Rafael Villafuerte

Spanish National Research Council | CSIC · Instituto de Estudios Sociales Avanzados

As a top predator, the Iberian Lynx plays a critical role in regulating mesocarnivore communities across the Iberian Peninsula. While species such as the red fox, the Egyptian mongoose, or the European wildcat develop spatial or temporal avoidance behaviours to minimise potentially lethal encounters with the lynx, the relationship between the Euras...

Despite increased conservation efforts, the European rabbit (Oryctolagus cuniculus), a keystone species in the Iberian Peninsula, continues declining due to habitat degradation and viral diseases. Following the 2011 outbreak of Rabbit Hemorrhagic Disease virus GI.2, the species was listed as Endangered by the International Union for Conservation of...

Human‐wildlife conflicts have increased and are particularly acute when predators are involved. A frequent source of conflict is some people's misbeliefs related to the alleged impact of predators on game species and livestock. In this context, quantifying the impact of expanding predators on their prey can be useful in designing conflict mitigatio...

Humans have moved domestic animals around the globe for thousands of years. These have occasionally established feral populations in nature, often with devastating ecological consequences. To understand how natural selection shapes re-adaptation into the wild, we investigated one of the most successful colonizers in history, the European rabbit. By...

Prey species develop anti-predatory strategies as a response to minimising the risk of being predated. However, how the European rabbit (Oryctolagus cuniculus) adapts to different predator pressure is not fully known. Here, we studied the adap-tive anti-predatory responses of European rabbits exposed to different terrestrial predation pressure. To...

The development of evidence-based tools that help to monitor wildlife populations is essential to assess the success of management interventions. Here, we evaluated the reliability of a simple method to estimate the abundance of the European rabbit (Oryctolagus cuniculus), which is likely one of the most managed vertebrate species worldwide. Cooke'...

Understanding the biogeography of species in space and time is essential for the development of evidence‐based conservation and management plans. In this paper we propose a biogeographical spatial modelling approach based on the favourability function, and developed under a fuzzy logic framework, to unravel the historical biogeography of the two Eu...

Although hunters often blame predators for the decline of the red-legged partridge, predation is just one of a number of possible causal factors. The main mammalian predators of partridges are those associated with humanized environments (feral dogs and cats). Other partridge predators include raptors, carnivores, rodents, insectivores and wild boa...

The assessment of the human dimensions of wildlife reintroduction projects is essential for their success. To date, few longitudinal studies (if any) have compared attitudes and perceived impacts before and after human‐assisted large predator reintroduction. In this study, we evaluated public (n = 1582) and hunters' (n = 773) support and perceived...

Context Some prey species can shift their daily activity patterns to reduce the risk of encountering predators, and, in turn, predators develop strategies to increase their chances of meeting prey. European rabbit (Oryctolagus cuniculus) is a key species in Iberian Mediterranean ecosystems. It is the main prey for many vertebrate predators. It is a...

Counting latrines is a standard method to estimate European wild rabbits (Oryctolagus cuniculus) abundance. This method plays an important role in endangered predators’ conservation programs in the Iberian Peninsula, especially in potential reintroduction areas for the Iberian lynx (Lynx pardinus). However, since the last half-century, rabbit popul...

Accurate methods for age determination are critical to the knowledge of wildlife populations' age structure and, therefore, to their successful management. The reliability of age estimation may have profound economic and ecological consequences on the management of the European wild rabbits, Oryctolagus cuniculus, in its native and introduced range...

Optimal foraging theory predicts that in situations of high prey abundance, predators will select the largest ones if the cost of capture is similar. This relationship is not clear in species of large owls. We aimed to evaluate the selection by the Eagle Owl (Bubo bubo) of different body sizes of a profitable prey, the European Rabbit (Oryctolagus...

Studies connecting microbiome composition and functional performance in wildlife have received little attention and understanding their connections with wildlife physical condition are sorely needed. We studied the variation in gut microbiota (hard fecal pellets) between allopatric subspecies of the European wild rabbit in wild populations and in c...

