Biology subjects

Sales, N.

Publications and source records attributed to Sales, N..

6 recordsLinked to original sources

bioRxiv2025

DNA metabarcoding and environmental DNA across Brazilian biomes: trends, challenges, and conservation applications

Brazil harbors the greatest biodiversity on the planet; however, the application of emerging technologies to enhance biodiversity assessment and monitoring remains limited. In recent years, DNA metabarcoding and environmental DNA (eDNA) surveys have revolutionized the assessment of biodiversity, offering new tools to evaluate ecological and conservation trends and patterns worldwide. Yet, their application in Brazil is still in its early stages, underscoring the paradox of a megadiverse country with limited adoption of cutting-edge tools for monitoring its natural wealth. This review provides a comprehensive synthesis of the application of DNA metabarcoding and eDNA analyses across different ecosystems in Brazil, integrating findings from 47 studies published between 2015 and 2025. Trends in ecosystem types, taxonomic groups, molecular markers, geographic distribution, and patterns of authorship and funding were analyzed. Most studies focused on terrestrial (42.5%) and freshwater (34%) environments, followed by marine (19.1%) and estuarine (4.2%) systems. DNA metabarcoding predominated in terrestrial studies (52.1%), while eDNA was more frequent in freshwater, marine, and estuarine environments. The mitochondrial 12S marker was the most widely used, primarily for detecting fish and amphibians. We observed a predominance of Brazilian first and senior authors, with weak signs of parachute science. However, challenges persist, including limited access to funding and underrepresentation of some biomes and taxonomic groups. Our findings highlight a growing national capacity in the use of DNA metabarcoding and eDNA research while underscoring the need for strategic investments in infrastructure, database development, and equitable scientific collaboration.

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↗

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↗

bioRxiv2023

Coupling remote sensing and eDNA to monitor environmental impact: A pilot to quantify the environmental benefits of sustainable agriculture in the Brazilian Amazon

Monitoring is essential to ensure that environmental goals are being achieved, including those of sustainable agriculture. Growing interest in environmental monitoring provides an opportunity to improve monitoring practices. Approaches that directly monitor land cover change and biodiversity annually by coupling the wall-to-wall coverage from remote sensing and the site-specific community composition from environmental DNA (eDNA) can provide timely, relevant results for parties interested in the success of sustainable agricultural practices. To ensure that the measured impacts are due to the environmental projects and not exogenous factors, sites where projects have been implemented should be benchmarked against counterfactuals (no project) and control (natural habitat) sites. Results can then be used to calculate diverse sets of indicators customized to monitor different projects. Here, we report on our experience developing and applying one such approach to assess the impact of shaded cocoa projects implemented by the Instituto de Manejo e Certificacao Florestal e Agricola (IMAFLORA) near Sao Felix do Xingu, in Para, Brazil. We used the Continuous Degradation Detection (CODED) and LandTrendr algorithms to create a remote sensing-based assessment of forest disturbance and regeneration, estimate carbon sequestration, and changes in essential habitats. We coupled these remote sensing methods with eDNA analyses using arthropod-targeted primers by collecting soil samples from intervention and counterfactual pasture field sites and a control secondary forest. We used a custom set of indicators from the pilot application of a coupled monitoring framework called TerraBio. Our results suggest that, due to IMAFLORAs shaded cocoa projects, over 400 acres were restored in the intervention area and the community composition of arthropods in shaded cocoa is closer to second-growth forests than that of pastures. In reviewing the coupled approach, we found multiple aspects worked well, and we conclude by presenting multiple lessons learned.

ecology↗

bioRxiv2022

Shark-dust: High-throughput DNA sequencing of processing residues unveils widespread trade in threatened sharks and rays

Illegal fishing, unregulated bycatch, and market demand for certain products (e.g. fins) are largely responsible for the rapid global decline of shark and ray populations. Controlling trade of endangered species remains difficult due to product variety, taxonomic ambiguity and trade complexity. The genetic tools traditionally used to identify traded species typically target individual tissue samples, are time-consuming and/or species-specific. Here, we performed high-throughput sequencing of trace DNA fragments retrieved from dust and scraps left behind by trade activities. We metabarcoded shark-dust samples from seven processing plants in the worlds biggest shark landing site (Java, Indonesia), and identified 54 shark and ray taxa (representing half of all chondrichthyan orders), half of which could not be recovered from tissue samples collected in parallel from the same sites. Importantly, over 80% of shark-dust sequences were found to belong to CITES-listed species. We argue that this approach is likely to become a powerful and cost-effective monitoring tool wherever wildlife is traded. One-Sentence SummaryShark-dust, the traces of biological material left behind from the processing of shark products, can now be DNA-sequenced in bulk to accurately reconstruct the biodiversity underlying trade.

genetics↗