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In a recent paper, "Environmental DNA: What's behind the term? Clarifying the terminology and recommendations for its future use in biomonitoring," Pawlowski et al. argue that the term eDNA should be used to refer to the pool of DNA isolated from environmental samples, as opposed to only extra-organismal DNA from macro-organisms. We agree with this view. However, we are concerned that their proposed two-level terminology specifying sampling environment and targeted taxa is overly simplistic and might hinder rather than improve clear communication about environmental DNA and its use in biomonitoring. This terminology is based on categories that are often difficult to assign and uninformative, and it overlooks a fundamental distinction within eDNA: the type of DNA (organismal or extra-organismal) from which ecological interpretations are derived., Molecular Ecology, 30 (19), ISSN:0962-1083, ISSN:1365-294X

18 pages, 8 figures, supplementary material https://www.frontiersin.org/articles/10.3389/fmars.2022.969071/full#supplementary-material, The Norway lobster, Nephrops norvegicus, supports a key European fishery. Stock assessments for this species are mostly based on trawling and UnderWater TeleVision (UWTV) surveys. However, N. norvegicus are burrowing organisms and these survey methods are unable to sample or observe individuals in their burrows. To account for this, UWTV surveys generally assume that “1 burrow system = 1 animal”, due to the territorial behavior of N. norvegicus. Nevertheless, this assumption still requires in-situ validation. Here, we outline how to improve the accuracy of current stock assessments for N. norvegicus with novel ecological monitoring technologies, including: robotic fixed and mobile camera-platforms, telemetry, environmental DNA (eDNA), and Artificial Intelligence (AI). First, we outline the present status and threat for overexploitation in N. norvegicus stocks. Then, we discuss how the burrowing behavior of N. norvegicus biases current stock assessment methods. We propose that state-of-the-art stationary and mobile robotic platforms endowed with innovative sensors and complemented with AI tools could be used to count both animals and burrows systems in-situ, as well as to provide key insights into burrowing behavior. Next, we illustrate how multiparametric monitoring can be incorporated into assessments of physiology and burrowing behavior. Finally, we develop a flowchart for the appropriate treatment of multiparametric biological and environmental data required to improve current stock assessment methods, The present research was carried out within the framework of the activities of the Spanish Government through the “Severo Ochoa Centre Excellence” accreditation to ICM-CSIC (CEX2019-000928-S) and the Research Unit Tecnoterra (ICM-CSIC/UPC). Other projects that supported the work were those of the Plan Estatal de Investigación Científica y Técnica y de Innovación 2017-2020 of the Spanish government: BITER-LANDER (PID2020-114732RB-C32); BITER-ECO (PID2020-114732RB-C31); BITER-AUV (PID2020-114732RB-C33); PLOME (PLEC2021-007525/AEI/10.13039/501100011033). Moreover, part of the conceptual development, falls within the framework of EU LIFE Project ECOREST (LIFE20 NAT/ES/001270), which also funded DC. SaF acknowledges the HGF-project (Helmholtz-Future Topic Project) ARCHES (Autonomous Robotic Networks to Help Modern Societies) and HGF POF IV funding for conducting this research. NR was funded by the Spanish Government (Agencia Española de Investigación; AEI) through the ‘Severo Ochoa Centre of Excellence’ accreditation (CEX2019-000928-S)

Intermittent rivers and ephemeral streams (IRES) compose the majority of draining networks on Earth, supporting a unique fraction of biodiversity. Despite their high ecological value, IRES are increasingly threatened by global change and require appropriate biomonitoring and restoration tools. However, indices and indicators used in routine biomonitoring programs are often confounded by drying effects. This occurs because most pollutionsensitive taxa are lost over drying gradients, limiting the utility of current biomonitoring tools in IRES. To address this challenge, there is a need to evaluate which taxa should be used to calculate biomonitoring metrics and indicators over the different portions of the drying gradient. Here, using high-resolution drying data from 33 unpolluted streams, we explored the drying preferences of macroinvertebrates to identify their potential as biomonitoring indicators in IRES. To do this, we characterized macroinvertebrate drying niches and identified those with drying resistance and sensitivity preferences. Next, we evaluated the capacity of functional traits to predict drying specialization and affinity. Finally, to identify potential biomonitoring metrics and indicators for IRES, we evaluated how drying influenced the density, relative abundance and richness of taxa in drying sensitive and drying-resistant niches. Our results identified three macroinvertebrate groups with drying resistant niches (partly tolerant, generalist and specialist taxa) and one group of drying-sensitive taxa. We also found that functional traits had a limited capacity to represent differences in drying niches, with shredding trophic preferences and body size showing the strongest correlations. In addition, we observed that the density, relative abundance and richness of drying-resistant taxa were less influenced by drying intensity than those of drying-sensitive taxa. Finally, we found that some pollution-sensitive taxa with partial (e.g., Lepidostoma), moderate (e.g., Corduliidae) or high drying tolerance (e.g., Nemoura) can serve as potential indicators in IRES. Taken together, our results demonstrate that characterizing drying niches can be a useful strategy for developing biomonitoring tools in IRES and for highlighting the limitations of taxonomic and trait-based approaches.

