Pedro Beja

Pedro Beja
University of Porto | UP · Centro de Investigação em Biodiversidade e Recursos Genéticos (CIBIO)

PhD

About

374
Publications
143,596
Reads
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8,179
Citations
Citations since 2017
183 Research Items
5104 Citations
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Introduction
Deputy Director and EDP Biodiversity Chair at CIBIO - Research Centre in Biodiversity and Genetic Resources and InBIO – Research Network in Biodiversity and Evolutionary Biology (Portugal). Conservation biologist interested in the natural and anthropogenic drivers of biodiversity change in human-dominated landscapes. Involved in the application of conservation science, from species reintroductions and thecreation and management of protected areas, to impact assessment and corporate biodiversity.
Additional affiliations
January 2007 - December 2012
University of Porto
January 1999 - December 2009
Education
January 1991 - December 1995
University of Aberdeen
Field of study
  • Zoology
September 1983 - November 1989
University of Lisbon
Field of study
  • Biology

Publications

Publications (374)
Article
1.Spatial variation in species composition (β-diversity) is an important component of farmland biodiversity, which together with local richness (α-diversity) drives the number of species in a region (γ-diversity). However, β-diversity is seldom used to inform conservation, due to limited understanding of its responses to agricultural management, an...
Article
Full-text available
Conserving biodiversity on farmland is an essential element of worldwide efforts for reversing the global biodiversity decline. Common approaches involve improving the natural component of the landscape by increasing the amount of natural and seminatural habitats (e.g., hedgerows, woodlots, and ponds) or improving the production component of the la...
Article
Full-text available
Mitigating conflicts associated with predation on livestock is essential for conserving large carnivores in human dominated landscapes. This is generally addressed by targeting at individual management practices affecting predation risk, often disregarding that different livestock husbandry systems (i.e., groups of farms sharing similar resource ba...
Article
Full-text available
In bats, sexual segregation has been described in relation to differential use of roosting and foraging habitats. It is possible that variation may also exist between genders in the use of different prey types. However, until recently this idea was difficult to test due to poorly resolved taxonomy of dietary studies. Here we use high throughput seq...
Article
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Assessing the spatio-temporal impact of agricultural intensification on species and communities is key for biodiversity conservation. Here, we investigated the seasonal effects of olive grove intensification at both local (farming practices and grove structural complexity) and landscape scale (land-cover diversity) on birds and bats, at species and...
Article
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Background The Trichoptera are an important component of freshwater ecosystems. In the Iberian Peninsula, 380 taxa of caddisflies are known, with nearly 1/3 of the total species being endemic in the region. A reference collection of morphologically identified Trichoptera specimens, representing 142 Iberian taxa, was constructed. The InBIO Barcoding...
Article
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Monitoring the occupancy and abundance of wildlife populations is key to evaluate their conservation status and trends. However, estimating these parameters often involves time and resource-intensive techniques, which are logistically challenging or even unfeasible for rare and elusive species that occur patchily and in small numbers. Hence, survey...
Article
Information about biotic interactions (e.g. competition, predation, parasitism, diseases, mutualism, allelopathy) is fundamental to better understand species distribution and abundance, ecosystem functioning, and ultimately guide conservation efforts. However, conservation planning often overlooks these important interactions. Here, we aim to demon...
Article
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Bees are a diverse group with more than 1000 species known from the Iberian Peninsula. They have increasingly received special attention due to their important role as pollinators and providers of ecosystem services. In addition, various rapid human-induced environmental changes are leading to the decline of some of its populations. However, we kno...
Article
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Arthropod declines have been linked to agricultural intensification. However, information about the impacts of intensification is still limited for many crops, as is our understanding of the responses of different arthropod taxa and trophic groups, thus hindering the development of effective mitigation measures. We investigated the impacts of olive...
Article
Full-text available
Aim: Reconstructing species' glacial refugial history and demographic changes over time has greatly relied on comparing inferences from multiple methods while not sufficiently acknowledging their limitations. Here, we aim to integrate as fully as possible complementary methods in ecology, genomics and palaeobiology to improve the reconstruction of...