Conflicts over the management of wildlife species that impact human livelihoods are increasingly frequent. In Spanish farmland areas, the European rabbit, one of the most important game species, can cause considerable crop damage. Tensions typically emerge between farmers who advocate rabbit reduction and hunters who are responsible for controlling...

Predation is a key factor in prey population dynamics and could impact population recovery. One common means employed to recover prey populations is that of translocations, but most fail owing to high predation during the early stages. We tested whether conditioned odor aversion can reduce predation during animal translocations by using the predati...

The European rabbit Oryctolagus cuniculus faces a paradoxical situation in its native range, the Iberian Peninsula. While many populations have declined sharply due to a new variant of the rabbit haemorrhagic disease virus (RHDV-b), others remain healthy. The latter populations, which flourish mostly in farmland, are even causing significant crop d...

The recreational use of natural resources requires the implementation of sustainable management systems. However, the existence of socioeconomic interests and the difficulty involved in applying evidence-based information often hinder this implementation. The European wild rabbit (Oryctolagus cuniculus) is an appropriate case with which to study th...

This article presents results of a qualitative study on the opinions and attitudes of stakeholders of the areas affected by the moratorium on European eel (Anguilla anguilla) fishing (declared in 2010) in the Guadalquivir River marshlands of southern Spain. Results suggest that the stakeholders were sustaining different principles, criterions, and...

The European rabbit (Oryctolagus cuniculus) is a key species of great ecological and economical interest in the Mediterranean ecosystem. During the last decades important changes in the land use have transformed part of its natural habitat, a problem that has been aggravated by the incidence of two viral diseases, myxomatosis and hemorrhagic diseas...

No solamente los rumores y las referencias de agricultores y cazadores, también diversos medios de comunicación y bases de datos internacionales hablan de la introducción de S. floridanus en España, conejo mucho mayor que los autóctonos y capacitado para subir a los árboles-lo que se achacaba al hecho de que podría tratarse de un conejo americano,...

Pest species cause significant ecological, social and economic impacts, and programs to control them usually target specific landscape features when pests use these to disperse. Roads or railways are often used by pest species as dispersal corridors, but little is known about the specific characteristics of these human infrastructures that facilita...

Understanding use of space in free ranging populations that cause damage to agriculture can help in the design of measures aimed at reducing their impact. Food availability is known to determine use of space in terrestrial vertebrates so, providing alternative food sources during a specific time period may help the management of vertebrate pests by...

El conejo europeo (Oryctolagus cuniculus) es una especie clave y de gran interés económico y ecológico en los ecosistemas Mediterráneos. Durante las últimas décadas los drásticos cambios en los usos del territorio han transformado parte de él, modificando los hábitats naturales, problemática que se ha visto agravada con la incidencia de dos enferme...

Context Humans have introduced lagomorph species in areas outside their native ranges for their meat, fur or value as game species. Assessing the rate of success of lagomorph introductions is vital to address the ecological damage they may cause. Cases of failed lagomorph introductions in apparently suitable areas may also shed light on mechanisms...

Aim of study: Monitoring and control the hunting activity is primordial to guarantee its sustainability. However, the governmental agencies responsible to manage hunting commonly are unable to adequately do this job because the thousands of small private hunting states, associated exclusively by political-administrative criteria. In this work, we p...

Significance A common feature of all domestic animals is their tame behavior and lack of fear for humans. Consistent with this, we have previously demonstrated that genes with a role in brain or neural development have been particularly targeted during rabbit domestication. Here we show, using high-resolution magnetic resonance imaging, that domest...

Speciation is a process proceeding from weak to complete reproductive isolation. In this continuum, naturally hybridizing taxa provide a promising avenue for revealing the genetic changes associated with the incipient stages of speciation. To identify such changes between two subspecies of rabbits that display partial reproductive isolation, we stu...

