Pedro Beja

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

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...

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...

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...

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...

To address the biodiversity crisis, global and regional policy frameworks like the Kunming-Montreal Global Biodiversity Framework and the European Green Deal demand to monitor biodiversity. Despite these efforts, existing approaches for monitoring biodiversity remain fragmented and lack data integration. Here, we review and synthesize crucial infor...

Environmental DNA (eDNA) analysis is a promising tool for monitoring wild animal populations and, more recently, their genetic variability. In this study, we used the mitochondrial Cytochrome B gene to develop and apply new eDNA metabarcoding assays targeting amphibian families and genera in order to estimate both inter‐ and intraspecific genetic d...

Understanding the demography of local populations within ephemeral habitat patches is crucial for effective local (site-based) conservation management in spatially and temporally heterogeneous environments. Evidence suggests that species persisting in networks of ephemeral patches often exhibit source-sink dynamics, where certain local populations...

Extensive farmland in Europe hosts high biodiversity levels but is threatened by land use changes associated with market and agricultural policy drivers. We show that a nationwide replacement of rainfed cereals in favor of beef production in Portugal has coincided with a nearly 80% decline in the population of a ground‐nesting raptor, the Montagu's...

Our commentary explores the increase in cashew cultivation across West Africa, drawing attention to its impacts on biodiversity and livelihoods. We summarize the issue regionally, then showcase Guinea‐Bissau, where we unravel the dynamics between cashew expansion, habitat and biodiversity loss, and livelihoods. Finally, we propose concrete policy m...

To achieve the goals of the 2030 Global Biodiversity Framework, the European Biodiversity Strategy, and the EU Green Deal, biodiversity monitoring is critical. Monitoring efforts in Europe, however, suffer from gaps and biases in taxonomy, spatial coverage, and temporal resolution, resulting in fragmented and disconnected data. To assess user and p...

The Corubal (Guinea-Bissau) is a wild but underexplored river in West Africa. This study underscores the potential of environmental DNA (eDNA) surveys to fill biodiversity knowledge gaps in the region. We filtered large water volumes at 11 sites along the watershed, amplified multiple molecular markers, and performed high PCR (polymerase chain reac...

Wildlife anthropogenic mortality is increasing worldwide, yet there is limited understanding regarding its population level impacts. Territorial species stand out in this context, as they possess distinctive characteristics that are often overlooked but may significantly affect their vulnerability. In particular, population impacts may depend on th...

Background The InBIO Barcoding Initiative (IBI) Dataset - DS-IBILP08 contains records of 2350 specimens of moths (Lepidoptera species that do not belong to the superfamily Papilionoidea). All specimens have been morphologically identified to species or subspecies level and represent 1158 species in total. The species of this dataset correspond to a...

Background The InBIO Barcoding Initiative (IBI) Orthoptera dataset contains records of 420 specimens covering all the eleven Orthoptera families occurring in Portugal. Specimens were collected in continental Portugal from 2005 to 2021 and were morphologically identified to species level by taxonomists. A total of 119 species were identified corresp...

Modern humans widely shaped present ecosystems through intentional and unintentional geographical redistribution of wildlife, both in historical and pre‐historical times. However, the patterns of ancient human‐mediated indirect changes in wildlife range are largely unknown, and the mechanisms behind them remain obscure. We used a multidisciplinary...

EuropaBON EBV workflow templates The information provided here represents the EBV workflow templates collected during the EuropaBON online workshop on Essential Biodiversity Variable (EBV) workflows from 22–24 February 2023. The templates were designed to capture comprehensive descriptions about the three workflow components (data collection and s...

The information represents the EBV workflow templates collected during the EuropaBON online workshop on Essential Biodiversity Variable (EBV) workflows from 22–24 February 2023. The templates were designed to capture comprehensive descriptions about the three workflow components (data collection and sampling, data integration, and modelling) that...

Agriculture is vital for supporting human populations, but its intensification often leads to landscape homogenization and a decline in non-provisioning ecosystem services. Ecological intensification and multifunctional landscapes are suggested as nature-based alternatives to intensive agriculture, using ecological processes like natural pest regul...

Bees are important actors in terrestrial ecosystems and are recognised for their prominent role as pollinators. In the Iberian Peninsula, approximately 1,100 bee species are known, with nearly 100 of these species being endemic to the Peninsula. A reference collection of DNA barcodes, based on morphologically identified bee specimens, representing...

Biocontrol services are widely recognized to provide key incentives for bat conservation. However, we have virtually no information on whether and how disruptions in bat‐mediated biocontrol services are driven by mismatches between the temporal activity patterns of insectivorous bats and insect pests. We investigated the temporal relationship betwe...

Arable plant diversity has been dramatically declining due to agriculture intensification, with several arable species currently included in national Red Lists. This is particularly relevant in the case of plant communities of the traditional Mediterranean agricultural systems. Despite the current knowledge about the factors affecting this diversit...

Optimal Foraging Theory (OFT) predicts that a population's trophic niche expansion should occur in periods of food scarcity as individuals begin to opportunistically exploit sub-optimal food items. However, the Niche Variation Hypothesis (NVH) posits that niche widening may result from increased among-individual differentiation due to food partitio...

The highlands and escarpments of Angola and Namibia (HEAN) consist of a series of high-elevation plateaus, escarpment ridges and inselbergs. They are known for their increased capacity to promote speciation and species persistence, but the importance of this area as an endemism centre for mammals remains poorly documented. Here we describe the ende...

