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Background: Out-of-hospital cardiac arrest (OHCA) incidence and survival often vary within regions according to patient-related and contextual factors. This study aims to establish the overall spatial dependence of incidence, bystander cardiopulmonary resuscitation (BCPR) and 48-h survival of OHCA with their associated demographic and socioeconomic characteristics in a Swiss region. Methods: We conducted a retrospective study using data of all OHCAs recorded between 2007 and 2019 in the canton of Vaud and, more specifically, in the Lausanne area. Provision of BCPR and 48-h survival were analysed using Getis-Ord Gi statistics and OHCA incidence by local Moran’s I with empirical Bayes standardised rates. Demographic and socioeconomic characteristics were compared between incidence clusters generated by local Moran’s I method. Results: Significant spatial variations of OHCA incidence, BCPR and 48-h mortality were observed. Although BCPR was statistically more likely in rural areas, 48-h survival was improved in a few main cities. At the cantonal level, postcode areas with a higher incidence of OHCAs were less densely inhabited with lower salary levels, more Swiss citizens, and an older population. At city level, small area variations were detected within urban neighbourhoods. The more affected hectares with more OHCAs were less inhabited, with a better median salary, more Swiss citizens, and off-centre. Conclusions: Spatial variations associated with demographic and socioeconomic factors were observed for OHCA incidence and survival, with sparsely populated areas particularly at risk. These data suggest an unmet need for targeted prevention interventions and structural modifications of the existing prehospital system at the cantonal level.

Abstract Landscape genomic analyses associating genetic variation with environmental variables are powerful tools for studying molecular signatures of species' local adaptation and for detecting candidate genes under selection. The development of landscape genomics over the past decade has been spurred by improvements in resolutions of genomic and environmental datasets, allegedly increasing the power to identify putative genes underlying local adaptation in non‐model organisms. Although these associations have been successfully applied to numerous species across a diverse array of taxa, the spatial scale of environmental predictor variables has been largely overlooked, potentially limiting conclusions to be reached with these methods. To address this knowledge gap, we systematically evaluated performances of genotype–environment association (GEA) models using predictor variables at multiple spatial resolutions. Specifically, we used multivariate redundancy analyses to associate whole‐genome sequence data from the plant Arabis alpina L. collected across four neighboring valleys in the western Swiss Alps, with very high‐resolution topographic variables derived from digital elevation models of grain sizes between 0.5 m and 16 m. These comparisons highlight the sensitivity of landscape genomic models to spatial resolution, where the optimal grain sizes were specific to variable type, terrain characteristics, and study extent. To assist in selecting variables at appropriate spatial resolutions, we demonstrate a practical approach to produce, select, and integrate multiscale variables into GEA models. After generalizing fine‐grained variables to multiple spatial resolutions, a forward selection procedure is applied to retain only the most relevant variables for a particular context. Depending on the spatial resolution, the relevance for topographic variables in GEA studies calls for integrating multiple spatial scales into landscape genomic models. By carefully considering spatial resolutions, candidate genes under selection by a more realistic range of pressures can be detected for downstream analyses, with important applied implications for experimental research and conservation management of natural populations.

IntroductionSince its emergence in late 2019, the SARS-CoV-2 virus has led to a global health crisis, affecting millions and reshaping societies and economies worldwide. Investigating the determinants of SARS-CoV-2 diffusion and their spatiotemporal dynamics at high spatial resolution is critical for public health and policymaking.MethodsThis study analyses 194,682 georeferenced SARS-CoV-2 RT-PCR tests from March 2020 and April 2022 in the canton of Vaud, Switzerland. We characterized five distinct pandemic periods using metrics of spatial and temporal clustering like inverse Shannon entropy, the Hoover index, Lloyd’s index of mean crowding, and the modified space–time DBSCAN algorithm. We assessed the demographic, socioeconomic, and environmental factors contributing to cluster persistence during each period using eXtreme Gradient Boosting (XGBoost) and SHapley Additive exPlanations (SHAP), to consider non-linear and spatial effects.ResultsOur findings reveal important variations in the spatial and temporal clustering of cases. Notably, areas with flatter epidemics had higher total attack rate. Air pollution emerged as a factor showing a consistent positive association with higher cluster persistence, substantiated by both immission models and, to a lesser extent, tropospheric NO2 estimations. Factors including population density, testing rates, and geographical coordinates, also showed important positive associations with higher cluster persistence. The socioeconomic index showed no significant contribution to cluster persistence, suggesting its limited role in the observed dynamics, which warrants further research.DiscussionOverall, the determinants of cluster persistence remained across the study periods. These findings highlight the need for effective air quality management strategies to mitigate air pollution’s adverse impacts on public health, particularly in the context of respiratory viral diseases like COVID-19.