Background: Numerous small and medium-sized mammal pests cause widespread and economically significant damage to crops all over the globe. However, most research on pest species has focused on accounts of the level of damage. There are fewer studies concentrating on the description of crop damage caused by pests at large geographical scales, or on...

In many parts of the world, millions of wildlife species are hunted for sport, food, skins, and other products. In recent years, a backlash has emerged from certain groups of society against this long-standing human pursuit. However, attitudes towards the control of wild animals to reduce the health risk to other animals, to lessen agricultural dam...

Myxomatosis is a viral disease that affects European rabbits (Oryctolagus cuniculus) worldwide. In Spain, populations of wild rabbits drastically decreased in the 1950s after the first outbreak of myxomatosis. Since that first appearance, it seems to be an annual epizootic in Spain with periodic outbreaks, predominantly in summer and autumn. Taking...

How foraging behaviour of predators is influenced by prey abundance is often not clear. Predators may behave as generalist or specialist depending on the relationship between the predator feeding behaviour and prey abundance, known as functional response. The European rabbit (Oryctolagus cuniculus) is a key species for most Iberian vertebrate preda...

Widespread generalist predators may affect declining keystone prey populations. However, this phenomenon is not well understood. In this paper, we assessed whether the abundance and population growth of European rabbits Oryctolagus cuniculus, a keystone prey species in Mediterranean Iberia, was related to the abundance and diet of red foxes, Vulpes...

The use of restocking of animals is common practice in the management of populations subject to hunting or recreational fishing. This practice encompasses the release of large numbers of individuals in an area where the species already exists, and thus it can have detrimental genetic impacts on the target populations, especially when captive-reared...

The climatic oscillations that have occurred in the last few million years have strongly affected species distribution ranges. Highly divergent genetic lineages arose, some of which correspond to recognized subspecies that currently occupy small geographical areas. Understanding the implications of the genetic differences between these subspecies i...

The climatic oscillations that have occurred in the last few million years have strongly affected species distribution ranges. Highly divergent genetic lineages arose, some of which correspond to recognized subspecies that currently occupy small geographical areas. Understanding the implications of the genetic differences between these subspecies i...

Biodiversity conflicts arise when the interests of different stakeholders over common resources compete. Typically, the more parties involved, the more complex situations become. Resolution of biodiversity conflicts requires an understanding of the ecological, social and economic factors involved, in other words the interests and priorities of each...

The genetic changes underlying the initial steps of animal domestication are still poorly understood. We generated a high-quality reference genome for the rabbit and compared it to resequencing data from populations of wild and domestic rabbits. We identified more than 100 selective sweeps specific to domestic rabbits but only a relatively small nu...

The analysis of introgression of genomic regions between divergent populations provides an excellent opportunity to determine the genetic basis of reproductive isolation during the early stages of speciation. However, hybridization and subsequent gene flow must be relatively common in order to localize individual loci that resist introgression. In...

The E uropean rabbit O ryctolagus cuniculus was designated as a protected species in S pain and P ortugal following sharp declines in many populations. The ongoing decline highlights the need to implement cost‐effective management strategies for this staple prey and important small game species of Iberian Mediterranean ecosystems. Habitat managemen...

In Mediterranean ecosystems, the European rabbit is a keystone species that has declined dramatically, with profound implications for conservation and manage-ment. Predation and disease acting on juveniles are con-sidered the likely causes. In the field, these processes are managed by removing predators, increasing cover to reduce predation risk an...

The European rabbit is a growing problem for agriculture in parts of its natural range. In this study, our aim was to use historical records over two periods within the last 50 years to analyze trends in the number of requests made for rabbit control in Central Spain. We gathered data on rabbit control applications made in 1967 from Rabbit and Hare...

We compared movement patterns and rhythms of activity of a top predator, the Iberian lynx Lynx pardinus, a mesopredator, the red fox Vulpes vulpes, and their shared principal prey, the rabbit Oryctolagus cuniculus, in relation to moon phases. Because the three species are mostly nocturnal and crepuscular, we hypothesized that the shared prey would...

