Adaptive divergence and genetic vulnerability of relict species under climate change: a case study of <i>Pterocarya macroptera</i>
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Aitken, 2016, Time to get moving: assisted gene flow of forest trees, Evolutionary Applications, 9, 271, 10.1111/eva.12293
Aitken, 2013, Assisted gene flow to facilitate local adaptation to climate change, Annual Review of Ecology, Evolution, and Systematics, 44, 367, 10.1146/annurev-ecolsys-110512-135747
Alexander, 2011, Enhancements to the ADMIXTURE algorithm for individual ancestry estimation, BMC Bioinformatics, 12, 246, 10.1186/1471-2105-12-246
Alexander, 2009, Fast model-based estimation of ancestry in unrelated individuals, Genome Research, 19, 1655, 10.1101/gr.094052.109
Andrews, 2010
Baird, 2008, Rapid SNP discovery and genetic mapping using sequenced RAD markers, PLoS One, 3, e3376, 10.1371/journal.pone.0003376
Bay, 2018, Genomic signals of selection predict climate-driven population declines in a migratory bird, Science, 359, 83, 10.1126/science.aan4380
Beaumont, 1996, Evaluating loci for use in the genetic analysis of population structure, Proceedings of the Royal Society of London. Series B: Biological Sciences, 263, 1619, 10.1098/rspb.1996.0237
Bolger, 2014, Trimmomatic: a flexible trimmer for Illumina sequence data, Bioinformatics, 30, 2114, 10.1093/bioinformatics/btu170
Brodribb, 2020, Hanging by a thread? Forests and drought, Science, 368, 261, 10.1126/science.aat7631
Cao, 2016, Evolution of East Asia’s Arcto-Tertiary relict Euptelea (Eupteleaceae) shaped by late Neogene vicariance and Quaternary climate change, BMC Evolutionary Biology, 16, 1, 10.1186/s12862-016-0636-x
Cao, 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, 10.1111/eva.12960
Capblancq, 2020, Genomic prediction of (mal)adaptation across current and future climatic landscapes, Annual Review of Ecology, Evolution, and Systematics, 51, 245, 10.1146/annurev-ecolsys-020720-042553
Catchen, 2013, Stacks: an analysis tool set for population genomics, Molecular Ecology, 22, 3124, 10.1111/mec.12354
Caye, 2019, LFMM 2: fast and accurate inference of gene-environment associations in genome-wide studies, Molecular Biology and Evolution, 36, 852, 10.1093/molbev/msz008
Cingolani, 2012, A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff, Fly, 6, 80, 10.4161/fly.19695
Chen, 2015, Chloroplast DNA phylogeographic analysis reveals significant spatial genetic structure of the relictual tree Davidia involucrata (Davidiaceae), Conservation Genetics, 16, 583, 10.1007/s10592-014-0683-z
Coop, 2010, Using environmental correlations to identify loci underlying local adaptation, Genetics, 185, 1411, 10.1534/genetics.110.114819
Danecek, 2011, The variant call format and VCFtools, Bioinformatics, 27, 2156, 10.1093/bioinformatics/btr330
Dauphin, 2020, Genomic vulnerability to rapid climate warming in a tree species with a long generation time, Global Change Biology, 27, 1181, 10.1111/gcb.15469
Davey, 2013, Special features of RAD sequencing data: implications for genotyping, Molecular Ecology, 22, 3151, 10.1111/mec.12084
Davis, 2001, Range shifts and adaptive responses to Quaternary climate change, Science, 292, 673, 10.1126/science.292.5517.673
Diniz-Filho, 2013, Mantel test in population genetics, Genetics and Molecular Biology, 36, 475, 10.1590/S1415-47572013000400002
Du, 2020, Contrasted patterns of local adaptation to climate change across the range of an evergreen oak, Quercus aquifolioides, Evolutionary Applications, 13, 2377, 10.1111/eva.13030
