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The integration of eDNA analysis into the population assessment and monitoring of sharks could greatly improve temporal and spatial data used for management purposes. This study aimed to compare eDNA detection against well-established seasonal changes in blacktip shark (Carcharhinus limbatus) abundance in Terra Ceia Bay (FL, USA). We used a species-specific real-time PCR approach to detect C. limbatus eDNA in the bay on a near monthly basis from spring through mid-fall in 2018 and 2019. Previous studies have shown that C. limbatus give birth in the bay in early summer and immature sharks occur there until late fall, when decreasing water temperatures cause them to move offshore and southwards. Water samples (2 L) were collected (4–6 per month) and filtered in the field, with each then being subjected to real-time PCR. Carcharhinus limbatus ‘positive’ filters were significantly more commonly collected during the April-July sampling period than during the August-October sampling period. While following the predicted pattern, eDNA concentration was generally too low for accurate quantification. Our results show that C. limbatus eDNA detection follows known seasonal residency patterns consistently over 2 years of monitoring. Species-specific eDNA analysis using real-time PCR could therefore represent a cost-effective, scalable sampling tool to facilitate improved shark population monitoring in semi-enclosed marine habitats.

Summary Proximity and size of the nearest market (‘market gravity’) have been shown to have strong negative effects on coral reef fish communities that can be mitigated by the establishment of closed areas. However, moray eels are functionally unique predators that are generally not subject to targeted fishing and should therefore not directly be affected by these factors. We used baited remote underwater video systems to investigate associations between morays and anthropogenic, habitat, and ecological factors in the Caribbean region. Market gravity had a positive effect on morays, while the opposite pattern was observed in a predator group subject to exploitation (sharks). Environmental DNA analyses corroborated the positive effect of market gravity on morays. We hypothesize that the observed pattern could be the indirect result of the depletion of moray competitors and predators near humans., Graphical Abstract, Highlights • Baited remote underwater videos and environmental DNA were used to assess morays • Market gravity had a strong positive effect on moray abundance • Morays and sharks were negatively associated • Lack of competitors and predators may explain increased morays on reefs near humans, Environmental science; ecology; biological sciences; zoology; animals; ethology

This book represents a synthesis of knowledge and best practice in the field of DNA-based biomonitoring at the time of writing. It has been written with end-users of molecular tools in mind, as well as those who are new to the field in research settings and are looking to gain an overall grounding in the subject area. For each of the main types of sample (water, soil / sediment, bulk invertebrates and diatoms), and for each stage of the field and laboratory processes, we outline key considerations, decisions that need to be made, factors that might influence those decisions, and trade-offs inherent in the choices made. We hope that this will help users, practitioners, and those commissioning DNA-based monitoring programmes to navigate this large field and critically evaluate the strengths and weaknesses of different analysis workflows based on context, project aims and available resources., ISBN:978-619-248-052-3, ISBN:978-619-248-053-0

Animal dietary information provides the foundation for understanding trophic relationships, which is essential for ecosystem management. Yet, in marine systems, high-resolution diet reconstruction tools are currently under-developed. This is particularly pertinent for large marine vertebrates, for which direct foraging behaviour is difficult or impossible to observe and, due to their conservation status, the collection of stomach contents at adequate sample sizes is frequently impossible. Consequently, the diets of many groups, such as sharks, have largely remained unresolved. To address this knowledge gap, we applied metabarcoding to prey DNA in faecal residues (fDNA) collected on cotton swabs from the inside of a shark's cloaca. We used a previously published primer set targeting a small section of the 12S rRNA mitochondrial gene to amplify teleost prey species DNA. We tested the utility of this method in a controlled feeding experiment with captive juvenile lemon sharks (Negaprion brevirostris) and on free-ranging juvenile bull sharks (Carcharhinus leucas). In the captive trial, we successfully isolated and correctly identified teleost prey DNA without incurring environmental DNA contamination from the surrounding seawater. In the field, we were able to reconstruct high-resolution teleost dietary information from juvenile C. leucas fDNA that was generally consistent with expectations based on published diet studies of this species. While further investigation is needed to validate the method for larger sharks and other species, it is expected to be broadly applicable to aquatic vertebrates and provides an opportunity to advance our understanding of trophic interactions in marine and freshwater systems.