Maintenance of genetic distinction in the face of gene flow is an important aspect of the speciation process. Here, we provide a detailed spatial and genetic characterization of a hybrid zone between two subspecies of the European rabbit. We examined patterns of allele frequency change for 22 markers located on the autosomes, X-chromosome, Y-chromo...

Agricultural intensification has led to the extreme simplification of agricultural landscapes. The subsequent impoverishment of farmland plant communities can drive dramatic changes in the associated food webs of agricultural systems, with potential implications for vertebrate pest management. Weeds may provide alternative food sources for damaging...

In many parts of the world, illegal poisoning of wild predators has increased abruptly in recent decades. Birds of prey and carnivores have been targeted directly or indirectly if these are perceived to impact game species or domestic animals. Non‐target species have experienced widespread declines, even local extinctions, as the result of illegal...

Wild predators are targeted if they are perceived to affect game species or domestic animals. Over the last century, the direct persecution of birds of prey and mammalian carnivores has led to their widespread decline, even local extirpations. Many such cases involved the illegal use of poisoned bait. We used 1,305 detected poisoning events and 59...

This work evaluates the effectiveness of fox control as a method to improve the survival of red-legged partridge (Alectoris rufa). We radio-tracked 89 adult partridges and their chicks (62 few days old chicks and 46 over one-month-old chicks) and monitored their nests (N = 45) on two hunting estates in northern Spain over two years. Generalist pred...

European rabbits (Oryctolagus cuniculus), a keystone species in the Iberian Mediterranean ecosystem, are the staple prey of the Iberian lynx (Lynx pardinus) and the Spanish imperial eagle (Aquila adalberti). These predators require medium to high rabbit densities and a low degree of human disturbance. We compared rabbit abundances in areas of centr...

Differentially expressed genes. (XLSX)

GO enrichment results. (XLS)

PCA of gene expression variation. Blue: domesticated/tame rat, red: wild/aggressive rat; circles: females, squares: males. (PDF)

Domestication-related genes. (XLSX)

Full details on samples and sequencing runs performed for this study. (XLS)

Gene expression values used in the analyses, stored as R objects. (ZIP)

PCA of SNV data. Blue: domesticated/tame rat, red: wild/aggressive rat; circles: females, squares: males. (PDF)

Transcript sequence differences to the reference genome in genes with common expression in domesticated animals. For each gene, the median fold change of expression in domesticated vs. wild animals is plotted as a function of the difference between wild and domesticated mean sequence difference to the reference genome. The p-values are from Wilcoxo...

PCA of expression data in all 12 rabbit samples. Note the large distance separating A115 from all other samples. Blue: domesticated, red: wild, circles: females, squares: males. (PDF)

“Extreme” and random permutations when testing for shared gene expression across domestication events. (DOCX)

Shown is the number of genes that are 1∶1 orthologues in the given comparison and that are “expressed” in both pairs (i.e. have >0 counts in at least half the samples in both species pairs that are compared). (DOCX)

Extreme and random permutations when searching for genes with shared expression in domesticated animals. A detailed step-by-step description of this Figure is provided in Note S1. A. Expression levels of a hypothetical gene in three pairs (circles, squares, triangles) of domesticated (blue) and wild (red) animals. The dotted line is the overall mea...

Q-Q plots comparing the p-value distribution of the un-permuted data to all possible extreme permutations for the analyses without guinea pigs. p-values are for the effect of domestication in the ANOVA analyses of dogs, pigs and rabbits, and were −log10 transformed. The real, un-permuted data is shown on the y-axis compared to each of the respectiv...

Q-Q plots comparing the p-value distribution of the un-permuted data to all possible extreme permutations for the analyses including guinea pigs. p-values are for the effect of domestication in the ANOVA analyses of dogs, pigs, rabbits and guinea pigs, and were −log10 transformed. The real, un-permuted data is shown on the respective y-axis compare...