Rachel Haderlé

Ports are increasingly recognized as distinct urban marine ecosystems (UME) shaped by intense human activities, yet their biodiversity remains poorly documented, particularly in tropical regions. Environmental DNA (eDNA) metabarcoding offers a powerful, non-invasive approach to assessing biodiversity in these complex and highly modified environments. In this study, we conducted, to our knowledge, the first eDNA-based inventory of marine vertebrates within the Grand Port Maritime de la Guadeloupe, a semi-enclosed coastal system embedded in a mosaic of coral reefs, seagrass beds, mangroves and restored habitats. Using a standardized sampling and taxonomic assignment protocol, we characterized vertebrate communities across four sites and compared them with a reference transect outside the port area. We detected 140 teleost taxa, representing more than one-third of the known regional diversity, including several species of management concern. Despite their proximity, sites exhibited compositional and phylogenetic contrasts, revealing fine-scale spatial structuring of eDNA signals within the port. Restored mangrove and seagrass areas combined high taxonomic richness with unexpectedly low phylogenetic diversity, suggesting colonization by closely related opportunistic species. By integrating taxonomic and phylogenetic metrics, our study highlights the unique biodiversity assemblages found in port ecosystems and demonstrates the value of eDNA-derived metrics for future biodiversity monitoring and marine spatial planning in UME.

Environmental DNA ( eDNA ) metabarcoding has emerged as a powerful tool for biodiversity monitoring because it is non‐invasive, applicable across broad taxonomic groups, and capable of detecting rare and cryptic species. However, the characteristics and limitations of eDNA vary among target organisms. Whereas studies of microorganisms and plankton often recover high‐quality DNA from whole or near‐whole organisms, surveys of marine macrofauna, particularly vertebrates, rely on trace, frequently degraded DNA . Combined with the lack of standardized protocols, inconsistent taxonomic resolution, limited quantitative information, and the absence of life‐stage information, these constraints hinder ecological interpretation and comparisons across studies. In this Perspective, we advocate a phylogenetic turn in eDNA analyses through the integration of phylogenetic diversity ( PD ), which quantifies the amount of evolutionary history represented by detected taxa. By considering evolutionary relatedness in addition to taxa identities, PD complements conventional taxonomic metrics and can provide additional ecological insight, particularly when taxonomic resolution is incomplete. We discuss both the opportunities and limitations of this approach, including its practical implementation in eDNA metabarcoding. To illustrate this framework, we compared five marine eDNA metabarcoding datasets (2021–2025) spanning tropical to Arctic ecosystems and contrasting anthropogenic contexts. Across these case studies, anthropized sites often showed higher taxonomic richness but reduced phylogenetic divergence, reflecting communities dominated by closely related evolutionary lineages, whereas less disturbed sites supported fewer taxa but encompassed broader evolutionary histories. These contrasting patterns illustrate how PD metrics can reveal ecological processes, including environmental filtering and community assembly, that may not be apparent from taxonomic richness alone. By proposing a reproducible workflow based on standardized eDNA datasets, we highlight the potential of phylogenetic diversity to strengthen biodiversity assessment from eDNA metabarcoding. Integrating evolutionary information alongside taxonomic information provides a complementary framework for biodiversity monitoring and offers promising perspectives for long‐term monitoring, conservation planning, and environmental policy.

