French Research Institute for Exploitation of the Sea
ArchiMer - Institutional Archive of IfremerNot a member yet
27944 research outputs found
Sort by
Development of a novel microhaplotype panel for steelhead/rainbow trout (Oncorhynchus mykiss) and application for phylogenetic analysis in California
No full textThe rapid advance of high-throughput sequencing has prompted a transition in wildlife and fisheries genetics from using microsatellites toward markers that are more amenable to genotyping by sequencing. Microhaplotypes are novel multi-allelic genetic markers that utilize a high-throughput genomic amplicon sequencing approach to genotype large numbers of individuals for parentage and kinship analysis and population genetic studies, including applications in monitoring and fisheries management. We describe the development of a panel of microhaplotypes for Oncorhynchus mykiss, a species of high cultural and economic importance both in its native range in the North American and the Kamchatka Peninsula of northeast Asia, and globally through introductions for aquaculture and due to its reputation as a prized sport fish among recreational fishers. The panel includes 124 loci presumed to be neutral, a marker for the sex determination locus (SdY), and 10 loci targeting previously identified adaptive genomic variants associated with important life-history traits in this species. We demonstrate that this panel provides high resolution for phylogeographic and other genetic analysis and provide an initial standardized reference population genetic baseline of California O. mykiss
Product User Manual for Sea Level Reprocessed In Situ Product INSITU_GLO_PHY_SSH_DISCRETE_MY_013_053
No full textThis document is the user manual of the Sea Level REProcessed In Situ product, INSITU_GLO_PHY_SSH_DISCRETE_MY_013_053, distributed by the Copernicus Marine Service In Situ Thematic Assembly Centre (In Situ TAC). It contains a description of the product, including how it is built, datasets, available data access services, and instructions for use of files and services. The Sea Level REP product is a global product that provides the best available version of in-situ historical sea level observations, reprocessed and validated in delayed mode at centralized level by the Production Centre. This is required for assessment of operational models and reanalysis, and for use by the research community. It integrates the in-situ sea level observations, mainly from tide gauges providing coastal sea level, aggregated from the Regional EuroGOOS consortium (Arctic-ROOS, BOOS, NOOS, IBIROOS, MONGOOS and Black Sea GOOS), National Data Centers (NODC’s), Hydrographic Offices or Metoffices, the Global Sea Level Observing System (GLOSS) and EMODnet Physics. The Copernicus Marine Service is not contributing to the maintenance and setting up of the observing systems it uses. The complete list of variables distributed by the In Situ TAC can be found in the Copernicus Marine In Situ TAC physical parameters list (https://doi.org/10.13155/53381). The product is updated twice a year after a delayed mode quality control and processing which includes visualization, computation of non-tidal residuals and hourly data, and check of datum stability by means of neighbour test or buddy-checking. Details are provided in the Quality Information Document (QuID) CMEMS-INS-QUID-013_053. Sea level data are available at the dedicated directory for sea level INSITU_GLO_PHY_SSH_DISCRETE_MY_013_053 of Copernicus Marine Service Dissemination System. It includes three different datasets: the first one contains the diverse original time sampling data available at the In Situ TAC NRT, which vary from 1-min to 1 hour, with updated quality control flags; a second one contains the homogeneous hourly data timeseries, validated and filtered from higher frequency observations, when available; and the third one contains an hourly dataset including astronomical tide and surge/non-tidal residuals for the IBI region. More detailed information can be obtained from the Copernicus Marine Service Copernicus Marine Service web page (https://marine.copernicus.eu/), and the In Situ TAC web page (http://www.marineinsitu.eu/). Information on operational issues on products and services can be found on our User Notification Service. If you have any questions, please contact us
Mesopelagic Fish Traits: Functions and Trade‐Offs
No full textFishes inhabiting the mesopelagic zone of the world's oceans are estimated to account for the majority of the world's fish biomass. They have recently attracted new attention because they are part of the biological carbon pump and have been reconsidered as a contribution to food security. Hence, there is an urgent need to understand how environmental conditions and species interactions shape their assemblages, and how they contribute to the functioning of marine ecosystems. Trait‐based approaches are valuable for addressing these types of questions. However, the biology and ecology of mesopelagic fishes are understudied compared to fishes in shallow and epipelagic waters. Here, we synthesise existing knowledge of traits of mesopelagic fishes and relate them to their role in survival, feeding and growth and reproduction, the key functions that contribute to fitness. Vertical migrations, specialised vision and the use of bioluminescence are among the most striking adaptations to the conditions in the mesopelagic realm. Many traits are interrelated as a result of trade‐offs, which may help to understand selection pressures. While morphological traits are straightforward to observe, major knowledge gaps exist for traits that require frequent sampling, assessment under experimental conditions or age determination. The unique adaptations of mesopelagic fishes need to be included in management strategies as well as fundamental research of the habitat
