A protocol for harvesting biodiversity data from Facebook.

The expanding use of community science platforms has led to an exponential increase in biodiversity data in global repositories. Yet, understanding of species distributions remains patchy. Biodiversity data from social media can potentially reduce the global biodiversity knowledge gap. However, practical guidelines and standardized methods for harvesting such data are nonexistent. Following data privacy and protection safeguards, we devised a standardized method for extracting species distribution records from Facebook groups that allow access to their data. It involves 3 steps: group selection, data extraction, and georeferencing the record location. We present how to structure keywords, search for species photographs, and georeference localities for such records. We further highlight some challenges users might face when extracting species distribution data from Facebook and suggest solutions. Following our proposed framework, we present a case study on Bangladesh's biodiversity-a tropical megadiverse South Asian country. We scraped nearly 45,000 unique georeferenced records across 967 species and found a median of 27 records per species. About 12% of the distribution data were for threatened species, representing 27% of all species. We also obtained data for 56 DataDeficient species for Bangladesh. If carefully harvested, social media data can significantly reduce global biodiversity knowledge gaps. Consequently, developing an automated tool to extract and interpret social media biodiversity data is a research priority.

Un protocolo para recolectar datos sobre biodiversidad en Facebook Resumen El uso creciente de plataformas de ciencia comunitaria ha causado un incremento exponencial de los datos sobre biodiversidad en los repositorios mundiales. Sin embargo, el conocimiento sobre la distribución de las especies todavía está incompleto. Los datos sobre biodiversidad obtenidos de las redes sociales tienen el potencial para disminuir el vacío de conocimiento sobre la biodiversidad mundial. No obstante, no existe una guía práctica o un método estandarizado para recolectar dichos datos. Seguimos los protocolos de privacidad y protección de datos para diseñar un método estandarizado para extraer registros de la distribución de especies de grupos en Facebook que permiten el acceso a sus datos. El método consta de tres pasos: selección del grupo, extracción de datos y georreferenciación de la localidad registrada. También planteamos cómo estructurar las palabras clave, buscar fotografías de especies y georreferenciar las localidades de dichos registros. Además, resaltamos algunos retos que los usuarios pueden enfrentar al extraer los datos de distribución de Facebook y sugerimos algunas soluciones. Aplicamos nuestro marco de trabajo propuesto a un estudio de caso de la biodiversidad en Bangladesh, un país tropical megadiverso en el sureste de Asia. Reunimos casi 45,000 registros georreferenciados únicos para 967 especies y encontramos una media de 27 registros por especie. Casi el 12% de los datos de distribución correspondió a especies amenazadas, que representaban el 27% de todas las especies. También obtuvimos datos para 56 especies deficientes de datos en Bangladesh. Si los datos de las redes sociales se recolectan con cuidado, éstos pueden reducir de forma significativa el vacío de conocimiento para la biodiversidad mundial. Como consecuencia, es una prioridad para la investigación el desarrollo de una herramienta automatizada para extraer e interpretar los datos sobre biodiversidad de las redes sociales.

Using social media records to inform conservation planning.

Citizen science plays a crucial role in helping monitor biodiversity and inform conservation. With the widespread use of smartphones, many people share biodiversity information on social media, but this information is still not widely used in conservation. Focusing on Bangladesh, a tropical megadiverse and mega-populated country, we examined the importance of social media records in conservation decision-making. We collated species distribution records for birds and butterflies from Facebook and Global Biodiversity Information Facility (GBIF), grouped them into GBIF-only and combined GBIF and Facebook data, and investigated the differences in identifying critical conservation areas. Adding Facebook data to GBIF data improved the accuracy of systematic conservation planning assessments by identifying additional important conservation areas in the northwest, southeast, and central parts of Bangladesh, extending priority conservation areas by 4,000-10,000 km2 . Community efforts are needed to drive the implementation of the ambitious Kunming-Montreal Global Biodiversity Framework targets, especially in megadiverse tropical countries with a lack of reliable and up-to-date species distribution data. We highlight that conservation planning can be enhanced by including available data gathered from social media platforms.