BackgroundTemperate subalpine lakes recovering from eutrophication in central Europe are experiencing harmful blooms due to the proliferation of Planktothrix rubescens, a potentially toxic cyanobacteria. To optimize the management of cyanobacteria blooms there is the need to better comprehend the combination of factors influencing the diversity and dominance of cyanobacteria and their impact on the lake’s ecology. The goal of this study was to characterize the diversity and seasonal dynamics of cyanobacteria communities found in a water column of Lake Geneva, as well as the associated changes on bacterioplankton abundance and composition.MethodsWe used 16S rRNA amplicon high throughput sequencing on more than 200 water samples collected from surface to 100 meters deep monthly over 18 months. Bacterioplankton abundance was determined by quantitative PCR and PICRUSt predictions were used to explore the functional pathways present in the community and to calculate functional diversity indices.ResultsThe obtained results confirmed that the most dominant cyanobacteria in Lake Geneva during autumn and winter was Planktothrix (corresponding to P. rubescens). Our data also showed an unexpectedly high relative abundance of picocyanobacterial genus Cyanobium, particularly during summertime. Multidimensional scaling of Bray Curtis dissimilarity revealed that the dominance of P. rubescens was coincident with a shift in the bacterioplankton community composition and a significant decline in bacterioplankton abundance, as well as a temporary reduction in the taxonomic and PICRUSt2 predicted functional diversity.ConclusionOverall, this study expands our fundamental understanding of the seasonal dynamics of cyanobacteria communities along a vertical column in Lake Geneva and the ecology of P. rubescens, ultimately contributing to improve our preparedness against the potential occurrence of toxic blooms in the largest lake of western Europe.

As the world’s population grows in cities, urban dwellers spend a large amount of time inside their home, making housing health ever more important. Critical for residents’ health, the interactions between indoor residential environments and outdoor environmental conditions (e.g. air pollution, noise, heat) are mediated by the controversial and evolving relationship between housing and the street. Currently, there is a lack of ways to integrate and explore synergies among the plurality of perspectives that have addressed the interactions between housing, street and health (HSH). This paper proposes a systemic research framework to address conceptually, spatially and temporally HSH interactions. With a focus on European cities, determinants of housing health are identified through six perspectives, comprising environmental health, domestic architecture, building technologies, socio-economic inequalities, housing prices and urban planning. Their interrelationships are organised in a causal loop diagram, which can be used to highlight gaps in research and data. Subsequently, the paper explores the research and practical applications of the resulting systemic understanding, taking the context of Geneva, Switzerland, as an example. In sum, this study illustrates ways to integrate systemic, transdisciplinary and spatiotemporal approaches essential to holistically address the complexity of HSH relationships. Practice relevance The interactions between housing, street and health (HSH) have been approached from different and often siloed perspectives, addressing issues ranging from diseases to architectural design and history, building technologies, socio-economic inequalities, housing prices and urban planning. This fragmentation hinders the coordination of interventions aimed at improving the health of residential environments, limiting the identification of synergies and trade-offs. This paper proposes a research framework enabling the integration of knowledge on the HSH interactions. The resulting holistic and systemic understanding is instrumental in fostering collaborations across disciplinary fields and among a variety of stakeholders, in raising awareness of the risks and opportunities associated with HSH interactions, and in supporting the design and implementation of health and wellbeing agendas at the building, neighbourhood or city level.

Summary: Background: Malnutrition and food insecurity might be driven not only by individual factors but also by contextual conditions, such as area-level deprivation or vulnerability. This study aimed to analyze the association between area-level vulnerability and i) household food insecurity and ii) malnutrition in children in Medellin, Colombia, during the years 2017 and 2018. Methods: We obtained data from two different sources: the Living Standards Measurement Survey (LSMS) and the nutrition surveillance system of Medellin. The main outcomes were food insecurity in households with children and anthropometric indicators for children under five. The main predictor was area-level vulnerability. Mixed effects Poisson regression with robust standard errors models were conducted to test the association of quintiles of deprivation with each outcome. Findings: Households with children living in areas with the highest deprivation had 1.9 times the prevalence of food insecurity as compared to those living in areas with the lowest deprivation (PR 1.91, 95% CI 1.42–2.57). Similar results were observed for underweight/risk of underweight (PR 1.26, 95% CI 1.11–1.42), stunting/risk of stunting (PR 1.36, 95% CI 1.22–1.53) and stunting (PR 1.93 95% CI 1.55–2.39) among children under five. We found no consistent associations with wasting/risk of wasting or excess weight/risk of overweight across quintiles of deprivation. Interpretation: This study sheds light on the role of area-level vulnerability on malnutrition in children in Medellin, Colombia, showing a pattern of increasing prevalence of food insecurity, underweight and stunting by quintile of deprivation. Funding: Swiss School of Public Health (SSPH+) and Centre for Global Health Inequalities Research (CHAIN).

