Biology subjects

Canals, O.

Publications and source records attributed to Canals, O..

6 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

Advancing ecological assessment: The integration of eDNA metabarcoding into an estuarine fish index

In the face of increasing anthropogenic pressures on estuarine ecosystems, methods to efficiently and reliably assess their ecological status are essential. This study explores the integration of environmental DNA analysis into the AZTIs Fish Index (AFI) to assess ecological status of estuarine ecosystems. Surface water eDNA sampling and bottom trawl surveys were performed across multiple estuaries in the Basque Country, Spain, and resulting species data were used to calculate AFI scores. eDNA metabarcoding consistently detected higher fish species richness than bottom trawling, while the latter remained more effective at capturing demersal species. In general, ecological classifications from eDNA- and bottom trawl derived data displayed low concordance, largely due to differing species assemblages and metric contributions. These results emphasize the respective strengths and weaknesses of each methodology and the necessity for method-specific calibration. Considering that the AFI is calibrated using bottom trawl data, its direct application to eDNA-derived species lists may lead to some inconsistencies. This study underscores the critical necessity to establish eDNA-specific reference conditions and to recalibrate index thresholds accordingly. While eDNA approach may not entirely replace traditional methods, its scalability, sensitivity, and minimal ecological disturbances establish it as an essential complementary application within estuarine assessment programs. This research strongly supports the urgent advancement of eDNA-based indices and the critical enhancement of reference conditions for their effective incorporation into ecological assessment frameworks under the Water Framework Directive.

ecology↗

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↗

bioRxiv2023

Increasing marine trophic web knowledge through DNA analyses of fish stomach contents: a step towards an Ecosystem Based Approach to fisheries research

Multispecies and ecosystem models, which are key for the implementation of ecosystem-based approaches to fisheries management, require extensive data on the trophic interactions between marine organisms, including changes over time. DNA metabarcoding (the simultaneous identification of all taxa in a sample by sequencing a short DNA region) could be used for speeding up large-scaled stomach content data collection. Yet, for DNA metabarcoding to be routinely implemented, technical challenges should be addressed, such as the potentially complicated sampling logistics, the detection of a high proportion of predator DNA, and the inability to provide reliable abundance estimations. Here, we present a DNA metabarcoding assay developed to examine the diet of five commercially important fish, which is feasible to be incorporated into routinary samplings. The method is devised to speed up the analysis process by avoiding the stomach dissection and content extraction steps, while preventing the amplification of predator DNA by using blocking primers. Tested in mock samples and in real stomachs, the method has proven effective and shows great effectiveness discerning diet variations due to predator ecology or prey availability. Additionally, by applying our protocol to mackerel stomachs previously analysed by visual inspection, we showcase how DNA metabarcoding could complement visually based data by detecting overlooked prey by the visual approach. We finally discuss how DNA metabarcoding-based data can contribute to trophic data collection. Our work reinforces the potential of DNA metabarcoding for the study and monitoring of fish trophic interactions and provides a basis for its incorporation into routine monitoring programs, which will be critical for the implementation of ecosystem-based approaches to fisheries management.

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↗

bioRxiv2021

Vertical stratification of environmental DNA in the open ocean captures ecological patterns and behavior of deep-sea fishes

The deep-sea remains among the most unknown ecosystems on Earth despite its relevant role in carbon sequestration and increasing threat due to interest by fishing and mining industries. This, together with the recent discovery that the upper layer of this ecosystem (mesopelagic zone) harbors about 90% of the fish biomass on Earth, claims for a deeper understanding of the deep-sea so that the foundations for a sustainable use of its resources can be established. The analysis of environmental DNA (eDNA) collected from the water column emerges as an alternative to traditional methods to acquire this elusive information, but its application to the deep ocean is still incipient. Here, we have amplified and sequenced the fish eDNA contained in vertical profile samples (from surface to 2000 m depth) collected during day and night-time throughout the Bay of Biscay. We found that eDNA-derived deep-sea fish richness and abundance follow a day-night pattern that is consistent with the diel migratory behavior of many mesopelagic species, and that eDNA can reveal species-specific distribution and movement through the water column. These results highlight the potential of eDNA-based studies to improve our knowledge on the species inhabiting the dark ocean before this still pristine ecosystem is exploited.

ecology↗