{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,12]],"date-time":"2026-10-12T09:51:04Z","timestamp":1791798664575,"version":"4.3.4"},"reference-count":105,"publisher":"Wiley","issue":"1","license":[{"start":{"date-parts":[[2026,10,12]],"date-time":"2026-10-12T00:00:00Z","timestamp":1791763200000},"content-version":"vor","delay-in-days":11,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"},{"start":{"date-parts":[[2026,10,1]],"date-time":"2026-10-01T00:00:00Z","timestamp":1790812800000},"content-version":"tdm","delay-in-days":0,"URL":"http:\/\/doi.wiley.com\/10.1002\/tdm_license_1.1"}],"funder":[{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["32570443"],"award-info":[{"award-number":["32570443"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["32070377"],"award-info":[{"award-number":["32070377"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["onlinelibrary.wiley.com"],"crossmark-restriction":true},"short-container-title":["The Plant Journal"],"published-print":{"date-parts":[[2026,10]]},"abstract":"<jats:title>SUMMARY<\/jats:title>\n                  <jats:p>\n                    Population genetic theory predicts that species with narrow geographic distributions experience stronger genetic drift, higher inbreeding, and greater mutational burden than their widespread relatives, yet how demographic history shapes the genomic basis of adaptation remains poorly understood. We hypothesized that (i) restricted\u2010range species exhibit reduced genetic diversity, elevated inbreeding, and greater mutation load owing to smaller long\u2010term effective population sizes; (ii) despite these demographic constraints, shared environmental pressures can still drive repeated adaptation; (iii) repeated adaptation may arise through ancestral standing genetic variation, adaptive introgression, or independent\n                    <jats:italic>de novo<\/jats:italic>\n                    mutations. We tested these hypotheses using two kiwifruit species,\n                    <jats:italic>Actinidia hemsleyana<\/jats:italic>\n                    (narrow\u2010ranged) and\n                    <jats:italic>Actinidia eriantha<\/jats:italic>\n                    (widespread), which differ markedly in demographic history and range size but occupy overlapping environments in subtropical China. We show that demographic contraction and inbreeding have eroded genome\u2010wide diversity in the range\u2010restricted species, accompanied by a substantially higher load of deleterious mutations. Despite these contrasting demographic legacies, both species exhibit repeated genomic responses to shared climatic gradients, with adaptation targeting similar genes. Such repeated adaptation was driven primarily by ancestral standing variation, with smaller contributions from adaptive introgression and only limited evidence for independent\n                    <jats:italic>de novo<\/jats:italic>\n                    mutations. These results reveal that demographic constraints shape genome\u2010wide diversity and mutation load but do not preclude repeated adaptation when shared genetic variation remains available.\n                  <\/jats:p>","DOI":"10.1111\/tpj.71163","type":"journal-article","created":{"date-parts":[[2026,10,12]],"date-time":"2026-10-12T09:40:21Z","timestamp":1791798021000},"update-policy":"https:\/\/doi.org\/10.1002\/crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["Repeated genetic adaptation under demographic limits in kiwifruit"],"prefix":"10.1111","volume":"128","author":[{"given":"Mengyun","family":"Qin","sequence":"first","affiliation":[{"name":"State Key Laboratory of Plant Diversity and Specialty Crops, Wuhan Botanical Garden Chinese Academy of Sciences  Wuhan Hubei 430074 China"},{"name":"University of Chinese Academy of Sciences  Beijing 100049 China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jingwen","family":"Huang","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Plant Diversity and Specialty Crops, Wuhan Botanical Garden Chinese Academy of Sciences  Wuhan Hubei 430074 China"},{"name":"University of Chinese Academy of Sciences  Beijing 100049 China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yufang","family":"Shen","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Plant Diversity and Specialty Crops, Wuhan Botanical Garden Chinese Academy of Sciences  Wuhan Hubei 430074 China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Quan","family":"Jiang","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Plant Diversity and Specialty Crops, Wuhan Botanical Garden Chinese Academy of Sciences  Wuhan Hubei 430074 China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7345-501X","authenticated-orcid":false,"given":"Na","family":"Wei","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Plant