[eng] The revolution in biologging and satellite telemetry technologies in the last two decades has led to a new era in seabird research. This thesis brings new insights into the spatial ecology and migration of the Cory’s and the Scopoli’s shearwaters (Calonectris borealis and C. diomedea, respectively), offering a comprehensive overview of these topics for the Spanish populations of these model species. In particular, the thesis provides new knowledge about the movement patterns, at-sea behaviour and the marine environment they inhabit year-round, through the use of GPS loggers and light-level geolocators. Along the chapters of the thesis, I illustrate the potential and applications of biologging in seabird research and conservation. To do so, I address different questions aimed to evaluate the role of environmental features, fisheries, and breeding constraints in the foraging strategies and at-sea behaviour of tracked birds. We found that females of Scopoli’s shearwater generally attended fisheries less than males, and both sexes associated less to fishing boats during unfavourable conditions. Sea surface temperature likely plays a role in individual decision-making: we found that birds may use this environmental feature to decide foraging trip destination. Moreover, we found variability in foraging trips at inter-annual scale, likely due to environmental fluctuations, but also at intra-annual scale, likely due to the different breeding constraints over the breeding period. We explored seabird behaviour from novel ways, deriving simple metrics that may enhance the use of seabirds as sentinel species. Last, we unveiled the role of individual differences in trophic ecology, and discussed the implications of such differences in the use of seabirds to monitor long term fluctuations in a complex upwelling ecosystem. This thesis compiles and summarises the previous knowledge of the Spanish populations of Cory’s and Scopoli’s shearwaters, and extends it with novel insights. Moreover, in a transversal way, I discuss the role of seabirds as indicator species, particularly considering the use of biologging to enhance their suitability as ocean sentinels within the framework of ecosystem-based management., [spa] La reciente revolución en tecnologías de seguimiento remoto y biologging en las dos últimas décadas ha desembocado en una nueva era en la investigación con aves marinas. Esta tesis contribuye a un mejor conocimiento sobre de la ecología espacial y los patrones migratorios de la pardela cenicienta atlántica (Calonectris borealis) y de la pardela cenicienta mediterránea (C. diomedea), enfocándose en las poblaciones españolas de ambas especies. La tesis recopila y resume el conocimiento previo sobre ambas especies, y aporta nueva información relevante para su conservación. A lo largo de los diferentes capítulos, se ilustra el potencial uso y las aplicaciones de las técnicas de biologging en la investigación y conservación de las aves marinas, en particular el empleo de registradores GPS y de geolocalizadores por niveles de luz. Se abordan diferentes temas de interés, desgranando el papel que juegan la variabilidad ambiental, las pesquerías, o las restricciones asociadas al periodo reproductor, en los patrones de comportamiento y movimientos inferidos con los datos recogidos. En conjunto, la tesis aporta nueva información sobre los movimientos en el mar, el comportamiento y el uso del hábitat marino a lo largo del año. Finalmente, a lo largo del trabajo y de forma transversal, se resalta la utilidad de las aves marinas como especies centinela, particularmente teniendo en cuenta que la aplicación de técnicas de seguimiento remoto y de biologging amplían el potencial de estas especies como indicadoras en el marco del manejo del medio marino basado en un enfoque ecosistémico.

