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Sharks are charismatic predators that play a key role in most marine food webs. Their demonstrated vulnerability to exploitation has recently turned them into flagship species in ocean conservation. Yet, the assessment and monitoring of the distribution and abundance of such mobile species in marine environments remain challenging, often invasive and resource-intensive. Here we pilot a novel, rapid and non-invasive environmental DNA (eDNA) metabarcoding approach specifically targeted to infer shark presence, diversity and eDNA read abundance in tropical habitats. We identified at least 21 shark species, from both Caribbean and Pacific Coral Sea water samples, whose geographical patterns of diversity and read abundance coincide with geographical differences in levels of anthropogenic pressure and conservation effort. We demonstrate that eDNA metabarcoding can be effectively employed to study shark diversity. Further developments in this field have the potential to drastically enhance our ability to assess and monitor elusive oceanic predators, and lead to improved conservation strategies.

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Our understanding of marine communities and their functions in an ecosystem relies on the ability to detect and monitor species distributions and abundances. Currently, the use of environmental DNA (eDNA) metabarcoding is increasingly being applied for the rapid assessment and monitoring of aquatic species. Most eDNA metabarcoding studies have either focussed on the simultaneous identification of a few specific taxa/groups or have been limited in geographical scope. Here, we employed eDNA metabarcoding to compare beta diversity patterns of complex pelagic marine communities in tropical coastal shelf habitats spanning the whole Caribbean Sea. We screened 68 water samples using a universal eukaryotic COI barcode region and detected highly diverse communities, which varied significantly among locations, and proved good descriptors of habitat type and environmental conditions. Less than 15% of eukaryotic taxa were assigned to metazoans, most DNA sequences belonged to a variety of planktonic “protists,” with over 50% of taxa unassigned at the phylum level, suggesting that the sampled communities host an astonishing amount of micro‐eukaryotic diversity yet undescribed or absent from COI reference databases. Although such a predominance of micro‐eukaryotes severely reduces the efficiency of universal COI markers to investigate vertebrate and other metazoans from aqueous eDNA, the study contributes to the advancement of rapid biomonitoring methods and brings us closer to a full inventory of extant marine biodiversity.

IntroductionThe Millennium Ecosystem Assessment (MEA) recognises the ecosystem services provided by seagrass beds, namely provisioning services, such as food; regulating services, such as atmospheric and climate regulation, waste processing, flood and storm protection, and erosion control; and cultural services reference [1,2]. The MEA also recognises food provisioning in the form of fisheries catch as one of the most important services derived from seagrasses [3]. Research in East Africa also confirms a diversity of seagrass related socialecological links important for the welfare of the local population [4]. Seagrass meadows provided fishing grounds for finfish and invertebrates, whilst creating substrate for seaweed cultivation and sites for bait collection. Studies from Indonesia report similar findings [5]. In addition, measures of the economic value of seagrasses place them as one of the world's most financially valuable natural systems [6,7]. This value is currently growing given greater understanding of their role in carbon sequestration [8], that is, as a regulating service.Despite such importance, seagrass meadows are being lost at rates possibly equal to or faster than coral reefs and rainforests [9]. The location of seagrasses in sheltered waters places them in conflict with human users of the coastal environment, as development and poor land management act as stressors on these ecosystems [1], with consequences for human 2 wellbeing [10]. Seagrass bed have suffered major losses in Mediterranean, Florida, and Australia and degradation is expected to accelerate, especially in the Caribbean [3]. Greater understanding of the social, economic and ecological circumstances that lead to such declines are required in order to facilitate effective conservation management, especially given that marine conservation policies often fail to appreciate the role of these habitats in supporting fisheries production [11].Effective conservation requires understanding not just the type of stressors currently acting but their historic origins. Past choices, for example about economic development priorities, may create path dependencies that make it difficult to address the cause of environmental deterioration in the contemporary period. Understanding how local people use seagrass resources is needed because communities can act as both a source of environmental degradation and as local environmental champions. In addition, conservation plans have to be followed by implementation efforts. This requires a system of public administration that has the capacity to engage in effective implementation. Devising conservation plans in abstraction from understanding what the administrative system is capable of supporting will lead at best to cynicism, at worst defeatism, about undertaking conversation efforts. This paper adopts an interdisciplinary approach to address this range of ecological, socioeconomic and administrative issues. The lens of food security in the Turks and Caicos Islands (TCI) is used to examine threats to seagra...