Biology subjects

Mauvisseau, Q.

Publications and source records attributed to Mauvisseau, Q..

12 recordsLinked to original sources

bioRxiv2026

On-site metabarcoding analysis of environmental DNA samples

Environmental DNA metabarcoding is a powerful monitoring tool for assessing aquatic biodiversity, as well as the sustainability and impacts of fisheries and aquaculture. However, conventional laboratory workflows remain time-consuming and dependent on dedicated infrastructures. Here, we present a field trial of a fully portable, off-grid eDNA metabarcoding pipeline that enables end-to-end analysis within a few days using compact equipment, including a BentoLab workstation and an Oxford Nanopore Technologies (ONT) MinION sequencer. The workflow was implemented during two international training courses in Norway and Brazil, where students and early career researchers collected environmental samples, extracted and amplified DNA, prepared DNA libraries, and sequenced on-site before performing bioinformatics and statistical analyses. In the case study detailed here, seven eDNA samples collected and analysed on-site in the Oslofjord allowed detection of 16 fish and elasmobranch species. Although overall diversity was lower than in earlier studies using Illumina-based sequencing, our protocol reliably detected key species and demonstrates that portable eDNA metabarcoding is feasible for rapid ecological assessment, surveillance of high-risk regions and/or deployment in remote or resourcelZllimited settings.

ecology↗

bioRxiv2025

Globally unified analysis of riverine eDNA reveals common associations of fish biodiversity with drainage characteristics

Freshwater biodiversity is declining at a pace that outstrips the capacity of existing monitoring approaches both in temporal and spatial dimensions, highlighting the urgent need for rapid and scalable assessment and attribution of biodiversity states and changes. Here, we present one of the first global assessments and unified analyses of riverine fish biodiversity using environmental DNA (eDNA) collected from 1818 sites across 113 river systems. We quantified species richness, functional redundancy, phylogenetic diversity, and genetic sequence diversity, and related them to drainage characteristics. Our results showed that eDNA effectively captured global patterns of multi-faceted riverine fish biodiversity and disentangled the roles of climate and human activities in shaping biodiversity-area relationships. Catchments in warmer climates consistently enhanced biodiversity accumulation with area, while higher human activity intensity weakened this scaling. Species richness, functional, and genetic sequence diversity exhibited stronger negative responses to human activities in larger catchments. In contrast, phylogenetic diversity showed the strongest negative effects in smaller catchments with these impacts diminishing as catchment area increased, highlighting the facet-dependent nature of biodiversity responses to environmental gradients. Our findings demonstrate the power of eDNA-based datasets for harmonized, multi-faceted biodiversity assessments, offering a scalable approach for detecting and attributing biodiversity change and informing conservation strategies under accelerating global change.

ecology↗

bioRxiv2025

Integrated reanalysis of global riverine fish eDNA datasets shows robustness and congruence of biodiversity conclusions

The analysis of environmental DNA (eDNA) has revolutionized biodiversity assessments in aquatic ecosystems, enabling non-invasive monitoring of fish communities across diverse regions. However, the global comparability of these eDNA datasets remains ambiguous due heterogeneous sampling protocols and bioinformatic workflows across studies, particularly regarding the robustness of their conclusions on biodiversity assessments. Here, we conducted a meta-analysis of 58 riverine fish eDNA metabarcoding datasets, covering 1,818 sampling sites worldwide, to evaluate the robustness of eDNA-derived biodiversity patterns. We found that species richness estimates and metrics of community structure derived under a common bioinformatic workflow were overall consistent with those of original analyses, despite the relatively high variability in bioinformatic analyses in the respective original studies. Contrastingly, congruence of species identity varied more extensively across datasets, mostly reflecting different completeness and regional relevance of reference databases. Restricting taxonomic assignment to basin-specific species pools improved species identification accuracy, while datasets lacking publicly accessible or well-curated reference data were more prone to mismatches. Year of sampling had a positive effect on taxonomic congruence, such that more recent studies showed increased robustness, also reflecting improved reference database coverage and enhanced species-level identification over time and overall method congruence in more recent years. Overall, the suitability and potential of eDNA for global biodiversity monitoring is corroborating overall robust biodiversity estimates, irrespective of the bioinformatic approaches. Our study underlines the effectiveness and need of further harmonization of bioinformatic workflows and strengthened region-specific reference databases for improved taxonomic resolution and comparability across studies.

ecology↗

bioRxiv2025

Recovering historical fish eDNA from museum-preserved Antarctic filter feeders via non-destructive metabarcoding.

