Biology subjects

Coscia, I.

Publications and source records attributed to Coscia, I..

11 recordsLinked to original sources

bioRxiv2025

Multi-seasonal eDNA metabarcoding highlights a resurgence in fish diversity across a severely impacted estuarine ecosystem

Aquatic ecosystems have been in an alarming state of decline for decades. Therefore, there is an urgent need for more accessible and rapid monitoring methods that will ultimately allow for restoration programmes to be implemented. In this study, we deployed environmental DNA (eDNA) metabarcoding as a fish monitoring tool in the Mersey estuarine system (UK), where ecosystem productivity has been severely impacted by water quality degradation since the Industrial Revolution. Monthly water samples were collected over a year (2023-2024) throughout the estuary, covering saline, brackish and freshwater zones. Overall, 69 species of fish were detected, increasing the number of known species within the estuary in comparison to both historical and contemporary records (46 and 39, respectively), with a generally higher observed richness within the upper estuary sampled zones where the water chemistry is predominantly freshwater. Notably, we identified several species returning to the system for the first time since pre-industrial times. Peak species richness was recorded during the winter season (December-February). Species compositions varied significantly by month and spatially by zone within months, but not when grouped seasonally. Furthermore, around [~]15% of the species detected were diadromous, with the endangered Atlantic salmon Salmo salar, for example, being frequently detected during its key migratory period. This study highlights the resurgence in fish diversity in a once biologically depleted estuarine ecosystem and demonstrates how eDNA metabarcoding can be implemented for detecting historically absent species, thereby enhancing restoration monitoring efforts globally.

ecology↗

bioRxiv2024

Performance of eDNA capture methods for monitoring fish biodiversity in a hyper-tidal estuary

Environmental DNA (eDNA) has become an established and efficient method for monitoring biodiversity in aquatic systems. However, there is a need to compare and standardise sampling methods across ecosystem types, particularly complex ecosystems such as estuaries where unique challenges for monitoring fish populations are present due to fluctuating environmental factors. Here, we compare fish biodiversity metrics obtained from eDNA metabarcoding data using four different eDNA filtering methods: three manual filtering methods with different pore sizes (0.45, 1.2 and 5 {micro}m) and a newly established passive method, the metaprobe. The study was applied across a salinity gradient in a hyper-tidal estuarine ecosystem. Overall, 44 fish species were detected across the four methods used. The 0.45 {micro}m filter recovered the highest richness (39 species), then the metaprobe method (35), followed by the 1.2 {micro}m (34) and 5 {micro}m (33) filters. Filter performance between salinity gradients revealed that the 0.45 {micro}m and the 1.2 {micro}m methods recovered the highest species richness across all sampled zones. The 0.45 {micro}m also had the most consistent detection probabilities using representative species from each zone. While the 0.45 {micro}m method appeared to be the optimal method, each of the methods can be considered as a viable and comparable option for biomonitoring in dynamic ecosystems such as estuaries and rivers. In particular, the passive metaprobe (used in a freshwater system for the first time here) performed well in comparison to the manual filtering methods despite a short deployment time. This study provides critical insights for optimising fish biodiversity assessments using eDNA metabarcoding in estuarine ecosystems, providing a valuable framework for future monitoring efforts in similar systems worldwide.

molecular biology↗

bioRxiv2023

Using Environmental DNA to Reconstruct Amphibian Communities at Sites Infected with Batrachochytrium salamandrivorans in the Netherlands