Abstract Though Switzerland has one of the highest life expectancies in the world, this global indicator may mask significant disparities at a local level. The present study used a spatial cluster detection approach based on individual death records to investigate the geographical footprint of life expectancy inequalities in the state of Geneva, Switzerland. Individual-level mortality data (n = 22,751) were obtained from Geneva’s official death notices (2009–2016). We measured life expectancy inequalities using the years of potential life lost or gained (YPLLG) metric, defined as the difference between an individual’s age at death and their life expectancy at birth. We assessed the spatial dependence of YPLLG across the state of Geneva using spatial autocorrelation statistics (Local Moran’s I). To ensure the robustness of the patterns discovered, we ran the analyses for ten random subsets of 10,000 individuals taken from the 22,751 deceased. We also repeated the spatial analysis for YPLLG before and after controlling for individual-level and neighborhood-level covariates. The results showed that YPLLG was not randomly distributed across the state of Geneva. The ten random subsets revealed no significant difference with the geographic footprint of YPLLG and the population characteristics within Local Moran cluster types, suggesting robustness for the observed spatial structure. The proportion of women, the proportion of Swiss, the neighborhood median income, and the neighborhood median age were all significantly lower for populations in low YPLLG clusters when compared to populations in high YPLLG clusters. After controlling for individual-level and neighborhood-level covariates, we observed a reduction of 43% and 39% in the size of low and high YPLLG clusters, respectively. To our knowledge, this is the first study in Switzerland using spatial cluster detection methods to investigate inequalities in life expectancy at a local scale and based on individual data. We identified clear geographic footprints of YPLLG, which may support further investigations and guide future public health interventions at the local level.

Abstract Most efforts to understand snakebite burden in Nepal have been localized to relatively small areas and focused on humans through epidemiological studies. We present the outcomes of a geospatial analysis of the factors influencing snakebite risk in humans and animals, based on both a national-scale multi-cluster random survey and, environmental, climatic, and socio-economic gridded data for the Terai region of Nepal. The resulting Integrated Nested Laplace Approximation models highlight the importance of poverty as a fundamental risk-increasing factor, augmenting the snakebite odds in humans by 63.9 times. For animals, the minimum temperature of the coldest month was the most influential covariate, increasing the snakebite odds 23.4 times. Several risk hotspots were identified along the Terai, helping to visualize at multiple administrative levels the estimated population numbers exposed to different probability risk thresholds in 1 year. These analyses and findings could be replicable in other countries and for other diseases.

BackgroundThe need for effective public health surveillance systems to track virus spread for targeted interventions was highlighted during the COVID-19 pandemic. It spurred an interest in the use of spatiotemporal clustering and genomic analyses to identify high-risk areas and track the spread of the SARS-CoV-2 virus. However, these two approaches are rarely combined in surveillance systems to complement each one's limitations; spatiotemporal clustering approaches usually consider only one source of virus transmission (i.e., the residential setting) to detect case clusters, while genomic studies require significant resources and processing time that can delay decision-making. Here, we clarify the differences and possible synergies of these two approaches in the context of infectious disease surveillance systems by investigating to what extent geographically-defined clusters are confirmed as transmission clusters based on genome sequences, and how genomic-based analyses can improve the epidemiological investigations associated with spatiotemporal cluster detection.MethodsFor this purpose, we sequenced the SARS-CoV-2 genomes of 172 cases that were part of a collection of spatiotemporal clusters found in a Swiss state (Vaud) during the first epidemic wave. We subsequently examined intra-cluster genetic similarities and spatiotemporal distributions across virus genotypes.ResultsOur results suggest that the congruence between the two approaches might depend on geographic features of the area (rural/urban) and epidemic context (e.g., lockdown). We also identified two potential superspreading events that started from cases in the main urban area of the state, leading to smaller spreading events in neighboring regions, as well as a large spreading in a geographically-isolated area. These superspreading events were characterized by specific mutations assumed to originate from Mulhouse and Milan, respectively. Our analyses propose synergistic benefits of using two complementary approaches in public health surveillance, saving resources and improving surveillance efficiency.

Coral reefs around the world are under threat from anomalous heat waves that are causing the widespread decline of hard corals. Different coral taxa are known to have different sensitivities to heat, although variation in susceptibilities have also been observed within the same species living in different environments. Characterizing such taxa-specific variations is key to enforcing efficient reef conservation strategies. Here, we combine worldwide-reef-survey data with remote sensed environmental variables to evaluate how local differences in taxa-specific coral cover are associated with past trends of thermal anomalies, as well as of non-heat related conditions. While the association with non-heat related environmental variation was seldom significant, we found that heat stress trends matched local differences in coral cover. Coral taxa were sorted based on the different patterns of associations with recent heat stress (measured the year before the survey) and past heat stress (measured since 1985). For branching, tabular and corymbose Acroporidae, reefs exposed to recent heat stress had lower coral cover than locally expected. Among such reefs, those previously exposed to frequent past heat stress displayed relatively higher coral cover, compared to those less frequently exposed. For massive and encrusting Poritidae, and for meandroid Favidae and Mussidae, we observed a negative association of coral cover with recent heat stress. However, unlike with Acroporidae, these associations were weaker and did not vary with past heat exposure. For Pocilloporidae, we found a positive association between coral cover and recent heat stress for reefs frequently exposed to past heat, while we found a negative association at reefs less frequently exposed to past heat. A similar pattern was observed for the branching Poritidae, although the associations were weaker and not statistically significant. Overall, these results show taxa-specific heat association patterns that might correspond to taxa-specific responses to past heat exposure, such as shifts in the assembly of coral communities, evolutionary adaptation or physiological acclimation.