The Arabian Gulf is a semi-enclosed sea with shallow waters. Its marine fauna must cope with extreme and recurring environmental conditions (high summer temperatures, hypersalinity, hypoxia). In addition, local human activities are very significant and have a marked impact on coastal areas, particularly in urban marine ecosystems (UME). Taken together, the Arabian Gulf’s low species richness, its exposure to multiple human-induced stressors, and the proximity of many taxa to their environmental tolerance limits create a particularly concerning situation. Monitoring marine wildlife must be a priority in this context, particularly with respect to marine vertebrates, difficult to study using integrative approaches. The present study aimed to generate relevant data on marine vertebrate biodiversity in the UME of Abu Dhabi, and to provide evidence-based information to inform conservation policy. In addition, investigating marine biodiversity in the world’s warmest sea in summer, the Arabian Gulf, will provide us with information of general interest in terms of the adaptation and evolution of marine fauna in the current period of global climate change. We conducted the first environmental DNA (eDNA)-based survey of marine vertebrate diversity in Abu Dhabi’s UME. Using a standardized process of water sampling, eDNA metabarcoding using a ~ 97 bp fragment of the mitochondrial 12S rRNA gene as barcode, and taxonomic assignment, we studied vertebrate biodiversity at four urban sites, including a marina, a newly developed area, a seagrass bed, and a protected urban mangrove. We identified 83 distinct taxa, including five birds, two elasmobranchs, one marine mammal, and 75 teleosts. The specific taxonomic richness did not vary significantly between sites. In contrast, phylogenetic diversity metrics revealed lower diversity than expected for the newly developed area, while the mangrove and, to a lesser extent, the seagrass bed exhibited a phylogenetic structure consistent with their species richness. This approach provides a powerful, non-invasive and integrative framework for long-term monitoring and supports evidence-based conservation planning for marine biodiversity in the Arabian Gulf.

Environmental DNA (eDNA) metabarcoding has become a powerful approach for large-scale biodiversity assessment, yet taxonomic assignment remains one of its most critical error-prone steps. Current bioinformatic pipelines rely on molecular similarity searches against reference databases, but assignment accuracy is constrained not only by short marker length and database incompleteness, but also by fundamental limitations, including recent species radiations, incomplete lineage sorting, introgression, NUMTs, and the imperfect correspondence between genetic variation and species boundaries. Here, we present TRIDENT (Taxonomic Resolution and IDentification using Environmental dNa Traces), an automated and simple protocol designed to improve taxonomic assignments in eDNA metabarcoding. Initially developed for marine vertebrates, TRIDENT may be used with any barcode and integrates three complementary sources of evidence: molecular similarity (NCBI/GenBank and BOLD), curated taxonomic information (WoRMS), and ecological plausibility derived from biogeographic occurrence data (GBIF). The workflow sequentially constructs candidate taxon lists based on sequence similarity, expands them through taxonomic hierarchies, and filters them using spatial occurrence constraints. It further identifies possible taxa lacking reference barcodes and evaluates their plausibility through CO1-based similarity if data exist in BOLD. TRIDENT has been implemented as a source-available Python tool and tested using empirical eDNA datasets from marine vertebrates as well as simulated communities. Results demonstrate that the tool produces taxonomic assignments consistent with expert manual curation while substantially reducing processing time and attention errors caused by manual processing of large datasets. By combining molecular, taxonomic, and ecological criteria within a single framework, TRIDENT improves transparency and reproducibility and provides a robust and flexible solution strengthening confidence in taxonomic identifications in eDNA-based biodiversity assessments.

Environmental DNA (eDNA) metabarcoding has transformed biodiversity monitoring, yet most analyses rely on taxonomic metrics that are sensitive to methodological variation and limit cross-study comparability. We propose a "phylogenetic turn" in eDNA analysis through the integration of phylogenetic diversity (PD) metrics. By incorporating evolutionary relationships, PD reduces dependence on species-level resolution, increases robustness to detection biases, and better captures the evolutionary "option value" of biodiversity. We synthesize key PD metrics across richness, divergence, and regularity, emphasizing the use of standardized effect sizes (SES) for ecological interpretation while addressing challenges in metric selection. We apply this framework to five marine eDNA datasets (2021-2025) spanning ecologically and geographically contrasting ecosystems, from tropical to Arctic regions, and encompassing a wide gradient of anthropogenic pressure. Across datasets, we identify consistent patterns: anthropized ecosystems exhibit high taxonomic richness but reduced phylogenetic diversity, indicating phylogenetic clustering, whereas less disturbed systems show lower richness but greater evolutionary breadth. These findings demonstrate that PD reveals ecological structure not captured by taxonomic metrics, including signatures of environmental filtering and community assembly processes. By providing a reproducible analytical workflow based on standardized eDNA datasets, we position phylogenetic diversity as a critical bridge between eDNA data and conservation frameworks. Ultimately, eDNA-based phylogenetic approaches open new avenues for decoding global biodiversity patterns across heterogeneous ecosystems.

