{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,12]],"date-time":"2026-09-12T08:07:38Z","timestamp":1789200458160,"version":"build-2803163510"},"reference-count":163,"publisher":"Oxford University Press (OUP)","issue":"9","license":[{"start":{"date-parts":[[2026,4,21]],"date-time":"2026-04-21T00:00:00Z","timestamp":1776729600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"UW-USDA NIFA","award":["2019-51181-30015"],"award-info":[{"award-number":["2019-51181-30015"]}]},{"DOI":"10.13039\/100007917","name":"USDA-ARS","doi-asserted-by":"crossref","award":["5090-21220-007-00-D"],"award-info":[{"award-number":["5090-21220-007-00-D"]}],"id":[{"id":"10.13039\/100007917","id-type":"DOI","asserted-by":"crossref"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2026,9,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>Wild populations of North American cranberry (Vaccinium macrocarpon Aiton) are reservoirs of genetic variation that may contribute to the improvement of breeding-relevant traits. However, the extent to which wild genetic variation is geographically structured and represented in elite germplasm remains unclear. We analysed 179 wild cranberry accessions from the upper Midwest and Eastern North America to estimate nucleotide diversity (\u03c0), population structure, and loci associated with genetic differentiation and environmental variables using a genome-informed targeted genotyping panel. Additionally, 14 demographic scenarios were evaluated using site-frequency-spectrum-based inference to identify historical events that could explain current genetic diversity. We observed extremely low nucleotide diversity within the targeted panel (\u03c0 = 5 \u00d7 10\u22126). Rare allele distributions strongly influenced \u03c0 and Tajima\u2019s D values, suggesting constrained diversity in the genomic regions assayed that is not captured by heterozygosity-based estimates alone. However, we interpreted these results as conservative lower bounds on genome-wide neutral diversity because the targeted panel is enriched for genic and conserved regions. A clear separation between the Midwest and East populations was observed, with inbreeding coefficients ranging from \u22120.13 to 0.15. Furthermore, site frequency spectrum inference from the targeted panel supported a demographic scenario consistent with a significant population reduction \u224815\u201314 thousand years ago (kya), followed by a divergence between the two regions \u224812 kya, and an asymmetric gene flow \u22481.3 kya. We detected 254 candidate loci showing regional allele-frequency differentiation. Several of these loci colocalized with candidate genes linked to stress response, development, and metabolic processes. To evaluate the representation of geographically differentiated wild alleles in a breeding context, we analysed Rutgers breeding materials (n\u2009=\u2009484) and found that this panel is enriched for common alleles in Eastern wild populations. These findings indicate regionally structured allele-frequency variation in wild cranberry, with potential relevance to environmental response and breeding. This study extends prior wild cranberry population-genetic research by providing targeted-panel estimates of diversity, comparisons of demographic models, and breeding insights on geographically differentiated alleles, while highlighting the importance of conserving wild cranberry germplasm for use in modern breeding programs.