Population genetic structure of the red fox (Vulpes vulpes) in the UK

Annual assessment of Echinococcus multilocularis surveillance reports submitted in 2024 in the context of commission delegated regulation (EU) 2018/772

This report comprises the 14th assessment of the Echinococcus multilocularis surveillance scientific reports, provided by Finland, Ireland, United Kingdom (Northern Ireland) and Norway on their respective surveillance programmes. Every year since 2012, EFSA presents the assessment to the European Commission in which the sampling strategy, data collection and detection methods used by these countries are evaluated. More specifically, the surveillance programmes of these four countries are evaluated by checking the information submitted by each of them and verifying that the technical requirements are fulfilled as laid down in Commission Delegated Regulation (EU) 2018/772 of 21 November 2017 supplementing Regulation (EU) No 576/2013 of the European Parliament and of the Council with regard to preventive health measures for the control of Echinococcus multilocularis infection in dogs, and repealing Delegated Regulation (EU) No 1152/2011. The information is divided into four different categories for assessment: the type and sensitivity of the detection method, the selection of the target population, the sampling strategy and the methodology. For each category, the main aspects that need to be considered in order to accomplish the technical requirements of the legislation are checked against compliance of several criteria. The countries participating in this surveillance (Finland, Ireland, the United Kingdom (Northern Ireland) and Norway) succeeded in the fulfilment of the technical legal requirements foreseen in Commission Delegated Regulation (EU) 2018/772 concerning these four different categories. None of the four countries recorded positive samples in the 12-month reporting period.

Mitogenomic exploration supports the historical hypothesis of anthropogenic diffusion of a zoonotic parasite Echinococcus multilocularis

Animal movement across regions owing to human activity can lead to the introduction of pathogens, resulting in disease epidemics with medical and socioeconomic significance. Here, we validated the hypothesis that human activity, such as the transportation of infected animals, has played a significant role in introducing the zoonotic parasite Echinococcus multilocularis into Hokkaido, Japan, by synthesizing and evaluating parasite genetic data in light of historical records. Our analysis indicates that a major genetic group in Hokkaido originated from St. Lawrence Island, USA, which is in accordance with the route suggested by historical descriptions. Moreover, we identified a minor genetic group closely related to parasites found in Sichuan, China. This fact implies that parasite invasion in Japan may result from complex and inadvertent animal translocations. These findings emphasize the anthropogenic impacts on zoonotic parasite spread and provide a crucial perspective for preventing future potential epidemics.

Annual assessment of Echinococcus multilocularis surveillance reports submitted in 2023 in the context of commission delegated regulation (EU) 2018/772

This report is part of the Echinococcus multilocularis surveillance scientific reports which are presented annually by EFSA to the European Commission and are intended to assess the sampling strategy, data collection and detection methods used by Finland, Ireland, United Kingdom (Northern Ireland) and Norway in their respective surveillance programmes. The surveillance programmes of these four countries were evaluated by checking the information submitted by each of them and verifying that the technical requirements were fulfilled as laid down in Commission Delegated Regulation (EU) 2018/772 of 21 November 2017 supplementing Regulation (EU) No 576/2013 of the European Parliament and of the Council with regard to preventive health measures for the control of Echinococcus multilocularis infection in dogs, and repealing Delegated Regulation (EU) No 1152/2011. The information was divided into four different categories for assessment: the type and sensitivity of the detection method, the selection of the target population, the sampling strategy and the methodology. For each category, the main aspects that need to be considered in order to accomplish the technical requirements of the legislation were checked against compliance of several criteria. The countries participating in this surveillance (Finland, Ireland, Norway and United Kingdom [Northern Ireland]) succeeded in the fulfilment of the technical legal requirements foreseen in Commission Delegated Regulation (EU) 2018/772 concerning these four different categories None of the four countries recorded positive samples in the 12-month reporting period.