Abstract Coral reefs are suffering a major decline due to the environmental constraints imposed by climate change. Over the last 20 years, three major coral bleaching events occurred in concomitance with anomalous heatwaves, provoking a severe loss of coral cover worldwide. The conservation strategies for preserving reefs, as they are implemented now, cannot cope with global climatic shifts. Consequently, researchers are advocating for preservation networks to be set‐up to reinforce coral adaptive potential. However, the main obstacle to this implementation is that studies on coral adaption are usually hard to generalize at the scale of a reef system. Here, we study the relationships between genotype frequencies and environmental characteristics of the sea (seascape genomics), in combination with connectivity analysis, to investigate the adaptive potential of a flagship coral species of the Ryukyu Archipelago (Japan). By associating genotype frequencies with descriptors of historical environmental conditions, we discovered six genomic regions hosting polymorphisms that might promote resistance against heat stress. Remarkably, annotations of genes in these regions were consistent with molecular roles associated with heat responses. Furthermore, we combined information on genetic and spatial distances between reefs to predict connectivity at a regional scale. The combination of these results portrayed the adaptive potential of this population: we were able to identify reefs carrying potential heat stress adapted genotypes and to understand how they disperse to neighbouring reefs. This information was summarized by objective, quantifiable and mappable indices covering the whole region, which can be extremely useful for future prioritization of reefs in conservation planning. This framework is transferable to any coral species on any reef system and therefore represents a valuable tool for empowering preservation efforts dedicated to the protection of coral reefs in warming oceans.

Introduction Evidence suggests that the built environment can influence the intensity of physical activity. However, despite the importance of the geographic context, most of the studies do not consider the spatial framework of this association. We aimed to assess individual spatial dependence of objectively measured moderate and vigorous physical activity (MVPA) and describe the characteristics of the built environment among spatial clusters of MVPA. Methods Cross-sectional data from the second follow-up (2014–2017) of CoLaus|PsyCoLaus, a longitudinal population-based study of the Lausanne area (Switzerland), was used to objectively measure MVPA using accelerometers. Local Moran’s I was used to assess the spatial dependence of MVPA and detect geographic clusters of low and high MVPA. Additionally, the characteristics of the built environment observed in the clusters based on raw MVPA and MVPA adjusted for socioeconomic and demographic factors were compared. Results Data from 1,889 participants (median age 63, 55% women) were used. The geographic distribution of MVPA and the characteristics of the built environment among clusters were similar for raw and adjusted MVPA. In the adjusted model, we found a low concentration of individuals within spatial clusters of high MVPA (median: 38.5mins; 3% of the studied population) and low MVPA (median: 10.9 mins; 2% of the studied population). Yet, clear differences were found in both models between clusters regarding the built environment; high MVPA clusters were located in areas where specific compositions of the built environment favor physical activity. Conclusions Our results suggest the built environment may influence local spatial patterns of MVPA independently of socioeconomic and demographic factors. Interventions in the built environment should be considered to promote physically active behaviors in urban areas.

Urban green infrastructure, especially trees, are widely regarded as one of the most effective ways to reduce urban temperatures in heatwaves and alleviate the adverse impacts of extreme heat events on human health and well-being. Nevertheless, urban planners and decision-makers are still lacking methods and tools to spatially evaluate the cooling effects of urban green spaces and exploit them to assess greening strategies at the urban agglomeration scale. This article introduces a novel spatially explicit approach to simulate urban greening scenarios by increasing the tree canopy cover in the existing urban fabric and evaluating their heat mitigation potential. The latter is achieved by applying the InVEST urban cooling model to the synthetic land use/land cover maps generated for the greening scenarios. A case study in the urban agglomeration of Lausanne, Switzerland, illustrates the development of tree canopy scenarios following distinct spatial distribution strategies. The spatial pattern of the tree canopy strongly influences the human exposure to the highest temperatures, and small increases in the abundance of tree canopy cover with the appropriate spatial configuration can have major impacts on human health and well-being. The proposed approach supports urban planning and the design of nature-based solutions to enhance climate resilience.

