Biology subjects

Pereira, H. M.

Publications and source records attributed to Pereira, H. M..

12 recordsLinked to original sources

bioRxiv2026

Forest degradation reshapes trophic functioning in vertebrate food webs across Amazonian forests

The Amazon is a mosaic of ecosystems, accounting for 13% of all known species globally, and responsible for providing a variety of ecosystem services, including a key role in global climate regulation. However, 18% of the Amazon forest cover has been lost completely and a further 38% degraded, threatening biodiversity and millions of local livelihoods. Currently, little is known about how this impacts the functioning of ecological communities. Here, we combine an energetic approach with biodiversity metrics to quantify ecosystem functioning in mammal and bird food webs across Amazonia, along a gradient of forest degradation linked to road proximity. We show that even under relatively low disturbance, ecosystem functions shift: carnivory increases closer to roads, driven by generalist species that persist under these conditions, whereas herbivory declines mainly due to reduced herbivore biomass and species richness. This suggests that processes associated with forest degradation can alter energy flow even where biodiversity metrics remain relatively unchanged, highlighting energetic approaches as sensitive indicators of ecosystem disruption.

ecology↗

bioRxiv2026

The Hidden Costs of Climate Change Tracking: Climate Velocity, Movement Energetics, and Connectivity in European Protected Areas

Rapid climate change is reducing the capacity of protected areas (PAs) to conserve biodiversity, but exposure metrics alone do not show whether species can reach areas where suitable climates persist. We developed a climate-informed connectivity framework integrating climate velocity, PA climatic residence time, PA size, and functional connectivity based on energetics-informed resistance surfaces from species distribution models. Using high-resolution climate projections and omnidirectional connectivity modelling across Europe, we show that climate-tracking opportunities are more limited and spatially uneven than structural connectivity alone suggests. Small, climate-exposed PAs are especially vulnerable because they provide little internal climatic buffering and are often embedded in landscapes with low movement feasibility, whereas larger and more climatically stable PAs are more often situated in landscapes that can support redistribution. These findings provide a spatially explicit basis for restoration and conservation planning to maintain the functionality of PA networks under future climate change. TeaserMany European protected areas are too isolated, climate-exposed, and energy-constrained to support climate-tracking connectivity.

ecology↗

bioRxiv2025

The carrying capacity of a fragmented landscape depends on the home-range size of a species

Population models have not considered the problem of home-range settlement when the grain of the landscape is smaller than the home-range size. We present an individual-based model addressing this problem that combines age-structured population dynamics, optimal foraging and habitat selection. During home-range settlement each juvenile tries to maximize her fitness, which depends on the proportion of high-quality habitat in her home range. We assume that home ranges do not overlap, which can happen because the home range is defended as a territory or because individuals avoid areas used by conspecifics. We show that the population supported by the landscape at equilibrium, the carrying capacity of the landscape, decreases with the amount of low-quality habitat cover. However, this decrease is non-linear, the carrying capacity starts to decline only below a critical habitat threshold. Furthermore, when the home-range size is larger than the grain of the landscape, the carrying capacity declines faster when the habitat is fragmented. Therefore species with small home-ranges persist in instances where species with large home-ranges go deterministically extinct. Species with large population growth rates have low critical habitat sizes, and are more resilient to habitat conversion.

ecology↗

bioRxiv2023

Threat of mining to African great apes

The rapid growth of clean energy technologies is driving a rising demand for critical minerals. In 2022 at the UN Biodiversity Conference (COP 15), seven major economies formed an alliance to enhance the sustainability of mining these essential decarbonization minerals. However, there is a scarcity of studies assessing the threat of mining to global biodiversity. By integrating a global mining dataset with ape density distribution estimates, we explored the potential negative impact of industrial mining on African great apes. Our findings reveal that up to one-third of Africas great ape population faces mining-related risks. This is especially pronounced in West Africa, where numerous mining areas overlap with fragmented ape habitats, often occurring in high-density ape regions. For 97% of mining areas, no ape survey data are available, underscoring the importance of increased accessibility to environmental data within the mining sector to facilitate research into the complex interactions between mining, climate, biodiversity and sustainability. TeaserMining for clean energy minerals could put one-third of Africas ape population at risk.

ecology↗

bioRxiv2023

Biodiversity monitoring in Europe: user and policy needs

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, resulting in fragmented and disconnected data which does not provide sufficient evidence for policy making. To assess user and policy needs in biodiversity monitoring, we employed with EuropaBON a four-step user-centred stakeholder engagement process, including an international public stakeholder workshop, a standardised online survey, semi-structured interviews, and an expert meeting with representatives of EU member states, the European Commission and the European Environment Agency. The resulting insights into national and European biodiversity monitoring schemes identify policy needs, current challenges and potential solutions. Based on this in-depth policy and science stakeholder assessment, we recommend the establishment of a European Biodiversity Observation Network through a permanent Biodiversity Monitoring and Coordinating Centre to optimise existing observation efforts, harmonise data, and enhance our ability to predict and respond to key challenges related to biodiversity loss in a changing climate in Europe.

