Genomic‐based species delimitation reveals cryptic diversity and semi‐permeable species boundaries in a Chorthippus (Orthoptera: Acrididae) grasshopper complex from Greece

Abstract Recent Pleistocene radiations often generate cryptic diversity and semi‐permeable species boundaries, challenging species delimitation and the reconstruction of evolutionary histories. Here, we investigate these processes in a species complex of Chorthippus grasshoppers from Greece using genome‐wide ddRAD‐seq data combined with geometric morphometrics. Phylogenomic analyses indicate that diversification occurred during the Middle Pleistocene and identify two major geographic clades separated by the Corinthian Gulf, followed by finer‐scale divergence within the Peloponnese Peninsula. Most taxa form well‐supported, reciprocally monophyletic lineages despite recent divergence, although several populations at range margins show signatures of historical hybridization, revealing semi‐permeable species boundaries shaped by secondary contact. Introgression is geographically restricted and strongly asymmetric, occurring primarily from long‐winged into short‐winged taxa, consistent with differences in dispersal capacity. Species delimitation analyses largely support current taxonomy but also identify three previously unrecognized evolutionary lineages corresponding to geographically restricted populations, uncovering additional cryptic diversity. Morphological analyses reveal pronounced stasis in shape‐related traits across lineages, with wing length emerging as the main axis of differentiation. Phylogenetic reconstructions indicate multiple independent reductions in wing size, highlighting repeated evolutionary transitions toward reduced dispersal. In at least one lineage, a pronounced geographic cline in wing length is mirrored by shallow phylogenetic structure, supporting an incipient evolutionary shift in dispersal capacity rather than phenotypic plasticity. Admixed populations consistently retain short‐winged phenotypes, suggesting strong selection on dispersal‐related traits despite genomic introgression. Overall, our results demonstrate how topographic complexity, Pleistocene climatic oscillations and dispersal‐related morphology interact to shape diversification and maintain lineage integrity in a Mediterranean biodiversity hotspot.