All is fish that comes to the net: metabarcoding for rapid fisheries catch assessment.

A line with no hook: longline-associated passive eDNA samplers for deep-sea fish monitoring.

Spatial and temporal changes of coastal demersal assemblages in the Gulf of Cadiz (SW Spain) in relation to environmental conditions

Fishery-dependent data, despite being a valuable resource, is often underutilized in addressing scientific inquiries comprehensively. Similar to citizen science data, it possesses significant potential to enhance our comprehension of changing species abundances and distributions. In this study, we present an illustrative example of harnessing available fishery-dependent data from the northeast United States to generate a valuable scientific output. Our approach involves combining data sets from two high-resolution fishery-dependent research and monitoring programs: (1) the Northeast Fisheries Science Center’s Study Fleet Program and (2) the Northeast Fisheries Observer Programs. By focusing on data collected from vessels employing bottom trawl gear, we construct a novel data set and establish a nominal catch per unit effort index specific to black sea bass (Centropristis striata), a commonly targeted species. To augment this data set, we incorporate additional variables pertaining to ecological and economic factors that could influence catch rates. The expanded data set is then used to develop a catch rate standardization using a generalized additive model. This study not only exemplifies how these unique, high-resolution data sets can be effectively leveraged for scientific purposes but also provides a detailed account of the methodology employed to compile these extensive data sets. We suggest that similar techniques could be applied to other species within the region or to analogous data sets from different regions. Advancing methodologies for utilizing fishery-dependent data in scientific research is a cost effective means for improving our understanding of species abundance and ecosystem dynamics. Moreover, it presents an opportunity to demonstrate the value of incorporating the knowledge and experiences of fishers and other stakeholders quantitatively into the scientific process. By tapping into the wealth of information provided by fishery-dependent data, we can make significant strides in expanding our scientific knowledge and informing sustainable management practices.

Stony reefs are ecologically important, providing irreplaceable ecosystem services. These fragile environments are recognised as conservation priorities by all relevant global and European policies. Bottom-contacting fisheries are an important source of anthropogenic disturbance to the seafloor’s physical and ecological integrity having immediate and destructive consequences on stony reefs and compromising ecological functions. This study, aimed to assess the ecological status (community composition and functions) of two stony reef areas -Northwest and Hinder Banks study sites -in Belgian waters using multiple remote sensing tools. Insights on the study sites’ geomorphological context and fishing patterns were gained using echo-sounding and publicly available satellite data. Video-based benthic community data were assessed against the exposure to fishing pressure using a trait-based approach linked to the biotas’ resistance and recovery potential. In the Northwest study site, between 2019 and 2022 there was a significant decline in the abundance of benthic species classified with low resistance and recovery potential to trawling. Conversely, there was a notable increase in species with moderate scores. During the same period, this site experienced an eight-fold increase in fishing effort and the hydroacoustic data revealed the presence of several trawl-marks in 2022. Similar changes in benthic communities were observed in the Hinder Banks too. Here, the abundance of species with low resistance and recovery potential was significantly lower in locations that were geomorphologically exposed to trawling compared to sheltered ones. Exposed locations had a higher abundance of opportunistic species, with moderate to high scores. The presence of several trawl marks on the seafloor was observed in the exposed locations, corresponding to fishing hotspots identified in the satellite data. Trawling activities marginally impacted richness and total abundance, but negatively altered benthic functional composition. The findings of this study provide scientific evidence of the detrimental impact of bottom-contacting fisheries on conservation priority biotopes and argues against the coexistence of such activities with Marine Protected Areas. The results of our investigation are of interest to environmental managers for the adequate implementation of environmental legislation in the face of rapid and widespread anthropogenic changes.

