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1. The American mink Neogale vison is an invasive alien species in Europe that threatens endemic biodiversity and can transmit zoonotic diseases, including the SARS-CoV-2 virus. The last attempt to map the geographic range of this species in Europe, at continental scale, dates back to 2007. 2. We aimed to update the distribution map of the feral American mink and assess its temporal trends. The information we collected was critically analysed with the aim of improving future monitoring protocols and data collection. 3. We gathered and standardised data from 34 databases, covering 32 countries. Through 3 five-year periods from 2007 to 2021, changes in range size, hunting bags and capture statistics were analysed. We also reviewed the current situation of mink farming in the different European countries and recorded population control schemes. 4. The American mink is now widespread in the Baltic States, France, Germany, Iceland, Ireland, Poland, Scandinavia, Spain and the UK. The species is reported to be absent in some areas (e.g. parts of the UK, Iceland and Norway). Data are deficient for several countries, mainly in south-eastern Europe. These findings indicate that, during the last 15 years, the species has continued to spread across the continent, increasing its potential extent of occurrence in most countries. Our effort to collect and harmonise data across international borders highlighted information gaps and heterogeneity in data quality. 5. Updated distribution data on the species provided here will aid risk assessment and risk management policies. These actions require a coordinated effort for population monitoring at continental level. Monitoring effort and data collection should be intensified in south-eastern Europe to improve data on the current distribution of this invasive species.

In order to monitor wildlife populations in a manner that supports policy makers and natural resource managers, data must be collected using frameworks and methodologies that allow for comparisons between projects and across time. Though hunting statistics may represent a reliable data source for monitoring population trends in game species, a standardised framework for collecting and analysing this data has never been established in Europe, even within countries. Here we describe a case study on the use of hunting statistics in Spain in order to (i) describe the variability in big game statistics collection frameworks across mainland regions of Spain and (ii) propose a minimum common denominator for a standardised approach at the country level. The main differences in methodologies identified are that each region collects different variables, uses different spatial and temporal resolution, and follows different methodologies. We described spatial patterns by grouping regions based on similarities in the hunting data collection system and identified socio-economic factors as a potential driver of differences in methodologies among regions. Hunting effort-related variables and improved temporal resolution (to the event level) must be incorporated in order to achieve country-level standardisation of methodologies. The use of application software to collect information from the field in a standardised way is recommended, which necessitates engaging stakeholders as part of the monitoring process. Applications software should be designed intentionally, and only after clear objectives for the monitoring program have been defined. Making hunting data open access will improve collaboration and information transfer to scientific and professional sectors. Our recommendations can be adapted to other European countries, which would make hunting data more useful for population monitoring and wildlife policy-making at large spatial scales. Initiatives such as the “European Wildli

The goal of this report is modelling the occurrence for carnivores at the European scale and to compare the output of occurrence with observed hunting yield (HY) density models for red fox (Vulpes vulpes) and badger (Meles meles). Random Forest function was used for modelling occurrence of species. Occurrences available from the past 30 years (1990-2020), and HY data (period 2012-2021) from records submitted to ENETWILD were considered for modelling. Like previous models based on HY for ungulates, the response variable was the maximum number of carnivores hunted in that period divided by the area in km2 of the corresponding administrative unit (HY density). Models based on HY were statistically downscaled to make predictions to 10x10 km2. Occurrence data models indicated a good predictive performance for most species, showing that the model framework proposed for ungulates can also be applied for carnivores. Realistic distribution maps of carnivore species were achieved under this framework, except for those ones which are expanding their range, the golden jackal (Canis aureus), or those considered alien species, raccoon (Procyon lotor) and raccoon dog (Nyctereutes procyonoides); or those having a very limited distribution as the Iberian lynx (Lynx pardinus) or the steppe polecat (Mustela eversmanii): in those cases the obtained models were underestimating their suitability in Europe. Suitability has potential to be used as a proxy for abundance of red fox and badger. Validation of suitability on HY suggested the potential to be used as a proxy for abundance of red fox and badger but depending on each species. The calibration plots for HY models showed a good and linear predictive performance for fox and badger as well as an expected pattern of abundance of species, according to the data. However, differences in type of hunting and regulations in game carnivores between countries must be playing an important role in the patterns obtained. We conclude that (i) the fr

The European Observatory of Wildlife (EOW) as part of the ENETWILD project aims progressively developing integrated wildlife monitoring (population abundance and pathogens). The present report shows how to link the wildlife population monitoring (by camera trapping) and wildlife disease surveillance at European scale, by using environmental sampling over 15 study areas of the EOW from 10 Countries (4 study areas in 4 countries will be incorporated next). We specifically focused on multi-host pathogens Mycobacterium tuberculosis Complex (bacteria, MTC), and Hepatitis E virus (HEV). The aims of this trial were, first, to evaluate the harmonized implementation of a simple field sampling protocol for detecting zoonotic pathogens in environmental samples (standing water) through a network of wildlife professionals at European level. Secondly, we got insights for future improved strategies of wildlife integrated monitoring through environmental sampling. This trial prioritized the inclusion of a diverse array of study areas and a simple sampling approach rather than complex protocols and illustrated. We evidenced the importance of supporting such a coordinate network of wildlife professionals to progressively improve strategies, protocols, the general design, sampling, target matrix, selected pathogens, preservation and transport of samples, analytical techniques, and sample and data flow. We discuss specific results on pathogens, remarking the detection of the MTC in certain areas.

The red-legged partridge, as the other Alectoris partridges, is an appreciated game bird subject to intensive management and high hunting demand. Red-legged partridges are raised on game farms, often if not always being hybridized with more prolific chukar partridges, to be released into natural populations for shooting. Massive captive rearing and releasing of partridges is not only homogenizing the natural genetic structuring of wild populations but also contaminating the gene pool of the red-legged partridge with the genome of the exotic chukar partridge. We review analytical approaches used to detect partridge hybridization and describe the status of anthropogenic hybridization in wild and farm populations. Finally, we assess the evidences of the fitness consequences of hybridization or domestication on red-legged partridge populations and incorporate some considerations and concerns about the use of current molecular tools to manage and research partridge genetic integrity.

It is essential to provide tools to wildlife professionals and researchers in order to facilitate data collection on wildlife density estimation following standardized protocols in the field. This is relevant for efficient harmonized data management systems, from the field to final reporting. Our main objective was to facilitate the collection of information in the field using established density estimation protocols. The specific objectives were (i) to evaluate and use already existing data registration IT tools for collecting and storing the data in the field; (ii) to make these data available in real time (cloud-based solution), and (iii) being flexible enough to incorporate new protocols and species, as methods (such as camera trap-based) and needs continuously evolves. We improved an already existing tool, Spatial Monitoring and Reporting Tool (SMART; https://smartconservationtools.org/). It is an open source software, which allows easily collect, visualize, store, analyze, report and act on a wide range of field data relevant for wildlife monitoring. The integration of SMART tools on EOW was successfully done for (i) distance sampling, (ii) hunting data and (iii) camera trap protocols. ENETWILD, therefore, made now available new IT functionalities to wildlife professionals and researchers to facilitate and harmonize wildlife data collection systems.

