French Research Institute for Exploitation of the Sea
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High residual additive genetic variability in a Pacific blue shrimp Litopenaeus stylirostris population after 36 generations of domestication from only 4 estimated founders
No full textSome cultured shrimp populations have been domesticated from a very small number of founders, which likely limits their genetic variability and heightens inbreeding. The population of Pacific blue shrimp Litopenaeus stylirostris in New Caledonia is one such case. It has undergone domestication since 1980 (36 generations at the time of this study) but was based on only four initial founders. Polymorphic SNPs for pedigree assignment and assessment of genetic variability were identified by partial RAD sequencing. The low genetic variability of this domesticated population compared with a wild Mexican population of reference was confirmed with 820 SNP markers.
To estimate genetic parameters, full-sib and half-sib families (n = 148) were bred from 74 dams and 92 sires using a double-sire insemination of each dam with spermatophores from two sires, the first time that this method has been used in shrimp genetics. At 6 months of age (14.5 g), 1200 progenies were then phenotyped for body weight and external color by digital vision, before and after cooking, using the CIE L*a*b* color space international reference system. This allowed 99.4 % of the progenies were to be successfully assigned to parents with 171 SNP markers.
Heritability was high for body weight and color traits before and after cooking (h2 = 0.41–0.59). Correlations between the blue color (b*) of uncooked shrimps and body weight did not differ from zero (rg = −0.23 to −0.11). The blue (b*) value of uncooked shrimps was positively correlated with the red (a*) value of cooked shrimps (rg = 0.48 ± 0.14).
All results are favorable to pursuing a selective breeding program for blue shrimp in New Caledonia using this population despite its limited number of initial founders and more than 36 generations of domestication. Genetic factors potentially contributing to the results are discussed
Petrogenetic processes in alkaline magmatism in the southern Mozambique Channel
No full textWhereas the northern part of the Mozambique Channel, between the eastern coast of Africa and Madagascar, is intensively studied, the southern part remains poorly investigated. The 2014 PAMELA-MOZ01 and 2015 PAMELA-MOZ04 cruises enabled us to collect volcanic rocks from the submarine flanks of the Bassas da India-Europa complex, including Bassas da India atoll, Europa Island, and Jaguar and Hall Banks. Despite significant alteration, probably due to their prolonged stay in seawater and the hydrothermal circulation they underwent, we are able to describe the main petrological and geochemical aspects of these largely unknown lavas. To achieve this, we integrated petrographic and mineralogical observations with geochemical analyses of the dredged rocks, aiming to identify the key aspects of the alteration and to characterize their petrological and geochemical properties.
The volcanism of this region is characterized by strongly silica-undersaturated alkaline magmas. Here, we demonstrate that this volcanism is marked by a bimodal magmatic activity with ultrabasic and basic compositions, and more silica-rich compositions. Using isotopic signatures and trace elements, we suggest that magmas are produced by a low degree of partial melting (1 to 5 %) of a metasomatized mantle at about 80 km depth. These mafic magmas then rise from the source to the surface via several magma storage levels, located at about 25–30 km and 15 km depth, the latter corresponding to the mantle-crust boundary as identified by geophysical methods. Fragments of zoned sanidine phenocrysts within intermediate lavas (olivine-free nephelinite or tephri-phonolite) also suggest the presence of differentiated magma reservoirs. Our observations strongly support frequent magmatic recharges, coupled with magma differentiation through olivine + clinopyroxene crystallization/assimilation, in long-lived magma reservoirs. In many respects, this volcanism has similar characteristics (nature of the source, degree of partial melting, composition of the lavas, age, and spatial distribution) to those of the Miocene to Quaternary volcanic provinces of Madagascar, the northern Mozambique Channel or the East African Rift. We propose that this volcanism might result from regional extension through the Mozambique Channel and the southern part of the East African Rift System, coupled with a thermal erosion of a mantle plume
Deep Argo Improves the Accuracy and Resolution of Ocean Bathymetry
No full textOcean bathymetry plays an instrumental role in stirring ocean circulation and ocean mixing, shaping the transport of ocean heat, freshwater, oxygen, and carbon, influencing the propagation of tides and tsunamis, and controlling the dispersion of sediments, nutrients, and planktonic species. The dearth of direct ocean bathymetry measurements from shipboard echo sounders covering only 26% of the ocean floor calls for supplemental data. Satellites can provide bathymetry estimates in poorly-sampled regions, but intrinsic limitations of satellite measurements limit their ability to resolve features at horizontal scale 77% of data coverage) and higher vertical accuracy of the Deep Argo data set (3.9-4.2 m at 4,000-6,000 m depth). The inclusion of the Deep Argo bathymetry in the general bathymetric chart of the ocean shows 50-200 m range improvement in the accuracy of altimetrically derived predicted depths
Genomics of Neotropical biodiversity indicators: Two butterfly radiations with rampant chromosomal rearrangements and hybridization