BackgroundThe early detection of clusters of infectious diseases such as the SARS-CoV-2–related COVID-19 disease can promote timely testing recommendation compliance and help to prevent disease outbreaks. Prior research revealed the potential of COVID-19 participatory syndromic surveillance systems to complement traditional surveillance systems. However, most existing systems did not integrate geographic information at a local scale, which could improve the management of the SARS-CoV-2 pandemic. ObjectiveThe aim of this study is to detect active and emerging spatiotemporal clusters of COVID-19–associated symptoms, and to examine (a posteriori) the association between the clusters’ characteristics and sociodemographic and environmental determinants. MethodsThis report presents the methodology and development of the @choum (English: “achoo”) study, evaluating an epidemiological digital surveillance tool to detect and prevent clusters of individuals (target sample size, N=5000), aged 18 years or above, with COVID-19–associated symptoms living and/or working in the canton of Geneva, Switzerland. The tool is a 5-minute survey integrated into a free and secure mobile app (CoronApp-HUG). Participants are enrolled through a comprehensive communication campaign conducted throughout the 12-month data collection phase. Participants register to the tool by providing electronic informed consent and nonsensitive information (gender, age, geographically masked addresses). Symptomatic participants can then report COVID-19–associated symptoms at their onset (eg, symptoms type, test date) by tapping on the @choum button. Those who have not yet been tested are offered the possibility to be informed on their cluster status (information returned by daily automated clustering analysis). At each participation step, participants are redirected to the official COVID-19 recommendations websites. Geospatial clustering analyses are performed using the modified space-time density-based spatial clustering of applications with noise (MST-DBSCAN) algorithm. ResultsThe study began on September 1, 2020, and will be completed on February 28, 2022. Multiple tests performed at various time points throughout the 5-month preparation phase have helped to improve the tool’s user experience and the accuracy of the clustering analyses. A 1-month pilot study performed among 38 pharmacists working in 7 Geneva-based pharmacies confirmed the proper functioning of the tool. Since the tool’s launch to the entire population of Geneva on February 11, 2021, data are being collected and clusters are being carefully monitored. The primary study outcomes are expected to be published in mid-2022. ConclusionsThe @choum study evaluates an innovative participatory epidemiological digital surveillance tool to detect and prevent clusters of COVID-19–associated symptoms. @choum collects precise geographic information while protecting the user’s privacy by using geomasking methods. By providing an evidence base to inform citizens and local authorities on areas potentially facing a high COVID-19 burden, the tool supports the targeted allocation of public health resources and promotes testing. International Registered Report Identifier (IRRID)DERR1-10.2196/30444

BACKGROUND: Rapid access to a trauma centre for severely injured road accident victims, conceptualised as the Golden Hour, links access time to definitive treatment within 1 hour of trauma with reduced risks of morbidity and mortality. Access times have not been studied in Switzerland. The aim of this work was to model the transport time by ambulance of seriously injured road traffic accident victims to one of the 12 trauma centres in Switzerland and to investigate whether this time influenced mortality. METHODS: Isochronous travel curves in 10-minute increments were modelled around each of the 12 Swiss trauma centres to assess travel times at the Swiss national level, based on the shortest travel time from the location of a serious road accident to the nearest trauma centre. We used the national database of the Federal Roads Office, which provided the geolocation of these accidents occurring between 2011 and 2017. The association between mortality and transport time to the nearest trauma centre was then analysed. RESULTS: The current distribution of trauma centres allowed access time within the Golden Hour for accidents occurring on the Swiss plateau, but the time was more prolonged in the Alps or the Jura. An association existed between mortality and prehospital transport time from the site of an accident to the nearest trauma centre. For each additional 10-minute isochrone, an average increase of 0.4% in mortality was observed. CONCLUSION: This work showed an adequate distribution of trauma centres in Switzerland and suggests a positive relationship between transport time to the nearest trauma centre and mortality. The numerous confounding factors not systematically collected in publicly available databases limit the robustness of our results. This study confirms the importance of having a national trauma registry to allow quality analyses to guide public health decisions.

Objective: To investigate the association between socioeconomic deprivation and the persistence of SARS-CoV-2 clusters.Methods: We analyzed 3,355 SARS-CoV-2 positive test results in the state of Geneva (Switzerland) from February 26 to April 30, 2020. We used a spatiotemporal cluster detection algorithm to monitor SARS-CoV-2 transmission dynamics and defined spatial cluster persistence as the time in days from emergence to disappearance. Using spatial cluster persistence measured outcome and a deprivation index based on neighborhood-level census socioeconomic data, stratified survival functions were estimated using the Kaplan-Meier estimator. Population density adjusted Cox proportional hazards (PH) regression models were then used to examine the association between neighborhood socioeconomic deprivation and persistence of SARS-CoV-2 clusters.Results: SARS-CoV-2 clusters persisted significantly longer in socioeconomically disadvantaged neighborhoods. In the Cox PH model, the standardized deprivation index was associated with an increased spatial cluster persistence (hazard ratio [HR], 1.43 [95% CI, 1.28–1.59]). The adjusted tercile-specific deprivation index HR was 1.82 [95% CI, 1.56–2.17].Conclusions: The increased risk of infection of disadvantaged individuals may also be due to the persistence of community transmission. These findings further highlight the need for interventions mitigating inequalities in the risk of SARS-CoV-2 infection and thus, of serious illness and mortality.

