French Research Institute for Exploitation of the Sea
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The LIFEDEEPER Project : LIving together in the Future: vulnErability of DEEP sea Ecosystems facing potential mineral Resources exploitation
No full textSubmarine canyons, a challenge for the conservation of cold-water coral reefs exposed to global change
No full textParallel Selection in Domesticated Atlantic Salmon from Divergent Founders Including on Whole-Genome Duplication-derived Homeologous Regions
No full textDomestication and artificial selection for desirable traits have driven significant phenotypic changes and left detectable genomic footprints in farmed animals. Since the 1960s, intensive breeding has led to the rapid domestication of Atlantic salmon (Salmo salar), with multiple independent events that make it a valuable model for studying early domestication stages and the parallel evolution of populations of different origins subjected to similar selection pressures. Some aquatic species, including Atlantic salmon, have undergone whole-genome duplication (WGD), raising the possibility that genetic redundancy resulting from WGD has contributed to adaptation in captive environments, as seen in plants. Here, we examined the genomic responses to domestication in Atlantic salmon, focusing on potential signatures of parallel selection, including those associated with WGD. Candidate genomic regions under selection were identified by comparing whole-genome sequences from aquaculture and wild populations across 2 independently domesticated lineages (Western Norway and North America) using a genome-wide scan that combined 3 statistical methods: allele frequencies (FST), site frequency (Tajima's D), and haplotype differentiation (XP-EHH). These analyses revealed shared selective sweeps on identical SNPs in major histocompatibility complex (MHC) genes across aquaculture populations. This suggests that a combination of long-term balancing selection and recent human-induced selection has shaped MHC gene evolution in domesticated salmon. Additionally, we observed selective sweeps on a small number of gene pairs in homeologous regions originating from WGD, offering insights into how historical genome duplication events may intersect with recent selection pressures in aquaculture species
Diving into Diversity: Haslea berepwari (Bacillariophyceae, Naviculaceae), a new species of marine diatom from New Caledonia
No full textThe current article introduces and describes Haslea berepwarisp. nov., a new species of diatom discovered in the vicinity of Boulouparis, New Caledonia. Under light microscopy, H. berepwarisp. nov. strongly resembles Haslea pseudostrearia, but preliminary molecular barcoding conducted using partial 18S and rbcL genes suggested that it was a distinct species. This was confirmed first by scanning electron microscopy which showed the differences in stria densities between both species. A short-reads genome-skimming protocol applied on H. berepwarisp. nov. led us to obtain its complete mitochondrial and plastid genomes. The mitogenome is 36,572 bp in length and as already observed among other species of Haslea spp., the nad6 and nad2 genes are fused within a single open-reading frame. The plastome is 131,897 bp length, and unlike the mitogenome, it is not colinear with those of H. pseudostrearia. The results derived from the sequencing of the plastome allowed to perform a 123-gene multigene maximum likelihood phylogeny that associates H. berepwarisp. nov. to H. pseudostrearia with maximum support at the nodes but also strictly distinguishes them, suggesting a greater genetic distance between these species than what has been previously observed between other marennine-producing species
Analysis, quantification and identification of in situ bioluminescence signals by an innovative sensor (CEMSOR2)
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Diagnosis of near-surface horizontal momentum balance from SWOT altimetry, drifter trajectories and wind reanalysis in the Western Mediterranean Sea.
No full textFrom underwater to drone: A novel multi-scale knowledge distillation approach for coral reef monitoring
No full textDrone-based remote sensing combined with AI-driven methodologies has shown great potential for accurate mapping and monitoring of coral reef ecosystems. This study presents a novel multi-scale approach to coral reef monitoring, integrating fine-scale underwater imagery with medium-scale aerial imagery. Underwater images are captured using an Autonomous Surface Vehicle (ASV), while aerial images are acquired with an aerial drone. A transformer-based deep-learning model is trained on underwater images to detect the presence of 31 classes covering various coral morphotypes, associated fauna, and habitats. For aerial analysis these predictions are refined (some classes are merged, others are retained, while some are removed) resulting in a final set of 12 ecological categories that serve as annotations for training a second model applied to aerial images. The transfer of information across scales is achieved through a weighted footprint method that accounts for partial overlaps between underwater image footprints and aerial image tiles. The results show that the multi-scale methodology successfully extends fine-scale classification to larger reef areas, achieving a high degree of accuracy in predicting coral morphotypes and associated habitats. The method showed a strong alignment between underwater-derived annotations and ground truth data, reflected by an AUC (Area Under the Curve) score of 0.9251. This shows that the integration of underwater and aerial imagery, supported by deep-learning models, can facilitate scalable and accurate reef assessments. This study combines multi-scale imaging and AI to provide scientific information on coral reef monitoring and conservation. Our approach leverages underwater and aerial imagery, aiming for the precision of fine-scale analysis while extending it to cover a broader reef area
A story of Neomicrorbis: a widely distributed bathyal serpulid long hidden in museum collections