Low levels of genetic differentiation and structure in red fox populations in Eastern Canada and implications for Arctic fox rabies propagation potential

Rabies is a lethal zoonosis present in most parts of the world which can be transmitted to humans through the bite from an infected mammalian reservoir host. The Arctic rabies virus variant (ARVV) persists mainly in populations of Arctic foxes (Vulpes lagopus), and to a lesser extent in red fox populations (Vulpes vulpes). Red foxes are thought to be responsible for sporadic southward movement waves of the ARVV outside the enzootic area of northern Canada. In this study, we wanted to investigate whether red foxes displayed notable levels of genetic structure across the Quebec-Labrador Peninsula, which includes portions of the provinces of Quebec and Newfoundland-Labrador in Canada, and is a region with a history of southward ARVV movement waves. We combined two datasets that were collected and genotyped using different protocols, totalling 675 red fox individuals across the whole region and genotyped across 13 microsatellite markers. We found two genetic clusters across the region, reflecting a latitudinal gradient, and characterized by low genetic differentiation. We also observed weak but significant isolation by distance, which seems to be marginally more important for females than for males. These findings suggest a general lack of resistance to movement in red fox populations across the Quebec-Labrador Peninsula, regardless of sex. Implications of these findings include additional support for the hypothesis of long-distance southward ARVV propagation through its red fox reservoir host.

Annual assessment of Echinococcus multilocularis surveillance reports submitted in 2022 in the context of Commission Delegated Regulation (EU) 2018/772

This report is part of the Echinococcus multilocularis surveillance scientific reports which are presented annually by EFSA to the European Commission and are intended to assess the sampling strategy, data collection and detection methods used by Finland, Ireland, United Kingdom (Northern Ireland) and Norway in their respective surveillance programmes. The surveillance programmes of these four countries were evaluated by checking the information submitted by each of them and verifying that the technical requirements were fulfilled as laid down in Commission Delegated Regulation (EU) 2018/772 of 21 November 2017 supplementing Regulation (EU) No 576/2013 of the European Parliament and of the Council with regard to preventive health measures for the control of Echinococcus multilocularis infection in dogs, and repealing Delegated Regulation (EU) No 1152/2011. The information was divided into four different categories for assessment: the type and sensitivity of the detection method, the selection of the target population, the sampling strategy and the methodology. For each category, the main aspects that need to be considered in order to accomplish the technical requirements of the legislation were checked against compliance of several criteria. Three of the countries participating in this surveillance (Finland, Ireland and Norway (mainland)) succeeded in the fulfilment of the technical legal requirements foreseen in Commission Delegated Regulation (EU) 2018/772 concerning these four different categories. United Kingdom (Northern Ireland) fulfils those requirements, only assuming a diagnostic test sensitivity value of 0.99 (value provided by the national reference laboratory, higher than the conservative sensitivity value suggested by EFSA, i.e. 0.78). None of the four countries recorded positive samples in the 12-month reporting period.

Annual assessment of Echinococcus multilocularis surveillance reports submitted in 2021 in the context of Commission Delegated Regulation (EU) 2018/772

This report is part of the Echinococcus multilocularis surveillance scientific reports which are presented annually by EFSA to the European Commission and are intended to assess the sampling strategy, data collection and detection methods used by Finland, Ireland, United Kingdom (Northern Ireland) and Norway in their respective surveillance programmes. The surveillance programmes of these four countries were evaluated by checking the information submitted by each of them and verifying that the technical requirements were fulfilled as laid down in Commission Delegated Regulation (EU) 2018/772 of 21 November 2017 supplementing Regulation (EU) No 576/2013 of the European Parliament and of the Council with regard to preventive health measures for the control of Echinococcus multilocularis infection in dogs, and repealing Delegated Regulation (EU) No 1152/2011. The information was divided in four different categories for assessment: the type and sensitivity of the detection method, the selection of the target population, the sampling strategy and the methodology. For each category, the main aspects that need to be considered in order to accomplish the technical requirements of the legislation were checked against compliance of several criteria. Three of the countries participating in this surveillance (Finland, Ireland and Norway (mainland)) succeeded in the fulfilment of the technical legal requirements foreseen in Commission Delegated Regulation (EU) 2018/772 concerning these four different categories. Northern Ireland did not fulfil those requirements, not even assuming a diagnostic test sensitivity value of 0.99 (value provided by the national reference laboratory, higher than the conservative sensitivity value suggested by EFSA, i.e. 0.78). None of the four countries recorded positive samples in the 12‐month reporting period.