<\/jats:p>","DOI":"10.1093\/hr\/uhag161","type":"journal-article","created":{"date-parts":[[2026,4,21]],"date-time":"2026-04-21T09:09:29Z","timestamp":1776762569000},"source":"Crossref","is-referenced-by-count":0,"title":["Targeted population genomics uncovers demographic history and genetic divergence in north American wild cranberry"],"prefix":"10.1093","volume":"13","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-4612-7157","authenticated-orcid":false,"given":"Nicol\u00e1s Pandeli","family":"Jim\u00e9nez","sequence":"first","affiliation":[{"name":"P.E. Marucci Center for Blueberry and Cranberry Research and Extension, Rutgers, The State University of New Jersey , Chatsworth, NJ 08019 ,","place":["USA"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0003-5548-5201","authenticated-orcid":false,"given":"Maria Alejandra","family":"Torres-Meraz","sequence":"additional","affiliation":[{"name":"Department of Plant and Agroecosystem Sciences, University of Wisconsin-Madison , Madison, WI 53706 ,","place":["USA"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1991-5310","authenticated-orcid":false,"given":"Jeffrey L","family":"Neyhart","sequence":"additional","affiliation":[{"name":"USDA, Agricultural Research Service, Genetic Improvement for Fruits and Vegetables Laboratory , Chatsworth, NJ 08019 ,","place":["USA"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8840-3565","authenticated-orcid":false,"given":"Juan","family":"Zalapa","sequence":"additional","affiliation":[{"name":"Department of Plant and Agroecosystem Sciences, University of Wisconsin-Madison , Madison, WI 53706 ,","place":["USA"]},{"name":"United States Department of Agriculture-Agricultural Research Service, Vegetable Crops Research Unit , Madison, WI 53706 ,","place":["USA"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1056-1496","authenticated-orcid":false,"given":"Gina Maria","family":"Sideli","sequence":"additional","affiliation":[{"name":"P.E. Marucci Center for Blueberry and Cranberry Research and Extension, Rutgers, The State University of New Jersey , Chatsworth, NJ 08019 ,","place":["USA"]}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2026,4,21]]},"reference":[{"key":"2026091203521351000_ref1","doi-asserted-by":"crossref","first-page":"3477","DOI":"10.1093\/jxb\/erv122","article-title":"Exploiting genetic diversity from landraces in wheat breeding for adaptation to climate change","volume":"66","author":"Lopes","year":"2015","journal-title":"J Exp Bot"},{"key":"2026091203521351000_ref2","doi-asserted-by":"crossref","first-page":"47","DOI":"10.1016\/j.pbi.2015.01.008","article-title":"Patterns of genomic changes with crop domestication and breeding","volume":"24","author":"Shi","year":"2015","journal-title":"Curr Opin Plant Biol"},{"key":"2026091203521351000_ref3","doi-asserted-by":"crossref","first-page":"29","DOI":"10.1111\/eva.12680","article-title":"A 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Geographical Reference Maps: U.S. River Basins","author":"National Oceanic and Atmospheric Administration (NOAA)","year":"2025"},{"key":"2026091203521351000_ref33","doi-asserted-by":"crossref","first-page":"S13","DOI":"10.1186\/1753-6561-8-S1-S13","article-title":"Small sample properties of rare variant analysis methods","volume":"8","author":"Swartz","year":"2014","journal-title":"BMC Proc"},{"key":"2026091203521351000_ref34","doi-asserted-by":"crossref","first-page":"123","DOI":"10.1186\/s12864-016-2441-8","article-title":"The effects of sample size on population genomic analyses \u2013 implications for the tests of neutrality","volume":"17","author":"Subramanian","year":"2016","journal-title":"BMC Genomics"},{"key":"2026091203521351000_ref35","doi-asserted-by":"crossref","first-page":"11","DOI":"10.1038\/s10038-020-00845-2","article-title":"Unique roles of rare variants in the genetics of complex diseases in humans","volume":"66","author":"Momozawa","year":"2021","journal-title":"J Hum Genet"},{"key":"2026091203521351000_ref36","article-title":"Polygenic power calculator: statistical power and polygenic prediction accuracy of genome-wide association studies of complex traits","volume":"13","author":"Tian","year":"2022","journal-title":"Front Genet"},{"key":"2026091203521351000_ref37","doi-asserted-by":"crossref","first-page":"uhad202","DOI":"10.1093\/hr\/uhad202","article-title":"Blueberry