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- A global dataset of demosponge distribution recordsPublication . Vafeiadou, Ariadni; Fragkopoulou, Eliza; Assis, JorgeBiodiversity information in the form of species occurrence records is key for monitoring and predicting current and fu- ture biodiversity patterns, as well as for guiding conserva- tion and management strategies. However, the reliability and accuracy of this information are frequently undermined by taxonomic and spatial errors. Additionally, biodiversity in- formation facilities often share data in diverse incompatible formats, precluding seamless integration and interoperabil- ity. We provide a comprehensive quality-controlled dataset of occurrence records of the Class Demospongiae, which comprises 81% of the entire Porifera phylum. Demosponges are ecologically significant as they structure rich habitats and play a key role in nutrient cycling within marine ben- thic communities. The dataset aggregates occurrence records from multiple sources, employs dereplication and taxonomic curation techniques, and is flagged for potentially incorrect records based on expert knowledge regarding each species’ bathymetric and geographic distributions. It yields 417,626 records of 1,816 accepted demosponge species (of which 321,660 records of 1,495 species are flagged as potentially correct), which are provided under the FAIR principle of Find- ability, Accessibility, Interoperability and Reusability in the Darwin Core Standard. This dataset constitutes the most up- to-date baseline for studying demosponge diversity at the global scale, enabling researchers to examine biodiversity patterns (e.g., species richness and endemicity), and forecast
- Genetic diversity increases with depth in red gorgonian populations of the Mediterranean Sea and the Atlantic OceanPublication . Pilczynska, Joanna; Cocito, Silvia; Boavida, Joana; Serrao, Ester; Assis, J.; Fragkopoulou, Eliza; Queiroga, HenriqueIn the ocean, the variability of environmental conditions found along depth gradients exposes populations to contrasting levels of perturbation, which can be reflected in the overall patterns of species genetic diversity. At shallow sites, resource availability may structure large, persistent and well-connected populations with higher levels of diversity. In contrast, the more extreme conditions, such as thermal stress during heat waves, can lead to population bottlenecks and genetic erosion, inverting the natural expectation. Here we examine how genetic diversity varies along depth for a long-lived, important ecosystem-structuring species, the red gorgonian, Paramuricea clavata.
- Artificial intelligence convolutional neural networks map giant kelp forests from satellite imageryPublication . Marquez, L.; Fragkopoulou, Eliza; Cavanaugh, K. C.; Houskeeper, H. F.; Assis, J.Climate change is producing shifts in the distribution and abundance of marine species. Such is the case of kelp forests, important marine ecosystem-structuring species whose distributional range limits have been shifting worldwide. Synthesizing long-term time series of kelp forest observations is therefore vital for understanding the drivers shaping ecosystem dynamics and for predicting responses to ongoing and future climate changes. Traditional methods of mapping kelp from satellite imagery are time-consuming and expensive, as they require high amount of human effort for image processing and algorithm optimization. Here we propose the use of mask region-based convolutional neural networks (Mask R-CNN) to automatically assimilate data from open-source satellite imagery (Landsat Thematic Mapper) and detect kelp forest canopy cover. The analyses focused on the giant kelp Macrocystis pyrifera along the shorelines of southern California and Baja California in the northeastern Pacific. Model hyper-parameterization was tuned through cross-validation procedures testing the effect of data augmentation, and different learning rates and anchor sizes. The optimal model detected kelp forests with high performance and low levels of overprediction (Jaccard's index: 0.87 +/- 0.07; Dice index: 0.93 +/- 0.04; over prediction: 0.06) and allowed reconstructing a time series of 32 years in Baja California (Mexico), a region known for its high variability in kelp owing to El Nino events. The proposed framework based on Mask R-CNN now joins the list of cost-efficient tools for long-term marine ecological monitoring, facilitating well-informed biodiversity conservation, management and decision making.