AO_SCPLOWBSTRACTC_SCPLOWThe recently discovered Batrachochytrium salamandrivorans (Bsal) fungus can cause high mortality rates in some European salamanders and newts (urodelans) and has the potential to expand its currently small invasive range in Europe. Therefore, monitoring its distribution and better understanding both the species threatened and the mechanics of infection are essential in mitigating the damage Bsal may cause. Environmental DNA (eDNA) has emerged as a promising non-invasive method for detecting both this fungal pathogen and the amphibian communities in infected areas. We applied these methods in the province Gelderland, the Netherlands where the pathogen has previously been detected and is expanding its range, with the goal of detecting the natural amphibian community present. We sampled 27 water bodies in the region surrounding the known outbreak sites. We used data from a Bsal-specific qPCR assay to determine its presence-absence and applied an eDNA metabarcoding approach to characterize the amphibian communities using two different primer sets. The 12S vertebrate primer set outperformed the 16S amphibian primer set and detected all the expected amphibians in the study area: Bufo bufo, Lissotriton vulgaris, Pelobates fuscus, Pelophylax spp., Rana temporaria and Triturus cristatus. Bsal was detected at eight of the ponds. A distance-based redundancy analysis found a weak but significant relationship between Bsal presence and the composition of amphibian communities using eDNA. This study provides the foundation for future studies on Bsal and its relationship with amphibian communities in Europe, highlighting the need for further research into the mechanisms of persistence and transmission between water bodies.

ecology↗

bioRxiv2021

Evidence of stock connectivity, hybridization and misidentification in white anglerfish support the need for adopting a genetics-informed fisheries management approach

Understanding population connectivity within a species as well as potential interactions with its close relatives is crucial to define management units and to derive efficient management actions. However, although genetics can reveal mismatches between biological and management units and other relevant but hidden information such as species misidentification or hybridization, the uptake of genetic methods by the fisheries management process is far from having been consolidated. Here, we have assessed the power of genetics to better understand the population connectivity of white angelfish (Lophius piscatorius) and its interaction with its sister species, the black anglerfish (L. budegassa). Our analyses, based on thousands of genome-wide single nucleotide polymorphisms, show three findings that are crucial for white anglerfish management. We found i) that white anglerfish is likely composed of a single panmictic population throughout the Northeast Atlantic, challenging the three-stock based management, ii) that a fraction of specimens classified as white anglerfish using morphological characteristics are genetically identified as black anglerfish (L. budegassa) and iii) that the two Lophius species naturally hybridize leading to a population of hybrids of up to 20% in certain areas. Our results set the basics for a genetics-informed white anglerfish assessment framework that accounts for stock connectivity, revises and establishes new diagnostic characters for Lophius species identification and evaluates the effect of hybrids in the current and future assessments of the white anglerfish. Furthermore, our study contributes to provide additional evidence of the potentially negative consequences of ignoring genetic data for assessing fisheries resources.

evolutionary biology↗

bioRxiv2021

eDNA in a bottleneck: obstacles to fish metabarcoding studies in megadiverse freshwater systems

The current capacity of environmental DNA (eDNA) to provide accurate insights into the biodiversity of megadiverse regions (e.g., the Neotropics) requires further evaluation to ensure its reliability for long-term monitoring. In this study, we first evaluated the taxonomic resolution capabilities of a short fragment from the 12S rRNA gene widely used in fish eDNA metabarcoding studies, and then compared eDNA metabarcoding data from water samples with traditional sampling using nets. For the taxonomic discriminatory power analysis, we used a specifically curated reference dataset consisting of 373 sequences from 264 neotropical fish species (including 47 newly generated sequences) to perform a genetic distance-based analysis of the amplicons targeted by the MiFish primer set. We obtained an optimum delimitation threshold value of 0.5% due to lowest cumulative errors. The barcoding gap analysis revealed only a 50.38% success rate in species recovery (133/264), highlighting a poor taxonomic resolution from the targeted amplicon. To evaluate the empirical performance of this amplicon for biomonitoring, we assessed fish biodiversity using eDNA metabarcoding from water samples collected from the Amazon (Adolpho Ducke Forest Reserve and two additional locations outside the Reserve). From a total of 84 identified Molecular Operational Taxonomic Units (MOTUs), only four could be assigned to species level using a fixed threshold. Measures of -diversity analyses within the Reserve showed similar patterns in each site between the number of MOTUs (eDNA dataset) and species (netting data) found. However, {beta}-diversity revealed contrasting patterns between the methods. We therefore suggest that a new approach is needed, underpinned by sound taxonomic knowledge, and a more thorough evaluation of better molecular identification procedures such as multi-marker metabarcoding approaches and tailor-made (i.e., order-specific) taxonomic delimitation thresholds.

ecology↗

bioRxiv2020

Next-generation phylogeography resolves post-glacial colonization patterns in a widespread carnivore, the red fox (Vulpes vulpes), in Europe.

