[1]

Exposito-Alonso M, Booker TR, Czech L, Gillespie L, Hateley S, et al. 2022. Genetic diversity loss in the Anthropocene. Science 377:1431−35

doi: 10.1126/science.abn5642
[2]

Walther GR, Post E, Convey P, Menzel A, Parmesan C, et al. 2002. Ecological responses to recent climate change. Nature 416:389−95

doi: 10.1038/416389a
[3]

Aitken SN, Yeaman S, Holliday JA, Wang T, Curtis‐McLane S. 2008. Adaptation, migration or extirpation: climate change outcomes for tree populations. Evolutionary Applications 1:95−111

doi: 10.1111/j.1752-4571.2007.00013.x
[4]

Waldvogel AM, Feldmeyer B, Rolshausen G, Exposito-Alonso M, Rellstab C, et al. 2020. Evolutionary genomics can improve prediction of species' responses to climate change. Evolution Letters 4:4−18

doi: 10.1002/evl3.154
[5]

de Lafontaine G, Napier JD, Petit RJ, Hu FS. 2018. Invoking adaptation to decipher the genetic legacy of past climate change. Ecology 99:1530−46

doi: 10.1002/ecy.2382
[6]

Browne L, Wright JW, Fitz-Gibbon S, Gugger PF, Sork VL. 2019. Adaptational lag to temperature in valley oak (Quercus lobata) can be mitigated by genome-informed assisted gene flow. Proceedings of the National Academy of Sciences of the United States of America 116:25179−85

doi: 10.1073/pnas.1908771116
[7]

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
[8]

Rellstab C, Zoller S, Walthert L, Lesur I, Pluess AR, et al. 2016. Signatures of local adaptation in candidate genes of oaks (Quercus spp.) with respect to present and future climatic conditions. Molecular Ecology 25:5907−24

doi: 10.1111/mec.13889
[9]

Exposito-Alonso M. 2023. Understanding local plant extinctions before it is too late: bridging evolutionary genomics with global ecology. New Phytologist 237:2005−11

doi: 10.1111/nph.18718
[10]

Taylor SA, Larson EL, Harrison RG. 2015. Hybrid zones: windows on climate change. Trends in Ecology & Evolution 30:398−406

doi: 10.1016/j.tree.2015.04.010
[11]

Aguirre-Liguori JA, Morales-Cruz A, Gaut BS. 2022. Evaluating the persistence and utility of five wild Vitis species in the context of climate change. Molecular Ecology 31:6457−72

doi: 10.1111/mec.16715
[12]

Rieseberg LH, Wendel JF. 1993. Introgression and its consequences. In Hybrid zones and the evolutionary process, ed. Harrison RG. New York, USA: Oxford University Press. pp. 70–109 doi: 10.1093/oso/9780195069174.003.0004
[13]

Todesco M, Pascual MA, Owens GL, Ostevik KL, Moyers BT, et al. 2016. Hybridization and extinction. Evolutionary Applications 9:892−908

doi: 10.1111/eva.12367
[14]

Angert AL, Bontrager MG, Ågren J. 2020. What do we really know about adaptation at range edges? Annual Review of Ecology, Evolution, and Systematics 51:341−61

doi: 10.1146/annurev-ecolsys-012120-091002
[15]

Tigano A, Friesen VL. 2016. Genomics of local adaptation with gene flow. Molecular Ecology 25:2144−64

doi: 10.1111/mec.13606
[16]

Aitken SN, Whitlock MC. 2013. Assisted gene flow to facilitate local adaptation to climate change. Annual Review of Ecology, Evolution, and Systematics 44:367−88

doi: 10.1146/annurev-ecolsys-110512-135747
[17]

Brauer CJ, Sandoval-Castillo J, Gates K, Hammer MP, Unmack PJ, et al. 2023. Natural hybridization reduces vulnerability to climate change. Nature Climate Change 13:282−9

doi: 10.1038/s41558-022-01585-1
[18]

Hansen MM. 2023. Prepping for climate change by introgressive hybridization. Trends in Genetics 39:524−25

doi: 10.1016/j.tig.2023.03.007
[19]

Tang CQ, Dong YF, Herrando-Moraira S, Matsui T, Ohashi H, et al. 2017. Potential effects of climate change on geographic distribution of the Tertiary relict tree species Davidia involucrata in China. Scientific Reports 7:43822

doi: 10.1038/srep43822
[20]

