[1] |
Adler C, Wester P, Bhatt I, Huggel C, Insarov GE, et al. 2023. Mountains. In Climate Change 2022: Impacts, Adaptation and Vulnerability. Working Group II Contribution to the Sixth Assessment Report of the Intergovernmental Panel on Climate Change, eds. Pörtner HO, Roberts DC, Tignor M, Poloczanska ES, Mintenbeck K, et al, Cambridge, UK and New York, USA: Cambridge University Press. pp. 2273–318. https://doi.org/10.1017/9781009325844.022 |
[2] |
Capblancq T, Fitzpatrick MC, Bay RA, Exposito-Alonso M, Keller SR. 2020. Genomic prediction of (mal)adaptation across current and future climatic landscapes. Annual Review of Ecology, Evolution, and Systematics 51:245−69 doi: 10.1146/annurev-ecolsys-020720-042553 |
[3] |
Lovell JT, MacQueen AH, Mamidi S, Bonnette J, Jenkins J, et al. 2021. Genomic mechanisms of climate adaptation in polyploid bioenergy switchgrass. Nature 590:438−44 doi: 10.1038/s41586-020-03127-1 |
[4] |
Weigel D, Nordborg M. 2015. Population genomics for understanding adaptation in wild plant species. Annual Review of Genetics 49:315−38 doi: 10.1146/annurev-genet-120213-092110 |
[5] |
Dobzhansky T. 1937. Genetics and the origin of species. New York, US: Columbia University Press. xvi, 364 pp. |
[6] |
Wright S. 1943. Isolation by distance. Genetics 28:114−38 doi: 10.1093/genetics/28.2.114 |
[7] |
Savolainen O, Lascoux M, Merilä J. 2013. Ecological genomics of local adaptation. Nature Reviews Genetics 14:807−20 doi: 10.1038/nrg3522 |
[8] |
Savolainen O, Pyhäjärvi T, Knürr T. 2007. Gene flow and local adaptation in trees. Annual Review of Ecology, Evolution, and Systematics 38:595−619 doi: 10.1146/annurev.ecolsys.38.091206.095646 |
[9] |
Gougherty AV, Keller SR, Fitzpatrick MC. 2021. Maladaptation, migration and extirpation fuel climate change risk in a forest tree species. Nature Climate Change 11:166−71 doi: 10.1038/s41558-020-00968-6 |
[10] |
Singh HCP. 2013. Adaptation and mitigation strategies for climate-resilient horticulture. In Climate-Resilient Horticulture: Adaptation and Mitigation Strategies, eds. Singh HCP, Rao NKS, Shivashankar KS, India: Springer India. pp. 1–12. https://doi.org/10.1007/978-81-322-0974-4_1 |
[11] |
Li Y, Cao K, Li N, Zhu G, Fang W, et al. 2021. Genomic analyses provide insights into peach local adaptation and responses to climate change. Genome Research 31:592−606 doi: 10.1101/gr.261032.120 |
[12] |
Zhang X, Guo R, Shen R, Landis JB, Jiang Q, et al. 2023. The genomic and epigenetic footprint of local adaptation to variable climates in kiwifruit. Horticulture Research 10:uhad031 doi: 10.1093/hr/uhad031 |
[13] |
Kawecki TJ, Ebert D. 2004. Conceptual issues in local adaptation. Ecology Letters 7:1225−41 doi: 10.1111/j.1461-0248.2004.00684.x |
[14] |
Cheplick G. 2015. Approaches to Plant Evolutionary Ecology. New York, US: Oxford University Press. x, 291 pp. |
[15] |
Ågren J, Schemske DW. 2012. Reciprocal transplants demonstrate strong adaptive differentiation of the model organism Arabidopsis thaliana in its native range. New Phytologist 194:1112−22 doi: 10.1111/j.1469-8137.2012.04112.x |
[16] |
Hereford J. 2009. A Quantitative survey of local adaptation and fitness trade-offs. The American Naturalist 173:579−88 doi: 10.1086/597611 |
[17] |
Ramírez-Valiente JA, Solé-Medina A, Robledo-Arnuncio JJ, Ortego J. 2023. Genomic data and common garden experiments reveal climate-driven selection on ecophysiological traits in two Mediterranean oaks. Molecular Ecology 32:983−99 doi: 10.1111/mec.16816 |
[18] |
