Carlos Fonseca

University of Aveiro | UA · Department of Biology

The successful introduction of the common genet (Genetta genetta) into Europe has been traditionally associated to the Muslim invasion of Iberia, although diverse evidence suggested an earlier arrival. In this study, we assessed genetic variation at 11 microsatellite loci in 199 individuals from the Mediterranean Basin and used approximate Bayesian...

Traditional land use practices declined throughout many of Europe’s rural landscapes during the 20th century. Rewilding (i.e. restoring ecosystem functioning with minimal human intervention) is being pursued in many areas, and restocking or reintroduction of key species is often part of the rewilding strategy. Such programmes require ecological inf...

ContextThe conversion of natural environments into agricultural land has profound effects on the composition of the landscape, often resulting in a mosaic of human-altered and natural habitats. The response to these changes may however vary among organisms. Bats are highly vagile, and their requirements often imply the use of distinct habitats, whi...

1. The Iberian Peninsula is witnessing ever-faster environmental changes, and new challenges for wild ungulates are continuously emerging as they become more abundant and widespread. 2. We conducted a systematic review to analyse the knowledge on wild ungulates inhabiting the Iberian Peninsula. We used Web of Science and Scopus search engines, comp...

Livestock predation constitutes the primary source of conflict between humans and large carnivores. Moreover, human factors, such as attitudes and emotions, can affect people’s tolerance towards carnivores, exacerbating the conflict. Such conflicts often lead to retaliatory killing of carnivores, which not only poses significant threats to species...

Dasypus novemcinctus and Euphractus sexcinctus are common armadillo species in the Brazilian Pantanal. Due to their digging habits, they alter the surroundings providing environmental alternatives that can be used by other organisms. We therefore aimed to identify the animal species that utilize the burrows of these armadillos in the Pantanal Wetla...

Chapter about conservation status of Sus scrofa (wild boar)

The ongoing increase in wild boar populations across Europe has fostered human-wildlife conflicts, including the transmission of emerging pathogens with zoonotic importance. Blastocystis is a ubiquitous, faecal-oral transmitted protist that can cause gastrointestinal illnesses and is observed in humans and animals worldwide. The role of wildlife in...

Wildlife monitoring is key for the effective management of natural resources. Hunting-based data (e.g., hunting bag statistics) is an important source of information to overcome the financial constraints imposed to long-term monitoring. Here, taking advantage of three decades (1989–2022) of hunting bag statistics of wild mammals in Portugal, we pre...

Context Large carnivores have faced severe extinction pressures throughout Europe during the last centuries, where human-induced disturbances reached unprecedented levels. In the late twentieth century, the Cantabrian brown bear population was on the verge of extinction, due to poaching. Yet, the end of the last century was a turning point for this...

Human dimensions play a pivotal role in wolf management and conservation. To offer an informed basis to improve Human-Wolf coexistence, we explore how socio-demographic factors, fear, knowledge, and perceptions of costs and benefits of wolf presence drive human attitudes in the southern area of the Douro River, Portugal, a region inhabited by a sma...

The ongoing increase of wild boar populations across Europe has fostered human-wildlife conflicts, including the transmission of emerging pathogens with zoonotic importance. Blastocystis is a ubiquitous, faecal-oral transmitted protist that can cause gastrointestinal illnesses and is observed in humans and animals worldwide. The role of wildlife in...

The continuous growth of the global human population results in increased use and change of landscapes, with infrastructures like transportation or energy facilities being a particular risk to large carnivores. Environmental impact assessments were established to identify the probable environmental consequences of any new proposed project, find way...

The endangered Iberian wolf (Canis lupus signatus) populations have been decreasing in Portugal due to a combination of factors such as habitat destruction and human persecution. This is particularly worrying in Central Portugal, where packs are highly fragmented, isolated, and with few individuals. Human-Wildlife-Conflicts occur in this area due t...

Blastocystis is a ubiquitous intestinal protist in humans and animals worldwide. The traditional livestock free-roaming raising system in rural communities increases the risk of infection with contact with a wider range of pathogens transmitted via the faecal-oral route associated with that wildlife-livestock-human interface. However, no studies ha...

The human dimension of wildlife is increasingly addressed in socioecological studies on the growth of some wildlife populations in Europe, which frequently leads to conflicts, particularly when wild populations inhabit or reach humanized landscapes. In Europe, ungulates have been increasing in number and distribution, especially the wild boar (Sus...

