Between Ocean and Sea: population genetics and evolutionary history of Pinna rudis

The recent expansion of Pinna rudis Linnaeus, 1758 in the Mediterranean Sea, following the collapse of its congener P. nobilis Linnaeus, 1758, raises questions about the full understanding of its evolutionary history, population connectivity and the role of hybridisation in a rapidly changing marine system. Here, we combine mitochondrial phylogenetics, molecular dating and population genetic analyses across the Atlantic and Mediterranean basins to reconstruct the demographic and evolutionary history of P. rudis. By integrating mitochondrial phylogeography and temporal inference across the Atlantic and Mediterranean basins, we show that the evolutionary trajectory of P. rudis reflects both deep-time oceanographic reorganisation and mid-Pleistocene climatic instability. While the ancestral early lineages of the species emerged during major inter-oceanic restructuring in the late Pliocene, present-day mitochondrial diversity largely originated during mid-Pleistocene oscillations, resulting in independently evolving Atlantic and Mediterranean populations characterised by restricted connectivity. Basin-specific ecological contexts further contributed to different evolutionary dynamics, with Mediterranean populations shaped by bottlenecks during glacial periods and long-term coexistence with P. nobilis and Atlantic populations primarily influenced by climatic and habitat change. The detection of natural hybridisation in the Mediterranean adds an additional layer of evolutionary complexity in a system undergoing rapid demographic expansion. Together, these findings illustrate how historical processes, evolutionary forces, and contemporary perturbations interact to shape genetic diversity in marine populations.