Registros de las redes sociales para guiar la planeación de la conservación Resumen La ciencia ciudadana es importante para monitorear la biodiversidad e informar la conservación. Con el creciente uso de los teléfonos inteligentes, muchas personas comparten información de la biodiversidad en redes sociales, pero todavía no se usa ampliamente en la conservación. Analizamos la importancia de los registros de las redes sociales para las decisiones de conservación enfocados en Bangladesh, un país tropical megadiverso y mega poblado. Cotejamos los registros de distribución de especies de aves y mariposas en Facebook y Global Biodiversity Information Facility (GBIF), las agrupamos en datos sólo de GBIF o datos combinados de Facebook y GBIF e investigamos las diferencias en la identificación de las áreas de conservación críticas. La combinación de los datos de Facebook con los de GBIF mejoró la precisión de las evaluaciones de la planeación de la conservación sistemática al identificar otras áreas importantes de conservación en el noroeste, sureste y centro de Bangladesh, extendiendo así las áreas prioritarias de conservación en unos 4,000-10,000 km2 . Se requieren esfuerzos comunitarios para impulsar la implementación de los objetivos ambiciosos del Marco Global de Biodiversidad Kunming-Montreal, especialmente en países tropicales que carecen de datos confiables y actuales sobre la distribución de las especies. Destacamos que la planeación de la conservación puede mejorarse si se incluye información tomada de las redes sociales.

Daily activity rhythms, chronotypes, and risk-taking behavior in the signal crayfish.

Consistent inter-individual differences in daily activity rhythms (i.e., chronotypes) can have ecological consequences in determining access to food resources and avoidance of predators. The most common measure to characterize chronotypes in animals as well as humans is the onset of activity (i.e., early or late chronotypes). However, daily activity rhythms may also differ in the relative amount of activity displayed at particular time periods. Moreover, chronotypes may also be linked to other consistent inter-individual differences in behavior (i.e., personality), such as the propensity to take risks. Here, we used the signal crayfish Pacifastacus leniusculus to test the presence of chronotypes and risk-taking personality traits and a potential behavioral syndrome between these traits. We first exposed crayfish to 5 days of light-darkness to measure daily activity rhythms and then we applied a visual predator-simulating stimulus in 2 different contexts (neutral and food). Our results showed consistent (i.e., across 5 days) inter-individual differences in the relative nocturnal activity displayed in the early and middle, but not in the late part of darkness hours. Moreover, while crayfish displayed inter-individual differences in risk-taking behavior, these were not found to be consistent across 2 contexts. Therefore, we were not able to formally test a behavioral syndrome between these 2 traits. In conclusion, our study provides the first evidence of chronotypes in the relative amount of activity displayed at particular time periods. This could be a valuable information for applied ecological aspects related to the signal crayfish, which is a major invasive species of freshwater ecosystems.

Evolutionary Impact of Size-Selective Harvesting on Shoaling Behavior: Individual-Level Mechanisms and Possible Consequences for Natural and Fishing Mortality.

AbstractIntensive and size-selective harvesting is an evolutionary driver of life history as well as individual behavioral traits. Yet whether and to what degree harvesting modifies the collective behavior of exploited species are largely unknown. We present a multigeneration harvest selection experiment with zebrafish, Danio rerio, as a model species to understand the effects of size-selective harvesting on shoaling behavior. The experimental system is based on a large-harvested (typical of most wild-capture fisheries targeting larger size classes) and small-harvested (typical of specialized fisheries and gape-limited predators targeting smaller size classes) selection lines. By combining high-resolution tracking of fish behavior with computational agent-based modeling, we show that shoal cohesion changed in the direction expected by a trade-off between individual vigilance and the use of social cues. In particular, we document a decrease of individual vigilance in the small-harvested line, which was linked to an increase in the attention to social cues, favoring more cohesive shoals. Opposing outcomes were found for the large-harvested line, which formed less cohesive shoals. Using the agent-based model, we outline possible consequences of changes in shoaling behavior for both fishing and natural mortality. The changes in shoaling induced by large size-selective harvesting may decrease fishing mortality but increase mortality by natural predators. Our work suggests an insofar overlooked evolutionary mechanism by which size-selective harvesting can affect fishing and natural mortality of exploited fish.

Fisheries-induced changes of shoaling behaviour: mechanisms and potential consequences.

We outline key mechanisms by which fishing can change the shoaling tendency and collective behaviour of exploited species - an issue that is rarely considered and poorly understood. We highlight potential consequences for fish populations and food webs, and discuss possible repercussions for fisheries and conservation strategies.