and cranberry pangenomes as a resource for future genetic studies and breeding efforts","volume":"10","author":"Yocca","year":"2023","journal-title":"Hortic Res"},{"key":"2026091203521351000_ref38","article-title":"A high-recovery, high-density targeted genotyping platform for cranberry. Plant","volume":"19","author":"Clare","year":"2026","journal-title":"Genome"},{"key":"2026091203521351000_ref39","doi-asserted-by":"crossref","first-page":"84","DOI":"10.1186\/1471-2156-14-84","article-title":"Peach genetic resources: diversity, population structure and linkage disequilibrium","volume":"14","author":"Li","year":"2013","journal-title":"BMC Genet"},{"key":"2026091203521351000_ref40","doi-asserted-by":"crossref","first-page":"R55","DOI":"10.1186\/gb-2013-14-6-r55","article-title":"Comprehensive genotyping of the USA national maize inbred seed bank","volume":"14","author":"Romay","year":"2013","journal-title":"Genome Biol"},{"key":"2026091203521351000_ref41","doi-asserted-by":"crossref","first-page":"114","DOI":"10.1007\/s11295-016-1075-y","article-title":"Genetic diversity and genetic structure of Persian walnut (Juglans regia) accessions from 14 European, African, and Asian countries using SSR markers","volume":"12","author":"Ebrahimi","year":"2016","journal-title":"Tree 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Nat"},{"key":"2026091203521351000_ref93","doi-asserted-by":"crossref","first-page":"207","DOI":"10.1016\/j.yqres.2009.04.002","article-title":"Climate and vegetation history from a 14,000-year peatland record, Kenai peninsula, Alaska","volume":"72","author":"Jones","year":"2009","journal-title":"Quat Res"},{"key":"2026091203521351000_ref94","doi-asserted-by":"crossref","first-page":"96","DOI":"10.1016\/j.yqres.2014.04.016","article-title":"Holocene development of maritime ombrotrophic peatlands of the St. Lawrence north shore in eastern Canada","volume":"82","author":"Magnan","year":"2014","journal-title":"Quat Res"},{"key":"2026091203521351000_ref95","doi-asserted-by":"crossref","first-page":"6036","DOI":"10.1111\/mec.15989","article-title":"An overview of current population genomics methods for the analysis of whole-genome resequencing data in eukaryotes","volume":"30","author":"Bourgeois","year":"2021","journal-title":"Mol Ecol"},{"key":"2026091203521351000_ref96","first-page":"373","article-title":"An outline of north American deglaciation with emphasis on central and northern Canada","volume":"2","author":"Dyke","year":"2004","journal-title":"Dev Quat Sci"},{"key":"2026091203521351000_ref97","doi-asserted-by":"crossref","first-page":"357","DOI":"10.1007\/s10933-011-9550-9","article-title":"Mapping the phases of glacial Lake Algonquin in the upper Great Lakes region, Canada and USA, using a geostatistical isostatic rebound model","volume":"47","author":"Drzyzga","year":"2012","journal-title":"J Paleolimnol"},{"key":"2026091203521351000_ref98","doi-asserted-by":"crossref","first-page":"453","DOI":"10.1139\/cjes-2019-0076","article-title":"A younger glacial Lake Iroquois in the Lake Ontario basin, Ontario and New York: re-examination of pollen stratigraphy and radiocarbon dating","volume":"57","author":"Lewis","year":"2020","journal-title":"Can J Earth Sci"},{"key":"2026091203521351000_ref99","doi-asserted-by":"crossref","first-page":"837","DOI":"10.1111\/j.1469-185X.2010.00129.x","article-title":"The role of hydrochory in structuring riparian and wetland vegetation","volume":"85","author":"Nilsson","year":"2010","journal-title":"Biol Rev"},{"key":"2026091203521351000_ref100","doi-asserted-by":"crossref","first-page":"4071","DOI":"10.5194\/bg-9-4071-2012","article-title":"Northern peatland carbon stocks and dynamics: a review","volume":"9","author":"Yu","year":"2012","journal-title":"Biogeosciences"},{"key":"2026091203521351000_ref101","doi-asserted-by":"crossref","first-page":"929","DOI":"10.5194\/bg-10-929-2013","article-title":"Climate-related