Background In the absence of a vaccine or effective treatment for COVID-19, countries have adopted nonpharmaceutical interventions (NPIs) such as social distancing and full lockdown. An objective and quantitative means of passively monitoring the impact and response of these interventions at a local level is needed. Objective We aim to explore the utility of the recently developed open-source mobile health platform Remote Assessment of Disease and Relapse (RADAR)–base as a toolbox to rapidly test the effect and response to NPIs intended to limit the spread of COVID-19. Methods We analyzed data extracted from smartphone and wearable devices, and managed by the RADAR-base from 1062 participants recruited in Italy, Spain, Denmark, the United Kingdom, and the Netherlands. We derived nine features on a daily basis including time spent at home, maximum distance travelled from home, the maximum number of Bluetooth-enabled nearby devices (as a proxy for physical distancing), step count, average heart rate, sleep duration, bedtime, phone unlock duration, and social app use duration. We performed Kruskal-Wallis tests followed by post hoc Dunn tests to assess differences in these features among baseline, prelockdown, and during lockdown periods. We also studied behavioral differences by age, gender, BMI, and educational background. Results We were able to quantify expected changes in time spent at home, distance travelled, and the number of nearby Bluetooth-enabled devices between prelockdown and during lockdown periods (P Conclusions RADAR-base, a freely deployable data collection platform leveraging data from wearables and mobile technologies, can be used to rapidly quantify and provide a holistic view of behavioral changes in response to public health interventions as a result of infectious outbreaks such as COVID-19. RADAR-base may be a viable approach to implementing an early warning system for passively assessing the local compliance to interventions in epidemics and pandemics, and could help countries ease out of lockdown.

OBJECTIVE: To explore factors influencing perceptions and viewpoints on the responsibility for the presence of toxic substances in food, on enforcement of laws and regulations that control human exposure to toxic substances in food, and on the effectiveness of such regulations. METHODS: An online survey was completed by 740 individuals from several parts of Spain (median age, 47 years; 67% were women; 70% had completed university studies). RESULTS: Over 87% of respondents said that it was possible that throughout their lives they could have accumulated in their body toxic substances potentially dangerous to their health. The attribution of the responsibility for toxic substances in food to a larger number of social groups was more frequent among respondents who consulted information about the problem more often (odds ratio [OR]: 1.92), who correctly identified factors that increase the likelihood of toxic substances in food being harmful to human health (OR: 2.86), who better knew the health problems that may be caused by such substances (OR: 2.48), and who recognised more food groups that tend to have concentrations of toxic substances potentially harmful to health (OR: 2.92) (all p values

This is the peer reviewed version of the following article: Siegenthaler, A., Wangensteen Fuentes, O.S., Soto, A.Z., Benvenuto, C., Corrigan, L, & Mariani, S. (2018). Metabarcoding of shrimp stomach content: harnessing a natural sampler for fish biodiversity monitoring. Molecular Ecology Resources. https://doi.org/10.1111/1755-0998.12956, which has been published in final form at https://doi.org/10.1111/1755-0998.12956. This article may be used for non-commercial purposes in accordance with Wiley Terms and Conditions for Use of Self-Archived Versions. Given their positioning and biological productivity, estuaries have long represented key providers of ecosystem services, and consequently remain under remarkable pressure from numerous forms of anthropogenic impact. The monitoring of fish communities in space and time are one of the most widespread and established approaches to assess the ecological status of estuaries and other coastal habitats, but traditional fish surveys are invasive, costly, labour intensive and highly selective. Recently, the application of metabarcoding techniques, on either sediment or aqueous environmental DNA, has rapidly gained popularity. Here, we evaluate the application of a novel, high through‐put DNA‐based monitoring tool to assess fish diversity, based on the analysis of the gut contents of a generalist predator/scavenger, the European brown shrimp, Crangon crangon. Sediment and shrimp samples were collected from eight European estuaries and DNA metabarcoding (using both 12S and COI markers) was carried out to infer fish assemblage composition. We detected 32 teleost species (16 and 20, for 12S and COI respectively). Twice as many species were recovered using metabarcoding than by traditional net surveys. By comparing and interweaving trophic, environmental DNA and traditional survey‐based techniques, we show that the DNA‐assisted gut content analysis of a ubiquitous, easily accessible, generalist species may serve as a powerful, rapid and cost‐effective tool for large scale, routine estuarine biodiversity monitoring.

