Seascape connectivity studies, informing the level of exchange of individuals between populations, can provide extremely valuable data for marine population biology and conservation strategy definition. Here we used a multidisciplinary approach to investigate the connectivity of the marbled crab (Pachygrapsus marmoratus), a high dispersal species, in the Adriatic and Ionian basins. A combination of genetic analyses (based on 15 microsatellites screened in 314 specimens), Lagrangian simulations (obtained with a biophysical model of larval dispersal) and individual-based forward-time simulations (incorporating species-specific fecundity and a wide range of population sizes) disclosed the realized and potential connectivity among eight different locations, including existing or planned Marine Protected Areas (MPAs). Overall, data indicated a general genetic homogeneity, after removing a single outlier locus potentially under directional selection. Lagrangian simulations showed that direct connections potentially exist between several sites, but most sites did not exchange larvae. Forward-time simulations indicated that a few generations of drift would produce detectable genetic differentiation in case of complete isolation as well as when considering the direct connections predicted by Lagrangian simulations.Overall, our results suggest that the observed genetic homogeneity reflects a high level of realized connectivity among sites, which might result from a regional metapopulation dynamics, rather than from direct exchange among populations of the existing or planned MPAs. Thus, in the Adriatic and Ionian basins, connectivity might be critically dependent on unsampled, unprotected, populations, even in species with very high dispersal potential like the marbled crab. Our study pointed out the pitfalls of using wide-dispersing species with broad habitat availability when assessing genetic connectivity among MPAs or areas deserving protection and prompts for the careful consideration of appropriate dispersing features, habitat suitability, reproductive timing and duration in the selection of informative species.

• 314 samples of Pachygrapsus marmoratus were collected in the Adriatic and Ionian seas. Genomic DNA was extracted using a standard salting out protocol.
• 15 Fifteen polymorphic microsatellite loci specific for P. marmoratus were used for genetic analysis.
• Refer to the full article for details at https://doi.org/10.3389/fmars.2022.944851

The "Pachygrapsus marmoratus_rawdata.txt" and "Pachygrapsus marmoratus_genotypes.txt" files contain information on 15 microsatellite loci. Eight population samples are reported for a total of 314 individuals. Please note that locus pm108 was identifed as an outlier using LOSITAN (Amos et al. 2008) and DETSEL (Vitalis et al. 2012).

The file "Pachygrapsus marmoratus_rawdata.txt" is a tab separated text file, organized with a first header row identifying columns for population ID, individual ID and names of the loci (two alleles per locus). The following 314 rows report for each individual population ID, individual ID, followed by genotypes information for each locus. For each locus, the two corresponding columns report raw size in base pairs of each of the two alleles. 

The file "Pachygrapsus marmoratus_genotypes.txt" is a tab separated text file, organized with a first header row identifying columns for population ID, individual ID and names of the loci. The following 314 rows report for each individual population ID, individual ID, followed by genotypes information for each locus. Alleles are given in repeat numbers, after that binning was performed automatically with the software FlexiBin version 2 (Amos et al. 2007). Missing data are represented by '000'.