Thanks to the Pan-European Common Birds Monitoring Scheme and Breeding Bird Survey, the temporal changes in abundance of the Red-legged Partridge are known in most countries of its area of distribution. However, these are based on abundance indices and no strong inference is possible about potential causes of local trends. Robust estimates of abundance or densities at national scale are still lacking. Information from hunting bags cannot be used owing to the inclusion of released Red-legged Partridges in those numbers. Even in the absence of released individuals in hunting bags, these estimates cannot be used owing to a lack of knowledge of variations in reporting behaviour in Europe and potential age-specific mortality. Numbers at the local scale are obtained using similar (although not equal) methods across countries based on line/point transect methods. Given that some capture-recapture studies have been carried out from time to time in most of the distribution range, their results could help to estimate the demographic parameters required for management. Finally, given that these common methods are applied with, possibly, some avoidable differences, a more integrative strategy of methodological design and spatial sampling may make it possible to extrapolate estimates from regional to national/continental scale, and to provide assessments of abundance as well as spatial and temporal variation in Red-legged Partridge population size. This global approach may increase the current value of monitoring to all stakeholders interested in Red-legged Partridges.

In a previous report, ENETWILD proposed a generic model framework to predict habitat suitability and likely occurrence for wild ruminant species using opportunistic presence data (occurrence records for wild ungulate species from the Global Biodiversity Information Facility). In this report, for the first time, we develop models based on hunting yield data (HY) for the most widely distributed wild ruminant species in Europe: roe deer (Capreolus capreolus) and red deer (Cervus elaphus). We also update models based on occurrence (roe deer, red deer, fallow deer (Dama dama), European moose (Alces alces) and muntjac (Muntiacus reevesi), evaluate the performance of both approaches, and compare outputs. As for HY models, we could not conduct one model per bioregion as there are not enough data for modelling in some bioregions, and therefore, we calibrated a unique model, including eco-geographical variables as predictors. The calibration plots for HY models showed a good predictive performance for red deer in the Eastern bioregion and roe deer at Eastern and Western. The abundance distribution pattern of red deer HY was widely scattered over all Europe, as expected for a widely distributed species which shows high ecological plasticity, and roe deer presented the highest abundance in Atlantic and Eastern Europe, progressively decreasing towards Northern Mediterranean bioregions. Overall, calibration plot did not perform well in the Northern region, which could be due to the low availability of data for both species in this bioregion. As for occurrence data models, performances using our revised approach for most species showed similarly moderate predictive accuracy. To sum, HY model projections showed good patterns where good quality data was provided, while worst predictions are found in neighbouring countries/bioregions. Two approximations to be explored for next models are: (i) modelling HY per bioregion providing more flexibility to the models, even if data projection

The International Symposium on Wild Boar and Other Suids (IWBS 2022), which took place in Montseny Biosphere Reserve (Catalonia, Spain) in September 2022, provided to ENETWILD with the opportunity to meet in-person for the first time after 2.5 years, and meet the international scientific community with expertise on wild suids and other ungulates. Twelve members of ENETWILD consortium representing 6 partners were present. Bringing together international experts, stakeholders and ENETWILD collaborators was a perfect occasion to present the European Observatory of Wildlife (EOW). Two hundred and twenty-five wildlife experts from 25 countries were present at symposium, and at presentation of the EOW. Overall, 3 'Plenary Talks' and 118 presentations (62 oral and 56 posters) were made. The meeting has gone through all the possible topics regarding wild suids, from genetics to monitoring and management. This was the optimal context to introduce the EOW to an ideal target audience, both in terms of interest and in terms of potential new member of the Network. From our presentation, it emerged the importance of comparable data on geographical distribution and abundance of wildlife hosts in Europe, fundamental to develop the best management policies and to perform effective risk assessments for shared emergent diseases. The adoption of a common and effective protocol adopted throughout the continent would ensure such comparability. Moreover, the discussion highlighted the need of extending the network to as many European countries as possible and, when feasible, of having multiple sites within each country. A number of participants manifested their interest to join the EOW during the 2023 campaign. Such a capillary distribution of observation points would provide solid and comparable density estimates as well as effective feedback about the field protocol implemented by the EOW. A number of questions were raised by the audience during the presentation of the EOW.

The goal of this report is i) to model the occurrence and hunting yield (HY) density of wild ungulates not only for widely distributed species in Europe, but also for those ones which have a constrained distribution and ii) to compare the output of occurrence with observed HY. Random Forest function was used for modelling occurrence of species. We used occurrence data available from the past 30 years, and HY data (period 2015-2020) from records collected by ENETWILD. Like previous models based on HY, the response variable was the maximum number of wild ruminants annually hunted in 2015-2020 hunting seasons divided by the area (km2) of the corresponding administrative unit (HY density). Models based on HY were statistically downscaled to make predictions to 10x10km squares. Occurrence data models indicated a good predictive performance for most species, showing that the model framework proposed have improved results in comparison to previous models. The transferability of models into new regions was limited by the exposure of species to environmental conditions. As for HY models, the calibration plots showed a good and linear predictive performance for widely distributed species, as well as constrained distributed species. Overall, our results were consistent with the expected abundance distribution of widely distributed species. The removal of zeros on the validation datasets affected the calibration plots of all regions, showing a better predictive performance when zeros were removed for widely distribution species, but the opposite was evidenced for species with limited distributions. We conclude that (i) the importance of co-correlation variables when variable importance is inferenced from random forest model results, (ii) manipulation presence and absence locations could yield further improvement in occurrence model outputs, and (iii) HY model projections displayed good abundance patterns for most of species, showing that the three frameworks proposed were a goo

Predation is just one of several possible causal factors of the red-legged partridge decline. It is a key factor affecting the success of red-legged partridge nests, but agricultural activities can be the main cause of nest loss in some areas. Because hatchlings are more vulnerable to predation, this stage represents a critical bottleneck for partridge populations. Most restocking programmes fail due to predation due to the partridges’ inability to adapt to the new situation. Although predator control is a widespread game management practice for the red-legged partridge it has limited effects in most management situations. Some measures indirectly affecting the effects of predation, such as habitat management, could represent a long-lasting measure for reducing partridge predation preferable over traditional predator control, and they could revert current negative trends.

The new-born European Observatory of Wildlife (EOW)2 is a part of the EFSA-funded ENETWILD project, and has the aim of improving the European capacities 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 monitoring. As a next step, the EOW has engaged and enhanced the existing network of collaborators, and a number of participants are currently preparing field operations to estimate wild mammal density (focused on wild ungulates and other medium to big sized mammals) in certain areas from their respective countries. A field camera trap (CT) based protocol provided by the EOW is going to be applied. An online training course held in May 2022 provided specific training on camera trapping methods and protocols, specifically the random encounter method (REM) and other methods which do not require individual recognition. Here we also present the new field protocol, which is compatible with the subsequent application of artificial intelligence to process and analyze photo trappings using the online app AGOUTI. This strategy aims at promoting a network of professionals/researchers capable of designing, developing field work and analysing data, contributing also to disseminate the experience and train other colleagues in their respective countries. By now, the overall number of countries participating in the EOW is 25. Some participants from 12 countries could already estimate mammal densities during the previous seasons 2019/2020/2021, which will also apply the same methodology in different populations during 2022 in their respective countries. The number of density values finally obtained through this experience by the end of 2022 will exceed 40 different locations in a total of at least 30 countries, since some countries are on the process to confirm their participation. The EOW website is presented.