Article
Full-text available
Over the last 30 years, olive farming has experienced a fast and large-scale intensification process across its Mediterranean range, that is reshaping Mediterranean farmland landscapes with associated impacts on biodiversity and ecosystem services. This study aims to analyze irrigated olive grove spatial expansion patterns across a 27–year period i...
Article
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Recent advances in molecular biomonitoring open new horizons for aquatic ecosystem assessment. Rapid and cost-effective methods based on organismal DNA or environmental DNA (eDNA) now offer the opportunity to produce inventories of indicator taxa that can subsequently be used to assess biodiversity and ecological quality. However, the integration o...
Conference Paper
The Douro is a unique region of deep valleys and Mediterranean character, nestled between two important Portuguese mountains and the Iberian plateau. The original geological, morphological, and climatic characteristics allow for the survival of an extraordinary diversity of plants and animals, which is why this territory has been occupied, since pr...
Data
The dataset contains eight records of moth specimens (Lepidoptera, Ypsolophidae) collected in 2019 in continental Portugal. Specimens were detected and captured by direct search of the environment during the day, with adults’ hand-netted and larvae reared to adulthood, and by night using mercury-vapor lamps or UV light traps to attract the insects....
Article
Large scale afforestation (i.e., establishment of forests on farmland, grassland and other land not previously forested) is increasingly regarded as a cost-effective option to mitigate climate change by promoting carbon sequestration. However, this strategy can have negative biodiversity impacts, potentially causing the loss and fragmentation of op...
Article
Agricultural policies in the European Union (EU) are increasingly promoting organic management and integrated pest management (IPM) as environmentally friendly alternatives to high-input conventional management. While there is consensus that organic management is largely beneficial for biodiversity, including the natural enemies of crop pests, IPM...
Preprint
Full-text available
In this report, we present the analysis of the different available biodiversity data streams at the EU and national level, both baseline biodiversity data and monitoring data. We assess how these biodiversity data inform and trigger policy action and identify the related challenges the different European countries and relevant EU agencies face and...
Article
Full-text available
Evaluating species responses to anthropogenic infrastructures and other habitat changes is often used to assess environmental impacts and to guide conservation actions. However, such studies are generally carried out at the population-level, disregarding inter-individual variability. Here, we investigate population- and individual-level responses t...
Article
Full-text available
Traditional detection of aquatic invasive species via morphological identification is often time-consuming and can require a high level of taxonomic expertise, leading to delayed mitigation responses. Environmental DNA (eDNA) detection approaches of multiple species using Illumina-based sequencing technology have been used to overcome these hindran...
Preprint
Full-text available
Observations are key to understand the drivers of biodiversity loss, and the impacts on ecosystem services and ultimately on people. Many EU policies and initiatives demand unbiased, integrated and regularly updated biodiversity and ecosystem service data. However, efforts to monitor biodiversity are spatially and temporally fragmented, taxonomical...
Article
The sudden loss of habitats due to natural or anthropogenic disturbances causes displacement of mobile animals from affected areas to refuge habitats, where large but often transitory concentrations of individuals may occur. While these local density increases have been previously described, the hypothesis that crowding disrupts demographic process...
Article
• In farmland landscapes worldwide, there are pervasive trends for either intensification or abandonment. Intensification is a widely recognised driver of wild bee declines, but little is known about the consequences of land abandonment, though it involves major habitat shifts from fallows, pastures and meadows, to shrublands and forests. • Focusin...
Data
Supporting Information for Morgado et al., 2021 - Preserving wintering frugivorous birds in agro‐ecosystems under land use change: Lessons from intensive and super‐intensive olive orchards
Article
Full-text available
The InBIO Barcoding Initiative (IBI) Diptera 02 dataset contains records of 412 crane fly specimens belonging to the Diptera families: Limoniidae, Pediciidae and Tipulidae. This dataset is the second release by IBI on Diptera and it greatly increases the knowledge on the DNA barcodes and distribution of crane flies from Portugal. All specimens were...
Article
Aim The road network is increasing globally but the consequences of roadkill on the viability of wildlife populations are largely unknown. We provide a framework that allows us to estimate how risk of extinction of local populations increases due to roadkill and to generate a global assessment that identifies which mammalian species are most vulner...