changes in peatland carbon accumulation during the last 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The Holocene"},{"key":"2026091203521351000_ref103","doi-asserted-by":"crossref","first-page":"2435","DOI":"10.1046\/j.0962-1083.2001.01366.x","article-title":"Rapid genetic divergence in postglacial populations of threespine stickleback (Gasterosteus aculeatus): the role of habitat type, drainage and geographical proximity","volume":"10","author":"Reusch","year":"2001","journal-title":"Mol Ecol"},{"key":"2026091203521351000_ref104","doi-asserted-by":"crossref","first-page":"381","DOI":"10.2307\/2960511","article-title":"Vaccinium oxycoccos L. (Oxycoccus palustris Pers.) and Vaccinium microcarpum (Turcz. Ex Rupr.) Schmalh. (Oxycoccus microcarpus Turcz. Ex Rupr.)","volume":"85","author":"Jacquemart","year":"1997","journal-title":"J Ecol"},{"key":"2026091203521351000_ref105","doi-asserted-by":"crossref","first-page":"175","DOI":"10.1139\/cjb-2021-0086","article-title":"Traditional uses and beneficial effects of various species of berry-producing plants in eastern Canada","volume":"100","author":"Weber","year":"2022","journal-title":"Botany"},{"key":"2026091203521351000_ref106","doi-asserted-by":"crossref","DOI":"10.1201\/9781315118116","volume-title":"Aquatic Dicotyledons of North America: Ecology, Life History, and Systematics","author":"Les","year":"2017"},{"key":"2026091203521351000_ref107","doi-asserted-by":"crossref","first-page":"3883","DOI":"10.1002\/ece3.2682","article-title":"Asymmetry matters: a genomic assessment of directional biases in gene flow between hybridizing spruces","volume":"7","author":"Lafontaine","year":"2017","journal-title":"Ecol Evol"},{"key":"2026091203521351000_ref108","doi-asserted-by":"crossref","first-page":"191","DOI":"10.1007\/978-1-4419-0763-9_6","article-title":"American cranberry fruit breeding","volume-title":"Fruit Breeding","author":"Vorsa","year":"2012"},{"key":"2026091203521351000_ref109","doi-asserted-by":"crossref","first-page":"279","DOI":"10.1002\/9781119616801.ch8","article-title":"Domestication, genetics, and genomics of the American cranberry","volume":"43","author":"Vorsa","year":"2019","journal-title":"Plant Breed Rev"},{"key":"2026091203521351000_ref110","doi-asserted-by":"crossref","first-page":"1389","DOI":"10.3732\/ajb.1000522","article-title":"From forest to field: perennial fruit crop domestication","volume":"98","author":"Miller","year":"2011","journal-title":"Am J Bot"},{"key":"2026091203521351000_ref111","doi-asserted-by":"crossref","first-page":"338","DOI":"10.3390\/plants11030338","article-title":"Coping with abiotic stress in plants \u2013 an endomembrane trafficking perspective","volume":"11","author":"Sampaio","year":"2022","journal-title":"Plants"},{"key":"2026091203521351000_ref112","doi-asserted-by":"crossref","first-page":"146","DOI":"10.1093\/plcell\/koab235","article-title":"Molecular mechanisms of endomembrane trafficking in plants","volume":"34","author":"Aniento","year":"2022","journal-title":"Plant Cell"},{"key":"2026091203521351000_ref113","doi-asserted-by":"crossref","first-page":"499","DOI":"10.1016\/j.bbrc.2017.10.092","article-title":"Loss of ribosomal protein L24A (RPL24A) suppresses proline accumulation of Arabidopsis thaliana ring zinc finger 1 (atrzf1) mutant in response to osmotic stress","volume":"494","author":"Park","year":"2017","journal-title":"Biochem Biophys Res Commun"},{"key":"2026091203521351000_ref114","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pone.0062577","article-title":"Loss of the Arabidopsis thaliana P4-ATPase ALA3 reduces adaptability to temperature stresses and impairs vegetative, pollen, and ovule development","volume":"8","author":"McDowell","year":"2013","journal-title":"PLoS