Population Genetics of the Invasive Red Fox, Vulpes vulpes, in South-Eastern Australia

The use of genetic information in conservation biology has become more widespread with genetic information more readily available for non-model organisms. It has also been recognized that genetic information from invasive species can inform their management and control. The red fox poses a significant threat to Australian native fauna and the agricultural industry. Despite this, there are few recently published studies investigating the population genetics of foxes in Australia. This study investigated the population genetics of 94 foxes across the Illawarra and Shoalhaven regions of New South Wales, Australia. Diversity Array sequencing technology was used to genotype a large number of single nucleotide polymorphisms (N = 33,375). Moderate genetic diversity and relatedness were observed across the foxes sampled. Low to moderate levels of inbreeding, high-levels of identity-by-state values, as well as high identity-by-descent values were also found. There was limited evidence for population genetic structure among the foxes across the landscape sampled, supporting the presence of a single population across the study area. This indicates that there may be no barriers hindering fox dispersal across the landscape.

Annual assessment of Echinococcus multilocularis surveillance reports submitted in 2020 in the context of Commission Delegated Regulation (EU) 2018/772

This report is part of the Echinococcus multilocularis surveillance scientific reports which are presented annually by EFSA to the European Commission and are intended to assess the sampling strategy, data collection and detection methods used by Finland, Ireland, the UK and Norway in their respective surveillance programmes. The surveillance programmes of these four countries were evaluated by checking the information submitted by each of them and verifying that the technical requirements were fulfilled as laid down in Commission Delegated Regulation (EU) 2018/772 of 21 November 2017 supplementing Regulation (EU) No 576/2013 of the European Parliament and of the Council with regard to preventive health measures for the control of E. multilocularis infection in dogs, and repealing Delegated Regulation (EU) No 1152/2011. Due to the UK exiting the European Union and under the Withdrawal Act, the data submitted by the UK after the 31 January 2020 are excluded from this assessment. The information was divided in four different categories for assessment: the type and sensitivity of the detection method, the selection of the target population, the sampling strategy and the methodology. For each category, the main aspects that need to be considered in order to accomplish the technical requirements of the legislation were checked against compliance of several criteria. All the countries participating in this surveillance (Finland, the UK, Ireland and Norway) succeeded in the fulfilment of the technical legal requirements foreseen in Commission Delegated Regulation (EU) 2018/772 concerning these four different categories. Within the UK, Northern Ireland fulfils those requirements only when assuming a diagnostic test sensitivity value of 0.99, provided by the national reference laboratory, which is higher than the sensitivity value suggested by EFSA (conservative value of 0.78) and not supported by adequate scientific evidence. None of the four countries recorded positive samples in the 12‐month reporting period.