Diversity and Specialty Crops, Wuhan Botanical Garden Chinese Academy of Sciences  Wuhan Hubei 430074 China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8398-1232","authenticated-orcid":false,"given":"Xiaohong","family":"Yao","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Plant Diversity and Specialty Crops, Wuhan Botanical Garden Chinese Academy of Sciences  Wuhan Hubei 430074 China"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"311","published-online":{"date-parts":[[2026,10,12]]},"reference":[{"key":"e_1_2_10_2_1","doi-asserted-by":"crossref","first-page":"68","DOI":"10.1093\/botlinnean\/boae089","article-title":"Narrow endemism of Dyckia (Bromeliaceae) species within a vegetative mosaic region in the Midwest Brazil: insights from the phylogeographic patterns","volume":"209","author":"Aguiar\u2010Melo C.","year":"2025","journal-title":"Botanical Journal of the Linnean Society"},{"key":"e_1_2_10_3_1","doi-asserted-by":"crossref","first-page":"2274","DOI":"10.1093\/bioinformatics\/bts419","article-title":"OmegaPlus: a scalable tool for rapid detection of selective sweeps in whole\u2010genome datasets","volume":"28","author":"Alachiotis N.","year":"2012","journal-title":"Bioinformatics"},{"key":"e_1_2_10_4_1","doi-asserted-by":"crossref","first-page":"1655","DOI":"10.1101\/gr.094052.109","article-title":"Fast model\u2010based estimation of ancestry in unrelated individuals","volume":"19","author":"Alexander D.H.","year":"2009","journal-title":"Genome Research"},{"key":"e_1_2_10_5_1","doi-asserted-by":"crossref","first-page":"38","DOI":"10.1016\/j.tree.2007.09.008","article-title":"Adaptation from standing genetic variation","volume":"23","author":"Barrett R.","year":"2008","journal-title":"Trends in Ecology & Evolution"},{"key":"e_1_2_10_6_1","doi-asserted-by":"crossref","first-page":"169","DOI":"10.1105\/tpc.16.00847","article-title":"Protein phosphatase 2Cs and microtubule\u2010associated stress protein 1 control microtubule stability, plant growth, and drought response","volume":"29","author":"Bhaskara G.B.","year":"2017","journal-title":"Plant Cell"},{"key":"e_1_2_10_7_1","doi-asserted-by":"crossref","first-page":"4448","DOI":"10.1111\/mec.16061","article-title":"Annual and perennial Medicago show signatures of parallel adaptation to climate and soil in highly conserved genes","volume":"30","author":"Blanco\u2010Pastor J.L.","year":"2021","journal-title":"Molecular Ecology"},{"key":"e_1_2_10_8_1","doi-asserted-by":"crossref","first-page":"396","DOI":"10.1016\/j.tree.2023.11.007","article-title":"Divergence time shapes gene reuse during repeated adaptation","volume":"39","author":"Bohut\u00ednsk\u00e1 M.","year":"2024","journal-title":"Trends in Ecology & Evolution"},{"key":"e_1_2_10_9_1","doi-asserted-by":"crossref","DOI":"10.1073\/pnas.2022713118","article-title":"Genomic basis of parallel adaptation varies with divergence in Arabidopsis and its relatives","volume":"118","author":"Bohut\u00ednsk\u00e1 M.","year":"2021","journal-title":"Proceedings of the National Academy of Sciences"},{"key":"e_1_2_10_10_1","doi-asserted-by":"crossref","first-page":"330","DOI":"10.1111\/eva.12872","article-title":"The type of bottleneck matters: insights into the deleterious variation landscape of small managed populations","volume":"13","author":"Bortoluzzi C.","year":"2020","journal-title":"Evolutionary Applications"},{"key":"e_1_2_10_11_1","doi-asserted-by":"crossref","first-page":"3228","DOI":"10.1093\/molbev\/msu256","article-title":"Standing genetic variation drives repeatable experimental evolution in outcrossing populations of Saccharomyces cerevisiae","volume":"31","author":"Burke M.K.","year":"2014","journal-title":"Molecular Biology and Evolution"},{"key":"e_1_2_10_12_1","doi-asserted-by":"crossref","first-page":"5825","DOI":"10.1093\/molbev\/msab293","article-title":"eggNOG\u2010mapper v2: functional annotation, orthology assignments, and domain prediction at the metagenomic scale","volume":"38","author":"Cantalapiedra C.P.","year":"2021","journal-title":"Molecular Biology and Evolution"},{"key":"e_1_2_10_13_1","doi-asserted-by":"crossref","first-page":"2298","DOI":"10.1111\/2041-210X.13722","article-title":"Redundancy analysis: a Swiss army knife for landscape genomics","volume":"12","author":"Capblancq T.","year":"2021","journal-title":"Methods in Ecology and Evolution"},{"key":"e_1_2_10_14_1","doi-asserted-by":"crossref","first-page":"5451","DOI":"10.1111\/mec.17132","article-title":"Understanding natural selection and similarity: convergent, parallel, and repeated evolution","volume":"32","author":"Cerca J.","year":"2023","journal-title":"Molecular Ecology"},{"key":"e_1_2_10_15_1","doi-asserted-by":"crossref","DOI":"10.1111\/tpj.70175","article-title":"Conservation