This is the pre-peer reviewed version of the following article: Collins, R.A., Bakker, J., Wangensteen, O.S., Soto, A.Z., Corrigan, L., Sims, D.W. ... Mariani, S. (2019). Non-specific amplification compromises environmental DNA metabarcoding with COI. Methods in Ecology and Evolution, 10(11), 1985-2001, which has been published in final form at https://doi.org/10.1111/2041-210X.13276. . This article may be used for non-commercial purposes in accordance with Wiley Terms and Conditions for Use of Self-Archived Versions. Metabarcoding extra‐organismal DNA from environmental samples is now a key technique in aquatic biomonitoring and ecosystem health assessment. Of critical consideration when designing experiments, and especially so when developing community standards and legislative frameworks, is the choice of genetic marker and primer set. Mitochondrial cytochrome c oxidase subunit I (COI), the standard DNA barcode marker for animals, with its extensive reference library, taxonomic discriminatory power and predictable sequence variation, is the natural choice for many metabarcoding applications. However, for targeting specific taxonomic groups in environmental samples, the utility of COI has yet to be fully scrutinized. Here, by using a case study of marine and freshwater fishes from the British Isles, we quantify the in silico performance of twelve primer pairs from four mitochondrial loci – COI, cytochrome b, 12S and 16S – in terms of reference library coverage, taxonomic discriminatory power and primer universality. We subsequently test in vitro four primer pairs – three COI and one 12S – for their specificity, reproducibility, and congruence with independent datasets derived from traditional survey methods at five estuarine and coastal sites around the English Channel and North Sea. Our results show that for aqueous extra‐organismal DNA at low template concentrations, both metazoan‐targeted and fish‐targeted COI primers perform poorly in comparison to 12S, exhibiting low levels of reproducibility due to non‐specific amplification of prokaryotic and non‐target eukaryotic DNAs. An ideal metabarcode would have an extensive reference library upon which custom primers could be designed, either for broad assessments of biodiversity, or taxon specific surveys. Such a database is available for COI, but low primer specificity hinders practical application, while conversely, 12S primers offer high specificity, but lack adequate references. The latter, however, can be mitigated by expanding the concept of DNA barcodes to include whole mitochondrial genomes generated by genome‐skimming existing tissue collections.

Environmental DNA reveals unsuspected shark diversity and calls for monitoring and protection of residual populations., In the era of “Anthropocene defaunation,” large species are often no longer detected in habitats where they formerly occurred. However, it is unclear whether this apparent missing, or “dark,” diversity of megafauna results from local species extirpations or from failure to detect elusive remaining individuals. We find that despite two orders of magnitude less sampling effort, environmental DNA (eDNA) detects 44% more shark species than traditional underwater visual censuses and baited videos across the New Caledonian archipelago (south-western Pacific). Furthermore, eDNA analysis reveals the presence of previously unobserved shark species in human-impacted areas. Overall, our results highlight a greater prevalence of sharks than described by traditional survey methods in both impacted and wilderness areas. This indicates an urgent need for large-scale eDNA assessments to improve monitoring of threatened and elusive megafauna. Finally, our findings emphasize the need for conservation efforts specifically geared toward the protection of elusive, residual populations.