One"},{"key":"2026091203521351000_ref115","doi-asserted-by":"crossref","first-page":"1025","DOI":"10.1105\/tpc.13.5.1025","article-title":"The Arabidopsis mutant cev1 has constitutively active jasmonate and ethylene signal pathways and enhanced resistance to pathogens","volume":"13","author":"Ellis","year":"2001","journal-title":"Plant Cell"},{"key":"2026091203521351000_ref116","doi-asserted-by":"crossref","first-page":"1557","DOI":"10.1105\/tpc.002022","article-title":"The Arabidopsis mutant cev1 links cell wall signaling to jasmonate and ethylene responses","volume":"14","author":"Ellis","year":"2002","journal-title":"Plant Cell"},{"key":"2026091203521351000_ref117","doi-asserted-by":"crossref","first-page":"242","DOI":"10.1104\/pp.15.01874","article-title":"Anisotropic cell expansion is affected through the bidirectional mobility of cellulose synthase complexes and phosphorylation at two critical residues on CESA3","volume":"171","author":"Chen","year":"2016","journal-title":"Plant Physiol"},{"key":"2026091203521351000_ref118","doi-asserted-by":"crossref","first-page":"3823","DOI":"10.1105\/tpc.109.069906","article-title":"Auxin response in Arabidopsis under cold stress: underlying molecular mechanisms","volume":"21","author":"Shibasaki","year":"2009","journal-title":"Plant Cell"},{"key":"2026091203521351000_ref119","doi-asserted-by":"crossref","first-page":"805","DOI":"10.1111\/j.1365-313X.2012.05121.x","article-title":"The putative auxin efflux carrier OsPIN3t is involved in the drought stress response and drought tolerance","volume":"72","author":"Zhang","year":"2012","journal-title":"Plant J"},{"key":"2026091203521351000_ref120","doi-asserted-by":"crossref","first-page":"9319","DOI":"10.1073\/pnas.1400966111","article-title":"Plant roots use a patterning mechanism to position lateral root branches toward available water","volume":"111","author":"Bao","year":"2014","journal-title":"Proc Natl Acad Sci USA"},{"key":"2026091203521351000_ref121","doi-asserted-by":"crossref","first-page":"1661","DOI":"10.1111\/nph.17687","article-title":"Osmotic stress represses root growth by modulating the transcriptional regulation of PIN-FORMED3","volume":"232","author":"Yuan","year":"2021","journal-title":"New Phytol"},{"key":"2026091203521351000_ref122","doi-asserted-by":"crossref","first-page":"2401","DOI":"10.1016\/j.febslet.2007.04.060","article-title":"Characterisation of the ATP-dependent phosphofructokinase gene family from Arabidopsis thaliana","volume":"581","author":"Mustroph","year":"2007","journal-title":"FEBS Lett"},{"key":"2026091203521351000_ref123","doi-asserted-by":"crossref","first-page":"257","DOI":"10.1105\/tpc.112.107045","article-title":"HDA18 affects cell fate in Arabidopsis root epidermis via histone acetylation at four kinase genes","volume":"25","author":"Liu","year":"2013","journal-title":"Plant Cell"},{"key":"2026091203521351000_ref124","doi-asserted-by":"crossref","first-page":"37","DOI":"10.1093\/aob\/mcab122","article-title":"Cytosolic phosphofructokinases are important for sugar homeostasis in leaves of Arabidopsis thaliana","volume":"129","author":"Perby","year":"2022","journal-title":"Ann Bot"},{"key":"2026091203521351000_ref125","doi-asserted-by":"crossref","first-page":"289","DOI":"10.1105\/tpc.110.075911","article-title":"The FRIGIDA complex activates transcription of FLC, a strong flowering repressor in Arabidopsis, by recruiting chromatin modification factors","volume":"23","author":"Choi","year":"2011","journal-title":"Plant Cell"},{"key":"2026091203521351000_ref126","doi-asserted-by":"crossref","first-page":"2186","DOI":"10.1038\/ncomms3186","article-title":"Two FLX family members are non-redundantly required to establish the vernalization requirement in 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coenzyme pyridoxal 5\u2032-phosphate in Arabidopsis","volume":"36","author":"Farkas","year":"2024","journal-title":"Plant