Rampant hybridization underlies cytonuclear discordance and shallow plastid divergence in Juniperus (Cupressaceae).

Reconstructing plant evolutionary history is complicated by processes such as hybridization, incomplete lineage sorting and the interplay of ecological adaptation with morphological innovation. These generate reticulate patterns that challenge tree-like models and can bias inferences from single genomic compartments. These issues are pronounced in long-lived woody lineages. To examine these dynamics, we analysed Juniperus, a widely distributed Northern Hemisphere gymnosperm genus, using near-complete taxon sampling, complete plastomes and >3000 nuclear single-copy genes recovered via target-enrichment 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-time 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-like leaves and blue seed cones facilitated colonization of high-elevation habitats. Together, these results demonstrate that plastid data alone underrepresent the complexity of Juniperus evolution and highlight the necessity of integrating nuclear and plastid genomes - alongside ecological and morphological evidence - to obtain temporally coherent and biologically informed reconstructions of diversification in plants shaped by reticulate evolution.