Size Selective Harvesting Does Not Result in Reproductive Isolation among Experimental Lines of Zebrafish, Danio rerio: Implications for Managing Harvest-Induced Evolution.

Size-selective mortality is common in fish stocks. Positive size-selection happens in fisheries where larger size classes are preferentially targeted while gape-limited natural predation may cause negative size-selection for smaller size classes. As body size and correlated behavioural traits are sexually selected, harvest-induced trait changes may promote prezygotic reproductive barriers among selection lines experiencing differential size-selective mortality. To investigate this, we used three experimental lines of zebrafish (Danio rerio) exposed to positive (large-harvested), negative (small-harvested) and random (control line) size-selective mortality for five generations. We tested prezygotic preferences through choice tests and spawning trials. In the preference tests without controlling for body size, we found that females of all lines preferred males of the generally larger small-harvested line. When the body size of stimulus fish was statistically controlled, this preference disappeared and a weak evidence of line-assortative preference emerged, but only among large-harvested line fish. In subsequent spawning trials, we did not find evidence for line-assortative reproductive allocation in any of the lines. Our study suggests that size-selection due to fisheries or natural predation does not result in reproductive isolation. Gene flow between wild-populations and populations adapted to size-selected mortality may happen during secondary contact which can speed up trait recovery.

Analyzing publicly available videos about recreational fishing reveals key ecological and social insights: A case study about groupers in the Mediterranean Sea.

iEcology and conservation culturomics are two emerging research approaches that rely on digital data for studying ecological patterns and human-nature interactions. We applied data mining of videos published on YouTube related to recreational fishing of four species of groupers (family: Epinephelidae) in Italy between 2011 and 2017 to learn whether digital user-supplied data help uncover key spatio-temporal ecological patterns characteristic of the studied species. Our results support an ontogenetic deepening of the dusky grouper (Epinephelus marginatus) as revealed by a positive relationship between body mass and depth of captures declared in spearfishing videos. In addition, the data support a northward expansion of the white grouper (Epinephelus aeneus) because the average latitude associated to the catch was found to be positively correlated with the years when the videos were uploaded on YouTube. Furthermore, the georeferenced data about the white grouper filled a knowledge gap in a well-established international occurrence records dataset. The approach presented here could help mitigating data deficiencies and inform about harvesting patterns shown by recreational anglers and spearfishers. Our work illustrates the value of digital data associated with recreational fishing for advancing fish and fisheries research. The approach can be broadened to larger spatial and temporal scales, and to different species, contributing to a better understanding of macroecological patterns, assessment and conservation of exploited species, and monitoring of recreational fisheries.

Size-selective mortality induces evolutionary changes in group risk-taking behaviour and the circadian system in a fish.

Intensive and trait-selective mortality of fish and wildlife can cause evolutionary changes in a range of life-history and behavioural traits. These changes might in turn alter the circadian system due to co-evolutionary mechanisms or correlated selection responses both at behavioural and molecular levels, with knock-on effects on daily physiological processes and behavioural outputs. We examined the evolutionary impact of size-selective mortality on group risk-taking behaviour and the circadian system in a model fish species. We exposed zebrafish Danio rerio to either large or small size-selective harvesting relative to a control over five generations, followed by eight generations during which harvesting was halted to remove maternal effects. Size-selective mortality affected fine-scale timing of behaviours. In particular, small size-selective mortality, typical of specialized fisheries and gape-limited predators targeting smaller size classes, increased group risk-taking behaviuor during feeding and after simulated predator attacks. Moreover, small size-selective mortality increased early peaks of daily activity as well as extended self-feeding daily activity to the photophase compared to controls. By contrast large size-selective mortality, typical of most wild capture fisheries, only showed an almost significant effect of decreasing group risk-taking behaviour during the habituation phase and no clear changes in fine-scale timing of daily behavioural rhythms compared to controls. We also found changes in the molecular circadian core clockwork in response to both size-selective mortality treatments. These changes disappeared in the clock output pathway because both size-selected lines showed similar transcription profiles. This switch downstream to the molecular circadian core clockwork also resulted in similar overall behavioural rhythms (diurnal swimming and self-feeding in the last hours of darkness) independent of the underlying molecular clock. To conclude, our experimental harvest left an asymmetrical evolutionary legacy in group risk-taking behaviour and in fine-scale daily behavioural rhythms. Yet, the overall timing of activity showed evolutionary resistance probably maintained by a molecular switch. Our experimental findings suggest that size-selective mortality can have consequences for behaviour and physiological processes.