The aim of the present study was to evaluate whether the variability in the structure of the epiphytic assemblages of leaves and rhizomes of the Mediterranean seagrassPosidonia oceanicadiffered between depths at a large spatial scale. A hierarchical sampling design was used to compare epiphytic assemblages at two different depths (10 and 20 m) in terms of both species composition and abundance and patterns of spatial variability in the Tuscan Archipelago (North Western Mediterranean Sea, Italy). Results showed significant differences in the structure of assemblages on rhizomes and leaves at different depths. These differences were related to species composition and abundance; differences were not significant for total biomass, total percentage cover and percentage cover of animals and algae. Whereas the higher variability was observed among shoots in all the studied systems, patterns of spatial variability at the other spatial scales investigated differed between the two studied depths. Moreover, in the present study, analogous patterns between depths resulted for both the assemblages of leaves and rhizomes, suggesting that factors that change with depth can be responsible for the spatial variability of both the assemblages (leaves and rhizomes), and operate regardless of the microclimatic conditions and the structure of assemblages.

A method for predicting species trajectories tested with trees in barro colorado tropical forest

Because the effects of land‐use change on biodiversity have primarily been examined at or below the regional scale, it remains unclear whether such effects scale up to the macroecological scale (i.e. nationwide or continental scale). In Japan, forests have become more mature since the cessation of most forestry efforts in the 1970s. At a nationwide scale, this forest maturation may lead to reductions in the abundance of species that depend on early successional forests (early successional species) and increases in the abundance of species that depend on mature forests (mature forest species). Japan has met its high demand for wood through imports from South‐east Asia, resulting in deforestation there. Therefore, the abundance of mature forest species that migrate long distances to overwinter in South‐east Asia may decrease. We examined changes in the range sizes of birds in Japan over the past 20 years using the living planet index (LPI). The LPI indicated that the range sizes of early successional species decreased. For mature forest species, the range sizes of long‐distance migrants decreased, whereas those of short‐distance migrants and residents increased. Our predictions were generally supported. Our results indicate that the effects of land‐use change extend to the macroecological scale and that such changes in one country can affect the biodiversity dynamics in other countries. Forest maturation in Japan and concomitant deforestation in South‐east Asia have been caused by internationally coupled socioeconomic processes. Therefore, biodiversity conservation at the macroecological scale must consider the role of land use, and such efforts will require both international and socioeconomic perspectives.

Citizen science is on the rise, with growing numbers of initiatives, participants and increasing interest from the broader scientific community. iNaturalist is an example of a successful citizen science platform that enables users to opportunistically capture and share biodiversity observations. Understanding how data from such opportunistic citizen science platforms compare with and complement data from structured surveys will improve their use in future biodiversity research. We compared the opportunistic fish photographs from iNaturalist to those obtained from structured surveys at eight study reefs in Sydney, Australia over twelve years. iNaturalist recorded 1.2 to 5.5 times more fish species than structured surveys resulting in significantly greater annual species richness at half of the reefs, with the remainder showing no significant difference. iNaturalist likely recorded more species due to having simple methods, which allowed for broad participation with substantially more iNaturalist observation events (e.g., dives) than structured surveys over the same period. These results demonstrate the value of opportunistic citizen science platforms for documenting fish species richness, particularly where access and use of the marine environment is common and communities have the time and resources for expensive recreational activities (i.e., underwater photography). The datasets also recorded different species composition with iNaturalist recording many rare, less abundant, or cryptic species while the structured surveys captured many common and abundant species. These results suggest that integrating data from both opportunistic and structured data sources is likely to have the best outcome for future biodiversity monitoring and conservation activities.

Previous studies show that conservation actions have prevented extinctions, recovered populations, and reduced declining trends in global biodiversity. However, all studies to date have substantially underestimated the difference conservation action makes because they failed to account fully for what would have happened in the absence thereof. We undertook a scenario-based thought experiment to better quantify the effect conservation actions have had on the extinction risk of the world's 235 recognized ungulate species. We did so by comparing species' observed conservation status in 2008 with their estimated status under counterfactual scenarios in which conservation efforts ceased in 1996. We estimated that without conservation at least 148 species would have deteriorated by one International Union for Conservation of Nature (IUCN) Red List category, including 6 species that now would be listed as extinct or extinct in the wild. The overall decline in the conservation status of ungulates would have been nearly 8 times worse than observed. This trend would have been greater still if not for conservation on private lands. While some species have benefited from highly targeted interventions, such as reintroduction, most benefited collaterally from conservation such as habitat protection. We found that the difference conservation action makes to the conservation status of the world's ungulate species is likely to be higher than previously estimated. Increased, and sustained, investment could help achieve further improvements.