With the increasing recognition of the significance of arachnid conservation, it is crucial to allocate greater efforts towards implementing targeted monitoring programmes. Despite recent studies, our understanding of arachnid populations in Portugal remains limited. This study serves as the initial inventory of arachnids (Araneae and Opiliones) wi...

The BioSTP: DNA Barcoding of endemic birds from oceanic islands of the Gulf of Guinea dataset contains records of 155 bird specimens belonging to 56 species in 23 families, representing over 80% of the diversity of the breeding landbird community. All specimens were collected on Príncipe, São Tomé and Annobón Islands between 2002 and 2021 and morph...

Species responses to habitat disturbance can be variable and diverse across space and time. Yet, our understanding of how those responses impacting species persistence (e.g. demographic, genetic) in disturbed environments is still limited. This is particularly true for metapopulations consisting of small local populations inhabiting patchy ephemera...

Anthropogenic mortality can have a significant impact on population dynamics and broader ecological processes, particularly for long-lived top predators. Such populations are highly vulnerable due to their low intrinsic population growth rates, small population sizes, and large home ranges. As a result, conservation strategies for the most vulnerab...

The status of the forest elephant Loxodonta cyclotis in Guinea-Bissau has been in doubt since the last assessment in 2006. In 2020-2022 we carried out field surveys to update the species’ status. We found elephant signs within an area of c. 1,000km^2. Microsatellite genotyping of faeces identified four males. Females could not be individually ident...

Freshwater mussels are one of the most threatened animal groups in the world. In the European Union, threatened and protected mussel species are not adequately monitored, while species considered to be common and widespread receive even less attention. This is particularly worrying in the Mediterranean region, where species endemism is high and fre...

To implement the goals of the 2030 Global Biodiversity Framework, the European Biodiversity Strategy and the EU Green Deal, biodiversity monitoring is a pivotal instrument to achieve accountability and progress in conservation. Monitoring efforts in Europe, however, suffer from gaps and biases in taxonomy, spatial coverage, and temporal resolution,...

The herpetofauna of São Tomé and Príncipe consists of nine species of amphibians, all endemic, and 21 species of terrestrial reptiles, of which 17 are endemic. Our current knowledge regarding its natural history, ecology, and distribution is limited. Here two important tools are provided to support researchers, conservationists, and local authoriti...

Aquatic environmental DNA is increasingly used for biodiversity monitoring, such as surveying threatened and invasive species. Mainstreaming these methods in practical applications, however, still requires significant standardization and optimisation, namely regarding DNA capture methods. Here we evaluated how filter type (standard disc filters vs...

The reconstruction of species' glacial refugial history and demographic changes over time has generally been based on comparing inferences from single-method approaches, with no truly methodological integration. Here, we aimed to overcome this shortfall by integrating ecological, genomics and paleobiology methods while discussing each method's limi...

Species associations are not uniform across space and time. However, this context-dependency remains very difficult to measure, as field experiments are often performed in a limited number of locations and over a short time window. The Cabrera vole (Microtus cabrerae) and the southern water vole (Arvicola sapidus) are two Mediterranean species that...

Public health and environmental concerns are increasing the pressure to reduce chemical pesticide usage, thereby requiring management alternatives to control pest damage to crops. Retaining semi-natural habitats within agricultural landscapes is often assumed to be one such alternative, by contributing to boost natural enemy populations and reduce...

The goal of this task was to identify and characterise novel methods for biodiversity monitoring, and to assess their suitability for large scale deployment across Europe. To address this goal we combined extensive literature searches with expert consultation, namely using a survey and through an online workshop. The outcome of our searches is summ...

Metapopulation models examining the effects of patch size, quality, and connectivity on local abundance and rates of extinction and (re)colonization have been well studied. However, the relative contributions of these attributes to key demographic and genetic parameters that determine local population viability are still largely unknown. This is pa...

Increasing the policy impact and effectiveness of biodiversity monitoring in Europe: current state and gaps.

The EuropaBON project seeks to design a European Biodiversity Observation Network to monitor the status and trends of European biodiversity and ecosystems in the coming years. To accomplish this, the project has brought together biodiversity monitoring experts and other relevant stakeholders from various sectors (policy, NGO, academia, business, ci...

The co-design of a European Observatory Observation Network requires information on the existing monitoring capacity in Europe, including the quantity and quality of the data available to generate the Essential Biodiversity Variables (EBVs) identified in Task 4.1 at the spatial- and temporal resolutions desired by users and policy. In this document...

Background DNA barcoding technologies have provided a powerful tool for the fields of ecology and systematics. Here, we present a part of the InBIO Barcoding Initiative Database: contribution to the knowledge on DNA barcodes of cuckoo wasps (Hymenoptera, Chrysididae) dataset representing 144 specimens and 103 species, covering approximately 44% of...

EuropaBON harnesses the power of modelling Essential Biodiversity Variables (EBVs) to integrate different reporting streams, data sources, and monitoring schemes, and measure biodiversity change across multiple dimensions in space and time. Therefore, EBVs are at the core of the project and form the basis for several of the tasks feeding into the c...

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...

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...

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...

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...

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...

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...

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...

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...

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...

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...

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....

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...

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...

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...

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...

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...

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...

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...

• 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...