Expanding conservation culturomics and iEcology from terrestrial to aquatic realms.

The ongoing digital revolution in the age of big data is opening new research opportunities. Culturomics and iEcology, two emerging research areas based on the analysis of online data resources, can provide novel scientific insights and inform conservation and management efforts. To date, culturomics and iEcology have been applied primarily in the terrestrial realm. Here, we advocate for expanding such applications to the aquatic realm by providing a brief overview of these new approaches and outlining key areas in which culturomics and iEcology are likely to have the highest impact, including the management of protected areas; fisheries; flagship species identification; detection and distribution of threatened, rare, and alien species; assessment of ecosystem status and anthropogenic impacts; and social impact assessment. When deployed in the right context with awareness of potential biases, culturomics and iEcology are ripe for rapid development as low-cost research approaches based on data available from digital sources, with increasingly diverse applications for aquatic ecosystems.

Climate change, biological invasions, and the shifting distribution of Mediterranean fishes: A large-scale survey based on local ecological knowledge.

Climate change and biological invasions are rapidly reshuffling species distribution, restructuring the biological communities of many ecosystems worldwide. Tracking these transformations in the marine environment is crucial, but our understanding of climate change effects and invasive species dynamics is often hampered by the practical challenge of surveying large geographical areas. Here, we focus on the Mediterranean Sea, a hot spot for climate change and biological invasions to investigate recent spatiotemporal changes in fish abundances and distribution. To this end, we accessed the local ecological knowledge (LEK) of small-scale and recreational fishers, reconstructing the dynamics of fish perceived as "new" or increasing in different fishing areas. Over 500 fishers across 95 locations and nine different countries were interviewed, and semiquantitative information on yearly changes in species abundance was collected. Overall, 75 species were mentioned by the respondents, mostly warm-adapted species of both native and exotic origin. Respondents belonging to the same biogeographic sectors described coherent spatial and temporal patterns, and gradients along latitudinal and longitudinal axes were revealed. This information provides a more complete understanding of the shifting distribution of Mediterranean fishes and it also demonstrates that adequately structured LEK methodology might be applied successfully beyond the local scale, across national borders and jurisdictions. Acknowledging this potential through macroregional coordination could pave the way for future large-scale aggregations of individual observations, increasing our potential for integrated monitoring and conservation planning at the regional or even global level. This might help local communities to better understand, manage, and adapt to the ongoing biotic transformations driven by climate change and biological invaders.

Size-selective harvesting fosters adaptations in mating behaviour and reproductive allocation, affecting sexual selection in fish.

The role of sexual selection in the context of harvest-induced evolution is poorly understood. However, elevated and trait-selective harvesting of wild populations may change sexually selected traits, which in turn can affect mate choice and reproduction. We experimentally evaluated the potential for fisheries-induced evolution of mating behaviour and reproductive allocation in fish. We used an experimental system of zebrafish (Danio rerio) lines exposed to large, small or random (i.e. control) size-selective mortality. The large-harvested line represented a treatment simulating the typical case in fisheries where the largest individuals are preferentially harvested. We used a full factorial design of spawning trials with size-matched individuals to control for the systematic impact of body size during reproduction, thereby singling out possible changes in mating behaviour and reproductive allocation. Both small size-selective mortality and large size-selective mortality left a legacy on male mating behaviour by elevating intersexual aggression. However, there was no evidence for line-assortative reproductive allocation. Females of all lines preferentially allocated eggs to the generally less aggressive males of the random-harvested control line. Females of the large-harvested line showed enhanced reproductive performance, and males of the large-harvested line had the highest egg fertilization rate among all males. These findings can be explained as an evolutionary adaptation by which individuals of the large-harvested line display an enhanced reproductive performance early in life to offset the increased probability of adult mortality due to harvest. Our results suggest that the large-harvested line evolved behaviourally mediated reproductive adaptations that could increase the rate of recovery when populations adapted to high fishing pressure come into secondary contact with other populations.