The definition of the most relevant parameters that describe the wild boar (WB) population dynamics is essential to guide African swine fever (ASF) control policies. These parameters should be framed considering different contexts, such as geographic, ecological and management contexts, and gaps of data useful for the parameter definition should be identified. This information would allow better harmonized monitoring of WB populations and higher impact of ASF management actions, as well as better parametrizing population dynamics and epidemiological models, which is key to develop more efficient cost-benefit strategies. This report presents a comprehensive compilation and description of parameters of WB population dynamics, including general drivers, population demography, mortality, reproduction, and spatial behaviour. Beyond the collection of current available data, we provided an open data model to allow academics and wildlife professionals to continuously update new and otherwise hardly accessible data, e.g. those from grey literature which is often not publicly available or only in local languages. This data model, conceived as an open resource and collaborative approach, will be incorporated in the European Observatory of Wildlife (EOW) platform, and include all drivers and population parameters that should be specified in studies on wild boar, and wildlife in general, ecology and epidemiology at the most suitable spatio-temporal resolution. This harmonized approach should be extended to other taxa in the future as an essential tool to improve European capacities to monitor, to produce risk assessment and to manage wildlife under an international perspective.

This report presents the results of field activities in relation to the generation of reliable wild boar density values by camera trapping (CT) in 19 areas in Europe, mainly in East Europe. Random Encounter Model (REM) densities ranged from 0.35±0.24 to 15.25±2.41 (SE) individuals/km2. No statistical differences in density among bioregions were found. The number of contacts was the component of the trapping rate that determined the coefficient of variation (CV) the most. The daily range (DR) significantly varied as a function of management; the higher values were detected in hunting grounds compared to protected areas, indicating that movement parameters are population specific, and confirming the potential role of hunting activities in increasing wild boar movement and contact rates among individual or groups. The results presented in this report illustrate that a harmonized approach to actual wildlife density estimation (namely for terrestrial mammals) is possible at a European scale, sharing the same protocols, collaboratively designing the study, processing, and analysing the data. This report adds reliable wild boar density values that have the potential to be used for wild boar abundance spatial modelling, both directly or to calibrate outputs of model based on abundance (such as hunting bags) or occurrence data. Future REM developments should focus on improving the precision of estimates (probably through increased survey effort). Next steps require an exhaustive and representative design of a monitoring network to estimate reliable trends of wild boar populations as a function of different factors in Europe. In this regard, the newly created European Observatory of Wildlife will be a network of observation points provided by collaborators from all European countries capable to monitor wildlife population at European level.

One of the main objectives of ENETWILD consortium is to collect data on density, hunting statistics and wildlife occurrence in order to model the geographical distribution and abundance of wildlife species across Europe as a tool to support the assessment of risks associated, for example, with disease transmission. Created in the framework of the ENETwild project, the European Wildlife Observatory (EOW2) provides the backbone for an integrated, interdisciplinary, multi-sectoral and multi-institutional approach to wildlife monitoring, initially focusing on terrestrial mammals in Europe. The EOW applies similar camera-trapping-based protocols for population estimation and data collection standards to facilitate harmonization and interoperability. For this purpose, continuous training of the network of wildlife professionals in Europe is a key activity of the EOW. In this context, during the last few years the ENETWILD consortium has organized different online training courses and workshops on the use of camera traps, addressing different approaches from the design and handling of camera traps to the processing of the collected data. Many of the participants in our previous courses are now part of the EOW and require updated information on methodology to process with next steps in the field. The course here reported presented improvements and refinements in the sampling protocols, aimed specially at new collaborators to be incorporated in the network. Therefore, the objectives of this introductory online course held on 5th May 2022 were: (i) to present milestones and achievements of the ENETWILD project and the EOW, and (ii) to review scientific methods for determining wildlife abundance and density, providing specific training on camera trapping methods and protocols, specifically the random encounter method (REM) and other methods which do not require identification of individuals. This course was attended by 46 wildlife biologists, animal health professionals and wi

Reliable estimates of the distribution of species abundance are a key element in wildlife studies, but such information is usually difficult to obtain for large spatial or long temporal scales. Wildlife–vehicle collision (WVC) data is systematically registered in many countries and could be used as a proxy of population abundance if the number of WVC in each territory increase with the population abundance. However, factors such as road density or human population should be controlled to obtain accurate abundance estimations from WVC data. Here, we propose a hierarchical modeling approach using the Royle–Nichols model for detection–non-detection data to obtain population abundance indices from WVC. Relative abundance and individual detectability were modeled for two species, wild boar Sus scrofa and roe deer Capreolus capreolus at 10 × 10 km cells in mainland Spain from WVC data using environmental, anthropological and temporal covariates. For each cell, a detection was annotated if at least one WVC was recorded at each month (used as survey occasion). The predicted abundance indices were compared with raw hunting statistics at region level to assess the performance of the modeling approach. Site specific covariates such as road density or administrative region and the month of the year, affected individual detectability, with higher WVC probability between October and December for wild boar and between April and July for roe deer. Wild boar and roe deer abundance can be explained by both, bioclimatic and land cover covariates. Abundance indices obtained from WVC data were significantly positively correlated with regional raw hunting yields for both species. We presented empirical evidence supporting that accurate wildlife abundance indices at fine spatial resolution can be generated from WVC data when individual detectability is considered in the modeling process.

While reliable estimates of species abundance distribution are required for wildlife management and are greatly needed at broad spatial scales, such information is scarce. In this context, the usefulness of spatial modelling as a tool for predicting game species relative abundance and distribution from hunting yield data was studied. Hunting yield data is affected by several factors related to species management, hunting regulations, and hunting efficacy and some doubts have been raised about the use or reliability of this data for large-scale modelling. Some years ago, Acevedo et al. (2014) calibrated five spatially explicit models (one per bioregion) by using hunting yield data for wild boar Sus scrofa (from hunting seasons 2006 to 2009) for approximately 60% of mainland Spain. After internal validation, the models were extrapolated to produce predictions of species relative abundance for the whole mainland country. Here, we reviewed these previous models to evaluate their predictive performance on new data (from hunting seasons 2014 to 2018) in areas where the models had been calibrated (interpolation areas) and also when projected into new ones (extrapolation areas). Our results showed that the previous models were able to forecast current general patterns of wild boar relative abundance with population growth rates equivalent to those reported by other authors, although differences between bioregions were observed. Performance on interpolation areas was higher than that obtained on extrapolation areas. Accuracy of model predictions decreased when fine resolution assessment at hunting ground level was carried out. Our results suggest that spatial models calibrated on hunting yields could be a good option to predict general wild boar relative abundance distribution patterns, although critical assessment is needed, since models can fail when they are extrapolated to areas for which no information is available and at fine scale resolution. These results represent a