Coral reefs are under threat and innovative management strategies are urgently required. However, discoveries from innovative fields of coral reef research are rarely transposed in practical conservation actions. This is mainly due to the difficulties in knowledge exchange between scientists and conservation stakeholders. The ManaCo consortium (http://manaco.ird.nc/) is an international network federating conservation stakeholders and researchers in a common effort to preserve the coral reefs. The focus is on using modern tools to build a bridge between indigenous knowledge and scientific innovation. ManaCo aims to orientate research toward relevant conservation needs and to facilitate the transposition of research into concrete management strategies. This will allow to coordinate a collaborative response against coral reef decline. We invite anyone sharing the same interests in joining us.

The transhumance system, which consists in moving animals to high mountain pastures during summer, plays a considerable role in preserving both local biodiversity and traditions, as well as protecting against natural hazard. In cows, particularly, milk production is observed to decline as a response to food shortage and climatic stress, leading to atypical lactation curves that are barely described by current lactation models. Here, we relied on 5 million monthly milk records from over 200 000 Braunvieh and Original Braunvieh cows to devise a new model accounting for transhumance, and test the influence of environmental, physiological and morphological factors on cattle productivity. Counter to expectations, environmental conditions in the mountain showed a globally limited impact on milk production during transhumance, with cows in favourable conditions producing only 10% more compared with cows living in detrimental conditions, and with precipitation in spring and altitude revealing to be the most production-affecting variables. Conversely, physiological factors such as lactation number and pregnancy stage presented an important impact over the whole lactation cycle with 20% difference in milk production, and alter the way animals respond to transhumance. Finally, the considered morphological factors (cow height and foot angle) presented a smaller impact during the whole lactation cycle (10% difference in milk production). The present findings help to anticipate the effect of climate change and to identify problematic environmental conditions by comparing their impact with the effect of factors that are known to influence lactation.

Abstract Background Since goat was domesticated 10,000 years ago, many factors have contributed to the differentiation of goat breeds and these are classified mainly into two types: (i) adaptation to different breeding systems and/or purposes and (ii) adaptation to different environments. As a result, approximately 600 goat breeds have developed worldwide; they differ considerably from one another in terms of phenotypic characteristics and are adapted to a wide range of climatic conditions. In this work, we analyzed the AdaptMap goat dataset, which is composed of data from more than 3000 animals collected worldwide and genotyped with the CaprineSNP50 BeadChip. These animals were partitioned into groups based on geographical area, production uses, available records on solid coat color and environmental variables including the sampling geographical coordinates, to investigate the role of natural and/or artificial selection in shaping the genome of goat breeds. Results Several signatures of selection on different chromosomal regions were detected across the different breeds, sub-geographical clusters, phenotypic and climatic groups. These regions contain genes that are involved in important biological processes, such as milk-, meat- or fiber-related production, coat color, glucose pathway, oxidative stress response, size, and circadian clock differences. Our results confirm previous findings in other species on adaptation to extreme environments and human purposes and provide new genes that could explain some of the differences between goat breeds according to their geographical distribution and adaptation to different environments. Conclusions These analyses of signatures of selection provide a comprehensive first picture of the global domestication process and adaptation of goat breeds and highlight possible genes that may have contributed to the differentiation of this species worldwide.

Abstract Background Goat populations that are characterized within the AdaptMap project cover a large part of the worldwide distribution of this species and provide the opportunity to assess their diversity at a global scale. We analysed genome-wide 50 K single nucleotide polymorphism (SNP) data from 144 populations to describe the global patterns of molecular variation, compare them to those observed in other livestock species, and identify the drivers that led to the current distribution of goats. Results A high degree of genetic variability exists among the goat populations studied. Our results highlight a strong partitioning of molecular diversity between and within continents. Three major gene pools correspond to goats from Europe, Africa and West Asia. Dissection of sub-structures disclosed regional gene pools, which reflect the main post-domestication migration routes. We also identified several exchanges, mainly in African populations, and which often involve admixed and cosmopolitan breeds. Extensive gene flow has taken place within specific areas (e.g., south Europe, Morocco and Mali-Burkina Faso-Nigeria), whereas elsewhere isolation due to geographical barriers (e.g., seas or mountains) or human management has decreased local gene flows. Conclusions After domestication in the Fertile Crescent in the early Neolithic era (ca. 12,000 YBP), domestic goats that already carried differentiated gene pools spread to Europe, Africa and Asia. The spread of these populations determined the major genomic background of the continental populations, which currently have a more marked subdivision than that observed in other ruminant livestock species. Subsequently, further diversification occurred at the regional level due to geographical and reproductive isolation, which was accompanied by additional migrations and/or importations, the traces of which are still detectable today. The effects of breed formation were clearly detected, particularly in Central and North Europe. Overall, our results highlight a remarkable diversity that occurs at the global scale and is locally partitioned and often affected by introgression from cosmopolitan breeds. These findings support the importance of long-term preservation of goat diversity, and provide a useful framework for investigating adaptive introgression, directing genetic improvement and choosing breeding targets.