Article
Full-text available
Fleshy‐fruit production is becoming more intensive worldwide, but how this affects frugivorous birds is poorly known. In the Mediterranean region, intensive and super‐intensive olive orchards are fast expanding, potentially affecting millions of wintering songbirds. Here we test the idea that intensification may benefit frugivorous birds, at least...
Article
Full-text available
The orders Neuroptera and Raphidioptera include the species of insects known as lacewings and snake-flies, respectively. In Portugal, these groups account for over 100 species, some of which are very difficult to identify by morphological analysis. This work is the first to sample and DNA sequence lacewings and snakeflies of Portugal. A reference c...
Data
The dataset contains 135 records of Hemiptera species collected from 2015 to 2019 in continental Portugal (Sousa et al., 2021). The species represented in the dataset, 90 in total, correspond to about 7.5% of the known true bugs diversity of continental Portugal, and contribute to the knowledge on the DNA barcodes and distribution of Portuguese Hem...
Article
Full-text available
The InBIO Barcoding Initiative (IBI) Hemiptera 01 dataset contains records of 131 specimens of Hemiptera. Most specimens have been morphologically identified to species or subspecies level and represent 88 species in total. The species of this dataset correspond to about 7.3% of continental Portuguese hemipteran species diversity. All specimens wer...
Article
Freshwater macroinvertebrates provide valuable indicators for biomonitoring ecosystem change in relation to natural and anthropogenic drivers. DNA metabarcoding is an efficient approach for estimating such indicators, but its results may differ from morphotaxonomic approaches traditionally used in biomonitoring. Here we test the hypothesis that des...
Thesis
Full-text available
Biodiversity is not evenly distributed across our planet. Freshwater ecosystems hold a disproportionate amount of biodiversity when compared with other biomes, though it only covers a small portion of our planet surface. Because water is essential for human activities, population growth and economic development put an enormous pressure on freshwate...
Article
Full-text available
Mediterranean pastures are experiencing strong changes in management, involving shifts from sheep to cattle-based livestock systems. The impacts of such shifts on biodiversity are still poorly understood. Here, we sought to contrast the grazing regime, vegetation structure, bird species richness and abundance, between sheep and cattle grazed parcel...
Article
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In multifunctional landscapes, diverse communities of flying vertebrate predators provide vital services of insect pest control. In such landscapes, conservation biocontrol should benefit service-providing species to enhance the flow, stability, and resilience of pest control services supporting the production of food and fibre. However, this would...
Article
During the day, flying animals exploit the environmental energy landscape by seeking out thermal or orographic uplift, or extracting energy from wind gradients.1, 2, 3, 4, 5, 6 However, most of these energy sources are not thought to be available at night because of the lower thermal potential in the nocturnal atmosphere, as well as the difficulty...
Preprint
Full-text available
To understand community assembly, ecologists have long sought to extract the signal of biotic interactions from species co-occurrence patterns. These efforts face multiple difficulties such as confounding environmental effects, confounding indirect interactions between multiple species and asymmetry of interactions. To address these problems, we pr...
Article
Full-text available
Traditional detection of aquatic invasive species, via morphological identification is often time-consuming and can require a high level of taxonomic expertise, leading to delayed mitigation responses. Environmental DNA (eDNA) detection approaches of multiple species using Illumina-based sequencing technology have been used to overcome these hindra...
Article
Full-text available
Recent developments on ethanol-based DNA (etDNA) metabarcoding have shown that it is possible to extract meaningful information about macroinvertebrate community diversity and composition from the ethanol used to preserve bulk samples. The major advantages of this molecular approach are the reduced processing time and costs, and the possibility to...
Article
Full-text available
Aim: Understanding temporal changes in aquatic communities is essential to address the freshwater biodiversity crisis. In particular, it is important to understand the patterns and drivers of spatial variation in local community dynamics, generalising temporal trends from discrete locations to entire landscapes that are the main focus of management...
Data
The dataset contains 38 records of Blattodea collected from 2005 to 2019 in continental Portugal. Specimens were identified to species level, except for a single record identified to genus level. Of the eight species in the dataset, seven are cockroaches and one is a termite. Specimens were detected during fieldwork by direct search and stored in 9...