Long-term Video Tracking of Cohoused Aquatic Animals: A Case Study of the Daily Locomotor Activity of the Norway Lobster (Nephrops norvegicus).

We present a protocol related to a video-tracking technique based on the background subtraction and image thresholding that makes it possible to individually track cohoused animals. We tested the tracking routine with four cohoused Norway lobsters (Nephrops norvegicus) under light-darkness conditions for 5 days. The lobsters had been individually tagged. The experimental setup and the tracking techniques used are entirely based on the open source software. The comparison of the tracking output with a manual detection indicates that the lobsters were correctly detected 69% of the times. Among the correctly detected lobsters, their individual tags were correctly identified 89.5% of the times. Considering the frame rate used in the protocol and the movement rate of lobsters, the performance of the video tracking has a good quality, and the representative results support the validity of the protocol in producing valuable data for research needs (individual space occupancy or locomotor activity patterns). The protocol presented here can be easily customized and is, hence, transferable to other species where the individual tracking of specimens in a group can be valuable for answering research questions.

Annual rhythms of temporal niche partitioning in the Sparidae family are correlated to different environmental variables.

The seasonal timing of recurring biological processes is essential for organisms living in temperate regions. While ample knowledge of these processes exists for terrestrial environments, seasonal timing in the marine environment is relatively understudied. Here, we characterized the annual rhythm of habitat use in six fish species belonging to the Sparidae family, highlighting the main environmental variables that correlate to such rhythms. The study was conducted at a coastal artificial reef through a cabled observatory system, which allowed gathering underwater time-lapse images every 30 minutes consecutively over 3 years. Rhythms of fish counts had a significant annual periodicity in four out of the six studied species. Species-specific temporal patterns were found, demonstrating a clear annual temporal niche partitioning within the studied family. Temperature was the most important environmental variable correlated with fish counts in the proximity of the artificial reef, while daily photoperiod and salinity were not important. In a scenario of human-induced rapid environmental change, tracking phenological shifts may provide key indications about the effects of climate change at both species and ecosystem level. Our study reinforces the efficacy of underwater cabled video-observatories as a reliable tool for long-term monitoring of phenological events.

Tracking Fish Abundance by Underwater Image Recognition.

Marine cabled video-observatories allow the non-destructive sampling of species at frequencies and durations that have never been attained before. Nevertheless, the lack of appropriate methods to automatically process video imagery limits this technology for the purposes of ecosystem monitoring. Automation is a prerequisite to deal with the huge quantities of video footage captured by cameras, which can then transform these devices into true autonomous sensors. In this study, we have developed a novel methodology that is based on genetic programming for content-based image analysis. Our aim was to capture the temporal dynamics of fish abundance. We processed more than 20,000 images that were acquired in a challenging real-world coastal scenario at the OBSEA-EMSO testing-site. The images were collected at 30-min. frequency, continuously for two years, over day and night. The highly variable environmental conditions allowed us to test the effectiveness of our approach under changing light radiation, water turbidity, background confusion, and bio-fouling growth on the camera housing. The automated recognition results were highly correlated with the manual counts and they were highly reliable when used to track fish variations at different hourly, daily, and monthly time scales. In addition, our methodology could be easily transferred to other cabled video-observatories.

Fighting over burrows: the emergence of dominance hierarchies in the Norway lobster (Nephrops norvegicus).

Animals fight over resources such as mating partners, territory, food or shelter and repeated contests lead to stable social hierarchies in different phyla. The group dynamics of hierarchy formation are not characterized in the Norway lobster (Nephrops norvegicus). Lobsters spend most of the day in burrows and forage outside of them according to a diel (i.e. 24 h-based) activity rhythm. Here, we use a linear and generalized mixed model approach to analyse, in seven groups of four male lobsters, the formation of dominance hierarchies and rank-related changes in burrowing behaviour. We show that hierarchies emerge within 1-3 days and increase in steepness over a period of 5 days, while rank changes and number of fights gradually decrease over a 5-day period. The rank position determined by open area fights predicts the outcome of fights over burrows, the time spent in burrows, and the locomotor activity levels. Dominant lobsters are more likely to evict subordinate lobsters from their burrows and are more successful in defending their own burrows. They spend more time in burrows and display lower levels of locomotor activity outside the burrow. Lobsters do not change their diel activity rhythms as a result of a change in rank, and all tested individuals showed higher activity at night and dusk compared with dawn and daytime. We discuss how behavioural changes in burrowing behaviour could lead to rank-related benefits such as reduced exposure to predators and energy savings.