- A dataset of cold-water coral distribution recordsPublication . Balogh, Viktória; Fragkopoulou, Eliza; Serrao, Ester; Assis, JorgeSpecies distribution data are key for monitoring present and future biodiversity patterns and informing conservation and management strategies. Large biodiversity information facilities often contain spatial and taxonomic errors that reduce the quality of the provided data. Moreover, datasets are frequently shared in varying formats, inhibiting proper integration and interoperability. Here, we provide a qualitycontrolled dataset of the diversity and distribution of coldwater corals, which provide key ecosystem services and are considered vulnerable to human activities and climate change effects. We use the common term cold-water corals to refer to species of the orders Alcyonacea, Antipatharia, Pennatulacea, Scleractinia, Zoantharia of the subphylum Anthozoa, and order Anthoathecata of the class Hydrozoa. Distribution records were collated from multiple sources, standardized using the Darwin Core Standard, dereplicated, taxonomically corrected and flagged for potential vertical and geographic distribution errors based on peer-reviewed published literature and expert consulting. This resulted in 817,559 quality-controlled records of 1,170 accepted species of cold-water corals, openly available under the FAIR principle of Findability, Accessibility, Interoperability and Reusability of data. The dataset represents the most updated baseline for the global cold-water coral diversity, and it can be used by the broad scientific community to provide insights into biodiversity patterns and their drivers, identify regions of high biodiversity and endemicity, and project potential re-distribution under future climate change. It can also be used by managers and stakeholders to guide biodiversity conser-vation and prioritization actions against biodiversity loss. (c) 2023 The Authors. Published by Elsevier Inc. This is an open access article under the CC BY license ( http://creativecommons.org/licenses/by/4.0/ )
- Weak biodiversity connectivity in the European network of no-take marine protected areasPublication . Assis, J.; Fragkopoulou, Eliza; Serrão, Ester A.; e Costa, Horta; Gandra, Miguel; Abecasis, DavidThe need for international cooperation in marine resource management and conservation has been reflected in the increasing number of agreements aiming for effective and well-connected networks of Marine Protected Areas (MPAs). However, the extent to which individual MPAs are connected remains mostly unknown. Here, we use a biophysical model tuned with empirical data on species dispersal ecology to predict connectivity of a vast spectrum of biodiversity in the European network of marine reserves (i.e., no-take MPAs). Our results highlight the correlation between empirical propagule duration data and connectivity potential and show weak network connectivity and strong isolation for major ecological groups, resulting from the lack of direct connectivity corridors between reserves over vast regions. The particularly high isolation predicted for ecosystemstructuring species (e.g., corals, sponges, macroalgae and seagrass) might potentially undermine biodiversity conservation efforts if local retention is insufficient and unmanaged populations are at risk. Isolation might also be problematic for populations' persistence in the light of climate change and expected species range shifts. Our findings provide novel insights for management directives, highlighting the location of regions requiring additional marine reserves to function as stepping-stone connectivity corridors. (C) 2021 Elsevier B.V. All rights reserved.
- Bottom trawling threatens future climate refugia of rhodoliths globallyPublication . Fragkopoulou, Eliza; Serrao, Ester; Horta, Paulo A.; Koerich, Gabrielle; Assis, J.Climate driven range shifts are driving the redistribution of marine species and threatening the functioning and stability of marine ecosystems. For species that are the structural basis of marine ecosystems, such effects can be magnified into drastic loss of ecosystem functioning and resilience. Rhodoliths are unattached calcareous red algae that provide key complex three-dimensional habitats for highly diverse biological communities. These globally distributed biodiversity hotspots are increasingly threatened by ongoing environmental changes, mainly ocean acidification and warming, with wide negative impacts anticipated in the years to come. These are superimposed upon major local stressors caused by direct destructive impacts, such as bottom trawling, which act synergistically in the deterioration of the rhodolith ecosystem health and function. Anticipating the potential impacts of future environmental changes on the rhodolith biome may inform timely mitigation strategies integrating local effects of bottom trawling over vulnerable areas at global scales. This study aimed to identify future climate refugia, as regions where persistence is predicted under contrasting climate scenarios, and to analyze their trawling threat levels. This was approached by developing species distribution models with ecologically relevant environmental predictors, combined with the development of a global bottom trawling intensity index to identify heavily fished regions overlaying rhodoliths. Our results revealed the importance of light, thermal stress and pH driving the global distribution of rhodoliths. Future projections showed poleward expansions and contractions of suitable habitats at lower latitudes, structuring cryptic depth refugia, particularly evident under the more severe warming scenario RCP 8.5. Our results suggest that if management and conservation measures are not taken, bottom trawling may directly threaten the persistence of key rhodolith refugia. Since rhodoliths have slow growth rates, high sensitivity and ecological importance, understanding how their current and future distribution might be susceptible to bottom trawling pressure, may contribute to determine the fate of both the species and their associated communities.
