Holothuria atra is one of the most common and widest ranging tropical, coral reef sea cucumbers in the world, and here we examine population genetic structure based on mitochondrial COI to aid in determining the appropriate scale for coral reef management. Based on SAMOVA, AMOVA and BARRIER analyses, we show that despite its large range, H. atra has hierarchical, fine-scale population structure driven primarily by between-archipelago barriers, but with significant differences between sites within an archipelago as well. Migrate analyses along with haplotype networks and patterns of haplotype diversity suggest that Hawai‘i and Kingman reef are important centers of the genetic diversity in the region rather than an evolutionary dead-end for migrants from the Indo-Pacific. Finally we show that for H. atra Kingman Reef is the most likely stepping stone between Hawai‘i and the rest of the Pacific, not Japan or Johnston Atoll as previously presumed. Based on our data, Johnston Atoll can instead be seen as an outpost of the Northwestern Hawaiian Islands rather than a gateway to the Hawaiian Archipelago. 1. Introduction Echinoderms play a major role in structuring many marine ecosystems, and many are described as “keystone species” because of their profound influence on benthic community structure (e.g., [1–3], reviewed by Uthicke et al. [4]). In addition to their important ecosystem functions, many echinoderm species are also the focus of artisanal or commercial fishing efforts, particularly the sea urchins and sea cucumbers [5–7]. The influence of echinoderm harvest on a wide range of other commercial fisheries, such as abalone, lobster, kelp, and kelp-associated fin fish, has long stimulated discussions of multispecies approaches to managing their exploitation (e.g., [5], reviewed by Purcell [7]). Delineation of the appropriate spatial scales for management zones within a spatial management network requires a detailed understanding of dispersal pathways and population connectivity (reviewed by Hedgecock et al. [8], Thorrold et al. [9], Fogarty and Botsford [10]). Understanding connectivity in the sea is complicated by the fact that many marine organisms share a biphasic life cycle typified by an adult form that is relatively sedentary and a larval form that can potentially disperse across large expanses of open ocean [11–15]. For example, in the sea urchin genus Tripneustes, some well-known biogeographic barriers, such the Isthmus of Panama or the long stretch of deep water in the western Atlantic, are important barriers to dispersal whereas others, such as
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