Sex and tissue specific gene expression patterns identified following de novo transcriptomic analysis of the Norway lobster, Nephrops norvegicus.

BACKGROUND: The Norway lobster, Nephrops norvegicus, is economically important in European fisheries and is a key organism in local marine ecosystems. Despite multi-faceted scientific interest in this species, our current knowledge of genetic resources in this species remains very limited. Here, we generated a reference de novo transcriptome for N. norvegicus from multiple tissues in both sexes. Bioinformatic analyses were conducted to detect transcripts that were expressed exclusively in either males or females. Patterns were validated via RT-PCR. RESULTS: Sixteen N. norvegicus libraries were sequenced from immature and mature ovary, testis and vas deferens (including the masculinizing androgenic gland). In addition, eyestalk, brain, thoracic ganglia and hepatopancreas tissues were screened in males and both immature and mature females. RNA-Sequencing resulted in >600 million reads. De novo assembly that combined the current dataset with two previously published libraries from eyestalk tissue, yielded a reference transcriptome of 333,225 transcripts with an average size of 708 base pairs (bp), with an N50 of 1272 bp. Sex-specific transcripts were detected primarily in gonads followed by hepatopancreas, brain, thoracic ganglia, and eyestalk, respectively. Candidate transcripts that were expressed exclusively either in males or females were highlighted and the 10 most abundant ones were validated via RT-PCR. Among the most highly expressed genes were Serine threonine protein kinase in testis and Vitellogenin in female hepatopancreas. These results align closely with gene annotation results. Moreover, a differential expression heatmap showed that the majority of differentially expressed transcripts were identified in gonad and eyestalk tissues. Results indicate that sex-specific gene expression patterns in Norway lobster are controlled by differences in gene regulation pattern between males and females in somatic tissues. CONCLUSIONS: The current study presents the first multi-tissue reference transcriptome for the Norway lobster that can be applied to future biological, wild restocking and fisheries studies. Sex-specific markers were mainly expressed in males implying that males may experience stronger selection than females. It is apparent that differential expression is due to sex-specific gene regulatory pathways that are present in somatic tissues and not from effects of genes located on heterogametic sex chromosomes. The N. norvegicus data provide a foundation for future gene-based reproductive studies.

Influence of temperature on daily locomotor activity in the crab Uca pugilator.

Animals living in the intertidal zone are exposed to prominent temperature changes. To cope with the energetic demands of environmental thermal challenges, ectotherms rely mainly on behavioral responses, which may change depending on the time of the day and seasonally. Here, we analyze how temperature shapes crabs' behavior at 2 different times of the year and show that a transition from constant cold (13.5°C) to constant warm (17.5°C) water temperature leads to increased locomotor activity levels throughout the day in fiddler crabs (Uca pugilator) collected during the summer. In contrast, the same transition in environmental temperature leads to a decrease in the amplitude of the daily locomotor activity rhythm in crabs collected during the winter. In other words, colder temperatures during the cold season favor a more prominent diurnal behavior. We interpret this winter-summer difference in the response of daily locomotor activity to temperature changes within the framework of the circadian thermoenergetics hypothesis, which predicts that a less favorable energetic balance would promote a more diurnal activity pattern. During the winter, when the energetic balance is likely less favorable, crabs would save energy by being more active during the expected high-temperature phase of the day-light phase-and less during the expected low-temperature phase of the day-dark phase. Our results suggest that endogenous rhythms in intertidal ectotherms generate adaptive behavioral programs to cope with thermoregulatory demands of the intertidal habitat.

Identification, Characterization, and Diel Pattern of Expression of Canonical Clock Genes in Nephrops norvegicus (Crustacea: Decapoda) Eyestalk.