The sheep and goat were domesticated ~10,500 years ago in the same region of the Middle-East. Here, Alberto et al compare the genomes of wild Asiatic mouflon and Bezoar ibex with that of domestics from local, traditional and improved breeds and find common targets of selection related to domestication and improvement in sheep and goats.

Livestock radiated out from domestication centres to most regions of the world, gradually adapting to diverse environments, from very hot to sub-zero temperatures and from wet and humid conditions to deserts. The climate is changing; generally global temperature is increasing, although there are also more extreme cold periods, storms, and higher solar radiation. These changes impact livestock welfare and productivity. This review describes advances in the methodology for studying livestock genomes and the impact of the environment on animal production, giving examples of discoveries made. Sequencing livestock genomes has facilitated genome-wide association studies to localize genes controlling many traits, and population genetics has identified genomic regions under selection or introgressed from one breed into another to improve production or facilitate adaptation. Landscape genomics, which combines global positioning and genomics, has identified genomic features that enable animals to adapt to local environments. Combining the advances in genomics and methods for predicting changes in climate is generating an explosion of data which calls for innovations in the way big data sets are treated. Artificial intelligence and machine learning are now being used to study the interactions between the genome and the environment to identify historic effects on the genome and to model future scenarios.

The vulnerability of alpine environments to climate change presses an urgent need to accurately model and understand these ecosystems. Popularity in the use of digital elevation models (DEMs) to derive proxy environmental variables has increased over the past decade, particularly as DEMs are relatively cheaply acquired at very high resolutions (VHR; Arabis alpina, in two valleys in the western Swiss Alps, we show that both LiDAR and PHOTO technologies can be relevant for producing DEM-derived variables for use in SDMs. We demonstrate that PHOTO DEMs, up to a spatial resolution of at least 1 m, rivalled the accuracy of LiDAR DEMs, largely owing to the customizability of PHOTO DEMs to the study sites compared to commercially available LiDAR DEMs. We obtained DEMs at spatial resolutions of 6.25 cm–8 m for PHOTO and 50 cm–32 m for LiDAR, where we determined that the optimal spatial resolutions of DEM-derived variables in SDM were between 1 and 32 m, depending on the variable and site characteristics. We found that the reduced extent of PHOTO DEMs altered the calculations of all derived variables, which had particular consequences on their relevance at the site with heterogenous terrain. However, for the homogenous site, SDMs based on PHOTO-derived variables generally had higher predictive powers than those derived from LiDAR at matching resolutions. From our results, we recommend carefully considering the required DEM extent to produce relevant derived variables. We also advocate implementing a multiscale framework to appropriately assess the ecological relevance of derived variables, where we caution against the use of VHR-DEMs finer than 50 cm in such studies.

East Coast fever (ECF) is a fatal sickness affecting cattle populations of eastern, central, and southern Africa. The disease is transmitted by the tick Rhipicephalus appendiculatus, and caused by the protozoan Theileria parva parva, which invades host lymphocytes and promotes their clonal expansion. Importantly, indigenous cattle show tolerance to infection in ECF-endemically stable areas. Here, the putative genetic bases underlying ECF-tolerance were investigated using molecular data and epidemiological information from 823 indigenous cattle from Uganda. Vector distribution and host infection risk were estimated over the study area and subsequently tested as triggers of local adaptation by means of landscape genomics analysis. We identified 41 and seven candidate adaptive loci for tick resistance and infection tolerance, respectively. Among the genes associated with the candidate adaptive loci are PRKG1 and SLA2. PRKG1 was already described as associated with tick resistance in indigenous South African cattle, due to its role into inflammatory response. SLA2 is part of the regulatory pathways involved into lymphocytes' proliferation. Additionally, local ancestry analysis suggested the zebuine origin of the genomic region candidate for tick resistance.

