The Making of a Continental Radiation: The History of Carduus (Compositae) From the Messinian Salinity Crisis to Pliocene–Pleistocene Ecological Opportunities

Aim To reconstruct the evolutionary and biogeographical history of the thistle genus Carduus (Compositae, Cardueae) using phylogenomic data, and to investigate the main factors behind its biogeographic expansion and ecological diversification. Location Eurasia, North Africa and Macaronesia. Taxon Carduus L. (Compositae, Cardueae). Methods We inferred highly resolved phylogenies of Carduus based on 1026 nuclear loci and a broad sampling (52 Carduus taxa plus 6 outgroup species), using concatenation and coalescent approaches. Building on this phylogenetic framework, we inferred the genus's historical biogeography, habitat evolution, and life‐form transitions under likelihood‐based models. Results Our strongly supported phylogenies recovered Carduus as monophyletic, with all but one species structured into two main clades, and three species complexes found to be non‐monophyletic. Our results indicate that Carduus originated in the Late Miocene (~8.2 Ma) in the eastern Mediterranean and eastern Asia, from an ancestor reconstructed as short‐lived and associated with grassland, meadow, and rocky habitats. Its two main clades diverged during the Messinian Salinity Crisis (~5.8 Mya). Repeated intra‐Mediterranean dispersal, range expansion and contraction dominated subsequent biogeographic history, with punctual long‐distance dispersals to Macaronesia and the Himalayas. During the Pliocene and Pleistocene, repeated life‐form shifts and habitat transitions into more competitive environments occurred in both main clades. Main Conclusions Repeated cycles of range contraction, expansion, and long‐distance dispersal probably shaped the present‐day distribution of Carduus during the Pliocene and Pleistocene. The repeated habitat and life‐form shifts inferred in both main clades suggest substantial ecological lability, which may have contributed to this dynamic biogeographic history. Carduus exemplifies how ecological flexibility, dispersal ability, and climatic fluctuations may have interacted to shape diversification and range expansion in the Mediterranean flora.