Biology subjects

Santos, C. D.

Publications and source records attributed to Santos, C. D..

3 recordsLinked to original sources

bioRxiv2025

Freshwater fish community assessment using eDNA metabarcoding vs. capture-based methods: differences in efficiency and resolution coupled to habitat and ecology

Environmental DNA (eDNA) metabarcoding has revolutionized ecological and environmental research by describing communities without relying on direct observations, making it a powerful, non-invasive, and cost-effective tool in biodiversity monitoring. However, implementation of eDNA as a standard protocol in long-term monitoring programs, that have traditionally relied on capture-based methods, poses challenges in terms of data comparability. Here, we compared freshwater fish communities assessed through eDNA metabarcoding and electrofishing, across 35 sampling sites in the lower Tagus River basin, Portugal. For most species or species-groups analyzed individually (13 out of 17), there was a significant correspondence between electrofishing and eDNA metabarcoding detections. The correspondence was weaker when comparing the number of specimens captured by electrofishing with the number of eDNA metabarcoding reads, with seven out of 13 taxa showing significant relationships. Species richness estimates based on the two methods were very similar at the basin level. The methods yielded significantly different species compositions, although these differences were driven by samples collected in the Tagus main channel, which is wider and has higher flow rates than tributaries. Benthic and shoreline fish communities showed similar species composition in the two methods, but this was not the case for pelagic communities, probably due to the higher water turnover of the pelagic zone and electrofishing inefficiency. Our results highlight the high potential of eDNA metabarcoding as a complementary method to electrofishing for freshwater fish monitoring, though further validation is needed to assess biases related to site-specific hydrological conditions and the ecology of the target species.

ecology↗

bioRxiv2024

Improving whole biodiversity monitoring and discovery with environmental DNA metagenomics

Environmental DNA (eDNA) metagenomics sequences all DNA molecules present in environmental samples and has the potential of identifying virtually any organism from which they are derived. However, due to unacceptable levels of false positives and negatives, this approach is underexplored as a tool for biodiversity monitoring across the tree of life, particularly for non-microscopic eukaryotes. We present SEQIDIST, a framework that combines multilocus BLAST matches against several reference databases followed by analysis of sequence identity distribution patterns to disentangle false positives while revealing new biodiversity and increasing the accuracy of metagenomic approaches. We tested SEQIDIST on an eDNA metagenomic dataset from a riverine site and compare the results to those obtained with an eDNA metabarcoding approach for benchmarking purposes. We start by characterizing the biological community ([~] 2000 taxa) across the tree of life at low taxonomic levels and show that eDNA metagenomics has a higher sensitivity than eDNA metabarcoding in discovering new diversity. We show that limited representation of whole genome sequences in reference databases can lead to false positives. For non-microscopic eukaryotes, eDNA metagenomic data often consist of a few sparse, anonymous sequences scattered across the genome, making metagenome assembly methods unfeasible. Finally, we infer eDNA source and residency time using read length distributions as a measure of decay status. The higher accuracy of SEQIDIST opens the discussion of the archival potential of eDNA metagenomics and its implementation in biodiversity monitoring actions at large planetary and temporal scales.

ecology↗

bioRxiv2022

Extreme tolerable winds for seabirds are determined by morphology

Storms can cause widespread seabird strandings and wrecking1,2,3,4,5, yet little is known about the maximum wind speeds that birds are able to tolerate or the conditions they avoid. We analyzed > 300,000 hours of tracking data from 18 seabird species, including flapping and soaring fliers, to assess how flight morphology affects wind selectivity, both at fine scales (hourly movement steps) and across the breeding season. We found no general preference or avoidance of particular wind speeds within foraging tracks. This suggests seabird flight morphology is adapted to a "wind niche", with higher wing loading being selected for in windier environments. In support of this, wing loading was positively related to the median wind speeds on the breeding grounds, as well as the maximum wind speeds in which birds flew. Yet globally, the highest wind speeds occur in the tropics (in association with tropical cyclones) where birds are morphologically adapted to low median wind speeds. Tropical species must therefore show behavioral responses to extreme winds, including long-range avoidance of wind speeds that can be twice their operable maxima. In contrast, procellariiformes flew in almost all wind speeds they encountered at a seasonal scale. Despite this, we describe a small number of cases where albatrosses avoided strong winds at close-range, including by flying into the eye of the storm. Extreme winds appear to pose context- dependent risks to seabirds, and more information is needed on the factors that determine the hierarchy of risk, given the impact of global change on storm intensity 6,7.

animal behavior and cognition↗