Geographic Information Systems (GIS) are becoming increasingly popular in the context of molecular ecology and conservation biology thanks to their display options efficiency, flexibility and management of geodata. Indeed, spatial data for wildlife and livestock species is becoming a trend with many researchers publishing genomic data that is specifically suitable for landscape studies. GIS uniquely reveal the possibility to overlay genetic information with environmental data and, as such, allow us to locate and analyze genetic boundaries of various plant and animal species or to study gene-environment associations (GEA). This means that, using GIS, we can potentially identify the genetic bases of species adaptation to particular geographic conditions or to climate change. However, many biologists are not familiar with the use of GIS and underlying concepts and thus experience difficulties in finding relevant information and instructions on how to use them. In this paper, we illustrate the power of free and open source GIS approaches and provide essential information for their successful application in molecular ecology. First, we introduce key concepts related to GIS that are too often overlooked in the literature, for example coordinate systems, GPS accuracy and scale. We then provide an overview of the most employed open-source GIS-related software, file formats and refer to major environmental databases. We also reconsider sampling strategies as high costs of Next Generation Sequencing (NGS) data currently diminish the number of samples that can be sequenced per location. Thereafter, we detail methods of data exploration and spatial statistics suited for the analysis of large genetic datasets. Finally, we provide suggestions to properly edit maps and to make them as comprehensive as possible, either manually or trough programming languages.

BACKGROUND:In 2007, the Food and Agriculture Organization of the United Nations (FAO) initiated the Global plan of action for Farm Animal Genetic Resources (FAnGR). The main goal of this plan is to reduce further loss of genetic diversity in farm animals, so as to protect and promote the diversity of farm animal resources. An important step to reach this goal is to monitor and prioritize endangered breeds in the context of conservation programs. METHODOLOGY/WEB PORTAL IMPLEMENTATION:The GENMON WebGIS platform is able to monitor FAnGR and to evaluate the degree of endangerment of livestock breeds. The system takes into account pedigree and introgression information, the geographical concentration of animals, the cryo-conservation plan and the sustainability of breeding activities based on socio-economic data as well as present and future land use conditions. A multi-criteria decision tool supports the aggregation of the multi-thematic indices mentioned above using the MACBETH method, which is based on a weighted average using satisfaction thresholds. GENMON is a monitoring tool to reach subjective decisions made by a government agency. It relies on open source software and is available at http://lasigsrv2.epfl.ch/genmon-ch. RESULTS/SIGNIFICANCE:GENMON allows users to upload pedigree-information (animal ID, parents, birthdate, sex, location and introgression) from a specific livestock breed and to define species and/or region-specific weighting parameters and thresholds. The program then completes a pedigree analysis and derives several indices that are used to calculate an integrated score of conservation prioritization for the breeds under investigation. The score can be visualized on a geographic map and allows a fast, intuitive and regional identification of breeds in danger. Appropriate conservation actions and breeding programs can thus be undertaken in order to promote the recovery of the genetic diversity in livestock breeds in need. The use of the platform is illustrated by means of an example based on three local livestock breeds from different species in Switzerland.

Urban sprawl is nowadays a pervasive topic that is subject of a contentious debate among planners and researchers, who still fail to reach consensual solutions. This paper reviews controversies of the sprawl debate and argues that they owe to a failure of the employed methods to appraise its complexity, especially the notion that urban form emerges from multiple overlapping interactions between households, firms and governmental bodies. To address such issues, this review focuses on recent approaches to study urban spatial dynamics from the perspective of the complexity sciences. Firstly, spatial metrics from landscape ecology provide means of quantifying urban sprawl in terms of increasing fragmentation and diversity of land use patches. Secondly, cellular automata and agent-based models suggest that the prevalence of urban sprawl and fragmentation at the urban fringe emerge from negative spatial interaction between residential agents, which seem accentuated as the agent’s preferences become more heterogeneous. Then, the review turns to practical applications that employ such models to spatially inform urban planning and assess future scenarios. A concluding discussion summarizes potential contributions to the debate on urban sprawl as well as some epistemological implications.

BackgroundDuring the past decades, neutral DNA markers have been extensively employed to study demography, population genetics and structure in livestock, but less interest has been devoted to the evaluation of livestock adaptive potential through the identification of genomic regions likely to be under natural selection.Methodology/principal findingsLandscape genomics can greatly benefit the entire livestock system through the identification of genotypes better adapted to specific or extreme environmental conditions. Therefore we analyzed 101 AFLP markers in 43 European and Western Asian goat breeds both with Matsam software, based on a correlative approach (SAM), and with Mcheza and Bayescan, two FST based software able to detect markers carrying signatures of natural selection. Matsam identified four loci possibly under natural selection--also confirmed by FST-outlier methods--and significantly associated with environmental variables such as diurnal temperature range, frequency of precipitation, relative humidity and solar radiation.Conclusions/significanceThese results show that landscape genomics can provide useful information on the environmental factors affecting the adaptive potential of livestock living in specific climatic conditions. Besides adding conservation value to livestock genetic resources, this knowledge may lead to the development of novel molecular tools useful to preserve the adaptive potential of local breeds during genetic improvement programs, and to increase the adaptability of industrial breeds to changing environments.