. Genome-wide analysis of butterfly bush (Buddleja alternifolia) in three uplands provides insights into biogeography, demography and speciation. New Phytol. 232, 1463–1476 (2021).
Spence, J. P. & Song, Y. S. Inference and analysis of population-specific fine-scale recombination maps across 26 diverse human populations. Sci. Adv. 5, 9206 (2019).
Keightley, P. D. et al. Estimation of the spontaneous mutation rate in Heliconius melpomene. Mol. Biol. Evol. 32, 239–243 (2014).
Torres, A. P. et al. The fine-scale recombination rate variation and associations with genomic features in a butterfly. Genome Res. 33, 810–823 (2023).
Zhang, H. Genetic basis of camouflage in an alpine plant and its long-term coevolution with an insect herbivore. figshare https://doi.org/10.6084/m9.figshare.26891578.v2 (2024).