ecology↗

bioRxiv2023

Tailoring evidence into action: using a codesign approach for biodiversity information in the Tropical Andes

Biodiversity conservation is a complex and transdisciplinary problem that requires engagement and cooperation among scientific, societal, economic, and political institutions. However, historical approaches have often failed to bring together and address the needs of relevant stakeholders in decision-making processes. The Tropical Andes, a biodiversity hotspot where conservation efforts often conflict with socioeconomic issues and policies that prioritize economic development, provides an ideal model to develop and implement more effective approaches. In this study, we present a codesign approach that mainstreams and improves the flow of biodiversity information in the Tropical Andes, while creating tailored outputs that meet the needs of economic and societal stakeholders. We employed a consultative process that brought together biodiversity information users and producers at the local, national, and regional levels through a combination of surveys and workshops. This approach identified priority needs and limitations of the flow of biodiversity information in the region, which led to the co-design of user-relevant biodiversity indicators. By leveraging the existing capacities of biodiversity information users and producers, we were able to co-design multiple biodiversity indicators and prioritize two for full implementation ensuring that the data was findable, accessible, interoperable, and reusable based on the FAIR principles. This approach helped address limitations that were identified in the stakeholder engagement process, including gaps in data availability and the need for more accessible biodiversity information. Additionally, capacity-building workshops were incorporated for all stakeholders involved, which aimed to not only improve the current flow of biodiversity information in the region but also facilitate its future sustainability. Our approach can serve as a valuable blueprint for mainstreaming biodiversity information and making it more inclusive in the future, especially considering the diverse worldviews, values, and knowledge systems between science, policy, and practice.

ecology↗

bioRxiv2023

Predicting the timing of ecological phenomena across regions using citizen science data

Spatial predictions of intra-annual ecological variation enhance ecological understanding and inform decision-making. Unfortunately, it is often challenging to use statistical or machine learning techniques to make such predictions, due to the scarcity of systematic, long-term observational data. Conversely, opportunistic time-stamped observation records, supported by highly informative data such as photographs, are increasingly available for diverse ecological phenomena in many regions. However, a general framework for predicting such phenomena using opportunistic data remains elusive. Here, we introduce a novel framework that leverages the concept of relative phenological niche to model observation records as a sample of temporal environmental conditions in which the represented ecological phenomenon occurs. We demonstrate its application using two distinct, management-relevant, ecological events: the emergence of the adult stage of the invasive Japanese beetle (Popillia japonica), and of fruiting bodies of the winter chanterelle mushroom (Craterellus tubaeformis). The framework accounts for spatial and temporal biases in observation data, and it contrasts the temporal environmental conditions (e.g., in temperature, precipitation, wind speed, etc.) associated with the observation of these events to those available in their occurrence locations. To discriminate between the two sets of conditions, we employ machine-learning algorithms (boosted regression trees and random forests). The proposed approach can accurately predict the temporal dynamics of ecological events across large geographical scales. Specifically, it successfully predicted the intra-annual timing of occurrence of adult Japanese beetles and of winter chanterelle mushrooms across Europe and North America. We further validate the approach by successfully predicting the timing of occurrence of adult Japanese beetles in Northern Italy, a recent hotspot of invasion in continental Europe, and the winter chanterelle mushroom in Denmark, a country with a high number of records of this mushroom. These results were also largely insensitive to temporal bias in recording effort. Our results highlight the potential of opportunistic observation data to predict the temporal variation of a wide range of ecological phenomena in near real-time. Furthermore, the conceptual and methodological framework is intuitive and easily applicable for the large number of ecologists already using machine-learning and statistical-based predictive approaches.

ecology↗

bioRxiv2021

Atazanavir is a competitive inhibitor of SARS-CoV-2 Mpro, impairing variants replication in vitro and in vivo

Atazanavir (ATV) has already been considered as a potential repurposing drug to 2019 coronavirus disease (COVID-19), however, there are controversial reports on its mechanism of action and effectiveness as anti-severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Through the pre-clinical chain of experiments: enzymatic, molecular docking, cell-based, and in vivo assays, it is demonstrated here that both SARS-CoV-2 B.1 lineage and variant of concern gamma are susceptible to this antiretroviral. Enzymatic assays and molecular docking calculations showed that SARS-CoV-2 main protease (Mpro) was inhibited by ATV, with Morrisons inhibitory constant (Ki) 1.5-fold higher than boceprevir (GC376, a positive control). ATV was a competitive inhibition, increasing the Mpros Michaelis-Menten (Km) more than 6-fold. Cell-based assays indicated that SARS-CoV-2 gamma is more susceptible to ATV than its predecessor strain B.1. Using oral administration of ATV in mice to reach plasmatic exposure similar to humans, transgenic mice expression in human angiotensin converting enzyme 2 (K18-hACE2) were partially protected against lethal challenge with SARS-CoV-2 gamma. Moreover, less cell death and inflammation were observed in the lung from infected and treated mice. Our studies may contribute to a better comprehension of the Mpro/ATV interaction, which could pave the way to the development of specific inhibitors of this viral protease.