Moving far, staying close: red fox dispersal patterns revealed by SNP genotyping

The genetic structure of a population can provide important insights into animal movements at varying geographical scales. Individual and social behaviors, such as philopatry and dispersal, affect patterns of relatedness, age and sex structure, shaping the local genetic structure of populations. However, these fine scale patterns may not be detected within broader population genetic structure. Using SNP genotyping for pairwise relatedness estimates, we investigated the spatial and genetic structuring of 141 red foxes within south-central Sweden at two scales. First, we looked at broad scale population structuring among red foxes at the regional level. We then estimated pairwise relatedness values to evaluate the spatial and genetic structure of male, female and mixed sex pairs for patterns of philopatry and dispersal at a more localized scale. We found limited genetic differentiation at the regional scale. However, local investigations revealed patterns of female philopatry and male biased dispersal. There were significant differences in pairwise geographic distances between highly related same sex pairs with the average distance between related males, 37.8 km, being six times farther than that of related females, averaging 6.3 km. In summary, the low levels of genetic differentiation found in this study illustrates the mobility and dispersal ability of red foxes across scales. However, relatedness plays a strong role in the spatial organization of red foxes locally, ultimately contributing to male biased dispersal patterns.

Spatial distribution of sarcoptic mange (Sarcoptes scabiei) in urban foxes (Vulpes vulpes) in Great Britain as determined by citizen science

Urban areas may support high densities of wild carnivores, and pathogens can strongly influence carnivore populations. Red foxes (Vulpes vulpes) are hosts of sarcoptic mange (Sarcoptes scabiei), which infects numerous species, and transmission can be density dependent. In Great Britain, urban red foxes (Vulpes vulpes) have recently increased in population density and undergone range expansions. Here we investigate corresponding changes in urban fox mange prevalence. We predicted a higher prevalence closer to historic epi/enzootics and lower prevalence where urban features reduce fox density and movements, i.e. large areas of public green space, and fragmented habitat, as measured by road length and urban perimeter shape complexity. We visually assessed mange symptoms from georeferenced images of urban foxes submitted online by the public, thus surveying private land on a national scale. We measured the proportion of foxes apparently showing mange and used SATSCAN to identify spatial clusters of high infection risk. Landscape features were extracted from urban layers in GIS to determine associations. Although mange was widespread, we identified a single cluster of high prevalence (37.1%) in Northwest and Central England, which exceeded double mean prevalence overall (15.1%) and mirrors the northward expansion of urban fox distribution. Prevalence was positively correlated with perimeter shape complexity and negatively correlated with distance to the nearest city with mange, although the latter association was weak. Our findings show that citizen science can effectively monitor diseases with highly visible symptoms and suggest that fox movements are influential in explaining spatial patterns of prevalence.

Genetic and spatial characterization of the red fox (Vulpes vulpes) population in the area stretching between the Eastern and Dinaric Alps and its relationship with rabies and canine distemper dynamics

Information on the population dynamics of a reservoir species have been increasingly adopted to understand and eventually predict the dispersal patterns of infectious diseases throughout an area. Although potentially relevant, to date there are no studies which have investigated the genetic structure of the red fox population in relation to infectious disease dynamics. Therefore, we genetically and spatially characterised the red fox population in the area stretching between the Eastern and Dinaric Alps, which has been affected by both distemper and rabies at different time intervals. Red foxes collected from north-eastern Italy, Austria, Slovenia and Croatia between 2006–2012, were studied using a set of 21 microsatellite markers. We confirmed a weak genetic differentiation within the fox population using Bayesian clustering analyses, and we were able to differentiate the fox population into geographically segregated groups. Our finding might be due to the presence of geographical barriers that have likely influenced the distribution of the fox population, limiting in turn gene flow and spread of infectious diseases. Focusing on the Italian red fox population, we observed interesting variations in the prevalence of both diseases among distinct fox clusters, with the previously identified Italy 1 and Italy 2 rabies as well as distemper viruses preferentially affecting different sub-groups identified in the study. Knowledge of the regional-scale population structure can improve understanding of the epidemiology and spread of diseases. Our study paves the way for an integrated approach for disease control coupling pathogen, host and environmental data to inform targeted control programs in the future.

