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Projeto de investigação
Teaming to Upgrade to Excellence in Environmental Biology, Ecosystem Research and AgroBiodiversity
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Freshwater fish community assessment using eDNA metabarcoding vs. capture-based methods: Differences in efficiency and resolution coupled to habitat and ecology
Publication . Curto, Manuel; Batista, Sofia; Santos, Carlos D.; Ribeiro, Filipe; Nogueira, Sofia; Ribeiro, Diogo; Prindle, Benjamin; Licari, Daniel; Riccioni, Giulia; Dias, Diogo; Pina-Martins, Francisco; Jentoft, Sissel; Veríssimo, Ana; Alves, Maria Judite; Gante, Hugo F.
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, the adoption of eDNA as a standard protocol in long-term monitoring programs, which have traditionally relied on capture-based methods, presents 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 the majority of species or species-groups analysed individually (13 out of 17), a significant correspondence was observed between electrofishing and eDNA metabarcoding detections. A weaker correspondence was found between 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.
Predicting the expansion of invasive species: how much data do we need?
Publication . Santana, Joana; Sillero, Neftalí; Ribeiro, Joana; Capinha, César; Lopes, Ricardo Jorge; Reino, Luís
Ecological niche models (ENMs) are a powerful tool to predict the spread of invasive alien species (IAS) and support the implementation of actions aiming to reduce the impact of biological invasions. While calibrating ENMs with distribution data from species’ native ranges can underestimate the invasion potential due to possible niche shifts, using distribution data combining species’ native and invasive ranges may overestimate the invasion potential due to a reduced fitness and environmental tolerance of species in invaded ranges. An alternative may be using the increasingly available distribution data of IAS as they spread their invaded ranges, to iteratively forecast invasions as they unfold. However, while this approach accounts for possible niche shifts, it may also underestimate the species’ potential range, particularly at the early stages of the invasion when the most suitable conditions may not yet be represented in the distribution range data set. Here, we evaluate the capacity of ENMs to forecast the distribution of IAS based on distribution data on invaded ranges as these data become available. We further use dispersion models to assess the expansion process using the predicted potential distributions. Specifically, we used the common waxbill (Estrilda astrild) in the Iberian Peninsula as a model system. We built ENMs with 10×10 km grid cells distribution records cumulatively for each decade from 1960 to 2019, and yearly bioclimatic variables, to forecast the species potential range in the coming decades. Then, we assessed the performance of the models for each decade in forecasting the species’ observed range expansion in the following decades and evaluated how the number of distribution records determined the quality of the forecasts. Finally, we performed dispersal estimates (based on species traits, topography, climate and land cover) to analyse the prediction capacity of models as their uncertainty may be reduced when projecting them to the next decades. Our results show that invasion-only ENMs successfully forecasted the species’ range expansion over three decades after invasion, while dispersion models were not important in forecasting common waxbill expansion. Our study highlights the importance of constantly monitoring alien species, suggesting that iterative updating of ENMs with observed distribution data may accurately forecast the range expansion of alien species.
High‑resolution species distribution modelling reveals spatio‑temporal variability of habitat suitability in a declining grassland bird
Publication . Crispim‑Mendes, Tiago; Valerio, Francesco; Marques, Ana Teresa; Pita, Ricardo; Godinho, Sérgio; Silva, João Paulo
Context Species distribution models (SDMs) may
provide accurate predictions of species occurrence
across space and time, being critical for effective con-
servation planning.
Objectives Focusing on the little bustard (Tetrax
tetrax), an endangered grassland bird, we aimed to:
(i) characterise the drivers of the species distribution
along its key phenological phases (winter, breeding,
and post-breeding); and (ii) quantify spatio-temporal
variation in habitat suitability across phenological
phases and over the years 2005–2021.
Methods Combining remotely sensed metrics at
high temporal resolution (MODIS) with long-term
(> 12 years) GPS telemetry data collected for 91 individuals at one of the species’ main strongholds
within the Iberian Peninsula, we built SDMs (250 m
resolution) for the species key phenological phases.
Results The use of both dynamic and static pre-
dictors unveiled previously unknown ecological
responses by little bustards, revealing a marked
change in the spatial distribution of suitable habitat
among phenological phases. Long-term habitat suita-
bility trends showed considerable fluctuations, mainly
in the breeding and post-breeding phases. Overall,
SDM projections into the past revealed that while
the species’ winter and post-breeding habitats appar-
ently increased since 2005, suitable habitat during the
species’ most critical phenological phase, breeding,
apparently reduced in area over time.
Conclusions Our findings show that matching
remotely sensed data with GPS tracking data results
in accurate habitat suitability predictions throughout the yearly cycle. Additionally, our findings stress the
importance of quantifying habitat loss and its poten-
tial impact on little bustard decline over nearly 20
years. Spatio-temporal variations in habitat suitability
are also identified in this work, which can help pri-
oritize conservation areas, particularly the breeding
areas that have remained stable over time, as this is a
key requirement for little bustard lek breeding system.
Multi-species occupancy modeling reveals methodological and environmental effects on eDNA detection of amphibians in temporary ponds
Publication . Peixoto, Sara; Mota-Ferreira, Mário; Chaves, Cátia; Velo-Antón, Guillermo; Beja, Pedro; Egeter, Bastian
Aquatic environmental DNA is increasingly used for biodiversity monitoring, such as
surveying threatened and invasive species. Mainstreaming these methods in practi-
cal applications, however, still requires significant standardization and optimisation,
namely regarding DNA capture methods. Here we evaluated how filter type (standard
disc filters vs high-capacity capsules), number of sampling sites, volume of water fil-
tered and environmental factors affected amphibian detection in Mediterranean tem -
porary ponds. The study involved water filtering until clogging at one (capsules) and
five (discs) sites from 16 small and shallow ponds, where three urodele and seven anu-
ran species were recorded through sweep- netting and adult observations. Detection
probabilities were estimated from site occupancy models based on replicate sampling
and from an adaptation of time-to-detection models relating detection probability to
volume of water filtered. Discs filtered relatively small volumes (15–1250 mL), with
detection probabilities of the two abundant species (Pelobates cultripes, Hyla meridi-
onalis) increasing rapidly with sample size and water volume, reaching almost per-
fect detection (0.95) at four and seven discs, and 420 mL and 1860 mL, respectively.
However, reaching high detection probabilities for rare species (Pelodytes atlanticus,
Pleurodeles waltl, Triturus pygmaeus) would require larger sampling effort than that
used in our study. Despite filtering much larger volumes (600–5300 mL), filtering with
capsules at a single site per pond provided lower detection probabilities for abun-
dant species than filtering with discs at five sites. Rarer species showed no difference
between methods, which may be due to small sample sizes and reduced statistical
power for species with few detections. The effect of conductivity on species detect-
ability was largely negative, while the influence of water clarity varied across species,
and pH had no effects. Overall, our results suggest that eDNA amphibian surveys
in Mediterranean temporary ponds need to consider filter clogging, heterogeneous
DNA distribution, and highly conductive waters
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Entidade financiadora
European Commission
Programa de financiamento
H2020
Número da atribuição
857251