Despite widespread acceptance of non-equilibrial dynamics and recruitment limitation in coral reef fish communities, the empirical evidence for these processes is limited to assemblages of site-attached fish species on small, isolated patch reefs. Studies have indicated that the structure of these assemblages is unpredictable in space and time, but the extent to which this result can be extrapolated to vagile fish species and fish communities on connected reef habitats remains unclear. Few quantitative studies have examined spatial and temporal variation in populations of vagile fish species or whole communities on contiguous coral reef. The general aim of this study was to expand the database to the wider fish community and investigate relationships between the structure of fish communities and habitat characteristics on contiguous and patchy reef habitats at Heron and Wistari Reefs, Great Barrier Reef.To obtain baseline data on spatial variability in fish community structure, I examined the distribution and abundance of fish species varying widely in vagility on a number of sites on contiguous and patchy coral reef. Ordination and regression analyses indicated that spatial variation in the structure of fish assemblages on contiguous reef was significantly related to intrinsic habitat characteristics, including the composition and topographical complexity of the substratum, and depth. The structure of fish assemblages on patch reefs was unrelated to intrinsic habitat characteristics but was related to the connectivity of the patch to neighbouring patches. Separate multiple regression models explained significant proportions of spatial variation in the population densities of four site-attached and six vagile species on contiguous reef sites. For patch reef sites, models were significant for six species, five of which were not site- ttached. For site-attached species, models based on patch reef sites explained considerably less variability than models based on contiguous reef sites. For vagile species, there was little difference between models based on contiguous and patch reef sites. These result lend support to the importance of post-settlement migration in facilitating relationships between population density and habitat structure.In addition to examining spatial variation in community structure, I examined the degree of temporal variability in the structure of fish communities resident on contiguous and patch reef sites over a two year period. Ordination analyses indicated that most of the fish assemblages fluctuated randomly through time, although at some sites, communities tended to fluctuate around a stable community configuration. Community variation was highest during periods of high recruitment but recruitment events did not cause persistent shifts in community structure. For site-attached and moderately vagile species, but not highly vagile species, temporal variability in assemblage structure increased as sites became smaller and more isolated.To investigate further the mechanisms underlying spatial variation in the distribution and abundance of fish species, I reanalysed the data obtained from the surveys of contiguous and patch reef sites to examine spatial variation in species richness. Observed pattems were compared to those expected on the basis of two null models which randomly redistributed fish among sites to simulate stochastic non-equilibrial recmitment processes. Observed data differed significantly from the null models, suggesting that species richness was influenced by equilibrial interactions within fish communities (e.g., competition and predation). To compare the relationship between species richness and habitat structure on contiguous reef and patch reefs of different sizes, I used rarefaction and partial regression to remove the effect of sample size variation (number of fish at each site). Only a small amount of spatial variation in species richness was explained by habitat characteristics on contiguous reef sites (30%) and patch reef sites (25%). Much of the unexplained variability was likely due to species interactions within fish communities. ........

Environmental water management seeks to balance competing demands between the water needed to sustain human populations and their economic activities and that required to sustain functioning freshwater ecosystems and the species they support. It must be predicated on an understanding of the environmental, hydrological, and biological factors that determine the distribution and abundance of aquatic species. The Daly River of the wet–dry tropics of northern Australia consists of a perennially flowing main stem and large tributaries, as well as many small to large naturally intermittent tributaries, and associated off‐channel wetlands. Increased groundwater abstraction to support irrigated agriculture during the dry season threatens to reduce dry‐season flows that maintain perenniality and persistence of freshwater fishes. Fish assemblages were surveyed at 55 locations during the dry season over a 2‐year period with the goal of establishing the key landscape‐scale and local‐scale (i.e. habitat) drivers of fish species distribution. Longitudinal (upstream/downstream) and lateral (river/floodplain) gradients in assemblage structure were observed with the latter dependent on the position in the river landscape. Underlying these gradients, stream flow intermittency influenced assemblage composition, species richness, and body size distributions. Natural constraints to dispersal were identified and their influence on assemblage structure was also dependent on position within the catchment. Eight distinct assemblage types were identified, defined by differences in the abundance of species within five groups differing in functional traits describing body size, spawning requirements, and dispersal capacity. These functional groups largely comprised species widely distributed in northern Australia. The results of the study are discussed with reference to the environmental flow needs of the Daly River and other rivers of northern Australia. The findings may also be applied to environmental flow management in savannah rivers elsewhere.