Ebrahimzadeh, 2009, Essential oil composition and antioxidant activity of Pterocarya fraxinifolia, Pakistan Journal of Biological Sciences, 12, 957, 10.3923/pjbs.2009.957.963
Ellis, 2012, Gradient forests: calculating importance gradients on physical predictors, Ecology, 93, 156, 10.1890/11-0252.1
Fazan, 2020, The woody planet: from past triumph to manmade decline, Plants, 9, 1593, 10.3390/plants9111593
Feng, 2022, Landscape genomics in tree conservation under a changing environment, Frontiers in Plant Science, 13, 822217, 10.3389/fpls.2022.822217
Fick, 2017, WorldClim 2: new 1-km spatial resolution climate surfaces for global land areas, International Journal of Climatology, 37, 4302, 10.1002/joc.5086
Fitzpatrick, 2015, Ecological genomics meets community-level modelling of biodiversity: mapping the genomic landscape of current and future environmental adaptation, Ecology Letters, 18, 1, 10.1111/ele.12376
Forester, 2018, Comparing methods for detecting multilocus adaptation with multivariate genotype–environment associations, Molecular Ecology, 27, 2215, 10.1111/mec.14584
Frankel, 1995, The genetic diversity of wild plants, ., 10
Franks, 2012, Genetics of climate change adaptation, Annual Review of Genetics, 46, 185, 10.1146/annurev-genet-110711-155511
Fredriksen, 2020, Green gravel: a novel restoration tool to combat kelp forest decline, Scientific Reports, 10, 3983, 10.1038/s41598-020-60553-x
Frichot, 2015, LEA: an R package for landscape and ecological association studies, Methods in Ecology and Evolution, 6, 925, 10.1111/2041-210X.12382
Goslee, 2007, The ecodist package for dissimilarity-based analysis of ecological data, Journal of Statistical Software, 22, 1, 10.18637/jss.v022.i07
Goudet, 2005, HIERFSTAT, a package for R to compute and test hierarchical F-statistics, Molecular Ecology Notes, 5, 184, 10.1111/j.1471-8286.2004.00828.x
Gougherty, 2021, Maladaptation, migration and extirpation fuel climate change risk in a forest tree species, Nature Climate Change, 11, 166, 10.1038/s41558-020-00968-6
Günther, 2013, Robust identification of local adaptation from allele frequencies, Genetics, 195, 205, 10.1534/genetics.113.152462
Halbert, 2008, Patterns of genetic variation in US federal bison herds, Molecular Ecology, 17, 4963, 10.1111/j.1365-294X.2008.03973.x
Hijmans, 2021, Package ‘geosphere’
Jombart, 2010, Discriminant analysis of principal components: a new method for the analysis of genetically structured populations, BMC Genetics, 11, 94, 10.1186/1471-2156-11-94
Korunes, 2021, pixy: unbiased estimation of nucleotide diversity and divergence in the presence of missing data, Molecular Ecology Resources, 21, 1359, 10.1111/1755-0998.13326
Kozlowski, 2018, Wingnuts (Pterocarya) and walnut family. Relict trees: linking the past, present and future
Kremer, 2012, Long-distance gene flow and adaptation of forest trees to rapid climate change, Ecology Letters, 15, 378, 10.1111/j.1461-0248.2012.01746.x
Lefèvre, 2014, Considering evolutionary processes in adaptive forestry, Annals of Forest Science, 71, 723, 10.1007/s13595-013-0272-1
Li, 2009, Fast and accurate short read alignment with Burrows–Wheeler transform, Bioinformatics, 25, 1754, 10.1093/bioinformatics/btp324
Li, 2009, The sequence alignment/map format and SAMtools, Bioinformatics, 25, 2078, 10.1093/bioinformatics/btp352
Li, 2017, Ten years of landscape genomics: challenges and opportunities, Frontiers in Plant Science, 8, 2136, 10.3389/fpls.2017.02136
Li, 2018, Adaptive genetic differentiation in Pterocarya stenoptera (Juglandaceae) driven by multiple environmental variables were revealed by landscape genomics, BMC Plant Biology, 18, 306, 10.1186/s12870-018-1524-x