Carnivores tend to exhibit a lack of (or less pronounced) genetic structure at continental scales in both a geographic and temporal sense and this can confound the identification of post-glacial colonization patterns in this group. In this study we used genome-wide data (using Genotyping-by-Sequencing (GBS)) to reconstruct the phylogeographic history of a widespread carnivore, the red fox (Vulpes vulpes), by investigating broad-scale patterns of genomic variation, differentiation and admixture amongst contemporary populations in Europe. Using 15,003 single nucleotide polymorphisms (SNPs) from 524 individuals allowed us to identify the importance of refugial regions for the red fox in terms of endemism (e.g. Iberia). In addition, we tested multiple post-glacial re-colonization scenarios of previously glaciated regions during the Last Glacial Maximum using an Approximate Bayesian Computation (ABC) approach that were unresolved from previous studies. This allowed us to identify the role of admixture from multiple source population post-Younger Dryas in the case of Scandinavia and ancient land-bridges in the colonization of the British Isles. A natural colonization of Ireland was deemed more likely than an ancient human-mediated introduction as has previously been proposed and potentially points to an increased mammalian fauna on the island in the early post-glacial period. Using genome-wide data has allowed us to tease apart broad-scale patterns of structure and diversity in a widespread carnivore in Europe that was not evident from using more limited marker sets and provides a foundation for next-generation phylogeographic studies in other non-model species.

evolutionary biology↗

bioRxiv2020

Space-time dynamics in monitoring neotropical fish communities using eDNA metabarcoding

The biodiverse Neotropical ecoregion remains insufficiently assessed, poorly managed, and threatened by unregulated human activities. Novel, rapid and cost-effective DNA-based approaches are valuable to improve understanding of the biological communities and for biomonitoring in remote areas. Here, we evaluate the potential of environmental DNA (eDNA) metabarcoding for assessing the structure and distribution of fish communities by analysing sediments and water from 11 locations along the Jequitinhonha River catchment (Brazil). Each site was sampled twice, before and after a major rain event in a five-week period and fish diversity was estimated using high-through-put sequencing of 12S rRNA amplicons. In total, 252 Molecular Operational Taxonomic Units (MOTUs) and 34 fish species were recovered, including endemic, introduced, and previously unrecorded species for this basin. Spatio-temporal variation of fish assemblages was detected, richness during the first campaign was nearly twice as high as in the second sampling round; though peaks of diversity were primarily associated with only four locations. No correlation between {beta}-diversity and longitudinal distance or presence of dams was detected, but low species richness observed at sites located near dams indicates that these anthropogenic barriers might have an impact on local fish diversity. Unexpectedly high -diversity levels recorded at the river mouth suggest that these sections should be further evaluated as putative "eDNA reservoirs" for rapid monitoring. By uncovering spatio-temporal changes, unrecorded biodiversity components, and putative anthropogenic impacts on fish assemblages, we further strengthen the potential of eDNA metabarcoding as a biomonitoring tool, especially in regions often neglected or difficult to access.

ecology↗

bioRxiv2019

Assessing the potential of environmental DNA metabarcoding for monitoring Neotropical mammals: a case study in the Amazon and Atlantic Forest, Brazil

The application of environmental DNA (eDNA) metabarcoding as a biomonitoring tool has greatly increased in the last decade. However, most studies have focused on aquatic macro-organisms in temperate areas (e.g., fishes). We apply eDNA metabarcoding to detect the mammalian community in two high-biodiversity regions of Brazil, the Amazon and Atlantic Forest. We identified critically endangered and endangered mammalian species in the Atlantic Forest and Amazon respectively and found congruence with species identified via camera trapping in the Atlantic Forest. In light of our results, we highlight the potential and challenges of eDNA monitoring for mammals in these high biodiverse areas.