genomics of a threatened subtropical Rhododendron species highlights the distinct conservation actions required in marginal and admixed populations","volume":"122","author":"Chang Y.","year":"2025","journal-title":"The Plant Journal"},{"key":"e_1_2_10_16_1","doi-asserted-by":"crossref","first-page":"195","DOI":"10.1038\/nrg2526","article-title":"Effective population size and patterns of molecular evolution and variation","volume":"10","author":"Charlesworth B.","year":"2009","journal-title":"Nature Reviews Genetics"},{"key":"e_1_2_10_17_1","doi-asserted-by":"crossref","DOI":"10.1111\/mec.70180","article-title":"Identifying the degree of gene reuse during repeated adaptation","volume":"34","author":"Chaturvedi S.","year":"2025","journal-title":"Molecular Ecology"},{"key":"e_1_2_10_18_1","doi-asserted-by":"crossref","first-page":"1952","DOI":"10.1038\/s41559-022-01909-6","article-title":"Climatic similarity and genomic background shape the extent of parallel adaptation in Timema stick insects","volume":"6","author":"Chaturvedi S.","year":"2022","journal-title":"Nature Ecology and Evolution"},{"key":"e_1_2_10_19_1","doi-asserted-by":"crossref","first-page":"i884","DOI":"10.1093\/bioinformatics\/bty560","article-title":"Fastp: an ultra\u2010fast all\u2010in\u2010one FASTQ preprocessor","volume":"34","author":"Chen S.","year":"2018","journal-title":"Bioinformatics"},{"key":"e_1_2_10_20_1","doi-asserted-by":"crossref","DOI":"10.1126\/sciadv.adw3797","article-title":"Balancing selection of climate adaptive loci underlies the success of introduction of Eurasian tree sparrows","volume":"11","author":"Chen Y.L.","year":"2025","journal-title":"Science Advances"},{"key":"e_1_2_10_21_1","doi-asserted-by":"crossref","DOI":"10.1016\/j.plantsci.2021.111125","article-title":"Calcium\u2010dependent protein kinase 5 (CPK5) positively modulates drought tolerance through phosphorylating ABA\u2010responsive element binding factors in oilseed rape (Brassica napus L.)","volume":"315","author":"Cheng H.","year":"2022","journal-title":"Plant Science"},{"key":"e_1_2_10_22_1","doi-asserted-by":"crossref","first-page":"80","DOI":"10.4161\/fly.19695","article-title":"A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff: SNPs in the genome of Drosophila melanogaster strain w1118; iso\u20102; iso\u20103","volume":"6","author":"Cingolani P.","year":"2012","journal-title":"Fly"},{"key":"e_1_2_10_23_1","doi-asserted-by":"crossref","first-page":"2156","DOI":"10.1093\/bioinformatics\/btr330","article-title":"The variant call format and VCFtools","volume":"27","author":"Danecek P.","year":"2011","journal-title":"Bioinformatics"},{"key":"e_1_2_10_24_1","doi-asserted-by":"crossref","DOI":"10.1093\/gigascience\/giab008","article-title":"Twelve years of SAMtools and BCFtools","volume":"10","author":"Danecek P.","year":"2021","journal-title":"GigaScience"},{"key":"e_1_2_10_25_1","doi-asserted-by":"crossref","first-page":"516","DOI":"10.1038\/s41467-021-20958-2","article-title":"Life history, climate and biogeography interactively affect worldwide genetic diversity of plant and animal populations","volume":"12","author":"De Kort H.","year":"2021","journal-title":"Nature Communications"},{"key":"e_1_2_10_26_1","doi-asserted-by":"crossref","first-page":"491","DOI":"10.1038\/ng.806","article-title":"A framework for variation discovery and genotyping using next\u2010generation DNA sequencing data","volume":"43","author":"DePristo M.A.","year":"2011","journal-title":"Nature Genetics"},{"key":"e_1_2_10_27_1","doi-asserted-by":"crossref","first-page":"126","DOI":"10.1038\/ng.3186","article-title":"No evidence that selection has been less effective at removing deleterious mutations in Europeans than in Africans","volume":"47","author":"Do R.","year":"2015","journal-title":"Nature Genetics"},{"key":"e_1_2_10_28_1","article-title":"Isolation of plant DNA from fresh tissue","volume":"12","author":"Doyle J.J.T.","year":"1990","journal-title":"Focus"},{"key":"e_1_2_10_29_1","doi-asserted-by":"crossref","first-page":"961","DOI":"10.1016\/j.tree.2023.05.008","article-title":"Purging and accumulation of genetic load in conservation","volume":"38","author":"Dussex N.","year":"2023","journal-title":"Trends in Ecology & Evolution"},{"key":"e_1_2_10_30_1","doi-asserted-by":"crossref","first-page":"1170","DOI":"10.1111\/j.1365-294X.2007.03659.x","article-title":"Genetic variation across species' geographical ranges: the central\u2013marginal hypothesis and beyond","volume":"17","author":"Eckert C.G.","year":"2008","journal-title":"Molecular Ecology"},{"key":"e_1_2_10_31_1","doi-asserted-by":"crossref","first-page":"422","DOI":"10.1038\/nrg.2016.58","article-title":"Determinants of genetic