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Contemporary patterns of genomic variation in plant species often reflect past demographic processes linked to climate events such as Pleistocene glaciations. Dianthus sylvestris s.l. comprises a number of taxa distributed across southern and south- eastern Europe. We here used RAD-seq SNP data to unravel genomic variation in 165 populations, including all six currently described subspecies occurring in the Balkan Peninsula. Population genetic structure using Bayesian clustering revealed a north- western (NW) and south-eastern (SE) group, while an alternative model-free approach identified five genetic groups. We detected significant isolation by distance (IBD) within our populations, though with a visible discontinuity, and additional genetic connectivity analyses confirmed a sharp break between the two main groups of populations from NW and SE, suggesting that these groups derive from separate evolutionary lineages. Migration analyses revealed highest rates of gene flow between two subgroups of the NW cluster, while lower rates of gene flow were inferred between three subgroups of the SE cluster. The SE group showed higher inbreeding values compared to the NW group. Species distribution modelling (SDM) pointed to suitable habitats during the last glacial maximum (LGM) along the whole eastern Adriatic coast with higher suitability predicted in the south of the Balkans compared to the north. Overall, patterns of genomic variation and SDM suggest that D. sylvestris in the Balkans survived the Pleistocene glaciations in two separate glacial refugia located along the eastern Adriatic coast, with secondary contact of the two lineages in the area of Montenegro where admixed populations occur.

Delimiting species only on morphology may lead to taxonomic inflation, biasing conservation studies and actions, particularly in organisms recently diversified. For instance, the central Mediterranean Dianthus virgineus L. complex belongs to a lineage that evolved rapidly in Eurasia, and is characterized by high phenotypic variation. In the central Mediterranean, 21 taxa are currently accepted, albeit solely described according to qualitative morphological and phenological variation. Our objective is to apply an integrative taxonomic approach, including morphometry, karyology, and genetics, to test these taxonomic hypotheses. We genotyped thousands of genome-wide biallelic, unlinked SNPs from 123 populations from southern France, peninsular Italy, Corsica, Sardinia, and Sicily, through ddRAD sequencing and conducted an explorative PCA and STRUCTURE analysis to detect genetic differentiation. All across the study area there is an overall low genetic variability, albeit structured according to geographical distribution of populations. In particular, we detected a NW-SE cline from southern France to Calabria, and a second, orthogonal cline from central Italy to Sardinia through the Tuscan Archipelago and Corsica. Conversely, plants from Sicily form a genetic cluster that does not appear to follow clinal patterns recovered in the Italian Peninsula. We deduce that the number of genetically recognizable groups of the D. virgineus complex in central Mediterranean is much lower than the current taxonomic hypotheses, highlighting the importance of an integrative taxonomic approach to better circumscribe systematic units. However, taxonomic conclusions await thorough morphometric and karyological analyses, which are currently underway.