Li, 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, 10.1111/jse.12699
Li, 2023, Wind-dispersed seeds blur phylogeographic breaks: the complex evolutionary history of Populus lasiocarpa around the Sichuan Basin, Plant Diversity, 45, 156, 10.1016/j.pld.2022.10.003
Licausi, 2013, APETALA 2/ethylene responsive factor (AP2/ERF) transcription factors: mediators of stress responses and developmental programs, New Phytologist, 199, 639, 10.1111/nph.12291
Liu, 2004, Isolation, identification and antitumor activity of triterpenes from Pterocarya tonkinensis (Franch.) Dode, Chinese Journal of Medicinal Chemistry, 14, 165
López-Pujol, 2011, Centres of plant endemism in China: places for survival or for speciation, Journal of Biogeography, 38, 1267, 10.1111/j.1365-2699.2011.02504.x
Lu, 1999, Juglandaceae, Flora of China, 277
Luo, 2018, Phylogeography of rare fern Polystichum glaciale endemic to the subnival zone of the Sino-Himalaya, Plant Systematics and Evolution, 304, 485, 10.1007/s00606-018-1495-2
Luu, 2017, pcadapt: an R package to perform genome scans for selection based on principal component analysis, Molecular Ecology Resources, 17, 67, 10.1111/1755-0998.12592
Ma, 2015, Phylogeography of Davidia involucrata (Davidiaceae) inferred from cpDNA haplotypes and nSSR data, Systematic Botany, 40, 796, 10.1600/036364415X689267
Mantel, 1967, The detection of disease clustering and a generalized regression approach, Cancer Research, 27, 209
Martins, 2018, Landscape genomics provides evidence of climate-associated genetic variation in Mexican populations of Quercus rugosa, Evolutionary Applications, 11, 1842, 10.1111/eva.12684
Meinshausen, 2020, The shared socio-economic pathway (SSP) greenhouse gas concentrations and their extensions to 2500, Geoscientific Model Development, 13, 3571, 10.5194/gmd-13-3571-2020
Meng, 2015, Refugial isolation and range expansions drive the genetic structure of Oxyria sinensis (Polygonaceae) in the Himalaya-Hengduan Mountains, Scientific Reports, 5, 10396, 10.1038/srep10396
Meng, 2021, Biodiversity arks in the Anthropocene, Regional Sustainability, 2, 109, 10.1016/j.regsus.2021.03.001
Meng, 2022, Opening a door to the spatiotemporal history of plants from the tropical Indochina Peninsula to subtropical China, Molecular Phylogenetics and Evolution, 171, 107458, 10.1016/j.ympev.2022.107458
De Mita, 2013, Detecting selection along environmental gradients: analysis of eight methods and their effectiveness for outbreeding and selfing populations, Molecular Ecology, 22, 1383, 10.1111/mec.12182
Munwes, 2010, The change in genetic diversity down the core-edge gradient in the eastern spadefoot toad (Pelobates syriacus), Molecular Ecology, 19, 2675, 10.1111/j.1365-294X.2010.04712.x
Nachman, 2012, Recombination rate variation and speciation: theoretical predictions and empirical results from rabbits and mice, Philosophical Transactions of the Royal Society B: Biological Sciences, 367, 409, 10.1098/rstb.2011.0249
Naimi, 2014, Where is positional uncertainty a problem for species distribution modelling, Ecography, 37, 191, 10.1111/j.1600-0587.2013.00205.x
Nocchi, 2023, Genomic signals of local adaptation and hybridization in Asian white birch, Molecular Ecology, 32, 595, 10.1111/mec.16788
Oksanen, 2019, Vegan: Community Ecology Package
Parmesan, 2006, Ecological and evolutionary responses to recent climate change, Annual Review of Ecology, Evolution, and Systematics, 37, 637, 10.1146/annurev.ecolsys.37.091305.110100
Paschold, 2006, Using ‘mute’ plants to translate volatile signals, Plant Journal, 45, 275, 10.1111/j.1365-313X.2005.02623.x