The ecological plasticity of wild boar and their growing populations can generate conflicts with human activities and can be a threat to livestock and public health. Particularly, the emergence of African Swine Fever in Europe is of major importance. However, there are gaps in knowledge about wild boar ecology, population monitoring, management and population control that prevent the design and application of the best science-based ASF control policies, and/or adaptive evaluation of the actions taken. The effectiveness of wildlife policies is known to be directly proportional to their acceptance by stakeholders. However, it is unknown how the acceptance of these policies and different management scenarios vary among stakeholder groups, in different socio-economic and cultural contexts. Acceptance by stakeholders in different contexts determines the success of management strategies. Finally, factors that influence wild boar abundance and disease spread are not bound by national borders. Thus, there is need to coordinate national and international decision-making. In this context, this report presents research protocols to address a number of knowledge gaps previously identified by EFSA, and aims to improve the strategy to control ASF in the short-term. Twelve research objectives grouped into six categories address aspects of: (i) wild boar ecology, i.e. studies on basic aspects of wild boar population dynamics and assessment of the factors that determine the presence of wild boar near outdoor pig farms; (ii) wild boar monitoring, i.e. implementation of practical methods to estimate wild boar density and strategies to promote their application; (iii) wild boar management and population control, i.e. effect of feed availability, role and efficacy of recreational hunting and professional culling, efficacy of wild boar trapping and different fencing methods and the use of trained dogs in ASF affected areas; (iv) social acceptance by the stakeholders; (v) assessment and m

In the previous ENETWILD model, the predicted patterns of wild boar abundance based on hunting yield data reached an acceptable reliability when the model was downscaled to higher spatial resolution. This new approach, based on the modelling of hunting yield densities instead of hunting yield counts and the assessment of spatial autocorrelation, was only applied with simulated data and with data from two regions at hunting ground level, the smallest spatial resolution. In this report, (1) we evaluate whether this approach can correct the overpredictions for high-resolution predicted patterns when raw data are present at a different spatial resolution (i.e. the European region). For this purpose, hunting yield densities were incorporated as response variable (one model per bioregion) and predictions reliability at 10x10km and 2x2km spatial resolution were assessed. Internal validations and comparisons with the previous two-step model carried out at European scale were addressed, as well as an evaluation with external data at the same scale at country level. The model presented certain overprediction (much less than the previous model) of the total hunting bags reported per country, although a good correlation in terms of values and linearity between observed and predicted values was achieved. Secondly (2), a generic model framework to predict habitat suitability and likely occurrence for wildlife species using opportunistic presence data was proposed (occurrence records for wild ungulate species from the past 20 years exclusively from the Global Biodiversity Information Facility extracted on 9/12/2020). Across all wild ungulate species (elk (Alces alces), roe deer (Capreolus capreolus), red deer (Cervus elaphus), dam deer (Dama dama), muntjac (Muntiacus reevesi), wild boar (Sus scrofa)) the model framework performs well. For those species where area under the curve is below 0.7 we note lower accuracy in predicting absences, which requires further investigation to und

The 2nd ENETWILD Annual General Meeting took place on 5-6th October 2021, bringing together experts, stakeholders and ENETWILD collaborators in online workshop discussions. First, workshop discussions contributed to the analysis and proposal of approaches for a harmonized European-wide wildlife monitoring framework able of sustaining coordinated decision-making. Secondly, participants identified the key challenges that managers face in making decisions for wildlife in Europe and data needs for policies. Finally, we illustrated these challenges with the case of wild boar as a model species widely distributed across Europe. Inputs from the participants were collated into a plan of proposed steps and objectives for the mid-term (5-year time frame) to achieve progress on harmonised, coordinated, and integrated wildlife monitoring at the European level, which requires the contribution of experts from the early stages.. Specific proposed actions include the creation of a trans-disciplinary authority at the European level, effective points of reference for data collection and sharing at different administrative levels and countries, a standing committee to coordinate and exchange experience and capacities on data collection between countries, and expert groups for problem solving, with proper EU financial support, establishing regular policy meetings. . To provide useful results, wildlife monitoring must ensure proper design and data analysis for subsequent science-based management and best allocation of management resources. The 'Observatory' approach (a representative network of intensively monitored sites) can provide long-term systematic and representative insights, normally more feasible for comparative studies, providing less biases and support for decision-making. For international decision-making by wildlife managers and politicians based on scientific knowledge and interdisciplinary research, experts should define the foundations of a common European wildlife deci

In order to define the spatial interface between wild boar and domestic pigs in Europe, the ENETWILD consortium (www.enetwild.com) described in a preliminary report the different sources of data for domestic pigs at European scale, and developed a preliminary risk map of possible spatial interaction between both groups. This modelexplored and assessed the use of pig distribution data from Gridded Livestock of the Worlddatabase (GLW), FAO. However, in some specific countries used as cases, the GLW predictions did not reliably represent the pig abundance distribution within countries. The currently available census data of livestock at the European Union level (Eurostat) is limited to the spatial resolution at NUTS2. While Eurostat ensures that data can be potentially comparable,there is still needed to resolve definition issues regarding better spatial resolution (level of aggregation of information) and the pig production systems. In this context, the objectives of this report are (i) assessing the spatial interface between pigs and wild boar over Europe using the best quality data available (Eurostat data and ENETWILD spatial models). We(ii) secondly assessed the interface at higher spatial resolution, distinguishing pig production types in countries where data was available. Based on comparisons at different scales and quality of data, we propose future steps in both data collection and modelling approach.Precisespatial resolution of pig data is not available at European level yet, and the discrimination of extensive vs. intensive farms, backyards vs. commercial; outdoor vs. indoor, is essential to quantify and perform risk analyses separatelyfor each production system and/or considering this relevant source of variation in risk at the interface. The development of a framework to collect harmonised and standardised data at European scale athigher resolution is needed.

Besides being a threat to conservation, the American mink (Neovison vison) also has the potential to play a crucial role in the ongoing pandemic, as it was demonstrated to be a susceptible host for a mutant version of the SARS-CoV-2 and capable of transmitting it back to humans. This virus can potentially be present also in feral specimens. Despite control and eradication plans, the American mink is still quite widespread in the continent and there is lack of information about its distribution, with the last mapping in Europe dated 2006. The aim of the project was to gather information about the presence and distribution of this species, creating a harmonized map of Europe, pointing out the trends over the years and the issues concerning harmonization of population data. In the frame of the ENETWILD project, we managed to collect information about the presence of American mink in all the western European countries and most of the eastern ones. Data were harmonized from different sources and spatial resolutions, grouped by year and transformed in 10x10km grid of presence and absence. Maps were compared to outline changes over time. We took Spain as a model for a more detailed work, where data of captures were related to capture effort: allowing a density index to be created that gave a better picture of the situation. We also reviewed the European current mink farming situation and the existence of control schemes for feral populations. This information will be extremely useful for risk assessment at a European level: it could represent the basis for coordinating the efforts to control a still spreading species with a relevant health interest. Moreover, the issue of a harmonized data collection for wildlife species clearly emerges as key element to implement to obtain better quality and more useful data.

