Hybridization, incomplete lineage sorting and climatic oscillations can interact across evolutionary timescales, but their combined effects on plant diversification remain difficult to resolve. We investigated how these processes shaped the origin and geographic structure of Linum bienne, the putative progenitor of cultivated flax. We integrated genus-level Angiosperms353 phylogenomics across Linum with plastome analyses, low-depth nuclear resequencing, demographic inference and environmental niche modelling across the range of L. bienne. This framework allowed us to assess phylogenetic discordance, test for reticulation and reconstruct lineage history through time. Phylogenetic discordance was widespread across our genus-level sampling and largely consistent with incomplete lineage sorting. However, branch-length and maximum-likelihood network analyses detected additional signal of gene flow at the node including L. bienne, cultivated flax and the closest relatives. Within L. bienne, plastid and nuclear data recovered four geographically structured lineages across the species range, with cytonuclear discordance and demographic analyses supporting repeated secondary contact. Our results show that the evolutionary history of L. bienne reflects the interaction between deep reticulation, incomplete lineage sorting and Pleistocene range dynamics. This multiscale perspective highlights L. bienne as a genetically complex species and illustrates how reticulate evolution and climatic change can jointly shape plant diversification.
Landoni, B., Viruel, J., Bourgeois, Y., Allaby, R. G., Brennan, A. C., Perez-Barrales, R.
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