A comparison of brain gene expression levels in domesticated and wild animals

This is an open-access article distributed under the terms of the Creative Commons Attribution License.-- et al.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.This work was funded by the Max Planck Society and a European Research Council grant (233297, TWOPAN) to SP. FWA is supported by a grant from the German Science Foundation (DFG grant AL 1525/1-1). MS was supported by a CAS young scientists fellowship (2009Y2BS12) and a National Science Foundation of China research grant (31010022). JAB-A is supported by fellowship (SFRH/BPD/65464/2009).Peer Reviewe

The genomic architecture of population divergence between subspecies of the european rabbit

This is an open-access article distributed under the terms of the Creative Commons Attribution License.-- et al.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.This work was partially supported by POPH-QREN funds from the European Social Fund and Portuguese MCTES [postDoc grants to MC (BPD/72343/2010); JM-F (SFRH/BPD/43264/2008); JAB-A (SFRH/BPD/65464/2009), and RC (SFRH/BPD/64365/2009)], by FEDER funds through the COMPETE program and Portuguese national funds through the Fundação para a Ciência e a Tecnologia (PTDC/CVT/122943/2010; PTDC/BIA/EVF/111368/2009; POCI/CVT/61590/2004; PTDC/BIA/BDE/72304/2006; PTDC/BIA-BDE/72277/2006; CGL2009-11665; POII09-0099-2557), by a National Science Foundation international postdoctoral fellowship to JMG (OISE-0754461), by National Science Foundation and National Institutes of Health grants to MWN, and by the Max Planck Society.Peer Reviewe

Science-based wildlife disease response

et al.Peer reviewe

Is the interaction between rabbit hemorrhagic disease and hyperpredation by raptors a major cause of the red-legged partridge decline in Spain?

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.J.A. Blanco-Aguiar was supported by Fundação para a Ciência e a Tecnologia (SFRH/BPD/65464/2009) grant. M. Delibes-Mateos was supported by a Juan de la Cierva research contract awarded by the Ministerio de Ciencia e Innovación—Fondo European Social Fund. F. Casas was supported by a postdoctoral grant of the Junta de Comunidades de Castilla la Mancha (JCCM).Peer Reviewe

Biometrical analysis reveals major differences between the two subspecies of the European rabbit

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.This study was partially funded by Projects PAI06-170, VP-0119-07,POII09-0099-2557, CGL2009-11665, 2012-30E060, CGL2013-43197, CGL2013-43197-R, FCT research project (PTDC/BIA-EVF/111368/2009), and ‘Genomics Applied to Genetic Resources’ co-funded by North Portugal Regional Operational Programme 2007/2013 (ON.2 – O Novo Norte), under the National Strategic Reference Framework (NSRF), through the European Regional Development Fund (ERDF). C.F. was supported by a PhD grant (Ref. SFRH/BD/22084/2005) and a postdoctoral grant (Ref. SFRH/BPD/88643/2012), and J.B.-A. by a postdoctoral grant (Ref. SFRH/BPD/65464/2009) all from the Fundaçao para a Ciência e Tecnologia of the Ministêrio da Ciência, Tecnologia e Ensino Superior, Portuguese government. C.F. is currently supported by a Marie Curie Out going International Fellowship for Career Development (PIOF-GA-2013-621571) within the 7th Framework Programme of the European Union. M.D.-M. is currently funded by Consejería de Economía, Innovación, Ciencia y Empleo of Junta de Andalucía, and the European Union’s SeventhFramework Programme for research, technological development and demonstration under grant agreement 267226. C.A.R.-S. was supported by a doctoral grant from the National Council of Science and Technology of Mexico (CONACyT). P.C.A. was supportedby an FCT sabbatical grant (SFRH/BSAB/1278/2012) and by FLAD (Luso-American Foundation).Peer Reviewe

ENETWILD training: "First online course on the use of camera trapping for monitoring wildlife and density estimation in the framework of the European Observatory of Wildlife (5th May 2022)

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 wildlife experts from national hunting and forestry authorities. Detailed explanations, protocols, and examples for applying such protocols were provided.EFSA-Q-2022-00056Peer reviewe

Report based on comparison of case studies in different wild boar populations representative of the different management and habitat conditions across Europe

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Analysis of wild boar-domestic pig interface in Europe: spatial overlapping and fine resolution approach in several countries

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.Peer reviewe

Wild boar ecology: a review of wild boar ecological and demographic parameters by bioregion all over Europe

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.EFSA-Q-2022-00047Peer reviewe

Update of model for wild boar abundance based on hunting yield and first models based on occurrence for wild ruminants at European scale

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 understand the root cause; whether a result of underlying assumptions regarding the testing data or due to the model performance itself.EFSA-Q-2020-00678Peer reviewe