The ENETWILD consortium (www.enetwild.com) aims at defining the spatial interface between wild boar and domestic pigs in Europe, which is essential to evaluate the risk for ASF spread between wild and domestic. This report describes the different sources of data for domestic pigs in Europe and develops a preliminary risk map of possible spatial interaction between both groups. Specific cases from Romania and Spain where reliable data were available were assessed. This model of the interface was based on the data from Gridded Livestock of the World (GLW) database of FAO, which provides predictions on a 1x1 km scale globally and the wild boar abundance distribution model recently elaborated by ENETWILD consortium (2020). The present available census data of livestock at the European Union level (Eurostat) is restricted to a maximum spatial resolution of NUTS2, remarking the need of developing a framework to collect harmonised data with higher resolution. This will ensure that data can be comparable, validated and used. There is need also to resolve definition issues regarding the pig production systems. Our prediction model of the interface between pig and wild boar at European level indicated that the maximum risk is scattered over Central Europe, large parts of Spain, north-east France and Romania. Hungary, so as Serbia and Croatia in the Balkans are at the highest risk in that area. In the specific case of Romania, no statistically significant association between census data of pigs collected from national authorities and predicted values was found when assessing the GLW model, evidencing that GLW predictions do not reliably represents the pig abundance distribution within countries. When assessing the interface model in Spain, certain areas of interaction were lacked, e.g. where extensive farming is relevant. The current discrimination of extensive vs. intensive farms of predictive models (GLW) is not reliable to perform analyses separately for each production sys

Domestication has resulted in immense phenotypic changes in animals despite their relatively short evolutionary history. The European rabbit is one of the most recently domesticated animals, but exhibits distinct morphological, physiological, and behavioral differences from their wild conspecifics. A previous study revealed that sequence variants with striking allele frequency differences between wild and domestic rabbits were enriched in conserved noncoding regions, in the vicinity of genes involved in nervous system development. This suggests that a large proportion of the genetic changes targeted by selection during domestication might affect gene regulation. Here, we generated RNA-sequencing data for four brain regions (amygdala, hypothalamus, hippocampus, and parietal/temporal cortex) sampled at birth and revealed hundreds of differentially expressed genes (DEGs) between wild and domestic rabbits. DEGs in amygdala were significantly enriched for genes associated with dopaminergic function and all 12 DEGs in this category showed higher expression in domestic rabbits. DEGs in hippocampus were enriched for genes associated with ciliary function, all 21 genes in this category showed lower expression in domestic rabbits. These results indicate an important role of dopamine signaling and ciliary function in the evolution of tameness during rabbit domestication. Our study shows that gene expression in specific pathways has been profoundly altered during domestication, but that the majority of genes showing differential expression in this study have not been the direct targets of selection.

A recent publication by Carvalho et al. in “Virus Genes” (June 2017) reported the presence of the new variant of rabbit hemorrhagic disease virus (RHDV2) in the two larger islands of the archipelago of Madeira. Based on the capsid protein sequence, the authors suggested that the high sequence identity, along with the short time spanning between outbreaks, points to dissemination from Porto Santo to Madeira. By including information of the full RHDV2 genome of strains from Azores, Madeira, and the Canary Islands, we confirm the results obtained by Carvalho et al., but further show that several subtypes of RHDV2 circulate in these islands: non-recombinant RHDV2 in the Canary Islands, G1/RHDV2 in Azores, Porto Santo and Madeira, and NP/RHDV2 also in Madeira. Here we conclude that RHDV2 has been independently introduced in these archipelagos, and that in Madeira at least two independent introductions must have occurred. We provide additional information on the dynamics of RHDV2 in the Macaronesian archipelagos of Azores, Madeira, and the Canary Islands and highlight the importance of analyzing RHDV2 complete genome.

[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 that may deter invasion, which are useful in developing strategies for population control. In Spain, it has been suggested that hunters introduced the non-native eastern cottontail (Sylvilagus floridanus) to compensate for the recent drastic declines of the native European rabbit (Oryctolagus cuniculus). [Aims]: Our main goals were to investigate (1) whether Sylvilagus rabbits have indeed been introduced by hunters across Spain, and (2) whether the species has become established in Spanish ecosystems. [Methods]: We interviewed 311 hunters or naturalists across Spain. The questionnaires inquired about the characteristics of game management in each locality, including the frequency of rabbit restocking, and particularly whether Sylvilagus rabbits had been released in the surveyed localities. In addition, we sampled 192 rabbit populations (n = 3974 individuals) across Spain by using molecular analysis to determine whether Sylvilagus rabbits were present in these areas. [Key results]: Our interview results suggest that Sylvilagus rabbits may have been released in 6% of the 311 localities surveyed. However, molecular analyses failed to confirm their persistence, because all samples belonged to O. cuniculus. [Conclusions]: We infer that Sylvilagus rabbits failed to establish themselves in Spain, although interviewees reported their introduction. Several reasons may explain the unsuccessful establishment of this species, such as a low propagule pressure, competition with native species, predation, inability to cope with local pathogens and unsuitable climatic conditions. [Implications]: The risk of future introductions of non

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 studied patterns of allele frequency change across their hybrid zone using whole-genome sequencing. To connect levels and patterns of genetic differentiation with phenotypic manifestations of subfertility in hybrid rabbits, we further investigated patterns of gene expression in testis. Geographic cline analysis revealed 253 regions characterized by steep changes in allele frequency across their natural region of contact. This catalog of regions is likely to be enriched for loci implicated in reproductive barriers and yielded several insights into the evolution of hybrid dysfunction in rabbits: (i) incomplete reproductive isolation is likely governed by the effects of many loci, (ii) protein–protein interaction analysis suggest that genes within these loci interact more than expected by chance, (iii) regulatory variation is likely the primary driver of incompatibilities, and (iv) large chromosomal rearrangements appear not to be a major mechanism underlying incompatibilities or promoting isolation in the face of gene flow. We detected extensive misregulation of gene expression in testis of hybrid males, but not a statistical overrepresentation of differentially expressed genes in candidate regions. Our results also did not support an X chromosome-wide disruption of expression as observed in mice and cats, suggesting variation in the mechanistic basis of hybrid male reduced fertility among mammals.

The most characteristic feature of domestic animals is their change in behavior associated with selection for tameness. Here we show, using high-resolution brain magnetic resonance imaging in wild and domestic rabbits, that domestication reduced amygdala volume and enlarged medial prefrontal cortex volume, supporting that areas driving fear have lost volume while areas modulating negative affect have gained volume during domestication. In contrast to the localized gray matter alterations, white matter anisotropy was reduced in the corona radiata, corpus callosum, and the subcortical white matter. This suggests a compromised white matter structural integrity in projection and association fibers affecting both afferent and efferent neural flow, consistent with reduced neural processing. We propose that compared with their wild ancestors, domestic rabbits are less fearful and have an attenuated flight response because of these changes in brain architecture.

