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These generate reticulate patterns that challenge tree\u2010like models and can bias inferences from single genomic compartments. These issues are pronounced in long\u2010lived woody lineages. To examine these dynamics, we analysed\n                    <jats:italic>Juniperus<\/jats:italic>\n                    , a widely distributed Northern Hemisphere gymnosperm genus, using near\u2010complete taxon sampling, complete plastomes and &gt;3000 nuclear single\u2010copy genes recovered via target\u2010enrichment sequencing. We reconstructed a robust species tree resolving eight major clades and detected extensive historical and ongoing gene flow, producing cytonuclear discordance and pronounced heterogeneity among nuclear gene trees. Divergence\u2010time estimates from plastid and nuclear datasets differed markedly, with nuclear data indicating earlier splits of most lineages, many predating the Late Miocene. Trait reconstructions suggest that scale\u2010like leaves and blue seed cones facilitated colonization of high\u2010elevation habitats. Together, these results demonstrate that plastid data alone underrepresent the complexity of\n                    <jats:italic>Juniperus<\/jats:italic>\n                    evolution and highlight the necessity of integrating nuclear and plastid genomes \u2013 alongside ecological and morphological evidence \u2013 to obtain temporally coherent and biologically informed reconstructions of diversification in plants shaped by reticulate evolution.\n                  <\/jats:p>","DOI":"10.1111\/cla.70058","type":"journal-article","created":{"date-parts":[[2026,7,29]],"date-time":"2026-07-29T04:49:51Z","timestamp":1785300591000},"update-policy":"https:\/\/doi.org\/10.1002\/crossmark_policy","source":"Crossref","is-referenced-by-count":1,"title":["Rampant hybridization underlies cytonuclear discordance and shallow plastid divergence in\n                    <i>Juniperus<\/i>\n                    (Cupressaceae)"],"prefix":"10.1111","author":[{"given":"Yujiao","family":"Zhang","sequence":"first","affiliation":[{"name":"Key Laboratory of Bio\u2010Resource and Eco\u2010Environment of Ministry of Education, College of Life Sciences, State Key Laboratory of Hydraulics and Mountain River Engineering Sichuan University  Chengdu Sichuan China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1700-131X","authenticated-orcid":false,"given":"Jialiang","family":"Li","sequence":"additional","affiliation":[{"name":"Key Laboratory of Bio\u2010Resource and Eco\u2010Environment of Ministry of Education, College of Life Sciences, State Key Laboratory of Hydraulics and Mountain River Engineering Sichuan University  Chengdu Sichuan China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Perla","family":"Farhat","sequence":"additional","affiliation":[{"name":"Diversit\u00e9, Adaptation, D\u00e9veloppement des Plantes (DIADE) University of Montpellier, Institut de Recherche pour le D\u00e9veloppement (IRD)  Montpellier France"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Zhitong","family":"Han","sequence":"additional","affiliation":[{"name":"Key Laboratory of Bio\u2010Resource and Eco\u2010Environment of Ministry of Education, College of Life Sciences, State Key Laboratory of Hydraulics and Mountain River Engineering Sichuan University  Chengdu Sichuan China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0008-8624-6605","authenticated-orcid":false,"given":"Jiajin","family":"Cheng","sequence":"additional","affiliation":[{"name":"Key Laboratory of Bio\u2010Resource and Eco\u2010Environment of Ministry of Education, College of Life Sciences, State Key Laboratory of Hydraulics and Mountain River Engineering Sichuan University  Chengdu Sichuan China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jingge","family":"Kuang","sequence":"additional","affiliation":[{"name":"Key Laboratory of Bio\u2010Resource and Eco\u2010Environment of Ministry of Education, College of Life Sciences, State Key Laboratory of Hydraulics and Mountain River Engineering Sichuan University  Chengdu Sichuan China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Chris","family":"Dudley","sequence":"additional","affiliation":[{"name":"Institute of Molecular Plant Sciences The\u00a0University of Edinburgh  Edinburgh UK"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Wentao","family":"Wang","sequence":"additional","affiliation":[{"name":"Key Laboratory of Bio\u2010Resource and Eco\u2010Environment of Ministry of Education, College of Life Sciences, State Key Laboratory of Hydraulics and Mountain River Engineering Sichuan University  Chengdu Sichuan China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3871-6114","authenticated-orcid":false,"given":"Dayu","family":"Wu","sequence":"additional","affiliation":[{"name":"Key Laboratory of Bio\u2010Resource and Eco\u2010Environment of Ministry of Education, College of Life Sciences, State Key Laboratory of Hydraulics and Mountain River Engineering Sichuan University  Chengdu Sichuan China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jibin","family":"Miao","sequence":"additional","affiliation":[{"name":"Key Laboratory of Bio\u2010Resource and Eco\u2010Environment of Ministry of Education, College of Life Sciences, State Key Laboratory of Hydraulics and Mountain River Engineering Sichuan University  Chengdu Sichuan China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Tsam","family":"Ju","sequence":"additional","affiliation":[{"name":"School of Ecology and Environment Xizang University  Lhasa China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Richard I.","family":"Milne","sequence":"additional","affiliation":[{"name":"Institute of Molecular Plant Sciences The\u00a0University of Edinburgh  Edinburgh UK"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0071-1844","authenticated-orcid":false,"given":"Kangshan","family":"Mao","sequence":"additional","affiliation":[{"name":"Key Laboratory of Bio\u2010Resource and Eco\u2010Environment of Ministry of Education, College of Life Sciences, State Key Laboratory of Hydraulics and Mountain River Engineering Sichuan University  Chengdu Sichuan China"},{"name":"School of Ecology and Environment Xizang University  Lhasa China"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"311","published-online":{"date-parts":[[2026,7,28]]},"reference":[{"key":"e_1_2_9_2_1","first-page":"179","article-title":"Phylogeny of Juniperus using nrDNA and four cpDNA 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