Article
Full-text available
Although sexual dietary differentiation is well known in birds, it is usually linked with significant morphological dimorphism between males and females, with lower differentiation reported in sexually monomorphic or only slightly dimorphic species. However, this may be an artifact of poor taxonomic resolution achieved in most conventional dietary...
Data
The dataset contains one record of the species Borkhausenia crimnodes (Lepidoptera, Oecophoridae) collected in continental Portugal in 2014. This species, a southern hemisphere moth, had not been recorded in Europe before. The specimen was detected and captured by direct search of the environment and preserved in 96% ethanol. A tissue sample, one l...
Data
The dataset contains 11 records of moth specimens (Lepidoptera, Depressariidae) collected from 1988 to 2016 in seven South European and North African countries. Captured specimens were identified to species level. Captured specimens were preserved in 96% ethanol, with one exception kept in dry storage. A tissue sample, one leg, was collected from e...
Data
The dataset contains one record of the species Cochylimorpha punctiferana (Ragonot, 1881) (Lepidoptera, Tortricidae) collected in continental Portugal in 2016. A tissue sample, one leg, was removed to be used for DNA extraction. Sequencing of the 658 bp COI DNA barcode was conducted within the InBIO Barcoding Initiative (IBI) and the DNA sequence w...
Data
The dataset contains two records of moth specimens (Lepidoptera, Depressariidae) collected in 2011 and 2015 in continental Portugal. Captured specimens were identified to species level. Specimens were detected and captured using a mercury-vapor lamp to attract the insects. Captured specimens were preserved in 96% ethanol or in dry storage. From eac...
Data
The dataset contains five records of moth specimens of the genus Isotrias collected from 2012 to 2016 in continental Portugal. Specimens were detected and captured by direct search of the environment during the day, with adults’ hand-netted, and by night using mercury-vapor lamps to attract the insects. Captured specimens were identified to species...
Data
The dataset contains three records of moth specimens of the family Gelechiidae collected from 2015 to 2018 in continental Portugal. Specimens were detected and captured using mercury-vapor lamps to attract the insects. Captured specimens were identified to species level and preserved in 96% ethanol. A tissue sample, a leg, was collected from each i...
Data
The dataset contains five records of the alderfly genus Sialis Latreille, 1803 (Megaloptera, Sialidae) collected in 2011 and 2015 in northern continental Portugal. Specimens were detected by direct search on vegetation and rocks around river streams and captured with a hand-net. Captured specimens were identified to species level and preserved in 9...
Data
The dataset contains eight records of moth specimens of the genus Ypsolopha collected from 2015 to 2017 in continental Portugal. Specimens were detected and captured by direct search of the environment during the day, with adults hand-netted and larvae reared to adulthood, and by night using mercury-vapor lamps to attract the insects. Captured spec...
Data
The dataset contains one record of the species Wesmaelius subnebulosus (Stephens, 1836) (Neuroptera, Hemerobiidae), a brown lacewing species, collected in continental Portugal in 2017. The specimens was detected and captured using a light-trap setup. A tissue sample, one leg, was removed to be used for DNA extraction. Sequencing of the 658 bp COI D...
Article
Full-text available
DNA metabarcoding from the ethanol used to store macroinvertebrate bulk samples is a convenient methodological option in molecular biodiversity assessment and biomonitoring of aquatic ecosystems, as it preserves specimens and reduces problems associated with sample sorting. However, this method may be affected by errors and biases, which need to be...
Article
Full-text available
Environmental DNA (eDNA) is increasingly used for biodiversity monitoring, particularly in aquatic systems. However, each step, from sample collection to bioinformatic analysis, can introduce biases and influence the reliability of results. While much effort has been put into the optimization of laboratory methods, less attention has been devoted t...
Article
Full-text available
The number of non-native freshwater fishes in the Iberian Peninsula has been greatly increasing. In this study, individuals of the genus Phoxinus were detected in 18 out of 138 stream sites sampled across the Douro Basin in 2017 and 2018. A total of 26 individuals were barcoded using partial cytochrome c oxidase subunit I (COI) and cytochrome b (cy...