Cell"},{"key":"2026091203521351000_ref130","doi-asserted-by":"crossref","first-page":"2283","DOI":"10.1093\/molbev\/msu170","article-title":"Natural variation in abiotic stress responsive gene expression and local adaptation to climate in Arabidopsis thaliana","volume":"31","author":"Lasky","year":"2014","journal-title":"Mol Biol Evol"},{"key":"2026091203521351000_ref131","doi-asserted-by":"crossref","first-page":"672","DOI":"10.3389\/fgene.2018.00672","article-title":"Introns as gene regulators: a brick on the accelerator","volume":"9","author":"Rose","year":"2019","journal-title":"Front Genet"},{"key":"2026091203521351000_ref132","doi-asserted-by":"crossref","first-page":"627","DOI":"10.1038\/nature08800","article-title":"Genome-wide association study of 107 phenotypes in Arabidopsis thaliana inbred lines","volume":"465","author":"Atwell","year":"2010","journal-title":"Nature"},{"key":"2026091203521351000_ref133","doi-asserted-by":"crossref","first-page":"29","DOI":"10.1186\/1746-4811-9-29","article-title":"The advantages and limitations of trait analysis with GWAS: a review","volume":"9","author":"Korte","year":"2013","journal-title":"Plant Methods"},{"key":"2026091203521351000_ref134","first-page":"437","article-title":"Plant genome and transcriptome annotations: from misconceptions to simple solutions","volume":"19","author":"Bolger","year":"2018","journal-title":"Brief Bioinform"},{"key":"2026091203521351000_ref135","author":"Vander Kloet","year":"1988"},{"key":"2026091203521351000_ref136","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pone.0264966","article-title":"Contrasting a reference cranberry genome to a crop wild relative provides insights into adaptation, domestication, and breeding","volume":"17","author":"Kawash","year":"2022","journal-title":"PLoS One"},{"key":"2026091203521351000_ref137","doi-asserted-by":"crossref","first-page":"10","DOI":"10.14806\/ej.17.1.200","article-title":"Cutadapt removes adapter sequences from high-throughput sequencing reads","volume":"17","author":"Martin","year":"2011","journal-title":"EMBnet J"},{"key":"2026091203521351000_ref138","author":"Li","year":"2013"},{"key":"2026091203521351000_ref139","article-title":"Scaling accurate genetic variant discovery to tens of thousands of samples","author":"Poplin","year":"2017","journal-title":"BioRxiv"},{"key":"2026091203521351000_ref140","doi-asserted-by":"crossref","first-page":"2987","DOI":"10.1093\/bioinformatics\/btr509","article-title":"A statistical framework for SNP calling, mutation discovery, association mapping and population genetical parameter estimation from sequencing 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The variant call format and VCFtools","volume":"27","author":"Danecek","year":"2011","journal-title":"Bioinformatics"},{"key":"2026091203521351000_ref144","doi-asserted-by":"crossref","first-page":"184","DOI":"10.1111\/j.1471-8286.2004.00828.x","article-title":"Hierfstat, a package for R to compute and test hierarchical F-statistics","volume":"5","author":"Goudet","year":"2005","journal-title":"Mol Ecol Notes"},{"key":"2026091203521351000_ref145","first-page":"1358","article-title":"Estimating F-statistics for the analysis of population structure","volume":"38","author":"Weir","year":"1984","journal-title":"Evolution"},{"key":"2026091203521351000_ref146","doi-asserted-by":"crossref","first-page":"1655","DOI":"10.1101\/gr.094052.109","article-title":"Fast model-based estimation of ancestry in unrelated individuals","volume":"19","author":"Alexander","year":"2009","journal-title":"Genome Res"},{"key":"2026091203521351000_ref147","first-page":"250","article-title":"Ridge regression and other kernels for genomic selection with R package rrBLUP. Plant","volume":"4","author":"Endelman","year":"2011","journal-title":"Genome"},{"key":"2026091203521351000_ref148","volume-title":"R: A Language and