- Marine biodiversity exposed to prolonged and intense subsurface heatwavesPublication . Fragkopoulou, Eliza; Sen Gupta, Alex; Costello, Mark John; Wernberg, Thomas; Araújo, Miguel B.; Serrao, Ester; De Clerck, Olivier; Assis, JorgeMarine heatwaves (MHWs) are becoming increasingly common, with devastating ecosystem impacts. However, MHW understanding has almost exclusively relied on sea surface temperature with limited knowledge about their subsurface characteristics. Here we estimate global MHWs from the surface to 2,000 m depth, covering the period 1993-2019, and explore biodiversity exposure to their effects. We find that MHWs are typically more intense in the subsurface at 50-200 m and their duration increases up to twofold with depth, although with large spatial variability linked to different oceanographic conditions. Cumulative intensity (a thermal stress proxy) was highest in the upper 250 m, exposing subsurface biodiversity to MHW effects. This can be particularly concerning for up to 22% of the ocean, where high cumulative intensity overlapped the warm range edge of species distributions, thus being more sensitive to thermal stress. Subsurface MHWs can hence drive biodiversity patterns, with consequent effects on ecological interactions and ecosystem processes. The authors estimate the intensity, duration and number of global marine heatwaves from 1993 to 2019, from the surface to 2,000 m. They show generally higher intensity of marine heatwaves at 50-200 m, but increased duration with depth, and predict ocean regions of higher biodiversity exposure.
- Bio‐ORACLE v3.0. pushing marine data layers to the CMIP6 earth system models of climate change researchPublication . Assis, Jorge; Fernández Bejarano, Salvador Jesús; Salazar, Vinícius W.; Schepers, Lennert; Gouvêa, Lidiane; Fragkopoulou, Eliza; Leclercq, Frederic; Vanhoorne, Bart; Tyberghein, Lennert; Serrao, Ester; Verbruggen, Heroen; De Clerck, OlivierMotivation: Impacts of climate change on marine biodiversity are often projected with species distribution modelling using standardized data layers representing physical, chemical and biological conditions of the global ocean. Yet, the available data layers (1) have not been updated to incorporate data of the Sixth Phase of the Coupled Model Intercomparison Project (CMIP6), which comprise the Shared Socioeconomic Pathway (SSP) scenarios; (2) consider a limited number of Earth System Models (ESMs), and (3) miss important variables expected to influence future biodiversity distributions. These limitations might undermine biodiversity impact assessments, by failing to integrate them within the context of the most up-to-date climate change projections, raising the uncertainty in estimates and misinterpreting the exposure of biodiversity to extreme conditions. Here, we provide a significant update of Bio-ORACLE, extending biologically relevant data layers from present-day conditions to the end of the 21st century Shared Socioeconomic Pathway scenarios based on a multi-model ensemble with data from CMIP6. Alongside, we provide R and Python packages for seamless integration in modelling workflows. The data layers aim to enhance the understanding of the potential impacts of climate change on biodiversity and to support well-informed research, conservation and management. Main Types of Variable Contained: Surface and benthic layers for, chlorophyll-a, diffuse attenuation coefficient, dissolved iron, dissolved oxygen, nitrate, ocean temperature, pH, phosphate, photosynthetic active radiation, total phytoplankton, total cloud fraction, salinity, silicate, sea-water direction, sea-water velocity, topographic slope, topographic aspect, terrain ruggedness index, topographic position index and bathymetry, and surface layers for air temperature, mixed layer depth, sea-ice cover and sea-ice thickness. Spatial Location and Grain: Global at 0.05 degrees resolution. Time Period and GrainDecadal from present-day to the end of the 21st century (2000-2100). Major Taxa and Level of Measurement: Marine biodiversity associated with surface and epibenthic habitats. Software Format: A package of functions developed for Python and R software.