The Norway lobster, Nephrops norvegicus, is a burrowing decapod with a rhythmic burrow emergence (24 h) governed by the circadian system. It is an important resource for European fisheries and its behavior deeply affects its availability. The current knowledge of Nephrops circadian biology is phenomenological as it is currently the case for almost all crustaceans. In attempt to elucidate the putative molecular mechanisms underlying circadian gene regulation in Nephrops, we used a transcriptomics approach on cDNA extracted from the eyestalk, a structure playing a crucial role in controlling behavior of decapods. We studied 14 male lobsters under 12-12 light-darkness blue light cycle. We used the Hiseq 2000 Illumina platform to sequence two eyestalk libraries (under light and darkness conditions) obtaining about 90 millions 100-bp paired-end reads. Trinity was used for the de novo reconstruction of transcriptomes; the size at which half of all assembled bases reside in contigs (N50) was equal to 1796 (light) and 2055 (darkness). We found a list of candidate clock genes and focused our attention on canonical ones: timeless, period, clock and bmal1. The cloning of assembled fragments validated Trinity outputs. The putative Nephrops clock genes showed high levels of identity (blastx on NCBI) with known crustacean clock gene homologs such as Eurydice pulchra (period: 47%, timeless: 59%, bmal1: 79%) and Macrobrachium rosenbergii (clock: 100%). We also found a vertebrate-like cryptochrome 2. RT-qPCR showed that only timeless had a robust diel pattern of expression. Our data are in accordance with the current knowledge of the crustacean circadian clock, reinforcing the idea that the molecular clockwork of this group shows some differences with the established model in Drosophila melanogaster.

A new colorimetrically-calibrated automated video-imaging protocol for day-night fish counting at the OBSEA coastal cabled observatory.

Field measurements of the swimming activity rhythms of fishes are scant due to the difficulty of counting individuals at a high frequency over a long period of time. Cabled observatory video monitoring allows such a sampling at a high frequency over unlimited periods of time. Unfortunately, automation for the extraction of biological information (i.e., animals' visual counts per unit of time) is still a major bottleneck. In this study, we describe a new automated video-imaging protocol for the 24-h continuous counting of fishes in colorimetrically calibrated time-lapse photographic outputs, taken by a shallow water (20 m depth) cabled video-platform, the OBSEA. The spectral reflectance value for each patch was measured between 400 to 700 nm and then converted into standard RGB, used as a reference for all subsequent calibrations. All the images were acquired within a standardized Region Of Interest (ROI), represented by a 2 × 2 m methacrylate panel, endowed with a 9-colour calibration chart, and calibrated using the recently implemented "3D Thin-Plate Spline" warping approach in order to numerically define color by its coordinates in n-dimensional space. That operation was repeated on a subset of images, 500 images as a training set, manually selected since acquired under optimum visibility conditions. All images plus those for the training set were ordered together through Principal Component Analysis allowing the selection of 614 images (67.6%) out of 908 as a total corresponding to 18 days (at 30 min frequency). The Roberts operator (used in image processing and computer vision for edge detection) was used to highlights regions of high spatial colour gradient corresponding to fishes' bodies. Time series in manual and visual counts were compared together for efficiency evaluation. Periodogram and waveform analysis outputs provided very similar results, although quantified parameters in relation to the strength of respective rhythms were different. Results indicate that automation efficiency is limited by optimum visibility conditions. Data sets from manual counting present the larger day-night fluctuations in comparison to those derived from automation. This comparison indicates that the automation protocol subestimate fish numbers but it is anyway suitable for the study of community activity rhythms.

Sensory biology and behaviour of Nephrops norvegicus.

The Norway lobster is one of the most important commercial crustaceans in Europe. A detailed knowledge of the behaviour of this species is crucial in order to optimize fishery yields, improve sustainability of fisheries, and identify man-made environmental threats. Due to the cryptic life-style in burrows, the great depth and low-light condition of their habitat, studies of the behaviour of this species in its natural environment are challenging. Here, we first provide an overview of the sensory modalities (vision, chemoreception, and mechanoreception) of Nephrops norvegicus. We focus particularly on the role of the chemical and mechanical senses in eliciting and steering spatial orientation behaviours. We then concentrate on recent research in social behaviour and biological rhythms of Nephrops. A combination of laboratory approaches and newly developed tracking technologies has led to a better understanding of aggressive interactions, reproductive behaviours, activity cycles, and burrow-related behaviours. Gaps in our knowledge are identified and suggestions for future research are provided.