Biology subjects

Claver, C.

Publications and source records attributed to Claver, C..

4 recordsLinked to original sources

bioRxiv2025

Integrating eDNA and acoustic-trawl data to provide small pelagic biomass estimates for fisheries assessment

Accurate abundance estimates of fisheries resources are essential for sustainable fisheries management. In response to the growing need for developing more accurate and cost-effective biomass estimation methods, the analysis of environmental DNA (eDNA) has recently emerged as an alternative for fish abundance quantification. However, practical approaches for integrating eDNA data into fisheries assessment remain limited. Here, we introduce a Bayesian joint model that combines acoustic-trawl and eDNA data to estimate fish biomass. Utilizing 209 water eDNA samples and 196 acoustic transects, the model was applied to estimate the distribution and abundance of the European anchovy (Engraulis encrasicolus) in the Bay of Biscay. The joint model produced estimates consistent with known spatial patterns of anchovy, with eDNA data suggesting a broader distribution and potentially higher abundance. This research demonstrates the value of incorporating eDNA data as a complement to acoustic-trawl for stock assessment and illustrates the versatility of joint Bayesian models and their potential application to various species and datasets. Ultimately, our work opens new avenues for more holistic fisheries assessment, underscoring the growing role of eDNA in that context.

genetics↗

bioRxiv2025

Contribution of mesopelagic fish and cephalopods to the diet of rorquals (Balaenoptera spp) and sperm whales (Physeter macrocephalus) beyond their feeding grounds

Cetacean conservation requires ecosystem-scale management with special focus on food webs. Rorquals and sperm whales are top predators of complex open ocean food webs and, although mesopelagic fish and cephalopods are predated by these cetaceans, their contribution to their diets is not fully understood. Here, we aimed to better describe the consumption of mesopelagic fish and cephalopods by identifying preferred species consumed by rorquals and sperm whales at mid-latitudes. To do so, we combined the fish and cephalopod community composition inferred from whale faecal and marine environmental DNA samples. We analysed the prey availability and predator preferences by comparing the vertical distribution and abundance of fish and cephalopod species in the water column with the prey items found in faecal samples of rorquals and sperm whales. We found that rorqual consumed mesopelagic fish that perform diel vertical migrations (DVM) such as myctophids. These species were found in depths that matched the deep foraging behaviours during daytime and shallow foraging behaviours during night, confirming that rorquals rely on the DVM to feed at these latitudes. Also, although a high diversity of cephalopods was found across the water column, the faecal content of sperm whales was mainly composed by Histioteuthis bonellii, which was abundant between 600 and 1200 meters and matches the diving patterns described for this species in the area. In this study, we present the first comprehensive genetic analysis of the diets of rorquals and sperm whales, expanding our understanding of open ocean trophic ecology to promote effective cetacean conservation.

ecology↗

bioRxiv2025

Lessons learned from applying eDNA surveying to diadromous fish detection across the north-east Atlantic region

Regular monitoring of diadromous fishes is critical to inform their management and conservation. Yet, the in-situ data collection these species is challenging due to their complex life cycle and low abundance. Focusing on the sea lamprey (Petromyzon marinus, Petromyzontidae) and the European shads (Alosa alosa and A. fallax, Clupeidae), emblematic diadromous fishes in the Northeast Atlantic region, this study leverages the use of water environmental DNA (eDNA) samples to monitor their distribution range. For that aim, we developed quantitative PCR (qPCR) and digital PCR (dPCR) assays and applied them to detect sea lamprey and European shad DNA in a network of 44 river basins across Spain, France, Ireland, and the UK. We found that qPCR efficiently detected presence/absence of shads, while the higher sensitivity of dPCR was essential for detecting the lower abundant and partly sessile behaving sea lamprey in the amount of water collected. Moreover, sea lamprey showed significantly lower eDNA copies per litre of water compared to shads, probably due to their larvae spending several years burrowed within soft sediments, reducing eDNA shedding into the water column. The integration of historical datasets with this snapshot wide-ranging study enhances our understanding of the distribution of sea lamprey and European shad in Atlantic rivers. Importantly, the lessons learned within this international collaboration are critical towards a prevailing framework for conservation of migratory fishes, highlighting the need of well-designed sampling strategies coupled with species-specific assays applied to eDNA samples to bust long-term monitoring efforts of diadromous species.

ecology↗

bioRxiv2022

An automated workflow to assess completeness and curate GenBank for eDNA metabarcoding: the marine fish assemblage as case study

Expectations are high regarding the potential of eDNA metabarcoding for diversity monitoring. To make this approach suitable for this purpose, the completeness and accuracy of reference databases used for taxonomic assignment of eDNA sequences are among the challenges to be tackled. Yet, despite ongoing efforts to increase coverage of reference databases, sequences for key species are lacking, and incorrect records in widely used repositories such as GenBank have been reported. This compromises eDNA metabarcoding studies, especially for high diverse groups such as marine fishes. Here, we have developed a workflow that evaluates the completeness and accuracy of GenBank. For a given combination of species and barcodes a gap analysis is performed, and potentially erroneous sequences are identified. Our gap analysis based on the four most used genes (cytochrome c oxidase subunit 1, 12S rRNA, 16S rRNA and cytochrome b) for fish eDNA metabarcoding found that COI, the universal choice for metazoans, is the gene covering the highest number of Northeast Atlantic marine fishes (70%), while 12S rRNA, the preferred region for fish-targeting studies, only covered about 50% of the species. The presence of too close and too distant barcode sequences as expected by their taxonomic classification confirms presence of erroneous sequences in GenBank that our workflow can detect and eliminate. Comparing taxonomic assignments of real marine eDNA samples with raw and clean reference databases for the most used 12S rRNA barcodes (teleo and MiFish), we found that both barcodes perform differently, and demonstrated that the application of the database cleaning workflow can result in drastic changes in community composition. Besides providing an automated tool for reference database curation, this study confirms the need to increase 12S rRNA reference sequences for European marine fishes, encourages the use of a multi-marker approach for better community composition assessment, and evidences the dangers of taxonomic assignments by directly querying GenBank.

ecology↗