Aim The climatic niche is associated with diversification in many groups of animals and plants. However, the relationships between climatic‐niche breadth evolution, climatic‐niche position evolution, and speciation remain underexplored. It is particularly unclear whether changes in climatic‐niche breadth are related to diversification. We tested tw...

The Iberian Peninsula is witnessing ever-faster environmental changes, and new challenges upon wild ungulates are continuously emerging as they become more abundant and widespread. We conducted a systematic review to i) sum-up the available scientific knowledge on Iberian wild ungulates, and ii) highlight a set of open questions regarding different...

La creciente expansión y sobreabundancia de las poblaciones de jabalíes en toda Europa han aumentado los conflictos entre humanos y estos animales de vida libre, incluyendo la transmisión de patógenos emergentes de relevancia zoonósica. Blastocystis (Stramenopile) es un protista ubicuo de transmisión fecal-oral que puede causar enfermedad gastroint...

Enteric protozoan parasites Giardia duodenalis, Cryptosporidium spp., and, to a lesser extent, the ciliate Balantioides coli are responsible for severe human and animal intestinal disorders globally. However, limited information is available on the occurrence and epidemiology of these parasites in domestic, but especially wild species in Portugal....

Trophic rewilding is considered a conservation measure that aims to restore the trophic interactions. In north‐central Portugal, the Iberian wolf ( Canis lupus signatus ) is endangered mainly due to human persecution, triggered by wolf depredation on livestock. Several initiatives have occurred in this area to increase wolf wild prey availability b...

Context The expansion of exotic plantations can impose conservation challenges on wildlife, and the Iberian Peninsula has one of the widest planted areas of exotic Eucalyptus sp. in Europe. Since mesocarnivores are pivotal elements of ecosystems’ functioning and Eucalyptus have been modifying the Portuguese landscape context in the last half centur...

Livestock depredation is a common cause of human-carnivore conflicts. In Portugal, free-ranging dogs are increasingly abundant and overlap endangered Iberian wolf territories, with reports of livestock depredation. However, the lack of awareness about dogs’ possible role as predators leads to bias against wolves in cases of damages. Our goal was to...

Context The Mediterranean basin is characterized by a heterogeneous landscape historically shaped by human activities. Land abandonment and extensive monocultures, however, have led to increasing homogeneity of Mediterranean habitats. Albeit the effects of habitat heterogeneity on wildlife have been widely studied, the available information on how...

The European Observatory of Wildlife (EOW, https://wildlifeobservatory.org/) is an EFSA-funded (European Food and Safety Authority) initiative run by the ENETWILD project (www.enetwild.com). The EOW aims to improve harmonizing wildlife monitoring methods throughout the Europe and provide the possibilities to estimate the density of wildlife across...

Climate change will impact environments globally. These changes, however, can affect species or regions differently. The upward limitation of high-mountain species suggests these are especially prone to the effects of climate change. We assess the impact of future climate scenarios on high-mountain species' suitable climatic niches. We gathered 135...

Natural regeneration is crucial to maintaining local adaptative genetic pools of Pinus pinaster Ait. forests and their restoration following disturbance events. After a wildfire, weak-serotinous maritime pine populations may only depend on the viability of seeds exposed to fire to recover. Subsequently, summer drought during the early stages of the...

The European Observatory of Wildlife (EOW) as part of the ENETWILD project, aims to improve the European capacity for monitoring wildlife populations, implementing international standards for data collection, providing guidance on wildlife density estimation, and finally, to promote collaborative, open data networks to develop wildlife monitorin...

The phylum Microsporidia encompasses a diverse group of obligate, intracellular, and spore-forming organisms able to infect a wide range of animal hosts. Among them, Enterocytozoon bieneusi is the most frequently reported species in humans and animals. Despite the role of wildlife as reservoirs of zoonotic pathogens, there are only a few studies do...

Humans have been altering the Mediterranean landscapes for millennia. To diminish the probability of encounters with domestic animals, humans and their activities, many species adjust their behavior to become more nocturnal. Even habitat-generalist species, such as red fox and stone marten that are somehow tolerant to environmental changes, might b...

The phylum Microsporidia encompasses a diverse group of obligate, intracellular, and spore-forming organisms able to infect a wide range of animal hosts. Among them, Enterocytozoon bieneusi is the most frequently reported species in humans and animals. Little is known about the presence and epidemiology of E. bieneusi in wildlife. We investigated E...