Petit, 1998, Identifying populations for conservation on the basis of genetic markers, Biological Conservation, 12, 844, 10.1046/j.1523-1739.1998.96489.x
Pina-Martins, 2018, New insights into adaptation and population structure of cork oak using genotyping by sequencing, Global Change Biology, 25, 337, 10.1111/gcb.14497
Privé, 2020, Performing highly efficient genome scans for local adaptation with R package pcadapt version 4, Molecular Biology and Evolution, 37, 2153, 10.1093/molbev/msaa053
Purcell, 2007, PLINK: A tool set for whole-genome association and population-based linkage analyses, American Journal of Human Genetics, 81, 559, 10.1086/519795
Qiao, 2018, Evolutionary melting pots and reproductive isolation: a ring-shaped diversification of an odorous frog (Odorrana margaratea) around the Sichuan Basin, Molecular Ecology, 27, 4888, 10.1111/mec.14899
Qiu, 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, 10.1016/j.ympev.2011.01.012
Qiu, 2017, Phylogeography of East Asia’s Tertiary relict plants: current progress and future prospects, Biodiversity Science, 25, 24, 10.17520/biods.2016292
R Core Team, 2019, R: a language and environment for statistical computing
Razgour, 2019, Considering adaptive genetic variation in climate change vulnerability assessment reduces species range loss projections, Proceedings of the National Academy of Sciences of the USA, 116, 10418, 10.1073/pnas.1820663116
Rellstab, 2015, A practical guide to environmental association analysis in landscape genomics, Molecular Ecology, 24, 4348, 10.1111/mec.13322
Rellstab, 2016, Signatures of local adaptation in candidate genes of oaks (Quercus spp.) with respect to present and future climatic conditions, Molecular Ecology, 25, 5907, 10.1111/mec.13889
Root, 2003, Fingerprints of global warming on wild animals and plants, Nature, 421, 57, 10.1038/nature01333
Sang, 2022, Genomic insights into local adaptation and future climate-induced vulnerability of a keystone forest tree species in East Asia, Nature Communications, 13, 6541, 10.1038/s41467-022-34206-8
Santini, 2019, Addressing common pitfalls does not provide more support to geographical and ecological abundant-centre hypotheses, Ecography, 42, 692, 10.1111/ecog.04027
Savolainen, 2011, The genomic basis of local climatic adaptation, Science, 334, 49, 10.1126/science.1213788
Scheffers, 2016, The broad footprint of climate change from genes to biomes to people, Science, 354, aaf7671, 10.1126/science.aaf7671
Song, 2019, Pterocarya macroptera. The IUCN Red List of Threatened Species: e.T66816136A66816223
Song, 2020, Phylogeny, taxonomy, and biogeography of Pterocarya (Juglandaceae), Plants, 9, 1524, 10.3390/plants9111524
Song, 2021, Past, present and future suitable areas for the relict tree Pterocarya fraxinifolia (Juglandaceae): integrating fossil records, niche modeling, and phylogeography for conservation, European Journal of Forest Research, 140, 1323, 10.1007/s10342-021-01397-6
Sork, 2018, Genomic studies of local adaptation in natural plant populations, Journal of Heredity, 109, 3, 10.1093/jhered/esx091
Sork, 2013, Putting the landscape into the genomics of trees: approaches for understanding local adaptation and population responses to changing climate, Tree Genetics and Genomes, 9, 901, 10.1007/s11295-013-0596-x
Strimmer, 2008, fdrtool: a versatile R package for estimating local and tail area-based false discovery rates, Bioinformatics, 24, 1461, 10.1093/bioinformatics/btn209
Tang, 2018, Identifying long-term stable refugia for relict plant species in East Asia, Nature Communications, 9, 4488, 10.1038/s41467-018-06837-3