The Arctic is undergoing rapid and spatially heterogeneous warming, with Svalbard among the fastest-changing regions worldwide. These transformations are reshaping coastal ecosystems and marine vertebrate communities, yet biodiversity assessments remain limited by logistical constraints and protection regulations. Environmental DNA (eDNA) metabarcoding offers a non-invasive alternative capable of capturing taxonomic and phylogenetic diversity across habitats. Here, we surveyed marine vertebrates along the western coast of Svalbard using continuous seawater filtration (16 transects of 2.5 miles each) from a dedicated sailing vessel, covering glacier fronts, walrus haul-out sites, harbors, and both shallow and deep-water areas. Across 31 samples collected at 16 sites, we detected 36 taxa, including 19 fish, 8 mammals, 8 birds, and 1 elasmobranch species. The congruence between eDNA, visual observations, and acoustic detections confirms the feasibility and robustness of eDNA sampling under Arctic conditions. Contrary to expectations of homogeneous assemblages across nearby sites, we observed marked taxonomic and phylogenetic turnover among habitats. Harbors and walrus haul-out areas showed particularly high taxonomic richness and phylogenetic diversity, whereas glacier-influenced sites were dominated by a few closely related taxa, suggesting that local conditions constrain community composition. Several detections, including Gasterosteus aculeatus , increased Phoca vitulina occurrence, and widespread Branta leucopsis , are consistent with biogeographic shifts linked to Arctic warming. The identification of Red List species and elusive taxa further illustrates the sensitivity of eDNA for conservation-focused monitoring. Overall, this study establishes eDNA metabarcoding as an effective tool for characterizing Arctic marine vertebrate communities and provides a valuable baseline for tracking ecological responses to rapid environmental change.

Estuaries are ecologically vital yet highly impacted ecosystems that serve as transitional zones between land and sea. Monitoring their biodiversity is essential but challenging due to their dynamic nature and the transient presence of many species. Traditionally, actinopterygian monitoring in these systems still relies on conventional and intrusive methods such as gill nets and trawls. Environmental DNA (eDNA) metabarcoding offers a non‐invasive, multi‐taxa alternative that can complement these traditional approaches. Here, we applied an eDNA‐based metabarcoding approach to characterize vertebrate diversity in the Rance Estuary, located in the Brittany Region of France. Water samples were collected from five stations spanning marine to freshwater environments. Special attention was given to two stations located upstream and downstream of the tidal power plant (TPP) dam to assess its potential impact on ecological continuity. We detected a total of 124 distinct vertebrate MOTUs, comprising actinopterygians, birds, mammals, and amphibians. Taxonomic composition followed the estuarine gradient, with Jaccard dissimilarity increasing with distance from the sea and largely driven by species turnover. While taxonomic and phylogenetic diversity remained relatively stable across the vertebrate community, functional diversity revealed an increasing terrestrial influence. For actinopterygians, taxonomic diversity decreased upstream, whereas phylogenetic and functional diversity indicated fine‐scale structuring, even among nearby stations. This approach enabled the development of biodiversity metrics and facilitated comparisons with previous actinopterygian monitoring surveys in the same area based on conventional methods (scientific fishing using nets and dredges). Our results emphasize the potential of eDNA for holistic estuarine biomonitoring and establish a valuable baseline for future non‐invasive assessments.