diversity","volume":"17","author":"Ellegren H.","year":"2016","journal-title":"Nature Reviews Genetics"},{"key":"e_1_2_10_32_1","doi-asserted-by":"crossref","first-page":"156","DOI":"10.1890\/11-0252.1","article-title":"Gradient forests: calculating importance gradients on physical predictors","volume":"93","author":"Ellis N.","year":"2012","journal-title":"Ecology"},{"key":"e_1_2_10_33_1","doi-asserted-by":"crossref","first-page":"177","DOI":"10.1111\/tpj.16486","article-title":"Genome sequences and population genomics provide insights into the demographic history, inbreeding, and mutation load of two \u2018living fossil\u2019 tree species of Dipteronia","volume":"117","author":"Feng Y.","year":"2024","journal-title":"The Plant Journal"},{"key":"e_1_2_10_34_1","doi-asserted-by":"crossref","first-page":"925","DOI":"10.1111\/2041-210X.12382","article-title":"LEA: an R package for landscape and ecological association studies","volume":"6","author":"Frichot E.","year":"2015","journal-title":"Methods in Ecology and Evolution"},{"key":"e_1_2_10_35_1","doi-asserted-by":"crossref","first-page":"2678","DOI":"10.1111\/j.0014-3820.2003.tb01512.x","article-title":"How are deleterious mutations purged? Drift versus nonrandom mating","volume":"57","author":"Gl\u00e9min S.","year":"2003","journal-title":"Evolution"},{"key":"e_1_2_10_36_1","doi-asserted-by":"crossref","first-page":"862","DOI":"10.1126\/science.185.4154.862","article-title":"Amino acid difference formula to help explain protein evolution","volume":"185","author":"Grantham R.","year":"1974","journal-title":"Science"},{"key":"e_1_2_10_37_1","doi-asserted-by":"crossref","first-page":"1001","DOI":"10.1038\/s41467-020-14803-1","article-title":"Purging of highly deleterious mutations through severe bottlenecks in Alpine ibex","volume":"11","author":"Grossen C.","year":"2020","journal-title":"Nature Communications"},{"key":"e_1_2_10_38_1","doi-asserted-by":"crossref","first-page":"89","DOI":"10.1186\/s12870-022-03464-5","article-title":"Molecular phylogeography and species distribution modelling evidence of \u2018oceanic\u2019 adaptation for Actinidia eriantha with a refugium along the oceanic\u2013continental gradient in a biodiversity hotspot","volume":"22","author":"Guo R.","year":"2022","journal-title":"BMC Plant Biology"},{"key":"e_1_2_10_39_1","doi-asserted-by":"crossref","first-page":"95","DOI":"10.1007\/BF00120641","article-title":"Factors influencing levels of genetic diversity in woody plant species","volume":"6","author":"Hamrick J.L.","year":"1992","journal-title":"New Forests"},{"key":"e_1_2_10_40_1","doi-asserted-by":"crossref","first-page":"1240","DOI":"10.1111\/nph.13643","article-title":"Evidence for extensive parallelism but divergent genomic architecture of adaptation along altitudinal and latitudinal gradients in Populus trichocarpa","volume":"209","author":"Holliday J.A.","year":"2016","journal-title":"New Phytologist"},{"key":"e_1_2_10_41_1","volume-title":"Actinidia: taxonomy, resources, domestication, cultivation","author":"Huang H.W.","year":"2013"},{"key":"e_1_2_10_42_1","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pgen.1008658","article-title":"Parallelism in eco\u2010morphology and gene expression despite variable evolutionary and genomic backgrounds in a Holarctic fish","volume":"16","author":"Jacobs A.","year":"2020","journal-title":"PLoS Genetics"},{"key":"e_1_2_10_43_1","doi-asserted-by":"crossref","first-page":"733","DOI":"10.1016\/j.pld.2025.02.003","article-title":"Genomic signatures of local adaptation to precipitation and solar radiation in kiwifruit","volume":"47","author":"Jiang Q.","year":"2025","journal-title":"Plant Diversity"},{"key":"e_1_2_10_44_1","doi-asserted-by":"crossref","DOI":"10.1016\/j.agwat.2022.107675","article-title":"Effects of different photovoltaic shading levels on kiwifruit growth, yield and water productivity under \u201cagrivoltaic\u201d system in Southwest China","volume":"269","author":"Jiang S.Z.","year":"2022","journal-title":"Agricultural Water Management"},{"key":"e_1_2_10_45_1","doi-asserted-by":"crossref","first-page":"587","DOI":"10.1038\/nmeth.4285","article-title":"ModelFinder: fast model selection for accurate phylogenetic estimates","volume":"14","author":"Kalyaanamoorthy S.","year":"2017","journal-title":"Nature Methods"},{"key":"e_1_2_10_46_1","doi-asserted-by":"crossref","DOI":"10.3390\/f13040579","article-title":"Genetic diversity and structure of Quercus hondae, a rare evergreen oak species in Southwestern Japan","volume":"13","author":"Kamiya K.","year":"2022","journal-title":"Forests"},{"key":"e_1_2_10_47_1","doi-asserted-by":"crossref","first-page":"63","DOI":"10.1038\/hdy.2015.17","article-title":"Measuring individual inbreeding in the age of genomics: