While acquiring age information is crucial for efficient stock management and biodiversity conservation, traditional aging methods fail to offer a universal, non‐invasive, and precise way of estimating a wild animal's age. DNA methylation from tissue DNA (tDNA) was recently proposed as a method to overcome these issues and showed more accurate results than telomere‐length‐based age assessments. Here, we used environmental DNA (eDNA) for the first time as a template for age estimation, focusing on the larval phase (10–24 days post‐hatch) of cultured Dicentrarchus labrax (seabass), a species of major economic and conservation interest. Using third‐generation sequencing, we were able to directly detect various modification types (e.g., cytosine and adenosine methylation in all contexts) across the whole genome using amplification‐free nanopore sequencing. However, aging sites were only present in the mitogenome, which could be a specific feature of eDNA methylation or the consequence of better DNA protection within mitochondria. By considering qualitative and quantitative information about aging sites according to an objective model selection framework, our epigenetic clock reached a cross‐validated accuracy of 2.6 days (Median Absolute Error). Such performances are higher than those of previous clocks, notably for adult seabass even when scaling MAE to the age range, which could be linked to a more dynamic epigenome during early life stages. Overall, our pilot study proposes new methods to determine the potential of eDNA for simultaneous age and biodiversity assessments, although robust validation of our preliminary results along with methodological developments are needed before field applications can be envisaged.

Madagascar harbors a rich marine biodiversity, yet detailed knowledge of its fish species remains limited. Of the 1689 species listed in 2018, only 22% had accessible cytochrome oxidase I (COI) sequences in public databases. In response to growing pressure on fishery resources, this study aims to strengthen biodiversity monitoring tools. Its objectives were to enrich the COI database for Malagasy marine fishes, create the first 12S reference library, and evaluate the taxonomic resolution of different 12S metabarcodes for eDNA analysis, namely MiFish, Teleo1, AcMDB, Ac12S, and 12SF1/R1. An integrated approach combining morphological, molecular, and phylogenetic analyses was applied for specimen identification of fish captured using various types of fishing gear in Toliara and Ranobe Bays from 2018 to 2023. The Malagasy COI database now includes 2146 sequences grouped into 502 Barcode Index Numbers (BINs) from 82 families, with 14 BINs newly added to BOLD (The Barcode of Life Data Systems), and 133 cryptic species. The 12S library comprises 524 sequences representing 446 species from 78 families. Together, the genetic datasets cover 514 species from 84 families, with the most diverse being Labridae, Apogonidae, Gobiidae, Pomacentridae, and Carangidae. However, the two markers show variable taxonomic resolution: 67 species belonging to 35 families were represented solely in the COI dataset, while 10 species from nine families were identified exclusively in the 12S dataset. For 319 species with complete 12S gene sequences associated with COI BINs (Barcode Index Numbers), 12S primer sets were used to evaluate the taxonomic resolution of five 12S metabarcodes. The MiFish marker proved to be the most effective, with an optimal similarity threshold of 98.5%. This study represents a major step forward in documenting and monitoring Madagascar’s marine biodiversity and provides a valuable genetic reference for future environmental DNA (eDNA) applications.

Even though environmental DNA metabarcoding is revolutionizing biomonitoring, many critical steps remain unstandardized, leading to arbitrary choices, particularly regarding the selection of metabarcode, clustering method and similarity threshold, among others. Additionally, these studies were hindered by biases resulting from the presence of mislabeled sequences in international databases such as GenBank and the lack of explicit definitions for taxonomic resolution. To address these issues, we developed a robust framework to compare the performance of 22 metabarcodes derived from the same mitogenomes (all available for Actinopterygians in NCBI) against a standardized taxonomic baseline based on COI Barcode Index Numbers (BINs). This framework allows for the separate quantification of over‐splitting (splitting the same taxon/BIN) and over‐merging (merging different taxon/BIN). Comparison of OTUs obtained with multiple de novo clustering methods to BINs confirmed the metabarcode ranking based on error sums. Although each metabarcode exhibited varying sensitivities to over‐merging or over‐splitting errors, the clustering threshold emerged as the most important factor influencing biodiversity estimates whatever the clustering method. This led us to propose optimal thresholds for each metabarcode to delineate taxonomic levels (metabarcode gaps). Additionally, we found that taxonomic resolution varied significantly among genes, orders and community diversity, but independently of metabarcode length. Overall, the choice of metabarcode and clustering threshold should aim to minimize over‐merging or over‐splitting while ensuring accurate lower taxonomic delineations. A set of documented R functions makes this evaluation of taxonomic resolution easily applicable to any other taxonomic group for which a representative set of full genes or mitogenomes is available.