The epibiotic community associated to the European flat oyster: a function of the state of development of the reef
No full textWhen healthy, Ostrea edulis populations are capable of creating remarkable biogenic reefs, providing a unique habitat for marine biodiversity. At present, the biotic assemblages associated with flat oysters remain poorly defined. This study aims to analyze biodiversity associated with the reef's development stage by focusing on its epibiotic community. The studied oyster population is an old remnant bed located in the Bay of Brest, which has been undergoing restoration for 5 years. The epibiotic communities (>500 μm) of scattered individual living (n = 10) and dead (n = 9) oysters, as well as of aggregates from the ground (n = 10) and from a restored reef (n = 3) were compared. 137 species associated with oysters were found, among which 22 were specific to individual oysters and 55 to aggregates and reefs. Although reef samples formed a distinct group in the SIMPER analysis, Shannon's (between 2.25 and 2.52) and Simpson's (between 0.84 and 0.86) diversity indices remained constant for each reef development stage. Piélou's indices (between 0.71 and 0.80) were significantly lower for aggregates displaying a less evenly distributed community. Mean abundance and species richness per sample were higher for aggregated structures. However, when standardized to abundance per centimeter square of shell surface, both parameters were significantly higher for individual oysters. Therefore, while reefs may support a higher species richness at a larger spatial scale, at a smaller scale, single oysters have a higher species richness per unit area of shell. Seemingly, despite the poor state of their remnant populations, flat oysters are still hosting important macrofaunal biodiversity
Variability of the kinetic energy in seasonally ice-covered oceans.
No full textThe seasonality of Arctic sea ice cover significantly influences heat, salt, buoyancy fluxes, ocean-ice stresses, and the potential and kinetic energy stored in the ocean mixed layer. This study examines the seasonal variability of oceanic scales and cross-scale flux of kinetic energy in the seasonally ice-covered Arctic, using a high-resolution, idealized coupled ocean-sea ice model. Our simulations demonstrate pronounced seasonality in the scales of oceanic motion within the mixed layer, governed by distinct mechanisms during summer and winter. In summer, an inverse energy cascade sustains mesoscale dynamics and enhances kinetic energy. In winter, ice-induced dissipation suppresses kinetic energy and mesoscale, allowing only the persistence of submesoscale processes. These results underscore the critical role of sea ice in modulating the seasonal dynamics of oceanic motion and their dominant scales, a behavior markedly different from that in the open ocean. Thus, understanding these coupled processes is essential for improving predictions of the ocean's energy evolution as the Arctic transitions toward a summer ice-free regime
Breaking onset and breaking strength of focused wave packets: Linear prediction model and nonlinear numerical simulations
No full textThe possibility of predicting the occurrence of wave breaking and the intensity of the breaking events using linear wave models is investigated. For this purpose, a new linear breaking onset criterion is proposed, based on the definition of a linear-equivalent wave, which has the same energy and impulse as the associated nonlinear wave. The strength of breaking is characterized by the parameter introduced by Derakhtiet al. (2018) and we derive an empirical law to estimate the breaking strength from the linear-equivalent wave model. The predictive ability of this criterion is assessed through comparisons with results of fully nonlinear potential flow simulations, for focused wave packets of various characteristics. For the considered configurations, the proposed approach is able to predict the onset and strength of breaking with good accuracy
Otolith stable isotopes highlight the importance of local nursery areas as the origin of recruits to yellowfin tuna (Thunnus albacares) fisheries in the western Indian Ocean