Environment for Statistical Computing","author":"R Core Team","year":"2023"},{"key":"2026091203521351000_ref149","doi-asserted-by":"crossref","first-page":"526","DOI":"10.1093\/bioinformatics\/bty633","article-title":"Ape 5.0: an environment for modern phylogenetics and evolutionary analyses in R","volume":"35","author":"Emmanuel","year":"2019","journal-title":"Bioinformatics"},{"key":"2026091203521351000_ref150","doi-asserted-by":"crossref","first-page":"592","DOI":"10.1093\/bioinformatics\/btq706","article-title":"Phangorn: phylogenetic analysis in R","volume":"27","author":"Klaus","year":"2011","journal-title":"Bioinformatics"},{"key":"2026091203521351000_ref151","article-title":"Ggtree: a serialized data object for visualization of a phylogenetic tree and annotation data","volume":"1","author":"Shuangbin","year":"2022","journal-title":"Imeta"},{"key":"2026091203521351000_ref152","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pgen.1000695","article-title":"Inferring the joint demographic history of multiple populations from multidimensional SNP frequency data","volume":"5","author":"Gutenkunst","year":"2009","journal-title":"PLoS Genet"},{"key":"2026091203521351000_ref153","doi-asserted-by":"crossref","first-page":"716","DOI":"10.1109\/TAC.1974.1100705","article-title":"A new look at the statistical model identification problem","volume":"19","author":"Akaike","year":"1974","journal-title":"IEEE Trans Autom Control"},{"key":"2026091203521351000_ref154","doi-asserted-by":"crossref","DOI":"10.1017\/CBO9780511802843","volume-title":"Bootstrap Methods and their Applications","author":"Davison","year":"1997"},{"key":"2026091203521351000_ref155","doi-asserted-by":"crossref","first-page":"584","DOI":"10.1111\/1755-0998.13265","article-title":"Dsuite \u2013 fast D-statistics and related admixture evidence from VCF files","volume":"21","author":"Malinsky","year":"2021","journal-title":"Mol Ecol Resour"},{"key":"2026091203521351000_ref156","doi-asserted-by":"crossref","first-page":"725","DOI":"10.1038\/ng.2285","article-title":"A model-based approach for analysis of spatial structure in genetic data","volume":"44","author":"Yang","year":"2012","journal-title":"Nat Genet"},{"key":"2026091203521351000_ref157","doi-asserted-by":"crossref","first-page":"4302","DOI":"10.1002\/joc.5086","article-title":"WorldClim2: new 1-km spatial resolution climate surfaces for global land areas","volume":"37","author":"Fick","year":"2017","journal-title":"Int J Climatol"},{"key":"2026091203521351000_ref158","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pone.0105992","article-title":"SoilGrids1km \u2013 global soil information based on automated mapping","volume":"9","author":"Hengl","year":"2014","journal-title":"PLoS One"},{"key":"2026091203521351000_ref159","doi-asserted-by":"crossref","first-page":"1","DOI":"10.3835\/plantgenome2015.08.0073","article-title":"Software for genome-wide association studies in autopolyploids and its application to potato","volume":"9","author":"Rosyara","year":"2016","journal-title":"Plant Genome"},{"key":"2026091203521351000_ref160","doi-asserted-by":"crossref","first-page":"1243","DOI":"10.1093\/bioinformatics\/btw766","article-title":"QCEWAS: automated quality control of results of epigenome-wide association studies","volume":"33","author":"Van Der Most","year":"2017","journal-title":"Bioinformatics"},{"key":"2026091203521351000_ref161","doi-asserted-by":"crossref","first-page":"3292","DOI":"10.1038\/s41596-024-01020-z","article-title":"Using clusterProfiler to characterize multiomics data","volume":"19","author":"Xu Shuangbin","year":"2024","journal-title":"Nat Protoc"},{"key":"2026091203521351000_ref162","volume-title":"Org","author":"Carlson","year":"2024"},{"key":"2026091203521351000_ref163","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; 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