marker\u2010based measures are better than pedigrees","volume":"115","author":"Kardos M.","year":"2015","journal-title":"Heredity"},{"key":"e_1_2_10_48_1","doi-asserted-by":"crossref","first-page":"897","DOI":"10.1534\/genetics.118.301120","article-title":"Inferring the probability of the derived vs. the ancestral allelic state at a polymorphic site","volume":"209","author":"Keightley P.D.","year":"2018","journal-title":"Genetics"},{"key":"e_1_2_10_49_1","doi-asserted-by":"crossref","first-page":"4979","DOI":"10.1038\/s41467-021-25256-5","article-title":"Parallel adaptation in autopolyploid Arabidopsis arenosa is dominated by repeated recruitment of shared alleles","volume":"12","author":"Kone\u010dn\u00e1 V.","year":"2021","journal-title":"Nature Communications"},{"key":"e_1_2_10_50_1","doi-asserted-by":"crossref","first-page":"356","DOI":"10.1186\/s12859-014-0356-4","article-title":"ANGSD: analysis of next generation sequencing data","volume":"15","author":"Korneliussen T.S.","year":"2014","journal-title":"BMC Bioinformatics"},{"key":"e_1_2_10_51_1","doi-asserted-by":"crossref","first-page":"1359","DOI":"10.1111\/1755-0998.13326","article-title":"Pixy: unbiased estimation of nucleotide diversity and divergence in the presence of missing data","volume":"21","author":"Korunes K.L.","year":"2021","journal-title":"Molecular Ecology Resources"},{"key":"e_1_2_10_52_1","doi-asserted-by":"crossref","DOI":"10.7554\/eLife.102321","article-title":"Pleiotropy increases parallel selection signatures during adaptation from standing genetic variation","volume":"13","author":"Lai W.Y.","year":"2024","journal-title":"eLife"},{"key":"e_1_2_10_53_1","doi-asserted-by":"crossref","first-page":"125","DOI":"10.1093\/plcell\/koac267","article-title":"Genotype\u2013environment associations to reveal the molecular basis of environmental adaptation","volume":"35","author":"Lasky J.R.","year":"2023","journal-title":"The Plant Cell"},{"key":"e_1_2_10_54_1","doi-asserted-by":"crossref","first-page":"1591","DOI":"10.1534\/genetics.117.300417","article-title":"Distinguishing among modes of convergent adaptation using population genomic data","volume":"207","author":"Lee K.M.","year":"2017","journal-title":"Genetics"},{"key":"e_1_2_10_55_1","doi-asserted-by":"crossref","first-page":"1754","DOI":"10.1093\/bioinformatics\/btp324","article-title":"Fast and accurate short read alignment with Burrows\u2013Wheeler transform","volume":"25","author":"Li H.","year":"2009","journal-title":"Bioinformatics"},{"key":"e_1_2_10_56_1","doi-asserted-by":"crossref","DOI":"10.1111\/tpj.70597","article-title":"Genomic analysis of xerophyte Salweenia species provides insights into the alpine dry\u2013warm valleys divergence and survival history","volume":"124","author":"Liao M.","year":"2025","journal-title":"The Plant Journal"},{"key":"e_1_2_10_57_1","doi-asserted-by":"crossref","DOI":"10.1007\/s11032-017-0729-2","article-title":"Construction of a SNP\u2010based genetic linkage map for kiwifruit using next\u2010generation restriction\u2010site\u2010associated DNA sequencing (RADseq)","volume":"37","author":"Liu C.Y.","year":"2017","journal-title":"Molecular Breeding"},{"key":"e_1_2_10_58_1","doi-asserted-by":"crossref","DOI":"10.1093\/molbev\/msac008","article-title":"Demographic history and natural selection shape patterns of deleterious mutation load and barriers to introgression across Populus genome","volume":"39","author":"Liu S.Y.","year":"2022","journal-title":"Molecular Biology and Evolution"},{"key":"e_1_2_10_59_1","doi-asserted-by":"crossref","first-page":"877","DOI":"10.1111\/nph.14607","article-title":"Rapid radiations of both kiwifruit hybrid lineages and their parents shed light on a two\u2010layer mode of species diversification","volume":"215","author":"Liu Y.F.","year":"2017","journal-title":"New Phytologist"},{"key":"e_1_2_10_60_1","doi-asserted-by":"crossref","DOI":"10.3389\/fgene.2012.00246","article-title":"Replaying the tape of life: quantification of the predictability of evolution","volume":"3","author":"Lobkovsky A.E.","year":"2012","journal-title":"Frontiers in Genetics"},{"key":"e_1_2_10_61_1","doi-asserted-by":"crossref","first-page":"1533","DOI":"10.1111\/tpj.15399","article-title":"Chromosome\u2010level genome assembly and population genetic analysis of a critically endangered Rhododendron provide insights into its conservation","volume":"107","author":"Ma H.","year":"2021","journal-title":"The Plant Journal"},{"key":"e_1_2_10_62_1","doi-asserted-by":"crossref","first-page":"83","DOI":"10.1007\/s00344-021-10557-2","article-title":"Biological function and stress response mechanism of MYB transcription factor family genes","volume":"42","author":"Ma R.","year":"2023","journal-title":"Journal of Plant Growth