Reducing the impacts of leg hold trapping on critically endangered foxes by modified traps and conditioned trap aversion on San Nicolas Island, California, USA

Padded leg-hold live traps were used as the primary removal technique in the successful eradication of feral cats Felis silvestris catus from San Nicolas Island, California, USA. Risk of injury to endemic San Nicolas Island foxes Urocyon littoralis dickeyi, a similarly sized and more abundant non-target species, was mitigated by using a smaller trap size, modifying the trap and trap set to reduce injuries, and utilising a trap monitoring system to reduce time animals spent in traps. Impacts to foxes during the eradication campaign were further reduced by having a mobile veterinary hospital on island to treat injured foxes. Compared to other reported fox trapping efforts, serious injuries were reduced 2-7 times. Trapping efforts exceeded animal welfare standards, with 95% of fox captures resulting in minor or no injuries. Older foxes were more likely to receive serious injury. Fox captures were also reduced through aversive conditioning, with initial capture events providing a negative stimulus to prevent recaptures. Fox capture rates decreased up to six times during seven months of trapping, increasing trap availability for cats, and improving the efficacy of the cat eradication program. No aspect of the first capture event was significantly linked to the chance of recapture

The impact of model grid zooming on tracer transport in the 1999/2000 Arctic polar vortex

International audienceWe have used a 3D chemistry transport model to evaluate the transport of HF and CH4 in the stratosphere during the Arctic winter of 1999/2000. Several model experiments were carried out with the use of a zoom algorithm to investigate the effect of different horizontal resolutions. Balloon-borne and satellite-borne observations of HF and CH4 were used to test the model. In addition, air mass descent rates within the polar vortex were calculated and compared to observations. Outside the vortex the model results agree well with the observations, but inside the vortex the model underestimates the observed vertical gradient in HF and CH4, even when the highest available resolution (1°×1°) is applied. The calculated diabatic descent rates agree with observations above potential temperature levels of 450 K. These model results suggest that too strong mixing through the vortex edge could be a plausible cause for the model discrepancies, associated with the calculated mass fluxes, although other reasons are also discussed. Based on our model experiments we conclude that a global 6°×9° resolution is too coarse to represent the polar vortex, whereas the higher resolutions, 3°×2° and 1°×1°, yield similar results, even with a 6°×9° resolution in the tropical region

Trace gas transport in the 1999/2000 Arctic winter: comparison of nudged GCM runs with observations

International audienceWe have compared satellite and balloon observations of methane (CH4) and hydrogen fluoride (HF) during the Arctic winter 1999/2000 with results from the MA-ECHAM4 middle atmospheric general circulation model (GCM). For this purpose, the meteorology in the model was nudged towards ECMWF analyses. This nudging technique is shown to work well for this middle atmospheric model, and offers good opportunities for the simulation of realistic chemistry and transport processes. The current study focuses on transport of HF and CH4, initialized with satellite measurements from the HALOE instrument aboard the UARS satellite. We have compared the model results with HALOE data and balloon measurements throughout the winter, and analyzed the uncertainties associated with tracer initialization, boundary conditions and the passive tracer assumption. This comparison shows that the model represents the Arctic vortex well, including relatively small-scale features. However, while profiles outside the vortex match well, the model underestimates HF and overestimates CH4 concentrations inside the vortex, particularly in the middle stratosphere. This problem is also evident in a comparison of vortex descent rates based upon vortex average tracer profiles from MA-ECHAM4, and various observations, respectively. This could be due to an underestimate of diabatic subsidence in the model, or due to too much mixing between vortex and non-vortex air

Information retrieval and text mining technologies for chemistry

Efficient access to chemical information contained in scientific literature, patents, technical reports, or the web is a pressing need shared by researchers and patent attorneys from different chemical disciplines. Retrieval of important chemical information in most cases starts with finding relevant documents for a particular chemical compound or family. Targeted retrieval of chemical documents is closely connected to the automatic recognition of chemical entities in the text, which commonly involves the extraction of the entire list of chemicals mentioned in a document, including any associated information. In this Review, we provide a comprehensive and in-depth description of fundamental concepts, technical implementations, and current technologies for meeting these information demands. A strong focus is placed on community challenges addressing systems performance, more particularly CHEMDNER and CHEMDNER patents tasks of BioCreative IV and V, respectively. Considering the growing interest in the construction of automatically annotated chemical knowledge bases that integrate chemical information and biological data, cheminformatics approaches for mapping the extracted chemical names into chemical structures and their subsequent annotation together with text mining applications for linking chemistry with biological information are also presented. Finally, future trends and current challenges are highlighted as a roadmap proposal for research in this emerging field.A.V. and M.K. acknowledge funding from the European Community’s Horizon 2020 Program (project reference: 654021 - OpenMinted). M.K. additionally acknowledges the Encomienda MINETAD-CNIO as part of the Plan for the Advancement of Language Technology. O.R. and J.O. thank the Foundation for Applied Medical Research (FIMA), University of Navarra (Pamplona, Spain). This work was partially funded by Consellería de Cultura, Educación e Ordenación Universitaria (Xunta de Galicia), and FEDER (European Union), and the Portuguese Foundation for Science and Technology (FCT) under the scope of the strategic funding of UID/BIO/04469/2013 unit and COMPETE 2020 (POCI-01-0145-FEDER-006684). We thank Iñigo Garciá -Yoldi for useful feedback and discussions during the preparation of the manuscript.info:eu-repo/semantics/publishedVersio