Chen JM, Zhao SY, Liao YY, Gichira AW, Gituru RW, et al. 2015. Chloroplast DNA phylogeographic analysis reveals significant spatial genetic structure of the relictual tree Davidia involucrata (Davidiaceae). Conservation Genetics 16:583−93

doi: 10.1007/s10592-014-0683-z
[21]

Ma Q, Du YJ, Chen N, Zhang LY, Li JH, et al. 2015. Phylogeography of Davidia involucrata (Davidiaceae) inferred from cpDNA haplotypes and nSSR data. Systematic Botany 40:796−810

doi: 10.1600/036364415X689267
[22]

Ren Y, Zhang L, Yang X, Lin H, Sang Y, et al. 2024. Cryptic divergences and repeated hybridizations within the endangered "living fossil" dove tree (Davidia involucrata) revealed by whole genome resequencing. Plant Diversity 46:169−80

doi: 10.1016/j.pld.2024.02.004
[23]

Catchen J, Hohenlohe PA, Bassham S, Amores A, Cresko WA. 2013. Stacks: an analysis tool set for population genomics. Molecular Ecology 22:3124−40

doi: 10.1111/mec.12354
[24]

Bolger AM, Lohse M, Usadel B. 2014. Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics 30:2114−20

doi: 10.1093/bioinformatics/btu170
[25]

Li H, Durbin R. 2009. Fast and accurate short read alignment with Burrows–Wheeler transform. Bioinformatics 25:1754−60

doi: 10.1093/bioinformatics/btp324
[26]

Chen Y, Ma T, Zhang L, Kang M, Zhang Z, et al. 2020. Genomic analyses of a "living fossil": the endangered dove-tree. Molecular Ecology Resources 20:756−69

doi: 10.1111/1755-0998.13138
[27]

Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, et al. 2009. The sequence alignment/map format and SAMtools. Bioinformatics 25:2078−79

doi: 10.1093/bioinformatics/btp352
[28]

Narasimhan V, Danecek P, Scally A, Xue Y, Tyler-Smith C, et al. 2016. BCFtools/RoH: a hidden Markov model approach for detecting autozygosity from next-generation sequencing data. Bioinformatics 32:1749−51

doi: 10.1093/bioinformatics/btw044
[29]

Danecek P, Auton A, Abecasis G, Albers CA, Banks E, et al. 2011. The variant call format and VCFtools. Bioinformatics 27:2156−58

doi: 10.1093/bioinformatics/btr330
[30]

Purcell S, Neale B, Todd-Brown K, Thomas L, Ferreira MAR, et al. 2007. PLINK: a tool set for whole-genome association and population-based linkage analyses. The American Journal of Human Genetics 81:559−75

doi: 10.1086/519795
[31]

Alexander DH, Novembre J, Lange K. 2009. Fast model-based estimation of ancestry in unrelated individuals. Genome Research 19:1655−64

doi: 10.1101/gr.094052.109
[32]

Li H, Durbin R. 2011. Inference of human population history from individual whole-genome sequences. Nature 475:493−96

doi: 10.1038/nature10231
[33]

Gutenkunst RN, Hernandez RD, Williamson SH, Bustamante CD. 2009. Inferring the joint demographic history of multiple populations from multidimensional SNP frequency data. PLoS Genetics 5:e1000695

doi: 10.1371/journal.pgen.1000695
[34]

Liu X, Fu YX. 2020. Stairway Plot 2: demographic history inference with folded SNP frequency spectra. Genome Biology 21:280

doi: 10.1186/s13059-020-02196-9
[35]

Excoffier L, Marchi N, Marques DA, Matthey-Doret R, Gouy A, et al. 2021. fastsimcoal2: demographic inference under complex evolutionary scenarios. Bioinformatics 37:4882−85

doi: 10.1093/bioinformatics/btab468
[36]

Malinsky M, Matschiner M, Svardal H. 2021. Dsuite − Fast D‐statistics and related admixture evidence from VCF files. Molecular ecology resources 21:584−95

doi: 10.1111/1755-0998.13265
[37]

Patterson N, Moorjani P, Luo Y, Mallick S, Rohland N, et al. 2012. Ancient admixture in human history. Genetics 192:1065−93

doi: 10.1534/genetics.112.145037
[38]

Dray S, Pélissier R, Couteron P, Fortin MJ, Legendre P, et al. 2012. Community ecology in the age of multivariate multiscale spatial analysis. Ecological Monographs 82:257−75

doi: 10.1890/11-1183.1
[39]

Frichot E, François O. 2015. LEA: an R package for landscape and ecological association studies. Methods in Ecology and Evolution 6:925−29

doi: 10.1111/2041-210X.12382
[40]