The dwarf phenotype characterizes the smallest of rabbit breeds and is governed largely by the effects of a single dwarfing allele with an incompletely dominant effect on growth. Dwarf rabbits typically weigh under 1 kg and have altered craniofacial morphology. The dwarf allele is recessive lethal and dwarf homozygotes die within a few days of birth. The dwarf phenotype is expressed in heterozygous individuals and rabbits from dwarf breeds homozygous for the wild-type allele are normal, although smaller when compared to other breeds. Here, we show that the dwarf allele constitutes a ~ 12.1 kb deletion overlapping the promoter region and first three exons of the HMGA2 gene leading to inactivation of this gene. HMGA2 has been frequently associated with variation in body size across species. Homozygotes for null alleles are viable in mice but not in rabbits and probably not in humans. RNA-sequencing analysis of rabbit embryos showed that very few genes (4–29 genes) were differentially expressed among the three HMGA2/dwarf genotypes, suggesting that dwarfism and inviability in rabbits are caused by modest changes in gene expression. Our results show that HMGA2 is critical for normal expression of IGF2BP2, which encodes an RNA-binding protein. Finally, we report a catalog of regions of elevated genetic differentiation between dwarf and normal-size rabbits, including LCORL-NCAPG, STC2, HOXD cluster, and IGF2BP2. Levels and patterns of genetic diversity at the LCORL-NCAPG locus further suggest that small size in dwarf breeds was enhanced by crosses with wild rabbits. Overall, our results imply that small size in dwarf rabbits results from a large effect, loss-of-function (LOF) mutation in HMGA2 combined with polygenic selection.

Anthropogenic hybridization in wildlife has been identified as one of the main causes of genetic homogenization, highlighting the need for identification and evaluation of populations at risk. Relocation of wildlife for game management purposes is a widespread practice that may promote the admixing of genetically different populations, subspecies or species. We undertook a large-scale study on the Iberian Peninsula to assess the extent of hybridization in red-legged partridge Alectoris rufa populations, which have been subject to extensive restocking of farm-reared individuals. Using a polymerase chain reaction-restriction fragment length polymorphism technique to assess the prevalence of individuals with mtDNA from other species, we examined samples of A. rufa from museum specimens (229), extant wild populations (955) and game farms (530). We found widespread occurrence of chukar partridge Alectoris chukar mtDNA lineages in samples obtained from game farm partridges (63% of game farms) and from wild partridges (45% of populations), but no allochthonous mtDNA lineages were found in museum partridges. We also found that the probability of occurrence and the number of partridges with allochthonous lineages was higher in localities where recent restocking had occurred. In addition, investigation of trends in bag records and the numbers of game farms over the past 30 years suggests that the general decline of wild populations has been accompanied by an increase in game farm facilities. These results suggest that supplemental stocking practices are threatening the integrity of the wild population gene pool. We recommend that rural development policies and associated wildlife management programs focused on maintaining high stock densities for hunting also need to consider the impact of game management on the genetic integrity of game populations.

Anthropogenic hybridization in wildlife has been identified as one of the main causes of genetic homogenization, highlighting the need for identification and evaluation of populations at risk. Relocation of wildlife for game management purposes is a widespread practice that may promote the admixing of genetically different populations, subspecies or species. We undertook a large-scale study on the Iberian Peninsula to assess the extent of hybridization in red-legged partridge Alectoris rufa populations, which have been subject to extensive restocking of farm-reared individuals. Using a polymerase chain reaction-restriction fragment length polymorphism technique to assess the prevalence of individuals with mtDNA from other species, we examined samples of A. rufa from museum specimens (229), extant wild populations (955) and game farms (530). We found widespread occurrence of chukar partridge Alectoris chukar mtDNA lineages in samples obtained from game farm partridges (63% of game farms) and from wild partridges (45% of populations), but no allochthonous mtDNA lineages were found in museum partridges. We also found that the probability of occurrence and the number of partridges with allochthonous lineages was higher in localities where recent restocking had occurred. In addition, investigation of trends in bag records and the numbers of game farms over the past 30 years suggests that the general decline of wild populations has been accompanied by an increase in game farm facilities. These results suggest that supplemental stocking practices are threatening the integrity of the wild population gene pool. We recommend that rural development policies and associated wildlife management programs focused on maintaining high stock densities for hunting also need to consider the impact of game management on the genetic integrity of game populations.

We developed and tested 16 new polymorphic microsatellite markers for the red-legged partridge (Alectoris rufa): four dinucleotide, two trinucleotide, eight tetranucleotide and two pentanucleotide repeat loci. The number of alleles per locus ranged from two to 21, observed heterozygosity was from 0.03 to 1.00 and expected heterozygosity was comprised between 0.18 and 0.91. Cross-specific amplification in others members of the Phasianidae family highlighted the potential usefulness of these molecular markers for the study of related species.

El género Alectoris (orden Galliformes, familia Phasianidae) está compuesto por siete especies distribuidas a través de Europa, Asia y norte de África. Las especies de este género están claramente diferenciadas en análisis filogenéticos, existiendo hibridación natural en zonas de contacto. La perdiz roja (A. rufa) es endémica del mediterráneo occidental, donde su distribución natural comprende Portugal, España, Francia y noroeste de Italia. Esta especie es importante en el ecosistema mediterráneo, siendo un componente frecuente en la dieta de numerosas especies, pero la perdiz roja por lo que destaca es por ser la especie económicamente más importante de la caza menor y, debido a esto, está sometida a una intensa presión cinegética. La presión cinegética, la degradación de su hábitat, junto con el incremento de la agricultura intensiva y la utilización de pesticidas, han favorecido la disminución en abundancia de sus poblaciones. Esta disminución en abundancia se ha intentado contrarrestar con sueltas de perdices criadas en cautividad, apareciendo perdices híbridas lejos de zonas de contacto parapátricas. La hibridación puede tener como consecuencias la pérdida de acervo genético y homogeneización de las poblaciones. Respecto a los conocimientos genéticos previos en esta especie, se sabe que hay hibridación y que el origen está en las granjas. Aparte de esto, se desconoce la diversidad genética de la especie, cómo se distribuye espacialmente y los factores que modelan la variación de la diversidad genética. En esta tesis se han valorado factores antrópicos, es decir, la influencia de la hibridación, y factores naturales, mediante genética de poblaciones y análisis filogeográficos, para ver la distribución de la diversidad genética y el porqué de tal distribución. Para conseguir nuestro objetivo hemos testado y desarrollado distintos tipos de marcadores.