A citizen science based survey method for estimating the density of urban carnivores

Globally there are many examples of synanthropic carnivores exploiting growth in urbanisation. As carnivores can come into conflict with humans and are potential vectors of zoonotic disease, assessing densities in suburban areas and identifying factors that influence them are necessary to aid management and mitigation. However, fragmented, privately owned land restricts the use of conventional carnivore surveying techniques in these areas, requiring development of novel methods. We present a method that combines questionnaire distribution to residents with field surveys and GIS, to determine relative density of two urban carnivores in England, Great Britain. We determined the density of: red fox (Vulpes vulpes) social groups in 14, approximately 1km² suburban areas in 8 different towns and cities; and Eurasian badger (Meles meles) social groups in three suburban areas of one city. Average relative fox group density (FGD) was 3.72 km^-2, which was double the estimates for cities with resident foxes in the 1980’s. Density was comparable to an alternative estimate derived from trapping and GPS-tracking, indicating the validity of the method. However, FGD did not correlate with a national dataset based on fox sightings, indicating unreliability of the national data to determine actual densities or to extrapolate a national population estimate. Using species-specific clustering units that reflect social organisation, the method was additionally applied to suburban badgers to derive relative badger group density (BGD) for one city (Brighton, 2.41 km^-2). We demonstrate that citizen science approaches can effectively obtain data to assess suburban carnivore density, however publicly derived national data sets need to be locally validated before extrapolations can be undertaken. The method we present for assessing densities of foxes and badgers in British towns and cities is also adaptable to other urban carnivores elsewhere. However this transferability is contingent on species traits meeting particular criteria, and on resident responsiveness.

Evolution of life in urban environments

Our planet is an increasingly urbanized landscape, with over half of the human population residing in cities. Despite advances in urban ecology, we do not adequately understand how urbanization affects the evolution of organisms, nor how this evolution may affect ecosystems and human health. Here, we review evidence for the effects of urbanization on the evolution of microbes, plants, and animals that inhabit cities. Urbanization affects adaptive and nonadaptive evolutionary processes that shape the genetic diversity within and between populations. Rapid adaptation has facilitated the success of some native species in urban areas, but it has also allowed human pests and disease to spread more rapidly. The nascent field of urban evolution brings together efforts to understand evolution in response to environmental change while developing new hypotheses concerning adaptation to urban infrastructure and human socioeconomic activity. The next generation of research on urban evolution will provide critical insight into the importance of evolution for sustainable interactions between humans and our city environments.

Assessing Genetic Structure in Common but Ecologically Distinct Carnivores: The Stone Marten and Red Fox

The identification of populations and spatial genetic patterns is important for ecological and conservation research, and spatially explicit individual-based methods have been recognised as powerful tools in this context. Mammalian carnivores are intrinsically vulnerable to habitat fragmentation but not much is known about the genetic consequences of fragmentation in common species. Stone martens (Martes foina) and red foxes (Vulpes vulpes) share a widespread Palearctic distribution and are considered habitat generalists, but in the Iberian Peninsula stone martens tend to occur in higher quality habitats. We compared their genetic structure in Portugal to see if they are consistent with their differences in ecological plasticity, and also to illustrate an approach to explicitly delineate the spatial boundaries of consistently identified genetic units. We analysed microsatellite data using spatial Bayesian clustering methods (implemented in the software BAPS, GENELAND and TESS), a progressive partitioning approach and a multivariate technique (Spatial Principal Components Analysis-sPCA). Three consensus Bayesian clusters were identified for the stone marten. No consensus was achieved for the red fox, but one cluster was the most probable clustering solution. Progressive partitioning and sPCA suggested additional clusters in the stone marten but they were not consistent among methods and were geographically incoherent. The contrasting results between the two species are consistent with the literature reporting stricter ecological requirements of the stone marten in the Iberian Peninsula. The observed genetic structure in the stone marten may have been influenced by landscape features, particularly rivers, and fragmentation. We suggest that an approach based on a consensus clustering solution of multiple different algorithms may provide an objective and effective means to delineate potential boundaries of inferred subpopulations. sPCA and progressive partitioning offer further verification of possible population structure and may be useful for revealing cryptic spatial genetic patterns worth further investigation.