Groundfish surveys carried out between October 1992 and October 1996 were used to describe the demersal assemblages of the northern Benguela along the Namibian coast. Multivariate analyses indicated a clear separation between shelf and slope habitats, which were divided into three and two assemblages respectively. These divisions were distinct, with clear distributional boundaries separating them. Species determining the structure of these divisions and subdivisions and their relative abundances were identified. Depth, bottom temperature, bottom salinity and dissolved oxygen were all significantly correlated with the spatial distribution of the assemblages. Minor changes or shifts in the distribution of assemblages were observed over the study period, although patterns of species associations remained relatively constant.

The spatial and seasonal structures of fish assemblages in a tropical mangrove tidal creek, Tudor, Kenya, were analysed from monthly survey data, extending from October 2007 to July 2008, and covering the north-east (NEM; October–March) and south-east (SEM; April–July) monsoon seasons. A total of 2 118 individuals, representing 84 species belonging to 49 families, were caught. Gerres oyena, Terapon jarbua and Lutjanus fulviflamma were the dominant species in all seasons. There was within-creek seasonal variability in species abundance and diversity. Overall, the mean density (individuals m–2) was higher during the SEM season (0.368; SE 0.078) than the NEM season (0.255; SE 0.041). The NEM season had significantly more species (n 69) than the SEM season (n 63) (χ2 = 317.891, p < 0.0001). Two-way ANOVA indicated the influence of season and habitat on abundance of some species. The abundance of creek-resident species was significantly influenced by site whereas abundance of creekdependent and transient species was influenced by interaction between seasons and stations. Bray-Curtis cluster analysis defined two species assemblages, reflecting differences in temporal and spatial use of the creek by the fish species. Correspondence analysis indicated that seasonal fish assemblages were only distinct at the mouth of the creek with less clear seasonal structure in the upper region of the creek.

To better understand the succession process of vegetation restoration from the active sand dune to the inter-dune lowland, species diversity which refers to species richness and abundance across scales and along the slope were studies in Horqin Sandy Land, China. A 0.25 ha square sampling plot, which sampled on the ecotone, was divided into five grain sizes and equal distance intervals along the slope from the top to the bottom. The results showed that both species abundance and richness increased as the grain sizes increased and along the slope, but the decreasing CV values indicated that species diversity gradually vary from heterogeneity to relatively homogeneity. In conclusion, species abundance and richness showed asynchronous changes and their relationship are more closely across scales than along the slope. Except that, more studies on the biotic and abiotic factors interaction concerning the vegetation patterns of sand dune ecosystems should be conducted. These could not only improve our understanding the mechanisms of vegetation invasion and succession, but also be beneficial for vegetation management and biodiversity conservation in semi-arid sand dune ecosystems.

The presence of piscivorous fish has a significant effect on the structure of fish assemblages. Exotic, piscivorous largemouth bass (Micropterus salmoides) have been introduced to a number of Japanese farm ponds that were originally characterized by a high level of biodiversity. We evaluated the effects of exotic bass on the structure of the fish assemblage following their introduction into the farm ponds. We collected fish and measured environmental conditions in 14 ponds of northeastern Japan. The species richness of pond-dwelling fish assemblages was negatively correlated with the relative abundance of exotic bass. In addition, the relative abundance of lentic cyprinid species (e.g., Rhodeus ocellatus ocellatus, Pseudorasbora parva and Carassius sp.) was negatively correlated with the relative abundance of exotic bass. The abundance of these species was also influenced by environmental factors, including transparency and/or coverage of aquatic vegetation, likely related to their influence on the predatory efficiency of exotic bass. Our results suggest that the structure of fish assemblages in farm ponds with exotic piscivorous fish was influenced by both biotic (i.e., predation) and abiotic factors and that some environmental factors mediate the effects of exotic bass on fish species richness and composition.