No full textYellowfin tuna (Thunnus albacares) supports the second largest tuna fishery worldwide, and in the Indian Ocean, it is overfished and subject to overfishing. This situation presents a significant challenge to fisheries management, requiring effective measures to rebuild and then maintain the stock at sustainable levels. A single stock of yellowfin is currently assumed by the Indian Ocean Tuna Commission (IOTC) for stock assessments in the Indian Ocean. However, the relative contribution of different spawning components to the total catches, and the degree of mixing rates of yellowfin tuna in the Indian Ocean by individuals from different production zones, are still unknown. This study uses otolith core oxygen and carbon stable isotope composition (δ18O and δ13C) of young-of-the-year yellowfin tuna from nursery areas located in the western (FAO Area 51) and eastern (FAO area 57) Indian Ocean, either side of 80 ºE, to establish a reference baseline of isotopic signatures. Then, a mixed population program (HISEA) and Random Forest (RF) assignment approaches were used to predict the most likely origin (west or east) of sub-adult and adult yellowfin tuna captured from four fishery areas of the western Indian Ocean (offshore Pakistan, Seychelles, Reunion, and South Africa) by comparing their otolith core values to that of the baseline. Both approaches show that the western Indian Ocean fisheries are mainly composed of west origin fish (> 95 %). We also found some individuals with an otolith isotopic signature that was not characteristic of either of the samples available in the baseline. We simulated an alternative baseline group formed by individuals with mean and standard deviation δ13C and δ18O values above the maximum ranges of the original baseline. We then used RF to infer again the most likely origin of fish in the mixed sample considering 3 possible sources (west, east, alternative). About one third of the samples were assigned to the alternative group, possibly indicating that they differ in geographical or temporal terms with the origins represented in the original baseline. Findings of otolith stable isotope composition of yellowfin tuna in the western Indian Ocean can provide a more comprehensive understanding of the species’ spatial structure and connectivity beyond the current assumption of an ocean basin single stock
A multi-tagged SAR ocean image dataset identifying atmospheric boundary layer structure in winter tradewind conditions
No full textA dataset of multi-tagged sea surface roughness synthetic aperture radar (SAR) satellite images was established near Barbados from January to June 2016 to 2019. It is an advancement of the Sentinel-1 Wave Mode TenGeoP-SARwv (a labelled SAR imagery dataset of 10 geophysical phenomena from Sentinel-1 wave mode) dataset that targets SAR marine atmospheric boundary layer (MABL) coherent structures. Twelve tags define roll vortices, convective cells, mixed rolls and convective cells, fronts, rain cells, cold pools and low winds. Examples are provided for each signature. The final dataset is comprised of 2100 Sentinel-1 wave mode SAR images acquired at 36 incidence angle over an 8° × 8°region centered at 51° W, 15° N. Each image is tagged with one or multiple phenomena by five experts. This strategy extends the TenGeoP-SARwv by identifying coexisting phenomena within a single SAR image and by the addition of mixed roll/cell states and cold pools. The dataset includes PNG-formatted SAR image files along with two text files containing the file name, the central latitude/longitude, expert tags for each image, and all dataset metadata. There is a high degree of consensus among expert tags. The dataset complements existing hand-labelled ocean SAR image datasets and offers the potential for new deep-learning SAR image classification model developments. Future use is also expected to yield new insights into the tradewind MABL processes such as structure transitions and their relation to the stratification
PRDM9 drives the location and rapid evolution of recombination hotspots in salmonid fish
No full textIn many eukaryotes, meiotic recombination occurs preferentially at discrete sites, called recombination hotspots. In various lineages, recombination hotspots are located in regions with promoter-like features and are evolutionarily stable. Conversely, in some mammals, hotspots are driven by PRDM9 that targets recombination away from promoters. Paradoxically, PRDM9 induces the self-destruction of its targets and this triggers an ultra-fast evolution of mammalian hotspots. PRDM9 is ancestral to all animals, suggesting a critical importance for the meiotic program, but has been lost in many lineages with surprisingly little effect on meiosis success. However, it is unclear whether the function of PRDM9 described in mammals is shared by other species. To investigate this, we analyzed the recombination landscape of several salmonids, the genome of which harbors one full-length PRDM9 and several truncated paralogs. We identified recombination initiation sites in Oncorhynchus mykiss by mapping meiotic DNA double-strand breaks (DSBs). We found that DSBs clustered at hotspots positioned away from promoters, enriched for the H3K4me3 and H3K36me3 and the location of which depended on the genotype of full-length Prdm9. We observed a high level of polymorphism in the zinc finger domain of full-length Prdm9, indicating diversification driven by positive selection. Moreover, population-scaled recombination maps in O. mykiss, Oncorhynchus kisutch and Salmo salar revealed a rapid turnover of recombination hotspots caused by PRDM9 target motif erosion. Our results imply that PRDM9 function is conserved across vertebrates and that the peculiar evolutionary runaway caused by PRDM9 has been active for several hundred million years