Data
The dataset contains six records of Solifugae specimens collected from 2016 to 2018 in continental Portugal. All specimens were identified as Gluvia dorsalis (Latreille, 1817) that belongs to the Daesiidae family, and is the only Solifugae species known to occur in Portugal. Specimens were captured during fieldwork directed specifically for the sam...
Article
Full-text available
Increasing evidence for global insect declines is prompting a renewed interest in the survey of whole insect communities. DNA metabarcoding can contribute to assessing diverse insect communities over a range of spatial and temporal scales, but efforts are still needed to optimize and standardize procedures. Here, we describe and test a methodologic...
Article
Full-text available
The use of DNA barcoding allows unprecedented advances in biodiversity assessments and monitoring schemes of freshwater ecosystems; nevertheless, it requires the construction of comprehensive reference collections of DNA sequences that represent the existing biodiversity. Plecoptera are considered particularly good ecological indicators and one of...
Article
Full-text available
The advent and boom of DNA barcoding technologies have provided a powerful tool for the fields of ecology and systematics. Here, we present the InBIO Barcoding Initiative Database: Portuguese Bats (Chiroptera) dataset containing DNA sequences of 63 specimens representing the 25 bat species currently known for continental Portugal. For that, we sequ...
Data
The dataset contains 71 records of Plecoptera species collected from 2004 to 2018 in the Iberian Peninsula. All specimens have been morphologically identified to species level, and belong to 29 species in total. Specimens were captured during fieldwork directed specifically for the sampling of Plecoptera using different methodologies and stored in...
Data
The dataset contains 63 records of Chiroptera species collected in continental Portugal. All specimens were identified to species level, for a total of 26 species belonging to three different families. Bat samples were collected under the scope of several projects spanning from 2005 to 2018. All bats were captured during mist-netting sessions or us...
Data
The dataset contains 13 records of Scorpionflies (Panorpidae) species collected from 2008 to 2019 in continental Portugal. All captured specimens were identified as Panorpa meridionalis, so far the only species of Mecoptera known to exist in Portugal Specimens were detected and captured by direct search of the environment. Captured specimens were p...
Data
The dataset contains 56 records of Earwigs (Dermaptera) species collected from 2006 to 2019 in continental Portugal. All captured specimens were identified to species level, belonging to ten of the fourteen species of Dermaptera present in Portugal. Specimens were detected and captured by direct search of the environment. Captured specimens were pr...
Data
The dataset contains 18 records of Stick insects (Phasmatodea) species collected from 2006 to 2019 in continental Portugal. All captured specimens were identified to species level, belonging to the two species of Phasmatodea present in Portugal. Specimens were detected and captured by direct search of the environment. Captured specimens were preser...
Preprint
Full-text available
Traditional detection of aquatic invasive species, via morphological identification is often time-consuming and can require a high level of taxonomic expertise, leading to delayed mitigation responses. Environmental DNA (eDNA) detection approaches of multiple species using Illumina-based sequencing technology have been used to overcome these hindra...
Preprint
A protocol for the metabarcoding of DNA samples using nanopore technology, for the purposes of biomonitoring, biodiversity assessment, DNA-based diet analysis, or other related applications. The protocol is being used in our laboratory for detecting aquatic invasive bivalve species and for measuring biodiversity of fish and other vertebrates from w...
Article
Full-text available
Aim: Biological invasions are pervasive in freshwater ecosystems, often causing native species to contract into areas that remain largely free from invasive species impacts. Predicting the location of such ecological refuges is challenging, because they are shaped by the habitat requirements of native and invasive species, their biotic interactions...
Article
Adenoviruses (AdV) are pathogens capable of infecting animals and humans leading to a wide spectrum of diseases. They have a widespread geographical dissemination and infect several species, including red squirrels (Sciurus vulgaris). In the Iberian Peninsula, there are no reports of infection of red squirrels by AdV. In this study, we report for t...
Preprint
A protocol for the metabarcoding of DNA samples using nanopore technology, for the purposes of biomonitoring, biodiversity assessment, DNA-based diet analysis, or other related applications. The protocol is being used in our laboratory for detecting aquatic invasive bivalve species and for measuring biodiversity of fish and other vertebrates from w...