O_LIRecent technical advances have significantly enhanced the value of museum specimens for molecular research, with metagenomic and metabarcoding approaches expanding further the utility of museum collections. However, given the finite number of specimens, there is a critical need to move past destructive DNA extraction approaches and to explore non-destructive techniques. C_LIO_LIIn this study, we evaluated the feasibility of extracting historical fish eDNA from the ethanol preservative used to store Antarctic museum specimens. We compared a variety of extraction methods - centrifugation, evaporation, filtration, and precipitation - using ten replicate samples per treatment for statistical analyses. To assess potential differences in preservative-derived eDNA recovery across different filter-feeding taxonomic groups, we included a Bryozoa and two Porifera, i.e., Demospongiae and Hexactinellida. C_LIO_LIComparative analyses with tissue biopsies revealed that the total genomic DNA was significantly reduced for non-destructive approaches. However, 10 ml ethanol filtration performed equal to, or in some instances, outperformed tissue biopsies when investigating the historical eDNA of Antarctic fish using a 16S rRNA metabarcoding approach, both for the number of species detected (-diversity) and community characterisation ({beta}-diversity). C_LIO_LIOur findings demonstrate the potential of ethanol preservative as a valuable, non-destructive source of historical fish eDNA from museum-stored filter-feeding specimens. These results highlight the viability of non-destructive sampling for molecular research on museum collections, preserving specimen integrity while enabling biodiversity assessments. Further refinement of non-destructive eDNA extraction could expand its applicability across taxa, collection types, and preservation methods, ensuring the long-term sustainability of museum-based genomic research. C_LI

ecology↗

bioRxiv2025

Investigating the dynamics of the aquatic community in Oslofjord through time series analysis of eDNA

Understanding temporal dynamics of marine communities is critical for assessing ecosystem health and guiding conservation efforts. Here, we conducted a survey using environmental DNA (eDNA) metabarcoding with two primer sets, MiFish and Elas02, to investigate seasonal and interannual changes in the fish community of Oslofjord (Norway) over two consecutive years. Using the MitoFish reference database through the GBIF querying tool, we identified 61 fish species and found significant changes in the dominant taxa between seasons and years. Clupea harengus (Atlantic herring) consistently peaked in early spring, while Scomber scombrus (Atlantic mackerel) dominated winter months in the second year. The MiFish primer set showed increased species richness in the second year, whereas the Elas02 primer set showed stable richness despite compositional turnover. Non-metric multidimensional scaling (NMDS) revealed distinct community separation between years in presence/absence data, driven by species turnover rather than abundance read changes. Our findings support the use of eDNA metabarcoding to capture fine-scale temporal dynamics and emphasise the importance of multi-year datasets for distinguishing ecological trends from stochastic changes. This strategy improves monitoring practices for marine ecosystems under anthropogenic stressors.

ecology↗

bioRxiv2025

From Nets to Molecules: A Comparative Study of Stream Fish Diversity Recovery Using Different Sampling Methods in Eastern Amazonia

The Neotropical freshwaters of South America host an exceptional level of ichthyofaunal diversity with over 5,160 species, making it the richest continental fauna worldwide. Despite their richness, these freshwater ecosystems face severe threats from human activities, leading to significant declines in fish populations. Traditional fish sampling techniques, such as netting, have been fundamental to ichthyology, offering insights into species richness and abundance. However, the complexity of stream environments limits the effectiveness of conventional sampling tools. As a result, more elusive or niche species are often missed. In recent years, water environmental DNA (eDNA) has emerged as a complementary method to traditional sampling. It allows for detection of aquatic organisms from water samples, expanding the scope of biodiversity assessments. Nevertheless, eDNA filtration faces challenges, especially in turbid waters, including the likelihood of co-extracting inhibitors that can affect amplification and detection processes, as well as the downstream flow of eDNA signals, which means that samples predominantly detect upstream fauna. To address these limitations, the use of bulk samples, such as stomach contents, provides a robust alternative by directly analyzing biological tissues and leveraging the bidirectional mobility of organisms within the stream, enabling the detection of taxa from both upstream and downstream regions. Given these issues, this study combines traditional netting, water eDNA analysis, and dietary metabarcoding to assess the fish biodiversity in three Neotropical streams in the Capim River basin, Para, Brazil. The integration of multiple sampling techniques offers a more accurate picture of biodiversity, helping to overcome the limitations of each individual method and providing essential insights for conservation efforts.