As environmental DNA (eDNA) becomes an increasingly valuable resource for marine ecosystem monitoring, understanding variation in its persistence across contrasting environments is critical. Here, we quantify the breakdown of macrobial eDNA over a spatio-temporal axis of locally extreme conditions, varying from ocean-influenced offshore to urban-inshore, and between winter and summer. We report that eDNA degrades 1.6 times faster in the inshore environment than the offshore environment, but contrary to expectation we find no difference over season. Analysis of environmental covariables show a spatial gradient of salinity and a temporal gradient of pH, with salinity—or the biotic correlates thereof—most important. Based on our estimated inshore eDNA half-life and naturally occurring eDNA concentrations, we estimate that eDNA may be detected for around 48 h, offering potential to collect ecological community data of high local fidelity. We conclude by placing these results in the context of previously published eDNA decay rates., Rupert A. Collins et al. show that environmental DNA degrades faster in the inshore urban environment than the ocean-influenced offshore environment. This study suggests that environmental DNA can be reliably detected for two days, providing an optimal time window of high local fidelity.

6 pages, 8 figures, Scoring animal behavior is increasingly needed for better understanding ecological processes. For example, behavior shapes harvesting likelihood, thus management of harvested resources should improve after accounting for behavior-driven processes. Automatic video-recording at controlled arenas is the most widespread method for scoring behavior. However, long term tracking animals while keeping identity is still an opened challenge. Here, we develop an ad-hoc algorithm for multi-tracking objects during days or even weeks, to fulfill the particular needs for a behavioral assay concerning a fish species targeted by recreational fishing. Specifically, we overcome the challenge of keeping fish identity in a context where they often disappeared from the camera when entering a shelter, the pixel size was low compared to the size of the arena and the lighting was constrained by the wellbeing of the fish. This work may contribute to better assess the behavioral features of fish in long-lasting lab conditions, This work has been partially supported by the Spanish Government projects PHENOFISH with references: CTM2015-69126-C2-1-R and CTM2015-69126-2-R, and is a contribution of the Joint Research Unit IMEDEA-LIMIA. A.C.C. was supported by a FPU predoctoral fellowship (ref.FPU13/01440) from the Spanish Ministry of Education, Culture and Sports (MECD)