The gradual decline of cooperation in surveys jeopardises the viability of this tool in the future, despite it being one of the most useful in gaining knowledge of society. Since the last decade of the 20th century, substantial, in-depth research has been conducted into this social phenomenon, whilst at the same time there has been further “transparency” in the data collection process, as documents are disseminated which describe in detail the “events” that occurred during field work. This paper analyses the lack of response in face-to-face surveys conducted in Spain, considering not only those selecting interviewees by using random route and quotas, but also those using administrative documents, such as the population census. It concludes by providing a number of proven, efficient strategies for counteracting the effects of non-response.El paulatino descenso en la cooperación en las encuestas hace peligrar la viabilidad futura de esta herramienta, una de las mejores para el conocimiento de la sociedad. Desde la última década del pasado siglo numerosas investigaciones han estudiado el fenómeno en profundidad, al tiempo que se ha producido una mayor “transparencia” del proceso de recogida de datos al difundirse documentos donde se detallan con precisión los “sucesos” acontecidos durante el trabajo de campo. En este trabajo se analiza la no respuesta de las encuestas presenciales realizadas en España considerando las que seleccionan los entrevistados con rutas y cuotas, así como las que emplean documentos administrativos como el Padrón de Población. El trabajo termina con una serie de estrategias que han demostrado su eficacia para contrarrestar los efectos de la no respuesta.

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.

In the context of drastic cutbacks many Dutch municipalities consider citizens’ initiatives (CIs) as an attractive alternative for municipal policies aimed at improving the livability and safety in neighbourhoods, simultaneously building responsible citizenship. In this paper we combine different theoretical perspectives to analyse the institutional settings in which CIs are being realised, and how municipalities try to facilitate such initiatives. Municipalities can do this by either trying to structure the relevant networks or by various forms of process management. This analysis sheds light on how municipalities use a variety of instruments to mobilise citizens to participate in CIs. In using such instruments they can influence various factors (like motivations, personal resources, social capital and expected responsiveness; cf. Lowndes et al.’s CLEAR model) that increase the likelihood of civic engagement

A comparison of the community structure of juvenile hermatypic corals of 2 to 37 m depth at the fringing reefs of Curaçao between 1975 and 2005 shows a decline of 54.7% in juvenile coral abundance and a shift in species composition. Agaricia species and Helioseris cucullata, the most common juveniles in 1975, showed the largest decline in juvenile abundance (a 9 and 120 fold decrease in density respectively) with Helioseris cucullata being nearly extirpated locally. In 2005, Porites astreoides contributed most colonies to the juvenile coral community, increasing from 8.2% (in 1975) to 19.9% of the total juvenile community. Between 1975 and 2005, juveniles of brooding species decreased in relative abundance while the abundance of juveniles of broadcast spawning species increased or remained the same. These data illustrate the magnitude of the changes that have occurred in only three decades in the composition of juvenile coral communities.

We conducted a study among a group of 26 regional pig farmers to determine the methicillin-resistant Staphylococcus aureus prevalence rate and found it was >760 times greater than the rate of patients admitted to Dutch hospitals. While spa-type t108 is apparently a more widespread clone among pig farmers and their environment, we did find other spa-types.

Burgerinitiatieven zijn in de inleiding van dit themanummer omschreven als een vorm van burgerparticipatie. Deze initiatieven verschillen principieel van activiteiten waarin burgers participeren binnen de bestuurlijke arena’s van de overheid. Burgerinitiatieven spelen zich niet af in het stadhuis of op inspraakavonden, maar op straat, in een buurthuis of bij een toevallige ontmoeting in een supermarkt. Het is niet de overheid die burgers vraagt om mee te denken over beleid, maar het zijn burgers zelf, die zich op eigen initiatief inzetten voor dingen die zij belangrijk vinden. Bovendien bepalen zij zelf of, wanneer, waar en hoe zij in actie komen. Burgerinitiatieven zijn van alle tijden. In dat opzicht zijn ze dus niet nieuw. Nieuw is wel dat dergelijke initiatieven onderwerp van overheidsbeleid worden.

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., Water samples from four Caribbean areas were sampled and subjected to universal eukaryote DNA metabarcoding. Tens of thousands of species were recovered, the vast majority being unicellular protists, most of which poorly known taxonomically and ecologically. Multivariate analyses clearly separated samples according to both region and habitat of origin.