Regulation"},{"key":"e_1_2_10_63_1","doi-asserted-by":"crossref","first-page":"251","DOI":"10.1038\/s41559-020-01341-8","article-title":"Intercontinental genomic parallelism in multiple three\u2010spined stickleback adaptive radiations","volume":"5","author":"Magalhaes I.S.","year":"2021","journal-title":"Nature Ecology and Evolution"},{"key":"e_1_2_10_64_1","doi-asserted-by":"crossref","first-page":"1540","DOI":"10.1111\/eva.13216","article-title":"Genetic load has potential in large populations but is realized in small inbred populations","volume":"14","author":"Mathur S.","year":"2021","journal-title":"Evolutionary Applications"},{"key":"e_1_2_10_65_1","doi-asserted-by":"crossref","first-page":"4676","DOI":"10.1038\/s41467-022-32316-x","article-title":"Repeated genetic adaptation to altitude in two tropical butterflies","volume":"13","author":"Montejo\u2010Kovacevich G.","year":"2022","journal-title":"Nature Communications"},{"key":"e_1_2_10_66_1","doi-asserted-by":"crossref","first-page":"2557","DOI":"10.1038\/s41467-023-37909-8","article-title":"Selection\u2010driven trait loss in independently evolved cavefish populations","volume":"14","author":"Moran R.L.","year":"2023","journal-title":"Nature Communications"},{"key":"e_1_2_10_67_1","doi-asserted-by":"crossref","DOI":"10.1126\/sciadv.add0560","article-title":"Convergent genomic signatures of local adaptation across a continental\u2010scale environmental gradient","volume":"9","author":"Moreira L.R.","year":"2023","journal-title":"Science Advances"},{"key":"e_1_2_10_68_1","doi-asserted-by":"crossref","first-page":"268","DOI":"10.1093\/molbev\/msu300","article-title":"IQ\u2010TREE: a fast and effective stochastic algorithm for estimating maximum\u2010likelihood phylogenies","volume":"32","author":"Nguyen L.T.","year":"2015","journal-title":"Molecular Biology and Evolution"},{"key":"e_1_2_10_69_1","doi-asserted-by":"crossref","first-page":"2224","DOI":"10.1093\/molbev\/mst112","article-title":"SweeD: likelihood\u2010based detection of selective sweeps in thousands of genomes","volume":"30","author":"Pavlidis P.","year":"2013","journal-title":"Molecular Biology and Evolution"},{"key":"e_1_2_10_70_1","doi-asserted-by":"crossref","first-page":"1095","DOI":"10.1038\/s41559-020-1215-5","article-title":"Determinants of genetic variation across eco\u2010evolutionary scales in pinnipeds","volume":"4","author":"Peart C.R.","year":"2020","journal-title":"Nature Ecology and Evolution"},{"key":"e_1_2_10_71_1","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pbio.1002379","article-title":"Phylogenomics reveals three sources of adaptive variation during a rapid radiation","volume":"14","author":"Pease J.B.","year":"2016","journal-title":"PLoS Biology"},{"key":"e_1_2_10_72_1","doi-asserted-by":"crossref","first-page":"2084","DOI":"10.1111\/mec.13154","article-title":"Expansion load: recessive mutations and the role of standing genetic variation","volume":"24","author":"Peischl S.","year":"2015","journal-title":"Molecular Ecology"},{"key":"e_1_2_10_73_1","doi-asserted-by":"crossref","first-page":"746","DOI":"10.1016\/j.pld.2025.06.006","article-title":"Genomic and population genomic analyses reveal contrasting diversity and demographic histories in a critically endangered and a widespread Oreocharis species","volume":"47","author":"Peng N.","year":"2025","journal-title":"Plant Diversity"},{"key":"e_1_2_10_74_1","first-page":"349","article-title":"Parallel evolution of cold tolerance within Drosophila melanogaster","volume":"34","author":"Pool J.E.","year":"2017","journal-title":"Molecular Biology and Evolution"},{"key":"e_1_2_10_75_1","doi-asserted-by":"crossref","first-page":"1467","DOI":"10.1111\/j.0014-3820.2000.tb00693.x","article-title":"Compensating for our load of mutations: freezing the meltdown of small populations","volume":"54","author":"Poon A.","year":"2000","journal-title":"Evolution"},{"key":"e_1_2_10_76_1","doi-asserted-by":"crossref","first-page":"559","DOI":"10.1086\/519795","article-title":"PLINK: a tool set for whole\u2010genome association and population\u2010based linkage analyses","volume":"81","author":"Purcell S.","year":"2007","journal-title":"American Journal of Human Genetics"},{"key":"e_1_2_10_77_1","doi-asserted-by":"crossref","first-page":"4350","DOI":"10.1111\/mec.15648","article-title":"Genomic signatures of convergent adaptation to alpine environments in three Brassicaceae species","volume":"29","author":"Rellstab C.","year":"2020","journal-title":"Molecular Ecology"},{"key":"e_1_2_10_78_1","doi-asserted-by":"crossref","first-page":"3487","DOI":"10.1016\/j.cub.2018.08.066","article-title":"Purging of strongly deleterious mutations explains long\u2010term persistence and absence of inbreeding depression in island