For centuries, wolf depredation on livestock has triggered human–wildlife conflicts throughout Europe. Free-ranging dogs, however, are increasingly abundant and may also act as predators of livestock herds. This calls for combined efforts aimed at identifying the causes of depredation events and optimizing the procedures towards predators’ identifi...

Ungulate-vehicle collisions (UVC) have been steadily increasing throughout Europe, posing a risk to human safety, representing an extra factor of animals death. Here, we used information of a 2-year roadkill (2019–2020) monitoring of wild ungulates (wild boar, red deer and roe deer) to assess the drivers that influence the likelihood of UVC in Port...

European wildlife has been subjected to intensifying levels of anthropogenic impact throughout the Holocene, yet the main genetic partitioning of many species is thought to still reflect the late-Pleistocene glacial refugia. We analyzed 26,342 nuclear SNPs of 464 wild boar (Sus scrofa) across the European continent to infer demographic history and...

(Introducción): El jaguar (Panthera onca) es el felino más grande de América y debido a los vastos bosques conectados en la Amazonía tiene actualmente las mayores poblaciones de esta especie. (Objetivos): Estimamos la densidad de jaguares para 7 sitios en el Gran Paisaje Madidi-Tambopata en el noroeste de Bolivia y el sureste de Perú. (Metodologí...

At the end of the nineteenth century, massive population declines were observed in carnivores due to the emergence of infectious diseases. This study aims to investigate, by means of coprological analysis, the prevalence and intensity of the parasites that infect the endangered Iberian wolf Canis lupus signatus and two mesocarnivores (the red fox V...

European wolf populations are currently exposed to distinct sources of anthropogenic disturbance and mortality that can cause dispersal limitations and lead to isolation. The identification of factors that act as complete or partial barriers to movement, dispersal, or gene flow contribute to foster connectivity between populations. We reviewed the...

The mcr-1 gene spread is worldwide recognized as a public health threat at multidrug-resistant infections therapy level. Here, we report for the first time, to the best of our knowledge, the detection of the globally distributed IncX4 plasmid carrying mcr-1 (mcr-1/IncX4) in Escherichia coli isolated from a wild mammal in Portugal and Europe. This p...

Portugal enfrenta um problema estrutural relacionado com o desenvolvimento e a gestão das áreas rurais, agravado pelos efeitos das alterações climáticas. Os incêndios rurais são uma das consequências deste problema, representando uma séria ameaça à segurança das comunidades, à economia florestal, ao ambiente e ao desenvolvimento económico e social...

The WHO considers that antimicrobial resistance (AMR) is among the ten greatest global public health risks of the 21st century. The expansion of human populations and anthropogenically related activities, accompanied by the fragmentation of natural habitats, has resulted in increased human–wildlife interaction. Natural ecosystems are therefore subj...

The Iberian ibex is one of the most singular species of the Iberian Peninsula. Throughout the years, this species suffered several threats which led the population to its decline. Many reintroductions and translocations were made, however, none of those actions took into account the genetic patterns of both reintroduced individuals and the target p...

Eucalyptus plantations, the second most economically important exotic tree in Europe, cover circa 1,5 million hectares on this continent. However, little is known about their effect on the ecological patterns of widely distributed and increasing populations of wild ungulates. This lack of knowledge jeopardizes our ability to correctly manage these...

Antimicrobial resistance (AMR) is a global health concern. Nowadays, antibiotic resistance genes (ARGs) are considered emerging pollutants. This study followed the One Health framework, in which AMR surveillance in the environment, including in wild animals, is advisable to mitigate this problem. Here we investigated AMR associated with Eurasian ot...

[Introducción]: El jaguar (Panthera onca) es el felino más grande de América y debido a los vastos bosques conectados en la Amazonía tiene actualmente las mayores poblaciones de esta especie. [Objetivos]: Estimamos la densidad de jaguares para 7 sitios en el Gran Paisaje Madidi-Tambopata en el noroeste de Bolivia y el sureste de Perú. [Metodología]...

A data set of terrestrial, volant, and marine mammal occurrences in Portugal

The replacement of natural areas with forestry plantations is a worldwide expanding process with direct consequences for biodiversity and ecosystem functionality. In the Mediterranean region, Eucalyptus spp. plantations are widespread, forming monospecific landscapes that in Portugal dominate most of its forested areas. The reduction in the availab...

