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Temperate reefs are among the most threatened marine habitats due to impacts caused by high density of human settlements, coastal development, pollution, fisheries and tourism. Networks of marine protected areas (MPAs) are an important tool for ensuring long-term health and conservation of ecological processes in the marine environment. Design of the MPA network has to be based on deep understanding of spatial patterns of species distribution, and on the make-up of connectivity among populations. Most benthic invertebrates are sessile and/or sedentary in the adult phase, and their dispersal relies mainly on the gametes and/or larval behaviours. Genetic markers allow us to quantify gene flow and structuring among populations, and to infer patterns of genetic connectivity. Based on the information available in the peer reviewed literature on genetic connectivity in benthic invertebrates of temperate MPAs, we provide a comment about the gaps and the needs. Moreover, we propose a rationale to plan and optimise future studies on this topic. A conceptual framework for planning effective studies on genetic connectivity in an MPAs network is provided, including general recommendations on sampling design, key species and molecular markers to use.
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