Luikart G, Kardos M, Hand BK, Rajora OP, Aitken SN, Hohenlohe PA, et al. 2018. Population genomics: advancing understanding of nature. In Population Genomics: Concepts, Approaches and Applications, ed. Rajora OP, Cham: Springer International Publishing. pp. 3–79. https://doi.org/10.1007/13836_2018_60 |
[19] |
Allendorf FW, Hohenlohe PA, Luikart G. 2010. Genomics and the future of conservation genetics. Nature Reviews Genetics 11:697−709 doi: 10.1038/nrg2844 |
[20] |
Fitzpatrick MC, Keller SR. 2015. Ecological genomics meets community-level modelling of biodiversity: mapping the genomic landscape of current and future environmental adaptation. Ecology Letters 18:1−16 doi: 10.1111/ele.12376 |
[21] |
Balkenhol N, Dudaniec RY, Krutovsky KV, Johnson JS, Cairns DM, et al. 2017. Landscape genomics: understanding relationships between environmental heterogeneity and genomic characteristics of populations. In Population Genomics: Concepts, Approaches and Applications, ed. Rajora OP. Cham, Switzerland: Springer. pp. 261–322. https://doi.org/10.1007/13836_2017_2 |
[22] |
Joost S, Bonin A, Bruford MW, Després L, Conord C, et al. 2007. A spatial analysis method (SAM) to detect candidate loci for selection: towards a landscape genomics approach to adaptation. Molecular Ecology 16:3955−69 doi: 10.1111/j.1365-294X.2007.03442.x |
[23] |
Li Y, Zhang X, Mao R, Yang J, Miao C, et al. 2017. Ten years of landscape genomics: challenges and opportunities. Frontiers in Plant Science 8:2136 doi: 10.3389/fpls.2017.02136 |
[24] |
Bay RA, Harrigan RJ, Le Underwood V, Gibbs HL, Smith TB, et al. 2018. Genomic signals of selection predict climate-driven population declines in a migratory bird. Science 359:83−86 doi: 10.1126/science.aan4380 |
[25] |
Hoffmann AA, Weeks AR, Sgrò CM. 2021. Opportunities and challenges in assessing climate change vulnerability through genomics. Cell 184:1420−25 doi: 10.1016/j.cell.2021.02.006 |
[26] |
Sang Y, Long Z, Dan X, Feng J, Shi T, et al. 2022. Genomic insights into local adaptation and future climate-induced vulnerability of a keystone forest tree in East Asia. Nature Communications 13:6541 doi: 10.1038/s41467-022-34206-8 |
[27] |
Rellstab C, Dauphin B, Exposito-Alonso M. 2021. Prospects and limitations of genomic offset in conservation management. Evolutionary Applications 14:1202−12 doi: 10.1111/eva.13205 |
[28] |
Feng L, Du F. 2022. Landscape genomics in tree conservation under a changing environment. Frontiers in Plant Science 13:822217 doi: 10.3389/fpls.2022.822217 |
[29] |
Zhang X, Sun Y, Landis JB, Zhang J, Yang L, et al. 2020. Genomic insights into adaptation to heterogeneous environments for the ancient relictual Circaeaster agrestis (Circaeasteraceae, Ranunculales). New Phytologist 228:285−301 doi: 10.1111/nph.16669 |
[30] |
Cao Y, Zhu S, Chen J, Comes HP, Wang IJ, et al. 2020. Genomic insights into historical population dynamics, local adaptation, and climate change vulnerability of the East Asian Tertiary relict Euptelea (Eupteleaceae). Evolutionary Applications 13:2038−55 doi: 10.1111/eva.12960 |
[31] |
Razgour O, Forester B, Taggart JB, Bekaert M, Juste J, et al. 2019. Considering adaptive genetic variation in climate change vulnerability assessment reduces species range loss projections. Proceedings of the National Academy of Sciences of the United States of America 116:10418−23 doi: 10.1073/pnas.1820663116 |
[32] |
Wang IJ, Bradburd GS. 2014. Isolation by environment. Molecular Ecology 23:5649−62 doi: 10.1111/mec.12938 |
[33] |
Smouse PE, Long JC, Sokal RR. 1986. Multiple regression and correlation extensions of the mantel test of matrix correspondence. Systematic Biology 35:627−32 doi: 10.2307/2413122 |
[34] |
