Savalia savaglia is an Atlantic-Mediterranean zoantharian species with a patchy geographic and bathymetric distribution. Due to its longevity, S. savaglia may form large-sized colonies which play a crucial role in the ecosystem as habitat formers. Despite its ecological importance, little is known about the population structure and intraspecific genetic diversity of this species. Using ddRAD-Seq genotyping, we obtained genome-wide single nucleotide polymorphisms (SNPs) from 50 S. savaglia individuals collected at different depths (8–60 m) and localities across the Mediterranean Sea (Marseille, Sardinia, Puglia and Montenegro) and eastern Atlantic (Portugal). Our molecular observations were discussed with the reproductive behaviour of the species to understand the observed patterns of connectivity and gene flow. These results highlight the presence of three main genetic clusters (Marseille; Sardinia; and Montenegro + Portugal + Puglia), with some of the Mediterranean individuals being genetically closer to the Atlantic population rather than to other Mediterranean populations. The strong linkage disequilibrium recorded across loci and the detection of clonal individuals in the shallow populations suggest that asexual reproduction seems to be the dominant reproductive strategy among the S. savaglia populations sampled at lower depths. Our work highlights the potential of genome-wide SNP data to study the reproductive behaviour in species such as S. savaglia that are difficult to investigate in the field. The genetic connectivity data obtained in this study can be used in the future to better guide the development of effective management and conservation plans.
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