Estuaries are ecologically vital yet highly impacted ecosystems that serve as transitional zones between land and sea. Monitoring their biodiversity is essential but challenging due to their dynamic nature and the transient presence of many species. Traditionally actinopterygian monitoring in these systems still relies on conventional and intrusive methods such as gill nets and trawls. Environmental DNA (eDNA) metabarcoding offers a non-invasive, multi-taxa alternative that can complement these traditional approaches. Here, we applied an eDNA-based metabarcoding approach to characterize vertebrate diversity in the Rance Estuary, located in the Brittany Region of France. Water samples were collected from five stations spanning marine to freshwater environments. Special attention was given to two stations located upstream and downstream of the tidal power plant (TPP) dam to assess its potential impact on ecological continuity. We detected a total of 124 distinct vertebrate MOTUs—comprising actinopterygians, birds, mammals, and amphibians. Taxonomic composition followed the estuarine gradient, with Jaccard dissimilarity increasing with distance from the sea and largely driven by species turnover. While taxonomic and phylogenetic diversity remained relatively stable across the vertebrate community, functional diversity revealed an increasing terrestrial influence. For actinopterygians, taxonomic diversity decreased upstream, whereas phylogenetic and functional diversity indicated fine-scale structuring, even among nearby stations. This approach enabled the development of biodiversity metrics and facilitated comparisons with previous actinopterygian monitoring surveys in the same area based on conventional methods (scientific fishing using nets and dredges). Our results emphasise the potential of eDNA for holistic estuarine biomonitoring and establish a valuable baseline for future non-invasive assessments.

The success of environmental DNA (eDNA) approaches for species detection has revolutionized biodiversity monitoring and distribution mapping. Targeted eDNA amplification approaches, such as quantitative PCR, have improved our understanding of species distribution, and metabarcoding‐based approaches have enabled biodiversity assessment at unprecedented scales and taxonomic resolution. eDNA datasets, however, are often scattered across repositories with inconsistent formats, varying access restrictions, and inadequate metadata; this limits their interoperation, reuse, and overall impact. Adopting FAIR (Findable, Accessible, Interoperable, and Reusable) data practices with eDNA data can transform the monitoring of biodiversity and individual species and support data‐driven biodiversity management across broad scales. FAIR practices remain underdeveloped in the eDNA community, partly due to gaps in adapting existing vocabularies, such as Darwin Core (DwC) and Minimum Information about any (x) Sequence (MIxS), to eDNA‐specific needs and workflows. To address these challenges, we propose a comprehensive FAIR eDNA (FAIRe) Metadata Checklist, which integrates existing data standards and introduces new terms tailored to eDNA workflows. Metadata are systematically linked to both raw data (e.g., metabarcoding sequences, Ct/Cq values of targeted qPCR assays) and derived biological observations (e.g., Amplicon Sequence Variant (ASV)/Operational Taxonomic Unit (OTU) tables, species presence/absence). Along with formatting guidelines, tools, templates, and example datasets, we introduce a standardized, ready‐to‐use approach for FAIR eDNA practices. Through broad collaboration, we seek to integrate these guidelines into established biodiversity and molecular data standards, promote journal data policies, and foster user‐driven improvements and uptake of FAIR practices among eDNA data producers. In proposing this standardized approach and developing a long‐term plan with key databases and data standard organizations, the goal is to enhance accessibility, maximize reuse, and elevate the scientific impact of these valuable biodiversity data resources.

The common bottlenose dolphin (Tursiops truncatus) exhibits significant intraspecific diversity globally, with distinct ecotypes identified in various regions. In the Guadeloupe archipelago, the citizen science NGO OMMAG has been monitoring these dolphins for over a decade, documenting two distinct morphotypes. This study investigates whether these morphotypes represent coastal and oceanic ecotypes, which have not been previously identified in the region. We characterized morphological differences between the two morphotypes, analyzed genetic variation in individuals stranded around Guadeloupe over the past ten years, and modeled their habitats. Results revealed that these morphotypes align with the ecotypes described in the Atlantic Ocean, forming two distinct genetic groups corresponding to Caribbean ecotypes. Habitat modeling showed differences in habitat preferences between the morphotypes. These findings provide strong evidence for the existence of two distinct ecotypes of T. truncatus in Guadeloupe. Considering the varied risks of exposure to maritime traffic, our study suggests that these ecotypes should be managed as separate units within the species to better inform conservation strategies in the region.