Wang IJ. 2013. Examining the full effects of landscape heterogeneity on spatial genetic variation: a multiple matrix regression approach for quantifying geographic and ecological isolation. Evolution 67:3403−11 doi: 10.1111/evo.12134 |
[35] |
Wang IJ, Glor RE, Losos JB. 2013. Quantifying the roles of ecology and geography in spatial genetic divergence. Ecology Letters 16:175−82 doi: 10.1111/ele.12025 |
[36] |
Capblancq T, Forester BR. 2021. Redundancy analysis: A Swiss Army Knife for landscape genomics. Methods in Ecology and Evolution 12:2298−309 doi: 10.1111/2041-210X.13722 |
[37] |
Ellis N, Smith SJ, Pitcher CR. 2012. Gradient forests: calculating importance gradients on physical predictors. Ecology 93:156−68 doi: 10.1890/11-0252.1 |
[38] |
Ferrier S, Manion G, Elith J, Richardson K. 2007. Using generalized dissimilarity modelling to analyse and predict patterns of beta diversity in regional biodiversity assessment. Diversity and Distributions 13:252−64 doi: 10.1111/j.1472-4642.2007.00341.x |
[39] |
Zhao W, Sun Y, Pan J, Sullivan AR, Arnold ML, et al. 2020. Effects of landscapes and range expansion on population structure and local adaptation. New Phytologist 228:330−43 doi: 10.1111/nph.16619 |
[40] |
Excoffier L, Hofer T, Foll M. 2009. Detecting loci under selection in a hierarchically structured population. Heredity 103:285−98 doi: 10.1038/hdy.2009.74 |
[41] |
Coop G, Witonsky D, Di Rienzo A, Pritchard JK. 2010. Using environmental correlations to identify loci underlying local adaptation. Genetics 185:1411−23 doi: 10.1534/genetics.110.114819 |
[42] |
Foll M, Gaggiotti O. 2008. A genome-scan method to identify selected loci appropriate for both dominant and codominant markers: a bayesian perspective. Genetics 180:977−93 doi: 10.1534/genetics.108.092221 |
[43] |
Gautier M. 2015. Genome-wide scan for adaptive divergence and association with population-specific covariates. Genetics 201:1555−79 doi: 10.1534/genetics.115.181453 |
[44] |
Frichot E, Schoville SD, Bouchard G, François O. 2013. Testing for associations between loci and environmental gradients using latent factor mixed models. Molecular Biology and Evolution 30:1687−99 doi: 10.1093/molbev/mst063 |
[45] |
Rellstab C, Gugerli F, Eckert AJ, Hancock AM, Holderegger R. 2015. A practical guide to environmental association analysis in landscape genomics. Molecular Ecology 24:4348−70 doi: 10.1111/mec.13322 |
[46] |
Forester BR, Lasky JR, Wagner HH, Urban DL. 2018. Comparing methods for detecting multilocus adaptation with multivariate genotype–environment associations. Molecular Ecology 27:2215−33 doi: 10.1111/mec.14584 |
[47] |
Chen F, Song Y, Li X, Chen J, Mo L, et al. 2019. Genome sequences of fruit tree: past, present, and future. Horticulture Research 6:112 doi: 10.1038/s41438-019-0195-6 |
[48] |
Fagny M, Austerlitz F. 2021. Polygenic adaptation: integrating population genetics and gene regulatory networks. Trends in Genetics 37:631−38 doi: 10.1016/j.tig.2021.03.005 |
[49] |
Xu J, Hua K, Lang Z. 2019. Genome editing for horticultural crop improvement. Horticulture Research 6:113 doi: 10.1038/s41438-019-0196-5 |
[50] |
Zheng T, Li P, Li L, Zhang Q. 2021. Research advances in and prospects of ornamental plant genomics. Horticulture Research 8:65 doi: 10.1038/s41438-021-00499-x |
[51] |
Hu Y, Feng C, Yang L, Edger PP, Kang M. 2022. Genomic population structure and local adaptation of the wild strawberry Fragaria nilgerrensis. Horticulture Research 9:uhab059 doi: 10.1093/hr/uhab059 |
[52] |
Li L, Cushman SA, He Y, Ma X, Ge X, et al. 2022. Landscape genomics reveals genetic evidence of local adaptation in a widespread tree, the Chinese wingnut (Pterocarya stenoptera). Journal of Systematics and Evolution 60:386−97 doi: 10.1111/jse.12699 |