Oksanen J, Simpson G, Blanchet F, Kindt R, Legendre P, et al. 2022. Package 'vegan'. Community ecology package, version 2. pp.1−301 https://cran.r-project.org/web/packages/vegan/vegan.pdf
[41]

Cingolani P, Platts A, Wang LL, Coon M, Nguyen T, et al. 2012. A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff: SNPs in the genome of Drosophila melanogaster strain w1118; Iso-2; Iso-3. Fly 6:80−92

doi: 10.4161/fly.19695
[42]

Alexa A, Rahnenführer J. 2023. topGO: Enrichment Analysis for Gene Ontology. Bioconductor Improvement. doi:10.18129/B9.bioc.topGO
[43]

Phillips SJ, Anderson RP, Schapire RE. 2006. Maximum entropy modeling of species geographic distributions. Ecological Modelling 190:231−59

doi: 10.1016/j.ecolmodel.2005.03.026
[44]

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
[45]

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
[46]

Yang X, Kang M, Yang Y, Xiong H, Wang M, et al. 2019. A chromosome-level genome assembly of the Chinese tupelo Nyssa sinensis. Scientific Data 6:282

doi: 10.1038/s41597-019-0296-y
[47]

Eriksson ME, Millar AJ. 2003. The circadian clock. A plant's best friend in a spinning world. Plant Physiology 132:732−38

doi: 10.1104/pp.103.022343
[48]

Zheng B, Xu Q, Shen Y. 2002. The relationship between climate change and Quaternary glacial cycles on the Qinghai–Tibetan Plateau: review and speculation. Quaternary International 97:93−101

doi: 10.1016/S1040-6182(02)00054-X
[49]

Qiu YX, Fu CX, Comes HP. 2011. Plant molecular phylogeography in China and adjacent regions: tracing the genetic imprints of Quaternary climate and environmental change in the world's most diverse temperate flora. Molecular Phylogenetics and Evolution 59:225−44

doi: 10.1016/j.ympev.2011.01.012
[50]

Zhao YP, Fan G, Yin PP, Sun S, Li N, et al. 2019. Resequencing 545 Ginkgo genomes across the world reveals the evolutionary history of the living fossil. Nature Communications 10:4201

doi: 10.1038/s41467-019-12133-5
[51]

DE Carvalho D, Ingvarsson PK, Joseph J, Suter L, Sedivy C, et al. 2010. Admixture facilitates adaptation from standing variation in the European aspen (Populus tremula L.), a widespread forest tree. Molecular Ecology 19:1638−50

doi: 10.1111/j.1365-294X.2010.04595.x
[52]

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
[53]

Cao YN, Zhu SS, 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
[54]

Wang TR, Meng HH, Wang N, Zheng SS, Jiang Y, et al. 2023. Adaptive divergence and genetic vulnerability of relict species under climate change: a case study of Pterocarya macroptera. Annals of Botany 132:241−54

doi: 10.1093/aob/mcad083
[55]

Lu Y, Dong H, Fan S, Yuan L, Wang Y, et al. 2025. Local adaptation and climate change vulnerability of the relict tree species Taiwania cryptomerioides provide insights into its conservation and restoration. Evolutionary Applications 18:e70113

doi: 10.1111/eva.70113
[56]

DeWoody JA, Harder AM, Mathur S, Willoughby JR. 2021. The long-standing significance of genetic diversity in conservation. Molecular Ecology 30:4147−54

doi: 10.1111/mec.16051
[57]

Hoelzel AR. 2023. Where to now with the evolutionarily significant unit? Trends in Ecology & Evolution 38:1134−42

doi: 10.1016/j.tree.2023.07.005
[58]

Miller CV, Bossu CM, Sarraco JF, Toews DPL, Rushing CS, et al. 2024. Genomics-informed conservation units reveal spatial variation in climate vulnerability in a migratory bird. Molecular Ecology 33:e17199

doi: 10.1111/mec.17199
[59]

Kramer AT, Havens K. 2009. Plant conservation genetics in a changing world. Trends in Plant Science 14:599−607

doi: 10.1016/j.tplants.2009.08.005
[60]

Maunder M, Havens K, Guerrant E, Falk D. 2014. Ex situ methods: a vital but underused set of conservation resources. In Ex Situ Plant Conservation: Supporting species survival in the wild, eds. Guerrant E, Havens K, Maunder M. Washington, USA: Island Press. pp. 3–20 https://islandpress.org/books/ex-situ-plant-conservation