No full textA central question in evolutionary biology is what drives the diversification of lineages. Rapid, recent radiations are ideal systems for this question because they still show key morphological and ecological adaptations associated with speciation. While most research on recent radiations focuses on those occurring in insular environments, less attention has been given to continental radiations with complex species interactions. Here, we study the drivers of continental radiations of Melinaea and Mechanitis butterflies (Nymphalidae: Ithomiini), which have rapidly radiated in the continental Neotropics. They are classical models for Amazonian biogeography and color pattern mimicry and have been proposed as biodiversity indicators. We generated reference genomes for five species of each genus and whole-genome resequencing data of most species and subspecies covering a wide geographic range to assess phylogeographic relationships, hybridization patterns, and chromosomal rearrangements. Our data help resolve the classification of these taxonomically challenging butterflies and reveal very high diversification rates. We find rampant evidence of historical hybridization and putative hybrid species in both radiations, which may have facilitated their rapid diversification by enriching the genetic diversity. Moreover, we identified dozens of chromosomal fusions and fissions between congeneric species that have likely expedited reproductive isolation. We conclude that interactions between geography, hybridization and chromosomal rearrangements have contributed to these rapid radiations in the highly diverse Neotropical region. We hypothesize that rapid radiations may be spurred if repeated periods of geographic isolation are combined with lineage-specific rapid accumulation of incompatibilities, followed by secondary contact with some gene exchange
Producing a new in-situ wind speed product for the Southern Ocean based on acoustic meteorology from biologged southern elephant seals
No full textObtaining in-situ wind speed measurements over the Ocean is paramount to i) better calibrate numerical models and satellite imagery and ii) increase our understanding of upper ocean processes such as Mixed Layer Depth (MLD) dynamics and air–sea gas exchanges. For instance, increasing wind speeds deepen the MLD through surface turbulence and mixing. In this study, we evaluate the use of acoustic meteorology as an alternative to conventional reanalysis and scatterometer products by training regression models and Long Short-Term Memory (LSTM) neural networks on passive acoustic data recorded from biologged elephant seals. The study presents the first LSTM fine-tuned on wind speed data products from the China-France Oceanography SATellite (CFOSAT) mission, exhibiting remarkably low errors with an average error over all deployments of 0.86 m/s. Using an innovative validation protocol, by correlating wind speed predictions with co-located MLD measurement, the different models are compared. All models’ wind speed predictions exhibit better correlation coefficients with the MLD than the ERA5 re-analysis wind speed products, underscoring the added value of acoustic meteorology in resolving ocean-atmosphere coupling. This work highlights the potential of passive acoustic monitoring as a robust, scalable, and accurate tool for oceanographic and climate studies
Warming enhances primary production and respiration and changes plankton community structure in an estuarine upwelling system
No full textMarine heatwaves are expected to become more frequent and intense due to global climate change, potentially impacting plankton communities. In the present study, the effects of a simulated short‐term warming event on the structure and functioning of coastal plankton communities were investigated during a mesocosm experiment conducted with water from the Ría de Vigo, a productive estuary strongly influenced by coastal upwelling dynamics from the North‐Western (NW) Iberian Peninsula. A warming event was simulated in triplicate mesocosms by increasing their water temperature at +3°C compared to three other mesocosms, which followed the natural temperature of the Ría. High‐frequency monitoring from sensors immersed in all mesocosms was used to estimate gross primary production (GPP), community respiration (R), phytoplankton growth (μ), and loss (L) rates. Phytoplankton size structure and community composition, photosynthetic efficiency, and inorganic nutrient concentrations were assessed from daily manual sampling of the mesocosms. Warming induced a mismatch between phytoplankton growth and its grazers, as it enhanced μ at the beginning of the experiment, while L only increased after a few days. Warming also significantly enhanced both GPP and R, but the metabolic index (GPP : R ratio) was not significantly affected by warming, as both GPP and R were enhanced to a similar extent. Warming altered the phytoplankton community structure by favoring haptophytes at the expense of diatoms and dinoflagellates. Conducted during phosphorus‐depleted post‐upwelling conditions, this experiment highlights the positive effects of short‐term warming events on the metabolic and trophic functioning of plankton communities from coastal upwelling systems
Mutation of Brain Aromatase Impairs Behavior and Neuroplasticity in Adult Zebrafish