- Phenotypic plasticity in sargassum forests may not counteract projected biomass losses along a broad latitudinal gradientPublication . Gouvêa, Lidiane; Horta, Paulo A.; Fragkopoulou, Eliza; Gurgel, Carlos F. D.; Peres, Leticia M. C.; Bastos, Eduardo; Ramlov, Fernanda; Burle, Giulia; Koerich, Gabrielle; Martins, Cintia D. L.; Serrao, Ester; Assis, JorgePhenotypic plasticity and local adaptation can adjust individual responses to environmental changes across species' ranges. Studies addressing the implications of such traits have been underrepresented in the marine environment. Sargassum cymosum represents an ideal model to test phenotypic plasticity, as populations along the southwestern Atlantic Ocean display a sharp decrease in abundance toward distributional range limits. We (1) characterized the macroecological environment of S. cymosum across a latitudinal gradient, (2) evaluated potential differences in ecophysiological adjustments (biomass, photosynthetic pigments, phenolic compounds, total soluble sugars and proteins, and carbon-nitrogen-CN-content), and (3) tested for differences in thermal tolerance based on time series analyses produced from the present to contrasting representative concentration pathways scenarios (RCP) of future climate changes. Our results showed distinct macroecological environments, corresponding to tropical and warm temperate conditions, driving biomass and ecophysiological adjustments of S. cymosum. Populations from the two environments displayed contrasting thermal tolerances, with tropical individuals better coping with thermal stress when compared to more temperate ones (lethal temperatures of 33 degrees C vs. 30 degrees C); yet both populations lose biomass in response to increasing thermal stress while increasing secondary metabolites (for example, carotenoids and phenolic compounds) and decrease chlorophyll's content, Fv/Fm, total soluble sugars concentration and CN ratio, owing to oxidative stress. Despite evidence for phenotypic plasticity, significant future losses might occur in both tropical and warm temperate populations, particularly under the no mitigation RCP scenario, also known as the business as usual (that is, 8.5). In this context, broad compliance with the Paris Agreement might counteract projected impacts of climate change, safeguarding Sargassum forests in the years to come.
- Major expansion of marine forests in a warmer ArcticPublication . Assis, Jorge; Serrao, Ester; Duarte, Carlos M.; Fragkopoulou, Eliza; Krause-Jensen, DorteAccelerating warming and associated loss of sea ice are expected to promote the expansion of coastal marine forests (macrophytes) along the massive Arctic coastlines. Yet, this region has received much less attention compared to other global oceans. The available future projections of Arctic macrophytes are still limited to few species and regions, and mostly focused at lower latitude ranges, thus precluding well-informed IPCC impact assessments, conservation and management. Here we aim to quantify potential distributional changes of Arctic intertidal and subtidal brown macroalgae and eelgrass by the year 2100, relative to present. We estimate habitat suitability by means of species distribution modeling, considering changes in seawater temperature, salinity, nutrients and sea ice cover under two greenhouse gas emission scenarios, one consistent with the Paris Agreement (RCP 2.6) and the other representing limited mitigation strategies (RCP 8.5). As data on substrate conditions do not exist, the models were restricted to the depth range supporting Arctic macrophytes (down to 5 m for eelgrass and 30 m for brown macroalgae). Models projected major expansions of Arctic macrophytes between 69,940 and 123,360 km2, depending on the climate scenario, with polar distribution limits shifting northwards by up to 1.5 latitude degrees at 21.81 km per decade. Such expansions in response to changing climate will likely elicit major changes in biodiversity and ecosystem functions in the future Arctic. Expansions are, however, less intense than those already realized over the past century, indicating an overall slowing down despite accelerated warming as habitats become increasingly occupied..