Understanding the spatial pattern of genetic diversity may be pivotal to adaptive conservation management of a given taxon. The red-legged partridge (Alectorisrufa, Linnaeus 1758) is naturally widely distributed from the Mediterranean to humid temperate zones. According to a recent study, the genetic structure of this species comprises five clusters, three of which are in the Iberian Peninsula (glacial refugia). Partridge demographic expansion events and climatic shifts during Pleistocene glaciations have been used to test the hypotheses concerning Iberian red-legged partridge distribution. We tested the existence of climatic and geographic relationships on genetic diversity/distances. We employed markers from two different genetic systems, such as part of the mitochondrial DNA control region (n = 113) and 20 species-specific microsatellite DNA loci (n = 377), including climatic and geographic factors from the 14 Iberian localities where A. rufa populations were sampled. Our results showed a mitochondrial genetic diversity pattern associated with a thermic gradient, and a decrease of genetic diversity in peripheral populations that concurred with the ‘abundant centre’ hypothesis. Overall, current climatic variables reliably described genetic variation and differentiation in the red-legged partridge, which may be a result of local species adaptation.

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 is crucial for proper conservation of Evolutionarily Significant Units. We use the two European rabbit subspecies, Oryctolagus cuniculus cuniculus and O. c. algirus, in the Iberian Peninsula as a model to investigate the repercussions at the biometric level of their largely recognized genetic differentiation. To accomplish this we analysed the ear and hind foot length, and the body mass of 999 adult rabbits from 27 locations across the distribution range of both subspecies in their native range, the Iberian Peninsula. Our results show biometric differences between the two subspecies, also explained by geographical location and sex, O. c. algirus being lighter and having shorter ear and hind foot lengths. We examine these findings under an evolutionary framework, and discuss their implications for current conservation efforts. Future research should focus on the ecological implications of these biometric differences, namely potential different habitat use and anti-predatory strategies in the species' native range.

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 this study, we used next-generation sequencing to study genome-wide patterns of genetic differentiation between two hybridizing subspecies of rabbits (Oryctolagus cuniculus algirus and O. c. cuniculus) that are known to undergo high rates of gene exchange. Our primary objective was to identify specific genes or genomic regions that have resisted introgression and are likely to confer reproductive barriers in natural conditions. On the basis of 326,000 polymorphisms, we found low to moderate overall levels of differentiation between subspecies, and fewer than 200 genomic regions dispersed throughout the genome showing high differentiation consistent with a signature of reduced gene flow. Most differentiated regions were smaller than 200 Kb and contained very few genes. Remarkably, 30 regions were each found to contain a single gene, facilitating the identification of candidate genes underlying reproductive isolation. This gene-level resolution yielded several insights into the genetic basis and architecture of reproductive isolation in rabbits. Regions of high differentiation were enriched on the X-chromosome and near centromeres. Genes lying within differentiated regions were often associated with transcription and epigenetic activities, including chromatin organization, regulation of transcription, and DNA binding. Overall, our results from a naturally hybridizing system share important commonalities with hybrid incompatibility genes identified using laboratory crosses in mice and flies, highlighting general mechanisms underlying the maintenance of reproductive barriers.

Hyperpredation can be described as a restrictive case of apparent competition where an increased number of primary prey species indirectly induces the decrease of the secondary prey species through numerical response of predators to the primary prey dynamics. It has been proposed that rabbit hemorrhagic disease (RHD), which decimated populations of European wild rabbit (Oryctolagus cuniculus) in Spain, led to prey switching by raptors towards red-legged partridges (Alectoris rufa) causing declines in their populations as a peculiar case of hyperpredation. We have reviewed field studies that disagree with estimates (based on bag records) of recent increases of rabbit and partridge numbers in Spain. Because of an increase in releases of farm-reared animals, there is doubt about the use of bag records to accurately estimate population trends in recent decades. We also provide new data and discuss some analytical considerations related to the temporal and spatial scales that might affect the interpretation of data. Finally, we discuss why studies associated with raptor food habits, predator population dynamics and predator distribution suggest that diet data are not sufficient to link patterns and processes. Although we agree that the RHD outbreak has markedly affected rabbit populations, which has indirectly affected many other species in the Iberian Peninsula, we consider that hyperpredation mediated by raptors has not been clearly demonstrated. In contrast, endorsing the hypothesis of raptor-mediated hyperpredation without sufficient proof may have conflictive consequences if we consider the increased persecution of raptors in recent decades in Spain.

The nearly neutral theory of molecular evolution predicts that the efficacy of both positive and purifying selection is a function of the long-term effective population size (Ne) of a species. Under this theory, the efficacy of natural selection should increase with Ne. Here, we tested this simple prediction by surveying ∼1.5 to 1.8 Mb of protein coding sequence in the two subspecies of the European rabbit (Oryctolagus cuniculus algirus and O. c. cuniculus), a mammal species characterized by high levels of nucleotide diversity and Ne estimates for each subspecies on the order of 1 × 10. When the segregation of slightly deleterious mutations and demographic effects were taken into account, we inferred that >60 of amino acid substitutions on the autosomes were driven to fixation by positive selection. Moreover, we inferred that a small fraction of new amino acid mutations (<4) are effectively neutral (defined as 0 < Nes < 1) and that this fraction was negatively correlated with a gene's expression level. Consistent with models of recurrent adaptive evolution, we detected a negative correlation between levels of synonymous site polymorphism and the rate of protein evolution, although the correlation was weak and nonsignificant. No systematic X chromosome-autosome difference was found in the efficacy of selection. For example, the proportion of adaptive substitutions was significantly higher on the X chromosome compared with the autosomes in O. c. algirus but not in O. c. cuniculus. Our findings support widespread positive and purifying selection in rabbits and add to a growing list of examples suggesting that differences in Ne among taxa play a substantial role in determining rates and patterns of protein evolution.

Domestication has led to similar changes in morphology and behavior in several animal species, raising the question whether similarities between different domestication events also exist at the molecular level. We used mRNA sequencing to analyze genome-wide gene expression patterns in brain frontal cortex in three pairs of domesticated and wild species (dogs and wolves, pigs and wild boars, and domesticated and wild rabbits). We compared the expression differences with those between domesticated guinea pigs and a distant wild relative (Cavia aperea) as well as between two lines of rats selected for tameness or aggression towards humans. There were few gene expression differences between domesticated and wild dogs, pigs, and rabbits (30-75 genes (less than 1%) of expressed genes were differentially expressed), while guinea pigs and C. aperea differed more strongly. Almost no overlap was found between the genes with differential expression in the different domestication events. In addition, joint analyses of all domesticated and wild samples provided only suggestive evidence for the existence of a small group of genes that changed their expression in a similar fashion in different domesticated species. The most extreme of these shared expression changes include up-regulation in domesticates of SOX6 and PROM1, two modulators of brain development. There was almost no overlap between gene expression in domesticated animals and the tame and aggressive rats. However, two of the genes with the strongest expression differences between the rats (DLL3 and DHDH) were located in a genomic region associated with tameness and aggression, suggesting a role in influencing tameness. In summary, the majority of brain gene expression changes in domesticated animals are specific to the given domestication event, suggesting that the causative variants of behavioral domestication traits may likewise be different.