Most reef fishes possess an early pelagic stage that ensures the crucial role of maintaining connectivity between distant populations, as movements of older demersal stages are generally restricted. While classically considered passive, numerous studies show that most larvae largely influence dispersion scale and settlement rate by actively swimming horizontally/vertically in an oriented way during most of their pelagic phase. Laboratory measurements of active dispersal skills differ from natural behaviors of individuals observed by divers manually annotating depth and bearing every 30 s, while carrying a low‐speed flowmeter to estimate average speed. Here, we improved this protocol through the use of electronic measurement devices to achieve enhanced feasibility, replicability, efficiency, and safety. Bearing and depth could be precisely measured at high frequencies using a logger fixed on an optimized diving tray, which allowed us to reduce tracking duration from 10 to 5 min, to track more individuals. It also permitted studying in situ the temporal dynamics of vertical speed and direction changes. All further steps, including data entry, sensor calibration, circular statistics and 3D track reconstruction (Madwick filter), were automated within interactive pipelines, enabling us to obtain results within 3 h after dives during fieldwork. We conducted in situ trackings for a diversified set of species (32 per ocean) during developments in the Caribbean (Guadeloupe), before being routinely applied in the Indian Ocean (Maldives) with a majority of trackings successfully carried out (74%) despite offshore conditions. High individual orientation accuracy, combined with great swimming/sinking abilities possibly dependent on depth/current, suggests that pelagic larvae/juveniles can swim in a correlated random‐walk (CRW). This occurs even when orientation cues are too scarce for a consistent orientation among species/zones to emerge (biased CRW), marking a difference with their behavior in the coastal environment. Although biophysical models of dispersal ease the development of informed conservation strategies at large spatial scales, comparisons with genetic connectivity demonstrate that only models incorporating realistic active behaviors yield comparable outputs. Our methodological advances overcome various obstacles preventing the measurement of the parameters necessary for active models, not only for demersal fishes, but also for any small pelagic organism in any aquatic habitat.

Although larval stages ensure most connectivity between demersal fish populations, dispersal traits are increasingly less measured, despite the importance of correctly parametrizing biophysical models for spatial conservation planning. Moreover, existing data are scattered across a vast multidisciplinary literature. To address this mismatch between need and availability, we compiled data from 3,201 references into multiple datasets covering 35 key pelagic dispersal traits across fish early-life stages. We specifically compiled data on swimming speed, vertical position, and delayed settlement in demersal fishes (rafting or pelagic juveniles), as these traits exert a major yet understudied influence on dispersal scale. We systematically reported all descriptive statistics, enabling robust fitting of probability density functions to introduce particle-level variability in Lagrangian models. Overall, datasets comprise 32,988 species-level (1,709 for higher-taxon-level) records for 6,841 marine fish species worldwide, including 1,155 unpublished records (other teams), and 313 records newly collected during two fieldworks (Maldives & Guadeloupe). We also digitized 12,322 individual-level age-at-length/weight records from rearing experiments, enabling temperature-dependent growth model fitting to forecast global warming impacts on dispersal.

The hydrothermal compounds massively released into the sea by the geothermal power plant of Bouillante (Guadeloupe, Lesser Antilles) support the growth of sulphur-oxidising bacteria like around black smokers. Opportunistic animals of the bay were previously shown to actively seek and consume the bacterial biofilm. To investigate the role of these bacterial mats in enhancing the transfer of Hg, a highly toxic heavy metal, its concentrations were assessed in sediments, bacteria, and 6 low trophic levels animals from the Bouillante Bay and a Control Site nearby containing only natural sources of Hg. Concentrations of Hg in all samples from Bouillante were greater than those from the Control Site (2 to 627 times higher). A comparison with the Hg concentrations reported in the literature for similar samples types reveals that they are abnormally high in most Bouillante samples. Although bacterial biofilm contained high levels of Hg, the link between bacteria contribution to diet and Hg concentration was more complex than expected, which might be due to interspecific differences in Hg uptake and elimination rates. Species not consuming bacteria (i.e. filter feeders) still presented higher levels of Hg, suggesting that significant amounts of Hg are released along with discharge waters from the Bouillante geothermal plant, and are integrated through diffusion. Differences in Hg concentrations between tissues do not indicate that Hg contained in samples from animals was under the form of MeHg, lowering the biomagnification potential of Hg in the Bouillante Bay trophic food web. Overall, the Bouillante case study emphasises for the first time an important role played by sulphur bacteria mats as a vector of hydrothermal inorganic Hg, and potentially other trace metals emitted in vents area, through dietary pathways.