No full textNeomicrorbis Rovereto, 1903 is a serpulid taxon well represented in the Cretaceous and Tertiary fossil records and described as the bathyal extant species Neomicrorbis azoricus Zibrowius, 1972. This enigmatic species of uncertain taxonomic affinities exhibits a morphology intermediate between serpulids sensu stricto (Serpulinae and Filograninae) and Spirorbinae. Only recently the phylogenetic placement of these unique serpulids has been clarified, unequivocally positioning them as the sister group to all other Spirorbinae. Despite this advancement, most aspects of their biology, distribution, and even morphology remain largely unexplored. We provide detailed morphological descriptions of specimens from the Azores (type locality) in the Atlantic, as well as from the Indian and the Pacific Oceans, using both long-hidden material in museum collections and recently collected specimens. This study enhances the original description of N. azoricus, which was based on a single, poorly preserved juvenile specimen, by offering a comprehensive overview of the species’ morphology. Our analysis utilizes advanced imaging techniques such as scanning electron microscopy, microCT, and 3D visualization. Contrast-enhanced microCT scanning has proven exceptionally valuable for non-invasive visualization of the worms within their calcareous tubes. This method shows great promise for studying serpulids in natural history collections. Our findings reveal a remarkable morphological consistency across specimens from geographically remote regions, suggesting a wide distribution for the species. However, molecular data on Neomicrorbis are currently limited to recently collected specimens from the Indian Ocean. Further genetic studies are necessary to fully understand the population structure and genetic diversity of Neomicrorbis azoricus across its range
Global and regional sea-surface temperature changes over the Marine Isotopic Stage 9e and Termination IV
No full textThe Marine Isotope Stage (MIS) 9, occurring approximately from 300 to 335 ka, represents an important period for studying the dynamics of Earth's climate. Interest in studying this interglacial period stems from the fact that is associated with the highest atmospheric CO2 concentrations over the last 800 ka (excluding anthropogenic CO2 emissions). Numerous reconstructions of the sea surface temperatures (SST) are available over this time interval, but it is challenging to assess the regional and global patterns of climate variability and to infer temporal sequences of changes from numerous marine sediment records located in different parts of the world and whose chronologies originate from different dating strategies. In this study, we present the first spatio-temporal SST synthesis over the interval 300 to 350 ka, covering this interglacial period and its preceding deglaciation (Termination IV, ~335 to ~350 ka). We include 98 high-resolution SST reconstructions and we establish a common temporal framework between the selected marine records, based on the latest reference ice core chronology (AICC2023). We also homogenize the proxy-calibration strategy by applying a single method for each proxy. Chronological and calibration uncertainties are quantified using Bayesian and Monte Carlo procedures. Finally, through a Monte Carlo approach, we generate global and regional SST stacks relative to Pre-Industrial Era over Termination IV and MIS 9. We highlight significant differences in terms of temporal variability, amplitude, and timing of changes in the SST records across the globe across the studied time interval. While the patterns of SST changes are homogeneous at basin-scale, heterogeneous interglacial SST peaks are observed across ocean basins. The interglacial surface temperature peaks in extra-tropic basins are similar or warmer than the pre-industrial period (PI), while intra-tropic areas appears to be colder relative to PI during glacial optimum. In addition, the timing in interglacial surface temperature peaks differ across the different regions. These regional temperature variations suggest that atmospheric and oceanic dynamics played a greater role than global radiative forcing in shaping the MIS 9 climate. The heterogeneous timing of changes across the different regions contribute to a smoothed global response in terms of both timing and amplitude. Consequently, we find that at a global scale MIS 9e SST was as warm as the pre-industrial period (~ -0.2°C ± 0.3 °C). Converted into surface air temperatures (~ -0.4°C ± 0.6 °C), this estimate agrees within the uncertainty range with previous studies based on a smaller number of records with lower temporal resolution. We also compare our results on MIS 9 and Termination IV with published SST syntheses from more recent interglacial periods (MIS 5e and Holocene) and deglacial periods (Termination I and II). We find that the global deglacial surface air warming during Termination IV is similar in amplitude (~5.3 °C) to that observed during Terminations I and II. Finally, a comparison of deglacial warming rates for these three terminations to the warming trend of the last 60 years emphasizes that the rapidity of modern climate change is unprecedented within the context of these past deglaciations
What can go wrong for future Senegalese sole recruitment? Temperature and food availability as important drivers of early-life-history traits
No full textWater temperature and prey availability are key factors influencing the successful recruitment of early life stages in fish. Understanding how these variables modulate larval growth and survival is essential for modelling larval dynamics. In this study we reared S. senegalensis larvae under controlled laboratory conditions to assess the effects of temperature and feeding frequency on larval development. Three temperatures (17, 20, and 23˚C) and three feeding frequencies (Ff 2.5 fed 2.5 times per week, Ff 4 four times per week, and Ff 6 six times per week) were tested from 12 to 32 days post-hatch (dph) in both individual and group housing systems. Survival, growth, and metamorphosis progress were monitored, and the expression of six genes related to nutrition (tryp1a and apoA4Aa2), cellular stress (hsp90aa and hsp70), endocrine regulation (tgb), and muscle development (myf4) were monitored on S3 and S4 metamorphic larvae. The feeding frequency appeared as the primary driver influencing all investigated traits, while temperature played a less pronounced effect. These data demonstrate the critical role of energy provision in regulating growth, development, and survival, which interacts with temperature, particularly under conditions where metabolic and energy demands cannot be fully fulfilled. Additionally, the Senegalese sole larvae exhibited compensatory genomic adaptive responses to efficiently mobilize nutrients from the gut and adjust the thyroid axis and cellular responses to support metamorphosis transformation and metabolism when food availability was limited or when temperature approached physiological thresholds