Dispersal barriers may arise and disappear repeatedly over the course of a species’ distribution and can have different effects depending partially on the duration of the barrier and the species’ ecology. The red-legged partridge (Alectoris rufa) has a large natural distribution range extending from the Mediterranean to humid temperate zones. However, the genetic structure of this species is unknown. We investigated the potential impact of Pleistocene and Holocene range shifts on the phylogeographic patterns and genetic population structure of this species using mitochondrial DNA control-region and nuclear microsatellite loci. Our results imply that during the Pleistocene glaciations this species was affected by climatic changes and ephemeral geographic barriers, which led to their current shallow genealogical and genetic structure apportioned into five genetic groups: South-western, Central-eastern, North-western, Balearic, and French and Italian, which could be recognized as management units (stocks) of the A. rufa species. Future conservation and management plans of this species should take into account its wild genetic structure in regards of releases of captivebred partridges for restocking, avoiding the mixture of different gene pools and alteration of intraspecific diversity.

The Pleistocene climatic oscillations promoted the diversification in avian species during the last glacial period. The red-legged partridge (Alectoris rufa, Family Phasianidae) has a large natural distribution extending from the Mediterranean to humid temperate zones. However, the genetic structure for this species is unknown. The present study investigates the phylogeography, genetic structure and demographic history of A. rufa across its distribution, employing both mitochondrial DNA control region sequences and nuclear microsatellite loci. Our results propose that this species was greatly affected by Pleistocene glaciations. The mismatch analyses suggest that the current populations resulted from post-glacial expansion and subsequent differentiation resulting in five diagnosable genetic clusters: Southwestern, Central-eastern, Northwestern, Balearic and French and Italian. Further, we found evidence of three glacial refugia within the currently recognized Iberian glacial refugium. The intraspecific structure revealed by both maternal and biparental phylogeographic analyses was not resolved in the phylogenetic analyses. Based on all considerations, we recommended that five management units be recognized.

Studies of gene flow between closely related taxa can provide insight into the genetic basis of speciation. To evaluate the importance of the X chromosome in reproductive isolation between subspecies of the European rabbit and to study the genomic scale over which islands of differentiation extend, we resequenced a total of 34 loci distributed along the X chromosome and chromosome 14. Previous studies based on few markers suggested that loci in centromeric regions were highly differentiated between rabbit subspecies, whereas loci in telomeric regions were less differentiated. Here, we confirmed this finding but also discovered remarkable variation in levels of differentiation among loci, with FST values from nearly 0 to 1. Analyses using isolation-with-migration models suggest that this range appears to be largely explained by differential levels of gene flow among loci. The X chromosome was significantly more differentiated than the autosomes. On chromosome 14, differentiation decayed very rapidly at increasing distances from the centromere, but on the X chromosome distinct islands of differentiation encompassing several megabases were observed both at the centromeric region and along the chromosome arms. These findings support the idea that the X chromosome plays an important role in reproductive isolation between rabbit subspecies. These results also demonstrate the mosaic nature of the genome at species boundaries.

Knowledge of intrinsic and extrinsic factors associated with survival rates and the underlying causes of mortality is essential to understand both population dynamics and the causes of population declines. We studied the influence of habitat variables and body condition on survival of 151 radio-tracked Red-legged Partridges Alectoris rufa in four areas of Spain, representing a gradient from natural unmanaged areas to highly managed areas. We examined the effects of differences in game management practices, and seasonal and geographical variations in survival and causes of mortality over 4 years, from 1999 to 2002. Monthly survival rate was consistently over 90% for both sexes in the natural area. However, in two areas managed intensively for both hunting and agriculture, survival was low during the hunting period (72% for females and 79% for males), high during the breeding period for males (99%), and intermediate for females (89%) due mainly to diseases. Hunting was the main cause of Red-legged Partridge mortality in both hunting areas where driven partridge shooting was performed, affecting 50% of radio-tagged individuals, and was the main cause of mortality over all areas during both breeding and hunting periods. Disease was the next most common cause of mortality in managed areas, affecting mostly females during the breeding period, whereas predation was the main cause of mortality in unmanaged populations. Finally, we compared the habitat associations and body condition of living and dead individuals with varying causes of mortality. In general, high survival rates were associated with diverse vegetation, habitat edges and a good body condition index. Habitat diversity and a high edge index were also negatively associated with mortality due to predation and diseases. On the other hand, hunting mortality decreased with the proportion of scrubland and increased with the proportion of agricultural land. These results suggest that preventing declines of wild Red-le

To understand the factors contributing to the spatial behaviour of the red-legged partridge (Alectoris rufa), a radio-tracking study of free living partridges was carried out in Spain. During 2000–2002, 275 individuals were captured in four areas with different environmental and management characteristics. Sixty-nine adults and 23 juveniles were used to study space use distributions, including home range size, core area size and habitat selection. According to a generalized linear mixed model, 63% of the variability in home range size was explained by three landscape variables: edge index, average patch size and agricultural disturbance. Habitat selection was not influenced by age or sex because parents and juveniles remained together for most of the year, except during mating. The decline of the red-legged partridge in Spain was preceded by agricultural transformations related to land holding concentration and an increase in cultivated surface per property, which increased patch sizes and decreased edge and marginal areas across Spain.

Recently, it has been proposed that adult mortality schedules may be responsible for latitudinal patterns of life history variation in passerine birds, whereas nest predation only could explain within latitude patterns. Unfortunately, no independent test has been performed regarding the importance of nest predation with different taxa. In the present study, seasonality and nest predation hypotheses explaining variations in gestation time and litter size in 17 lagomorph species were tested. Among latitude patterns were analysed using the phylogenetic independent contrast method of Felsenstein and within latitude patterns were analysed by the pairwise comparative method. The results obtained indicate that latitudinal patterns observed in both variables are explained by different factors: seasonality for litter size and nest predation for gestation time. Litter size variations within latitudes are also explained by differences in nest predation, supporting previous hypotheses. In conclusion, the present study suggests that, when compared among latitudes, different life history traits (e.g. litter size and gestation time) may be shaped by different selective forces and that the effects of nest predation may be high both within and between latitudes.

Parasite community ecology has recently focused on understanding the forces structuring these communities. There are few surveys, however, designed to study the spatial repeatability and predictability of parasite communities at the local scale in one host. The purpose of our study was to address the relationship between infracommunity and component community richness, and to describe spatial variations on the local scale, of helminth parasite communities in an avian host, the red-legged partridge (Alectoris rufa). We sampled 235 wild partridges from 8 separate localities, with different partridge population densities, in the Ciudad Real and Toledo provinces of central Spain, and we determined their overall and intestinal helminth species. We found that habitat variables (mean temperature and land use) were not significantly associated with any component community. The partridge population abundance index was directly correlated with the prevalence and mean intensity of infection but not with component community species richness. There was a curvilinear relationship between infracommunity and component community species richness, as well as negative interspecific associations, for the helminth species assemblage parasitizing the intestine. A nestedness/anti-nestedness pattern, considered as part of a continuum, was associated with prevalence, mean intensity and partridge population abundance index, but not with component community richness. Increases in the partridge population abundance index and the prevalence and mean intensity of infection were associated with increases in helminth community nestedness. Although negative interactions between helminth species could not be ruled out as forces structuring helminth communities, our results suggest that parasite community structure in the red-legged partridge was primarily determined by the extrinsic influence of parasite habitat heterogeneity and its amplification of the differing probabilities of colonization of pa