No full textBrain aromatase, an enzyme responsible for the local synthesis of estrogens, plays a key role in regulating behavior and neuroplasticity in mammals. In teleost fish, brain aromatase is encoded by the cyp19a1b gene, which is strongly expressed in radial glial cells; however, the specific functions of this enzyme are currently unknown. To investigate its role, a cyp19a1b‐mutant zebrafish line was generated using gene‐editing techniques. Behavioral, neurogenic, and neurotransmission‐related parameters were assessed in adult male and female zebrafish. Behavioral analysis highlighted significant alterations in mutant zebrafish, including changes in swimming activity, boldness, sociability, and aggression, with a stronger effect in males compared to females. Beyond these behavioral modifications, mutant zebrafish exhibited disrupted cell proliferation patterns, as assessed by PCNA immunofluorescence in key forebrain regions. Specifically, proliferation decreased in the telencephalon and in the caudal hypothalamus of mutant zebrafish while increasing in the olfactory bulbs. The number of dopaminergic and serotonergic neurons, visualized by immunofluorescence, remained unchanged. Similarly, HPLC‐ED quantification of monoamines and their metabolites showed no significant differences between mutant and wild‐type zebrafish. To further explore the impact of the cyp19a1b mutation on gene expression, transcriptomic analysis was performed using BRB‐Seq technology. Gene expression analyses identified several processes affected by the mutation, including cell proliferation, apoptosis, estrogen signaling, neuroplasticity, and behavioral regulation, in a sex‐ and region‐dependent manner. In conclusion, our results demonstrate that several behaviors, including locomotor activity, sociability, aggressiveness, and anxiety, exhibit marked sexual dimorphism. They show that the cyp19a1b mutation affects locomotor activity in a context‐dependent manner, increases boldness, and reduces aggressiveness. In addition, transcriptomic analyses revealed widespread dysregulation of gene expression, which likely contributes to the observed behavioral alterations. Taken together, these findings underscore the crucial role of brain aromatase in the neurobiological regulation of diverse behaviors.imag
Evidence for gas hydrate-filled fractures forming at the sulfate-methane transition zone, Hikurangi subduction margin, New Zealand
No full textUsing high-resolution X-ray computed tomography (X-CT) of sediment cores from International Ocean Discovery Program Expedition 372 offshore New Zealand, we identify a network of near-vertical, low-density structures interpreted as relics of gas hydrate-filled fractures. These fractures occur at shallow depths near the sulfate-methane transition zone (SMTZ), with widths (thickness) ranging from 0.5 to 5 mm and vertical extents between 7 and 60 mm. They are characterized by diffuse boundaries and steep dip angles. In contrast to previously documented hydrate-filled fractures, which are typically larger (centimeter to meter scale) and located deeper within the sediment column, these findings suggest that hydrate fracture formation can initiate at much shallower depths. We propose that these fractures represent early-stage hydrate formation; these fractures may increase in size over time as microbial methane production increases. The formation, dissociation or dissolution of hydrate-filled fractures may alter sediment structure, fluid migration pathways, and microbial community dynamics during early diagenesis. Moreover, the existence of shallow, fracture-hosted gas hydrate could facilitate rapid methane transport to the seafloor if dissociated, with significant implications for climate-sensitive environments such as the Arctic. Similar features identified in other settings support the hypothesis that shallow hydrate-filled fractures may be widespread but remain underreported due to limited X-CT imaging of shallow sediment intervals in scientific drilling. Expanding the application of high-resolution X-CT scanning, particularly across the SMTZ, is crucial to improve detection and understanding of near-seafloor hydrate systems and their potential environmental impacts
Long Term Predictability of Southern Ocean Surface Nutrients Using Explainable Neural Networks
No full textThe Southern Ocean is a region of high surface nutrient content, reflecting an inefficient biological carbon pump. The variability, predictability, and causes of changes in these nutrient levels on interannual to decadal time scales remain unclear. We employ a deep learning approach, specifically a Temporal Convolution Attention Neural Network (TCANN), to conduct multi‐year forecasting of surface based on oceanic physical drivers. The TCANN successfully replicates testing data with a prediction skill extending to at least 4 years with the GFDL‐ESM4‐driven model and 1 year with the observation‐driven model. To benchmark the results, we compare the prediction skill of TCANN with a simple persistence model and two regression methods, a linear regression and a ridge regression. The TCANN model was able to predict variability with a higher skill than persistence and the two regression methods indicating that non‐linearities present in the system become too high to predict inter‐annual variability with traditional regression methods. To enhance the interpretability of the predictions, we explore three explainable AI techniques: occlusion analysis, integrated gradients, and Gradient Shap. The outcomes suggest a crucial role played by salinity processes and buoyancy/potential density fluxes on the prediction of on annual time scales. The deep learning tools' ability to provide skillful forecasts well into the future presents a promising avenue for gaining insights into how the Southern Ocean's surface nutrients respond to climate change based on physical quantities
Vers des approches respectueuses de la santé humaine et des écosystèmes dans les pratiques agricoles.