genetics↗

bioRxiv2024

eDNA replicates, polymerase and amplicon size impact inference of richness across habitats

Environmental DNA-based monitoring has been increasingly used in the last decade to monitor biodiversity in aquatic and terrestrial systems. Molecular-based surveys now allow quick and reliable production of baseline knowledge of species community composition on a large scale, allowing better understanding of ecosystem function and mitigation of stressors linked to anthropogenic activities. Despite this, technical hurdles often remain, and the impact of replicates, PCR polymerases and amplicon size on the recovered species richness is still poorly understood. Here, we conducted a large controlled experiment, with bulk samples collected from terrestrial, marine and freshwater environments to assess the impact of natural and technical replicates, PCR polymerases with different degrees of fidelity or proofreading activity, as well as amplicon size on species richness recovery across habitats. In this study, we consistently found variations in sample species richness depending on PCR polymerase choice. We further demonstrate the dissimilar impacts between natural and technical replicates on species richness recovery, and the necessity of increasing natural replications in eDNA based surveys. We highlight the benefits and limitations of replication strategies, polymerase choice and amplicon size across terrestrial, marine and freshwater habitats, and provide recommendations to increase the reliability of future eDNA-based metabarcoding studies.

molecular biology↗

bioRxiv2024

Assessing reliability and accuracy of qPCR, dPCR and ddPCR for estimating mtDNA copy number in songbird blood and sperm cells

Mitochondrial DNA copy number varies across species, individuals and cell types. Two avian cell types carrying a relatively low number of mitochondria are the red blood cells and spermatozoa. While previous studies investigating variation of mitochondrial abundance in animal sperm have generally used quantitative PCR (qPCR), this method shows potential limitations when quantifying low abundant targets. To mitigate such issues, we investigated and compared the reliability and accuracy of qPCR, digital PCR (dPCR) and droplet digital PCR (ddPCR) to quantify high and low concentration DNA. Using synthetic DNA, we found that both dPCR and ddPCR displayed lower Limit of Detection and Limit of Quantification than qPCR. Using DNA extracted from blood and sperm cells of Eurasian Siskin, we found that qPCR, dPCR and ddPCR reliably quantified mitochondrial DNA in sperm samples, but showed significant differences when analyzing typically lower levels of mtDNA in blood. We found that ddPCR consistently showed lower variation among replicates. These analyses provide critical insights and recommendations for future studies aiming to quantify target mtDNA. Our study indicates that dPCR and ddPCR are the preferred methods when working with samples with low abundance of mtDNA.

molecular biology↗

bioRxiv2024

tombRaider - improved species and haplotype recovery from metabarcoding data through artefact and pseudogene exclusion.

Environmental DNA metabarcoding has revolutionized ecological surveys of natural systems. By amplifying and sequencing small gene fragments from environmental samples containing complex DNA mixtures, scientists are now capable of exploring biodiversity patterns across the tree of life in a time-efficient and cost-effective manner. However, the accuracy of species and haplotype identification can be compromised by sequence artefacts and pseudogenes. Despite various strategies developed over the years, effective removal of artefacts remains challenging and inconsistent data reporting standards hinder reproducibility in eDNA metabarcoding experiments. To address these issues, we introduce tombRaider, an open-source command line software program (https://github.com/gjeunen/tombRaider) and R package (https://github.com/gjeunen/tombRaider_R) to remove artefacts and pseudogenes from metabarcoding data post clustering and denoising. tombRaider features a modular algorithm capable of evaluating multiple criteria, including sequence similarity, co-occurrence patterns, taxonomic assignment, and the presence of stop codons. We validated tombRaider using various published data sets, including mock invertebrate communities, air eDNA from a zoo, and salmon haplotypes from aquatic eDNA. Our results demonstrate that tombRaider effectively removed a higher proportion of artefacts while retaining authentic sequences, thus enhancing the accuracy and reliability of eDNA-derived diversity metrics. This user-friendly software program not only improves data quality in eDNA metabarcoding studies, but also contributes to standardised reporting practices, an aspect currently lacking in this emerging research field.