[cat] L’ecologia de poblacions és una branca multidisciplinària de l’ecologia que, al considerar les poblacions com a unitats biològiques fonamentals, permet establir nexes d’unió entre l’ecologia bàsica, els estudis evolutius i la biologia de la conservació. L’estudi de les respostes demogràfiques als canvis ambientals es realitza per mitjà del monitoratge de poblacions, però per a un coneixement detallat dels processos ecològics que determinen les dinàmiques poblacionals cal fer server eines d’anàlisi robustes que ens permetin estimar i modelitzar paràmetres poblacionals tenint en compte la detecció imperfecta dels processos ecològics. Aquest enfoc metodològic ha estat aplicat a l’anàlisi de les dades de monitoratge poblacional dut a terme en aquesta tesi, on cada capítol representa una aplicació metodològica per a respondre a qüestions biològiques específices al llarg de diferents nivells de complexitat ecològica. Els capitols 1 i 2 és centren en poblacions discretes de tortuga mediterrània i truita comuna, respectivament. En aquest capítols vaig aplicar diferents models de captura-recaptura per obtenir estimes de supervivència per a diferents estadis vitals, i, en el cas del capitol 2, estimes de creixement individual. L´ús de covariables va permetre avaluar l’efecte de la meteorologia en la supervivència, i en el cas de la tortuga, aquesta relació fóu utilitzada per a realitzar simulacions sota diferents escenaris de canvi climatic, proporcionant riscos d’extinció al llarg de tota la distribució mundial de l’espècie. Els capitols 3 i 4 es centren en l’estudi de xarxes poblacionals i en concret, en l’estudi de la dispersió i els processos d’extinció i colonització d’espècies fent servir com a models biològics la gavina corsa i la comunitat de papallones diurnes de Catalunya. En el cas de la gavina, vaig aplicar models de captura-recaptura multievent per controlar biaixos i obtenir estimes de dispersió adulta tant a dins com a fora de l’àrea d’estudi. L’aplicació de models d’ocupació dinàmica va perpetre obtindre estimes robustes de probabilitats d’extinció i clonització per a 73 espècies de papallones. En ambdòs casos, diferents variables externes varen ser examinades i es varen identificar diferents factors ambientals relacionats amb processos de dispersió i recanvi poblacional que poden ajudar al desenvolupament d’estratègies de conservació., [eng] Population ecology is a scientific discipline primarily interested in the ecological processes that make the number of individuals in a population to change over space and time, and by focusing on populations as fundamental units, this discipline allows studying processes at multiple scales of ecological complexity, linking basic ecological science with evolutionary studies and more applied disciplines such as conservation biology. Inference about the responses of population to change are made via observational studies that focus at either the individual or population level in order to estimate key vital rates and to determine the primary drivers of system dynamics. However, a problem of observational studies is that quite often the ecological and observational processes are confounded, leading to biased estimates and wrong conclusions about a population, so more specific and robust analytical approaches need to be applied for a correct scientific study of the populations. In this thesis, I have consistently applied a methodological approach that allows the study of population processes by separating ecological and observational processes via the estimation and modelling of key demographic parameters. By means of chapters 1 to 4, I provide several examples of this methodology via the analysis of demographic data belonging to different species and levels of population complexity that also reflect different biological questions and scientific applications. Field data for this thesis was collected using either capture-recapture or detection-non detection sampling techniques and were provided via collaborations with different researchers and institutions. Chapters 1 and 2 focus on discrete mediterranean tortoise (Testudo hermanni) and brown trout (Salmo trutta) populations, respectively. These populations are closed to dispersal processes and in both chapters I focused on stage-dependent local survival rates that were estimated using capture-recapture models that take into account recapture probabilities. Given that individuals were classified according to body size, in the case of the brown trout populations, I could apply multistate capture-recapture models to estimate individual growth and maturation rates across different populations. In both chapters, survival dynamics were modelled using external covariates (temperature and/or precipitation) that explained part of the observed variation in survival. In the case of tortoises, the obtained survival-precipitation relationship was used to perform several population viability analyses under future precipitation scenarios to forecast the extinction risk of the species across their global geographic distribution. Chapters 3 and 4 focus on population networks connected by dispersal processes. Chapter 3 is strictly focused on adult dispersal and so analyses a capture-recapture dataset collected over 4 local populations of Audouin’s gull (Larus audouinii) in the Western Mediterranean. In Chapter 4 I analysed a large database on butterfly species collected at 26 sites in Catalonia over 17 years and focused on species’ extinction-colonization dynamics at a large geographical scale. In both chapters, two relatively recent analytical approaches, the multievent modelling (chapter 3) and the multiseason or dynamic occupancy modelling (chapter 4) were applied. The application of such modelling tools allowed, in the case of gulls, to control recapture heterogeneities and to study individual dispersal both in and out of the study area, by means of the addition of unobservable states in the model. In the case of butterflies, a common candidate model set was applied to 73 butterfly species, obtaining specific extinction and colonization rates corrected for species’ detectability, which allowed assessing the influence of the species’ traits on occupancy dynamics. Covariate modelling became much more complex in these chapters, but allowed the identification of different habitat and environmental variables related to dispersal, extinction and colonization processes that are of high value in the conservation and management of the species under study.

30 páginas, 9 figuras, 1 tabla., We assessed spatio-temporal patterns of diversity in deep-sea sediment communities using metabarcoding. We chose a recently developed eukaryotic marker based on the v7 region of the 18S rRNA gene. Our study was performed in a submarine canyon and its adjacent slope in the Northwestern Mediterranean Sea, sampled along a depth gradient at two different seasons. We found a total of 5,569 molecular operational taxonomic units (MOTUs), dominated by Metazoa, Alveolata and Rhizaria. Among metazoans, Nematoda, Arthropoda and Annelida were the most diverse. We found a marked heterogeneity at all scales, with important differences between layers of sediment and significant changes in community composition with zone (canyon vs slope), depth, and season. We compared the information obtained from metabarcoding DNA and RNA and found more total MOTUs and more MOTUs per sample with DNA (ca. 20% and 40% increase, respectively). Both datasets showed overall similar spatial trends, but most groups had higher MOTU richness with the DNA template, while others, such as nematodes, were more diverse in the RNA dataset. We provide metabarcoding protocols and guidelines for biomonitoring of these key communities in order to generate information applicable to management efforts., The sampling was done in the framework of the DOSMARES project (CTM2010-21810) of the Spanish Government. MG benefitted from a FPI predoctoral contract of the Spanish Government. This research was funded by project CHALLENGEN CTM2013-48163 of the Spanish Government.