pharmacology and toxicology↗

bioRxiv2021

Deforestation projections imply range-wide population decline for critically endangered Bornean orangutan

Assessing where wildlife populations are at risk from future habitat loss is particularly important for land-use planning and avoiding biodiversity declines. Combining projections of future deforestation with species density information provides an improved way to anticipate such declines. Using the endemic and critically endangered Bornean orangutan (Pongo pygmaeus) as a case study we applied a spatio-temporally explicit deforestation model to forest loss data from 2001-2017 and projected future impacts on orangutans to the 2030s. Our projections point to continued deforestation across the island, amounting to a loss of forest habitat for 26,200 (CI: 19,500-34,000) orangutans. Populations currently persisting in forests gazetted for industrial timber and oil palm concessions, or unprotected forests outside of concessions, were projected to experience the worst losses within the next 15 years, amounting to 15,400 (CI: 12,000-20,500) individuals. Lowland forests with high orangutan densities in West and Central Kalimantan were also projected to be at high risk from deforestation, irrespective of land-use. In contrast, most protected areas and logging concessions currently harboring orangutans will continue to face low levels of deforestation. Our business-as-usual projections indicate the importance of protected areas, efforts to prevent the conversion of logged forests for the survival of highly vulnerable wildlife, and protecting orangutan habitat in plantation landscapes. The modeling framework could be expanded to other species with available density or occurrence data. Our findings highlight that species conservation should not only attempt to act on the current situation, but also be adapt to changes in drivers to be effective.

ecology↗

bioRxiv2020

Global trends in biodiversity and ecosystem services from 1900 to 2050

Despite the scientific consensus on the extinction crisis and its anthropogenic origin, the quantification of historical trends and of future scenarios of biodiversity and ecosystem services has been limited, due to the lack of inter-model comparisons and harmonized scenarios. Here, we present a multi-model analysis to assess the impacts of land-use and climate change from 1900 to 2050. During the 20th century provisioning services increased, but biodiversity and regulating services decreased. Similar trade-offs are projected for the coming decades, but they may be attenuated in a sustainability scenario. Future biodiversity loss from land-use change is projected to keep up with historical rates or reduce slightly, whereas losses due to climate change are projected to increase greatly. Renewed efforts are needed by governments to meet the 2050 vision of the Convention on Biological Diversity. One Sentence SummaryDevelopment pathways exist that allow for a reduction of the rates of biodiversity loss from land-use change and improvement in regulating services but climate change poses an increasing challenge.

ecology↗

bioRxiv2018

High impact journals in ecology cover proportionally more statistically significant findings

Unbiased scientific reporting is crucial for data and research synthesis. Previous studies suggest that statistically significant results are more likely to be published and more likely to be submitted to high impact journals. However, the most recent research on statistical significance in relation to journal impact factors in ecological research was published more than two decades ago or addressed a small subset of the literature. Here, we extract p-values from all articles published in 11 journals in 2012 and 2014 across a wide range of impact factors with six journals sampled in both years. Our results indicate that the proportion of statistically significant results increases with rising impact factor. Such a trend can have important consequences for syntheses of ecological data and it highlights the importance of covering a wide range of impact factors when identifying published studies for data syntheses. This trend can also lead to a biased understanding of the probability of true effects in ecology and conservation. We caution against the possible downplaying of non-significant results by either journals or authors.

scientific communication and education↗

bioRxiv2016

Extinction rate has a complex and non-linear relationship with area

Aim.Biodiversity loss, measured as count of extinction events, is a key component of biodiversity change, and can significantly impact ecosystem services. However, estimation of the loss has focused mostly on per-species extinction rates measured over limited numbers of spatial scales, with no theory linking small-scale extirpations with global extinctions. Here we provide such link by introducing the relationship between area and per-species probability of extinction (PxAR) and between area and count of realized extinction events in that area (NxAR). We show theoretical and empirical forms of these relationships, and we discuss their role in perception and estimation of the current extinction crisis.\n\nLocationUSA, Europe, Czech Republic, Barro Colorado Island\n\nMethodsWe derived the expected forms of PxAR and NxAR from a range of theoretical frameworks based on theory of island biogeography, neutral models, and species-area relationships. We constructed PxAR and NxAR in five empirical datasets on butterflies, plants, trees and birds, collected over range of spatial scales.\n\nResultsBoth the theoretical arguments and empirical data support monotonically decreasing PxAR, i.e. per-species extinction probability decreasing with increasing area; however, we also report a rare theoretical possibility of locally increasing PxAR. In contrast, both theory and data revealed complex NxAR, i.e. counts of extinction events follow variety of relationships with area, including nonlinear unimodal, multimodal and U-shaped relationships, depending on region and taxon.\n\nMain conclusionsThe uncovered wealth of forms of NxAR can explain why biodiversity change (the net outcome of losses and gains) also appears scale-dependent. Furthermore, the complex scale dependence of PxAR and NxAR means that global extinctions indicate little about local extirpations, and vice versa. Hence, effort should be made to understand and report extinction crisis as a scale-dependent problem. In this effort, estimation of scaling relationships such as PxAR and NxAR should be central.

ecology↗