Genetic diversity hotspot at the edge of the species range: integrating plastome phylogeography with ecological niche modelling for the conservation of Ulmus glabra Huds. in the Italian peninsula

Background: The Italian peninsula is a widely recognised genetic diversity hotspot and one of the main glacial refugia for European temperate trees, which are now increasingly threatened by climate change, anthropogenic pressure, and pathogens. This study, focusing on the wych elm (Ulmus glabra) in its Italian range, integrated plastome phylogeography with lineage-based ecological niche modelling (ENM) and protected area gap analysis, aiming at: (1) reconstructing the evolutionary history of the species and identifying main phylogenetic lineages; (2) assessing habitat suitability and evaluating the impacts of climate change on each lineage; (3) performing a spatially explicit conservation assessment, incorporating genetic and ecological information. Results: Phylogeographic analyses of 75 trees revealed 42 haplotypes and a deep separation between Alpine (ALP) and Apennine (APE) lineages, with the latter showing higher nucleotide diversity and substructuring into two haplogroups, corresponding to north-central and south-central Apennines. The deep separation between ALP and APE was confirmed by significant NST and GST statistics (NST > GST, p ≤ 0.01). Our findings suggest a multiple refugia scenario for the species in the Italian peninsula, with the Apennines supporting a 'refugia-within-refugia' model. Niche analysis highlighted significant ecological differentiation between ALP and APE (niche overlap D = 0.18). ENMs for the two lineages predicted a future decrease in habitat suitability, mainly in the arid regions of south-central Italy; however, while APE lineage was found to be well represented within protected areas, often coinciding with potential climatic refugia, most ALP populations are not protected. Conclusions: The strong genetic and ecological divergence between U. glabra lineages underscores the need for lineage-specific conservation. Priority actions should include expanding in situ conservation in the Alps, establishing Genetic Conservation Units in the identified climate-refugia and enhancing connectivity in south-central Italy. As a complementary measure, ex situ conservation should maximize genetic diversity, preserving all identified haplogroups.