bioinformatics↗

bioRxiv2019

Development and application of eDNA-based tools for the conservation of white-clawed crayfish

O_LIeDNA-based methods represent non-invasive and cost-effective approaches for species monitoring and their application as a conservation tool has rapidly increased within the last decade. Currently, they are primarily used to determine the presence/absence of invasive, endangered or commercially important species, but they also hold potential to contribute to an improved understanding of the ecological interactions that drive species distribution. However, this next step of eDNA-based applications requires a thorough method development. C_LIO_LIWe developed an eDNA assay for the white-clawed crayfish (Austropotamobius pallipes), a flagship species of conservation in the UK. Multiple subsequent in-situ and ex-situ validation tests aimed at improving method performance allowed us to apply eDNA-based surveys to evaluate interactions between white-clawed crayfish, crayfish plague and invasive signal crayfish. C_LIO_LIThe assay performed well in terms of specificity (no detection of non-target DNA) and sensitivity, which was higher than more established traditional species survey methods. Quantification of species biomass was, however, less reliable. C_LIO_LIComparison of eDNA sampling methods (precipitation vs. various filtration approaches) revealed that optimal sampling method differed across environments and might depend on inhibitor concentrations. C_LIO_LIFinally, we applied our methodology together with established assays for crayfish plague and the invasive signal crayfish and demonstrated their significant interactions in a UK river system. C_LIO_LIOur analysis highlights the importance of thorough methodological development of eDNA-based assays. Only a critical evaluation of methodological strengths and weaknesses will allow us to capitalise on the full potential of eDNA-based methods and use them as decision support tools in environmental monitoring and conservation practices. C_LI

ecology↗

bioRxiv2019

Improving detection capabilities of a critically endangeredfreshwater invertebrate with environmental DNA using digital droplet PCR

Isogenus nubecula is a critically endangered Plecoptera species. Considered extinct in the UK, the species was recently rediscovered in one location of the river Dee in Wales after 22 years of absence. As many species belonging to the Perlodidae, this species can be a bio-indicator, utilised for assessing water quality and health status of a given freshwater system. However, conventional monitoring of invertebrates via kick-sampling for example, is an invasive and expensive (time consuming). Further, such methods require a high level of taxonomic expertise. Here, we compared the traditional kick-sampling method with the use of eDNA detection using qPCR and ddPCR-analyses. In spring 2018, we sampled eDNA from twelve locations on the river Dee. I. nubecula was detected using kick-sampling in five of these locations, three locations using both eDNA detection and kick-sampling and one location using eDNA detection alone - resulting in a total of six known and distinct populations of this critically endangered species. Interestingly, despite the eDNA assay being validated in vitro and in silico, and results indicating high sensitivity, qPCR analysis of the eDNA samples proved to be ineffective. In contrast, ddPCR analyses resulted in a clear detection of I. nubecula at four locations suggesting that inhibition most likely explains the big discrepancy between the obtained qPCR and ddPCR results. It is therefore important to explore inhibition effects on any new eDNA assay. We also highlight that ddPCR may well be the best option for the detection of aquatic organisms which are either rare or likely to shed low levels of eDNA into their environment.

ecology↗

bioRxiv2018

First detection of a highly invasive freshwater amphipod (Crangonyx floridanus) in the United Kingdom

The freshwater gammarid, Crangonyx floridanus, originates from North America but has invaded and subsequently spread rapidly throughout Japan. We provide here the first genetic and microscopic evidence that C. floridanus has now also reached the United Kingdom. We found this species in two locations separated by more than 200 km (Lake Windermere in the North of the UK and Smestow Brook, West Midlands). The current distribution of C. floridanus is currently unknown, however both sites are well connected to other river and channel systems therefore the chance of further spread is high. Genetic analyses of C. floridanus indicate that British inland waters are colonised by the same linage, which also has invaded Japan. We recommend further work to assess the distribution of this species and its impact on the local fauna and flora.

ecology↗