Tang, 2022, Molecular phylogeography and evolutionary history of the pink rice borer (Lepidoptera: Noctuidae): implications for refugia identification and pest management, Systematic Entomology, 47, 371, 10.1111/syen.12535
Vranken, 2021, Genotype-environment mismatch of kelp forests under climate change, Molecular Ecology, 30, 3730, 10.1111/mec.15993
Wahid, 2007, Heat tolerance in plants: an overview, Environmental and Experimental Botany, 61, 199, 10.1016/j.envexpbot.2007.05.011
Waldvogel, 2020, Evolutionary genomics can improve prediction of species’ responses to climate change, Evolution Letters, 4, 4, 10.1002/evl3.154
Wang, 2021, New approaches for ecological adaptation study: from population genetics to landscape genomics, Scientia Sinica Vitae, 51, 167, 10.1360/SSV-2020-0265
Wang, 2019, Phylogeography of Excoecaria acerifolia (Euphorbiaceae) suggests combined effects of historical drainage reorganization events and climatic changes on riparian plants in the Sino-Himalayan region, Botanical Journal of the Linnean Society, 192, 350
Wei, 2016, Genetic evidence for central-marginal hypothesis in a Cenozoic relict tree species across its distribution in China, Journal of Biogeography, 43, 2173, 10.1111/jbi.12788
Whitlock, 2015, Reliable detection of loci responsible for local adaptation: inference of a null model through trimming the distribution of FST, American Naturalist, 186, S24, 10.1086/682949
Wiens, 2016, Climate-related local extinctions are already widespread among plant and animal species, PLoS Biology, 14, e2001104, 10.1371/journal.pbio.2001104
Woolbright, 2014, Climate relicts and their associated communities as natural ecology and evolution laboratories, Trends in Ecology and Evolution, 29, 406, 10.1016/j.tree.2014.05.003
Wu, 1996, A proposal for a new floristic kingdom (realm) – the E. Asiatic kingdom, its delimitation and characteristics, Proceedings of the First International Symposium on Floristic Characteristics and Diversity of East Asian Plants, 3
Wu, 2017, Mobile hotspots and refugia of avian diversity in the mountains of south-west China under past and contemporary global climate change, Journal of Biogeography, 44, 615, 10.1111/jbi.12862
Wu, 2020, The last primary forests of the Tertiary relict Glyptostrobus pensilis contain the highest genetic diversity, Forestry, 93, 359, 10.1093/forestry/cpz063
Xiao, 2002, Attraction of the cotton bollworm, Helicoverpa armigera (Hübner) (Lepidoptera: Noctuidae), to volatiles from wilted leaves of a non-host plant, Pterocarya stenoptera, Applied Entomology and Zoology, 37, 1, 10.1303/aez.2002.1
Xu, 2021, A test of the centre–periphery hypothesis using population genetics in an East Asian Tertiary relict tree, Journal of Biogeography, 48, 2853, 10.1111/jbi.14244
Yang, 2017, Molecular phylogeny, biogeography and ecological niche modelling of Cardiocrinum (Liliaceae): insights into the evolutionary history of endemic genera distributed across the Sino-Japanese floristic region, Annals of Botany, 119, 59, 10.1093/aob/mcw210
Yannic, 2014, Genetic diversity in caribou linked to past and future climate change, Nature Climate Change, 4, 132, 10.1038/nclimate2074
Yin, 2019, Chemical compositions and antimicrobial activities of the essential oil from Pterocarya stenoptera C. DC, Natural Product Research, 34, 2828, 10.1080/14786419.2019.1587426
Zhang, 2006, Analysis of the volatile components of fresh, wilts, dry China wingnut (Pterocarya stenoptera C. DC.) by SPME with GC-MS, Natural Product Research, 18, 778
Zhang, 2022, Dead-end hybridization in walnut trees revealed by large-scale genomic sequence data, Molecular Biology and Evolution, 39, msab308, 10.1093/molbev/msab308