Background Zoonoses are diseases common to humans and animals (livestock, wildlife, and pets). In 2018 about 360 000 zoonoses were reported in European Union. Shiga toxin-producing Escherichia coli (STEC) infections were among the most reported causes of these zoonotic diseases. Methods Faecal samples of mammal species (n=286) with distinct phenol...

Forestry plantations have increased considerably over recent decades to fulfil human demand for wood, pulp and paper. Eucalyptus globulus Labill is one of the most abundant plantation species, particularly in Europe, where its largest presence is in Portugal. Furthermore, plantations in Mediterranean areas, such as Portugal, frequently suffer from...

Extended-spectrum β-lactamases (ESBL)-producing Enterobacterales have been classified as critical priority pathogens by the World Health Organization (WHO). ESBL are universally distributed and, in 2006, were firstly reported on a wild animal. Understanding the relative contributions of wild animals to ESBL circulation in the environment is urgentl...

Mammals are threatened worldwide, with ~26% of all species being included in the IUCN threatened categories. This overall pattern is primarily associated with habitat loss or degradation, and human persecution for terrestrial mammals, and pollution, open net fishing, climate change, and prey depletion for marine mammals. Mammals play a key role in...

Humans have negatively impacted most ecosystems on Earth, altering how species use habitats and resources available to them, but also their circadian rhythms. Among many factors affecting animal activity patterns, conversion of native habitat into production forests and hunting are critical, and their impacts may be exacerbated by seasonal weather...

Pseudomonas aeruginosa is a ubiquitous bacterium, successfully exploiting a variety of environmental niches due to its remarkable metabolic versatility. The World Health Organization classifies P. aeruginosa as a “priority pathogen” due to its a great ability to overcome the action of antimicrobials, including carbapenems. Hitherto, most studies ha...

Identifying the role of quantitative variables on speciation rates is among the main purposes of trait-dependent diversification methods. ES-sim, a recent simulation-based approach that relies on Pearson’s correlations, allows testing trait-dependent diversification for single regression models. Here, we modified this approach to include generalize...

The emergence of antimicrobial resistance (AMR) is a global threat to public health. Antimicrobials are used in animal production and human medicine, which contribute to the circulation of antibiotic resistance genes (ARGs) in the environment. Wildlife can be reservoirs of pathogens and resistant bacteria. Furthermore, anthropogenic pressure can in...

In the last decades, the wildlife-human interface has been increasing due to several anthropogenic factors. Therefore, it is crucial to be aware of the impact of these new dynamics on the health of wild animals and its associated zoonotic disease risks. This study aimed to characterise the faecal microbiota of two populations of red deer (Cervus el...

Shiga toxin-producing Escherichia coli (STEC) is one of the most frequent bacterial agents associated with food-borne outbreaks in Europe. In humans, the infection can lead to life-threatening diseases. Domestic and wild animals can harbor STEC, and ruminants are the main STEC reservoirs, although asymptomatic. In the present study we have characte...

The INCREMENTO project attempts to evaluate the consequences of a progressive increase of wild ungulate (red deer, Cervus elaphus) abundance on the structure and functioning of two Mediterranean environments (Quintos de Mora, Toledo and Muela de Cortes, Valencia). We are conducting a manipulative approach based on the release of herds of female red...

The Iberian lynx (Lynx pardinus) is one of the most endangered felid species in the world. Conservation efforts have increased its population size and distribution and reinforced their genetic diversity through captive breeding and reintroduction programmes. Among several threats that the Iberian lynx faces, infectious and parasitic diseases have u...

Antimicrobial resistance (AMR) is a serious problem for public and animal health, and also for the environment. Monitoring and reporting the occurrence of AMR determinants and bacteria with the potential to disseminate is a priority for health surveillance programs around the world and critical to the One Health concept. Wildlife is a reservoir of...

In a recent paper, we presented new evidence and provided new insights on the status of Cantabrian brown bear subpopulations, relevant for this species conservation. Namely, we revealed the likely phylogeographic relation between eastern Cantabrian subpopulation and the historical Pyrenean population. We have also detected an asymmetric flow of all...

Measures of performance in wild ungulates must consider density dependent and stochastic factors such as parasitic rates (as natural enemies in intimae relation with hosts) along with the impact of population management. In order to standardize parasite counts to be useful ecological indicators, it is essential to test host and parasite responses t...