foxes","volume":"28","author":"Robinson J.A.","year":"2018","journal-title":"Current Biology"},{"key":"e_1_2_10_79_1","doi-asserted-by":"crossref","DOI":"10.3390\/genes14010174","article-title":"Genetic diversity, conservation, and utilization of plant genetic resources","volume":"14","author":"Salgotra R.K.","year":"2023","journal-title":"Genes"},{"key":"e_1_2_10_80_1","doi-asserted-by":"crossref","first-page":"807","DOI":"10.1038\/nrg3522","article-title":"Ecological genomics of local adaptation","volume":"14","author":"Savolainen O.","year":"2013","journal-title":"Nature Reviews Genetics"},{"key":"e_1_2_10_81_1","doi-asserted-by":"crossref","first-page":"650","DOI":"10.1111\/nph.16406","article-title":"Determinants of geographic range size in plants","volume":"226","author":"Sheth S.N.","year":"2020","journal-title":"New Phytologist"},{"key":"e_1_2_10_82_1","doi-asserted-by":"crossref","first-page":"1680","DOI":"10.1093\/bioinformatics\/btu861","article-title":"scrm: efficiently simulating long sequences using the approximated coalescent with recombination","volume":"31","author":"Staab P.R.","year":"2015","journal-title":"Bioinformatics"},{"key":"e_1_2_10_83_1","doi-asserted-by":"crossref","first-page":"1026","DOI":"10.1038\/nbt.3988","article-title":"MMseqs2 enables sensitive protein sequence searching for the analysis of massive data sets","volume":"35","author":"Steinegger M.","year":"2017","journal-title":"Nature Biotechnology"},{"key":"e_1_2_10_84_1","doi-asserted-by":"crossref","first-page":"78","DOI":"10.1016\/j.pld.2023.06.005","article-title":"Conservation genomic investigation of an endangered conifer, Thuja sutchuenensis, reveals low genetic diversity but also low genetic load","volume":"46","author":"Tao T.","year":"2024","journal-title":"Plant Diversity"},{"key":"e_1_2_10_85_1","doi-asserted-by":"crossref","DOI":"10.1007\/978-3-319-32274-2","volume-title":"The kiwifruit genome","author":"Testolin R.","year":"2016"},{"key":"e_1_2_10_86_1","doi-asserted-by":"crossref","first-page":"129","DOI":"10.1002\/evl3.106","article-title":"Parallel genetic evolution and speciation from standing variation","volume":"3","author":"Thompson K.A.","year":"2019","journal-title":"Evolution Letters"},{"key":"e_1_2_10_87_1","doi-asserted-by":"crossref","first-page":"3041","DOI":"10.1534\/g3.120.401527","article-title":"rdmc: an open source r package implementing convergent adaptation models of Lee and Coop (2017)","volume":"10","author":"Tittes S.","year":"2020","journal-title":"G3: Genes, Genomes, Genetics"},{"key":"e_1_2_10_88_1","doi-asserted-by":"crossref","first-page":"4102","DOI":"10.1111\/mec.15429","article-title":"Rapid repeatable phenotypic and genomic adaptation following multiple introductions","volume":"29","author":"Boheemen L.A.","year":"2020","journal-title":"Molecular Ecology"},{"key":"e_1_2_10_89_1","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1038\/nprot.2015.123","article-title":"SIFT missense predictions for genomes","volume":"11","author":"Vaser R.","year":"2016","journal-title":"Nature Protocols"},{"key":"e_1_2_10_90_1","doi-asserted-by":"crossref","first-page":"263","DOI":"10.1093\/molbev\/msaa213","article-title":"Genomic consequences of long\u2010term population decline in brown eared pheasant","volume":"38","author":"Wang P.","year":"2021","journal-title":"Molecular Biology and Evolution"},{"key":"e_1_2_10_91_1","doi-asserted-by":"crossref","first-page":"1908","DOI":"10.1111\/nph.18634","article-title":"Selective sweeps linked to the colonization of novel habitats and climatic changes in a wild tomato species","volume":"237","author":"Wei K.","year":"2023","journal-title":"New Phytologist"},{"key":"e_1_2_10_92_1","doi-asserted-by":"crossref","first-page":"418","DOI":"10.1007\/s00239-008-9146-9","article-title":"Divergence and polymorphism under the nearly neutral theory of molecular evolution","volume":"67","author":"Welch J.J.","year":"2008","journal-title":"Journal of Molecular Evolution"},{"key":"e_1_2_10_93_1","doi-asserted-by":"crossref","first-page":"97","DOI":"10.1093\/genetics\/16.2.97","article-title":"Evolution in Mendelian populations","volume":"16","author":"Wright S.","year":"1931","journal-title":"Genetics"},{"key":"e_1_2_10_94_1","article-title":"ClusterProfiler 4.0: a universal enrichment tool for interpreting omics data","volume":"2","author":"Wu T.","year":"2021","journal-title":"Innovation (Cambridge, Mass.)"