Planktonic larvae do not ensure gene flow in the edible sea urchin Paracentrotus lividus

Previous studies of the commercially harvested sea urchin Paracentrotus lividus revealed genetic differentiation between the Atlantic Ocean and the Mediterranean Sea and between the Adriatic and other Mediterranean basins, and reported an absence of genetic structure within basins. These studies used mitochondrial markers. We augmented these data with new mitochondrial (COI) and nuclear (calpain exon-primed intron crossing) sequences and renalyzed them. We found within-basin and within-region differentiation with each genetic marker, providing, for this species, the first report of a significant and consistent genetic structure within regions in which no stable or identified oceanographic barriers had ever been reported. This was unexpected given the long planktonic larval phase. With the mitochondrial marker, the easternmost population from Lebanon appeared strongly differentiated from other populations, with Phi(ST) values of the same order as those between Atlantic and Mediterranean basins, and a differentiation of the same magnitude was found for the northernmost population (Galway, Ireland). Among basins, gene flow appeared unidirectional, from the Atlantic to the Mediterranean Sea, and we found an admixture area between Adriatic and other Mediterranean populations. The divergence between Atlantic and Mediterranean basins was estimated to have started between 270 000 and 370 000 yr ago. Chaotic genetic patchiness appears unlikely to be the single factor responsible for such a differentiation, and some environmental or hydrological factors that are relatively stable over years, are probably involved. Methodological aspects such as sample sizes and the choice of statistics (F-ST versus Phi(ST)) contributed to the increased detection power of our study.