ecology↗

bioRxiv2019

Fine-scale seascape genomics of an exploited marine species, the common cockle Cerastoderma edule, using a multi-modelling approach

Population dynamics of marine species that are sessile as adults are driven by oceanographic dispersal of larvae from spawning to nursery grounds. This is mediated by life-history traits such as the timing and frequency of spawning, larval behaviour and duration, and settlement success. Here, we use 1725 single nucleotide polymorphisms (SNPs) to study the fine scale spatial genetic structure in the commercially important cockle species Cerastoderma edule and compare it to environmental variables and current-mediated larval dispersal within a modelling framework. Hydrodynamic modelling employing the NEMO Atlantic Margin Model (AMM15) was used to simulate larval transport and estimate connectivity between populations during spawning months (April - September), factoring in larval duration and seasonal variability of ocean currents. Results at neutral loci reveal the existence of three separate genetic clusters (mean FST=0.021) within a relatively fine spatial scale in the northwest Atlantic. Environmental association (EA) analysis indicates that oceanographic currents and geographical distance between the populations explain over 20% of the variance observed at neutral loci, while genetic variance (71%) at outlier loci was explained by sea surface temperatures extremes. These results fill an important knowledge gap in the management of a commercially important, overexploited species, and bring us closer to understanding the role of larval dispersal in connecting populations at a fine geographical scale.

evolutionary biology↗

bioRxiv2019

Fishing for mammals: landscape-level monitoring of terrestrial and semi-aquatic communities using eDNA from lotic ecosystems

O_LIEnvironmental DNA (eDNA) metabarcoding has revolutionised biomonitoring in both marine and freshwater ecosystems. However, for semi-aquatic and terrestrial animals, the application of this technique remains relatively untested.\nC_LIO_LIWe first assess the efficiency of eDNA metabarcoding in detecting semi-aquatic and terrestrial mammals in natural lotic ecosystems in the UK by comparing sequence data recovered from water and sediment samples to the mammalian communities expected from historical data. Secondly, we evaluate the detection efficiency of eDNA samples compared to multiple conventional non-invasive survey methods (latrine surveys and camera trapping) using occupancy modelling.\nC_LIO_LIeDNA metabarcoding detected a large proportion of the expected mammalian community within each area. Common species in the areas were detected at the majority of sites. Several key species of conservation concern in the UK were detected by eDNA in areas where authenticated records do not currently exist, but potential false positives were also identified for several non-native species.\nC_LIO_LIWater-based eDNA samples provided comparable results to conventional survey methods in per unit of survey effort for three species (water vole, field vole, and red deer) using occupancy models. The comparison between survey effort to reach a detection probability of [≥]0.95 revealed that 3-6 water replicates would be equivalent to 3-5 latrine surveys and 5-30 weeks of single camera deployment, depending on the species.\nC_LIO_LISynthesis and Applications. eDNA metabarcoding represents an extremely promising tool for monitoring mammals, allowing for the detection of multiple species simultaneously, and provides comparable results to widely-used conventional survey methods. eDNA from freshwater systems delivers a terrestrial dividend by detecting both semi-aquatic and terrestrial mammalian communities, and provides a basis for future monitoring at a landscape level over larger spatial and temporal scales (i.e. long-term monitoring at national levels).\nC_LI

ecology↗

bioRxiv2018

Environmental DNA metabarcoding as an effective and rapid tool for fish monitoring in canals

Environmental DNA (eDNA) metabarcoding has revolutionized biomonitoring of aquatic habitats. Man-made canal systems are among the least-studied environments in terms of biodiversity in Britain. Here we focus on a case study along an English canal comparing eDNA metabarcoding with two types of electrofishing techniques (wade-and-reach and boom-boat). In addition to corroborating data obtained by electrofishing, eDNA provided a wider snapshot of fish assemblages. Given the semi-lotic nature of canals, we encourage the use of eDNA as a fast and cost-effective tool to detect and monitor whole fish communities.

ecology↗