},{"key":"e_1_2_10_95_1","doi-asserted-by":"crossref","DOI":"10.1016\/j.ijbiomac.2024.136652","article-title":"MYB\u00a0transcription factors in plants: a comprehensive review of their discovery, structure, classification, functional diversity and regulatory mechanism","volume":"282","author":"Wu X.","year":"2024","journal-title":"International Journal of Biological Macromolecules"},{"key":"e_1_2_10_96_1","doi-asserted-by":"crossref","first-page":"231","DOI":"10.1016\/j.pld.2025.09.006","article-title":"Speciation, endangerment and adaptation in limestone rocky environment of Urophysa (Ranunculaceae)","volume":"48","author":"Xie D.F.","year":"2025","journal-title":"Plant Diversity"},{"key":"e_1_2_10_97_1","doi-asserted-by":"crossref","DOI":"10.1093\/molbev\/msab359","article-title":"Ancient demographics determine the effectiveness of genetic purging in endangered lizards","volume":"39","author":"Xie H.X.","year":"2021","journal-title":"Molecular Biology and Evolution"},{"key":"e_1_2_10_98_1","doi-asserted-by":"crossref","first-page":"164","DOI":"10.1079\/9781800620933.0011","volume-title":"Kiwifruit botany, production and uses","author":"Xiloyannis C.","year":"2023"},{"key":"e_1_2_10_99_1","doi-asserted-by":"crossref","first-page":"242","DOI":"10.1126\/science.aaa3952","article-title":"Mountain gorilla genomes reveal the impact of long\u2010term population decline and inbreeding","volume":"348","author":"Xue Y.","year":"2015","journal-title":"Science"},{"key":"e_1_2_10_100_1","doi-asserted-by":"crossref","first-page":"5449","DOI":"10.1038\/s41467-018-07913-4","article-title":"Genomic effects of population collapse in a critically endangered ironwood tree Ostrya rehderiana","volume":"9","author":"Yang Y.","year":"2018","journal-title":"Nature Communications"},{"key":"e_1_2_10_101_1","doi-asserted-by":"crossref","first-page":"294","DOI":"10.1016\/j.pld.2024.03.006","article-title":"Conservation genomics provides insights into genetic resilience and adaptation of the endangered Chinese hazelnut, Corylus chinensis","volume":"46","author":"Yang Z.","year":"2024","journal-title":"Plant Diversity"},{"key":"e_1_2_10_102_1","doi-asserted-by":"crossref","DOI":"10.1186\/s43897-022-00034-z","article-title":"The genome sequencing and comparative analysis of a wild kiwifruit Actinidia eriantha","volume":"2","author":"Yao X.H.","year":"2022","journal-title":"Molecular Horticulture"},{"key":"e_1_2_10_103_1","doi-asserted-by":"crossref","first-page":"1431","DOI":"10.1126\/science.aaf7812","article-title":"Convergent local adaptation to climate in distantly related conifers","volume":"353","author":"Yeaman S.","year":"2016","journal-title":"Science"},{"key":"e_1_2_10_104_1","doi-asserted-by":"crossref","first-page":"1522","DOI":"10.1111\/tpj.17064","article-title":"Genomic signatures of inbreeding and mutation load in tree ferns","volume":"120","author":"Yi H.","year":"2024","journal-title":"The Plant Journal"},{"key":"e_1_2_10_105_1","doi-asserted-by":"crossref","first-page":"1528","DOI":"10.1111\/tpj.16336","article-title":"Genomic analyses reveal dead\u2010end hybridization between two deeply divergent kiwifruit species rather than homoploid hybrid speciation","volume":"115","author":"Yu X.F.","year":"2023","journal-title":"The Plant Journal"},{"key":"e_1_2_10_106_1","article-title":"Development of single nucleotide polymorphism and phylogenetic analysis of Rhododendron species in Zhejiang province, China, using ddRAD\u2010Seq technology","volume":"14","author":"Zhu H.","year":"2025","journal-title":"Plants (Basel)"}],"container-title":["The Plant Journal"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/onlinelibrary.wiley.com\/doi\/pdf\/10.1111\/tpj.71163","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/onlinelibrary.wiley.com\/doi\/full-xml\/10.1111\/tpj.71163","content-type":"application\/xml","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/onlinelibrary.wiley.com\/doi\/pdf\/10.1111\/tpj.71163","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,10,12]],"date-time":"2026-10-12T09:40:37Z","timestamp":1791798037000},"score":1,"resource":{"primary":{"URL":"https:\/\/onlinelibrary.wiley.com\/doi\/10.1111\/tpj.71163"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,10]]},"references-count":105,"journal-issue":{"issue":"1","published-print":{"date-parts":[[2026,10]]}},"alternative-id":["10.1111\/tpj.71163"],"URL":"https:\/\/doi.org\/10.1111\/tpj.71163","archive":["Portico"],"relation":{},"ISSN":["0960-7412","1365-313X"],"issn-type":[{"value":"0960-7412","type":"print"},{"value":"1365-313X","type":"electronic"}],"subject":[],"published":{"date-parts":[[2026,10]]},"assertion":[{"value":"2026-02-28","order":0,"name":"received","label":"Received","group":{"name":"publication_history","label":"Publication History"}},{"value":"2026-09-25","order":2,"name":"accepted","label":"Accepted","group":{"name":"publication_history","label":"Publication History"}},{"value":"2026-10-12","order":3,"name":"published","label":"Published","group":{"name":"publication_history","label":"Publication History"}}],"article-number":"e71163"}}