No full textThe February 6, 2025 roundtable at ONIRIS in Nantes, co-organized by Carrefours de l'Innovation INRAE and ECOPHYTO recherche & innovation, took up and extended the presentation of the effects of plant protection products (PPPs) on human health and ecosystems. PPPs, designed to target pests and diseases, also affect non-target organisms, causing human illnesses (cancers, neurological and respiratory diseases) and ecological imbalances. Solid research, including an INSERM report, has established the degree of reliability of the links between exposure to PPPs and various pathologies, especially among agricultural workers, but also among children exposed in utero. On the environmental front, an INRAE-Ifremer study reveals widespread contamination, with a serious impact on biodiversity (bees, birds, invertebrates) and even the marine environment. The concept of “symbiotoxicity” underlines the disruption of organisms' microbiomes, accentuating their vulnerability. Research is still lacking data on PPP degradation products and their combined effects (cocktail effects). Training programs such as the ‘One Health’ Master's degree aim to train professionals capable of tackling these issues in a systemic way. Since 2020, a compensation fund has been supporting PPP victims, including children exposed before birth. Specialized pediatric consultations are emerging to provide better support for families. All this work unequivocally calls for a rapid and widespread agro-ecological transition, leading to far-reaching changes in farming practices, although at present the choice seems to be more towards a gradual approach and pragmatic actions that can be carried out without upsetting the foundations of the current choice of agriculture.La table ronde du 6 février 2025 à l’ONIRIS de Nantes, co-organisée par les Carrefours de l’Innovation INRAE et ECOPHYTO recherche & innovation, a repris et étendu l’exposé des effets des produits phytopharmaceutiques (PPP) sur la santé humaine et les écosystèmes. Les PPP, conçus pour cibler ravageurs et maladies, affectent aussi des organismes non ciblés, provoquant maladies humaines (cancers, maladies neurologiques, respiratoires) et déséquilibres écologiques. Des recherches solides, dont une expertise de l’INSERM, établissent le degré de fiabilité des liens entre exposition aux PPP et diverses pathologies, surtout chez les travailleurs agricoles, mais aussi chez les enfants exposés in utero. Sur le plan environnemental, une expertise INRAE-Ifremer révèle des contaminations généralisées impactant gravement la biodiversité (abeilles, oiseaux, invertébrés) jusqu’au sein même du milieu marin. Le concept de "symbiotoxicité" vient souligner les perturbations du microbiome des organismes, accentuant leur vulnérabilité. La recherche manque encore de données sur les produits de dégradation des PPP et leurs effets combinés (effets cocktail). Des programmes de formation comme le Master ‘One Health’ visent à former des professionnels capables d’aborder ces enjeux de manière systémique. Un fonds d’indemnisation soutient depuis 2020 les victimes des PPP, y compris les enfants exposés avant la naissance. Des consultations pédiatriques spécialisées émergent pour mieux accompagner les familles. L’ensemble des travaux menés appelle sans équivoque à une transition agroécologique rapide et généralisée devant conduire à des changements profonds dans les pratiques agricoles, bien qu’à l’heure actuelle, le choix semble plutôt s’orienter vers une approche graduelle et des actions pragmatiques que l’on peut conduire sans bouleverser les bases du choix actuel d’agricultur