Biology subjects

Delrieu-Trottin, E.

Publications and source records attributed to Delrieu-Trottin, E..

4 recordsLinked to original sources

bioRxiv2025

NeMO: a flexible R package for nested multi-species occupancy modelling and eDNA study optimization

Biodiversity monitoring using environmental DNA (eDNA) metabarcoding has expanded rapidly, providing a non-invasive tool widely adopted by ecologists and stakeholders. However, eDNA surveys are prone to imperfect detection, and non-detections are often misinterpreted as true absences - a critical issue when monitoring rare or elusive species. Despite its implications for biodiversity assessments, detection uncertainty is rarely quantified in eDNA-based studies. Occupancy modeling offers a powerful solution to this limitation but remains underused, partly due to a lack of accessible and flexible tools. We developed NeMO (Nested eDNA Metabarcoding Occupancy), a user-friendly R package for fitting multi-species occupancy models in a Bayesian framework. NeMO explicitly accounts for the nested structure of eDNA metabarcoding workflows - typically involving multiple replication steps such as field samples and PCR replicates - while accommodating presence/absence or read-count data. The framework estimates species occupancy, eDNA collection probability, amplification probability, and expected read counts, and allows users to assess the influence of environmental or methodological covariates on each process. Crucially, NeMO helps rigorously assess detectability and optimize resource allocation in eDNA surveys. It estimates the minimum number of eDNA samples, PCR replicates, and sequencing depth required to reliably detect species when present, thereby guiding study design. We illustrate its utility using a fish biodiversity dataset from the Rhone River (France). NeMO integrates key modelling features into a single streamlined framework, providing researchers and practitioners with an accessible and effective tool to assess detectability and optimize resource allocation in eDNA metabarcoding surveys. Our results highlight the importance of quantifying detection uncertainty, which has major implications for conservation monitoring and for designing cost-effective and reliable eDNA strategies. GRAPHICAL ABSTRACT O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=113 SRC="FIGDIR/small/655794v3_ufig1.gif" ALT="Figure 1"> View larger version (35K): org.highwire.dtl.DTLVardef@3a8f2borg.highwire.dtl.DTLVardef@8d8375org.highwire.dtl.DTLVardef@b1976forg.highwire.dtl.DTLVardef@14cfde5_HPS_FORMAT_FIGEXP M_FIG NeMO provides a flexible framework for modeling multi-species site occupancy from eDNA data, estimating species presence and detectability despite imperfect detection. It supports diverse experimental designs, enables model comparison, and guides study design optimization by calculating minimal sampling effort to detect species, helping ecologists balance detection accuracy and resource allocation. C_FIG

ecology↗

bioRxiv2024

Improving the monitoring of the invasive Blue Crab (Callinectes sapidus): combining environmental DNA and citizen observations

O_LIEarly detection is a crucial tool for identifying the spread of invasive species. C_LIO_LIIn this study, we validated a probe-based quantitative polymerase chain reaction (qPCR) assay for the detection of the invasive Blue Crab, Callinectes sapidus, in the Mediterranean Sea, using 22 initial eDNA environmental samples (eDNA) collected from three coastal lagoons. C_LIO_LIA subsequent large-scale eDNA sampling campaign (61 samples in 31 sites), conducted in collaboration with local stakeholders, was carried out to map the distribution of Callinectes sapidus along the Occitanie coastline (Western Mediterranean, France). C_LIO_LIUsing eDNA probe-based qPCR, Callinectes sapidus was detected in 32 out the 61 samples (52%), confirming its presence in 24 out of 31 sites surveyed, including the 13 lagoons where its occurrence had already been reported, as well as two additional lagoons and at sea where no prior records existed. C_LIO_LIOur results demonstrate the utility of eDNA probe-based qPCR for effective monitoring the invasive Blue Crab. The integration of eDNA analysis with citizen science observations enhances the monitoring framework, facilitating early detection and contributing to improved management strategies at the very beginning of species colonization when practical actions could be implemented. C_LI

ecology↗

bioRxiv2024

Otolith shape variability of labrid fish from Rapa Nui (Easter Island), southeastern Pacific

Fish otolith shape provides valuable insights into the taxonomic, phylogenetic, and ecological traits of fish species. This study aimed to assess and compare the phenotypic variation in otolith shape among four labrid species (Anampses femininus, Coris debueni, Pseudolabrus fuentesi and Thalassoma lutescens) inhabiting Rapa Nui (Easter Island) in the southeastern Pacific Ocean, utilizing geometric morphometrics and aging methods. Age estimation based on otolith structure indicated that collected specimens were adults, ranging between 1 and 3 years old. Allometric analysis revealed low but significant variation (5.40%), primarily driven by changes in otolith width, resulting in distinct morphologies. Principal Component Analysis (PCA) of sagittal otoliths elucidated significant morphospace variation among species, with the first two PCs explaining 60.3% of the total variance. PC1 distinguished between elongated sagittal shapes (e.g., P. fuentesi) and robust sagittae (e.g., T. lutescens), while PC2 correlated with otolith roundness, delineating variations within species. Canonical variate analysis further highlighted differences in otolith shape, with significant variations detected among all species. The Discriminant function analysis showed high levels of discrimination accuracy for most of species pairs. Except for C. debueni-P. fuentesi (89%) and C. debueni-T. lutescens (96%), all other species pairs achieved 100% discrimination, highlighting the reliability of otolith shape as a distinguishing characteristic for the studied species. Overall, our findings emphasize the value of otolith shape analysis for characterizing and distinguishing Rapa Nui labrid species. This offers potential applications such as identifying prey within the digestive systems of large fish or bird predators in the vicinity of this isolated island in the South Pacific Ocean or archaeofauna studies.

zoology↗

bioRxiv2021

DNA reconciles morphology and colouration in the drunk blenny genus Scartichthys (Teleostei: Blenniidae) and provides insights into their evolutionary history

The blenniids of the genus Scartichthys are one of the most common fishes of Central and South American Pacific coastal reefs. This being said, Scartichthys spp. remain difficult to identify in the field, and identification is particularly challenging across the ca. 6000 km where three of the four currently accepted species are known to occur in sympatry. A reason for this is that the main taxonomic characters from traditional taxonomy are indeed elusive. Additionally, At the same time, species can display multiple colour patterns in the field, depending on their ontogenetic stage, habitat association, and reproductive behaviour. Overall, molecular characterization is warranted to help address these issues. Here, we have used a novel approach to revise the genus by combining colouration, morphological, and molecular data of representative specimens of the four currently valid species and seven described colour patterns. From this, we show that only three of the four species should be considered as valid; Scartichthys gigas (Steindachner, 1876), S. variolatus (Valenciennes, 1836), and S. viridis (Valenciennes, 1836); while S. crapulatus Williams 1990 should be synonymized with S. viridis. In the same way, our analyses show that one of the colour patterns attributed so far only to S. gigas is characteristic of the juvenile stages of S. viridis. Our time-calibrated phylogeny shows that this genus is relatively young and that the estimated time of divergence between Scartichthys gigas and S. viridis is around 1.71 Ma. In comparison, the Desventuradas and Juan Fernandez Islands endemic S. variolatus diverged about 1.95 Ma. Our results help to clarify the taxonomy of Scartichthys. SIGNIFICANCE STATEMENTThe blenniids of the genus Scartichthys are one of the most common fishes of Central and South American Pacific coastal reefs. Here we provide an updated phylogeny of this genus, comparing for the first time morphological, coloration, and molecular data in combination to resolve a 30-year-old discord among ecologists and taxonomists and discuss the potential underlying evolutionary processes that led to their presentday distribution.

zoology↗