A functional response in resource selection links multi-scale responses of a large carnivore to human mortality risk

Theory suggests that animals make hierarchical, multiscale resource selection decisions to address the hierarchy of factors limiting their fitness. Ecologists have developed tools to link population-level resource selection across scales; yet, theoretical expectations about the relationship between coarse-and fine-scale selection decisions at the individual level remain elusive despite their importance to fitness. With GPS-telemetry data collected across California, USA, we evaluated resource selection of mountain lions (Puma concolor; n = 244) relative to spatial variation in human-caused mortality risk. With hierarchical resource selection, coarse-scale selection determines availability at finer scales. This simple relationship allowed us to demonstrate that functional responses in resource selection explicitly link individual-level resource selection decisions across scales. We show that individuals proactively avoiding risk when selecting home ranges are freed to relax this avoidance when making decisions within home ranges. However, individuals also exhibit reactive avoidance of risk at the finest scales along movement paths

Evaluation of the effects of multiple capture methods and immobilization drugs on mountain lion welfare

Using a dataset of 591 capture events between 2001–2019 in California, USA, we examined the impact of capture methods and immobilization drugs on mountain lion (Puma concolor) welfare. The 3 methods used to capture mountain lions were cage traps, trained hounds, and cable restraints. The drugs used to immobilize mountain lions were either tiletamine/zolazepam (Telazol®), ketamine/medetomidine, or ketamine/xylazine. Mortality occurred in 1.4% of captures, with only one mortality out of 310 captures occurring since 2012. We used a logistic regression framework to compare morbidity and vital parameters of mountain lions among the different capture methods and immobilization drugs used. Vomiting (a risk factor for developing aspiration pneumonia) was the most common severe risk factor associated with cage trapping and was only seen with the use of ketamine/medetomidine or ketamine/xylazine. Morbidity scores were not well predicted by any of the variables we accounted for. Animals immobilized with Telazol® were more likely to experience abnormal heart and respiratory rates, as well as high body temperatures, than those immobilized with the other two combinations. Although there are risks associated with each of the capture methods and drug combinations commonly used in mountain lion captures in California, our analyses demonstrated they are all relatively safe when following appropriate animal welfare practices. Our analyses suggested that unaccounted for factors are equally or more important in explaining injury and physiological abnormality rates, and we urge that agencies train personnel in best practices and conservative decision-making in order to assure that the welfare of the animal takes precedence over collaring. We suggest training on how to choose between several capture techniques, immobilization drugs and monitoring methods and how to reduce both detrimental effects to mountain lions and danger to humans

A Functional Response in Resource Selection Links Multiscale Responses of a Large Carnivore to Human Mortality Risk

Theory suggests that animals make hierarchical, multiscale resource selection decisions to address the hierarchy of factors limiting their fitness. Ecologists have developed tools to link population-level resource selection across scales; yet, theoretical expectations about the relationship between coarse- and fine-scale selection decisions at the individual level remain elusive despite their importance to fitness. With GPS-telemetry data collected across California, USA, we evaluated resource selection of mountain lions (Puma concolor; n = 244) relative to spatial variation in human-caused mortality risk. With hierarchical resource selection, coarse-scale selection determines availability at finer scales. This simple relationship allowed us to demonstrate that functional responses in resource selection explicitly link individual-level resource selection decisions across scales. We show that individuals proactively avoiding risk when selecting home ranges are freed to relax this avoidance when making decisions within home ranges. However, individuals also exhibit reactive avoidance of risk at the finest scales along movement paths.</p

The ecology of human-caused mortality for a protected large carnivore

Mitigating human-caused mortality for large carnivores is a pressing global challenge for wildlife conservation. However, mortality is almost exclusively studied at local (within-population) scales creating a mismatch between our understanding of risk and the spatial extent most relevant to conservation and management of wide-ranging species. Here, we quantified mortality for 590 radio-collared mountain lions statewide across their distribution in California to identify drivers of human-caused mortality and investigate whether human-caused mortality is additive or compensatory. Human-caused mortality, primarily from conflict management and vehicles, exceeded natural mortality despite mountain lions being protected from hunting. Our data indicate that human-caused mortality is additive to natural mortality as population-level survival decreased as a function of increasing human-caused mortality and natural mortality did not decrease with increased human-caused mortality. Mortality risk increased for mountain lions closer to rural development and decreased in areas with higher proportions of citizens voting to support environmental initiatives. Thus, the presence of human infrastructure and variation in the mindset of humans sharing landscapes with mountain lions appear to be primary drivers of risk. We show that human-caused mortality can reduce population-level survival of large carnivores across large spatial scales, even when they are protected from hunting

Adaptive divergence despite strong genetic drift: genomic analysis of the evolutionary mechanisms causing genetic differentiation in the island fox (\u3ci\u3eUrocyon littoralis\u3c/i\u3e)

The evolutionary mechanisms generating the tremendous biodiversity of islands have long fascinated evolutionary biologists. Genetic drift and divergent selection are pre- dicted to be strong on islands and both could drive population divergence and specia- tion. Alternatively, strong genetic drift may preclude adaptation. We conducted a genomic analysis to test the roles of genetic drift and divergent selection in causing genetic differentiation among populations of the island fox (Urocyon littoralis). This species consists of six subspecies, each of which occupies a different California Chan- nel Island. Analysis of 5293 SNP loci generated using Restriction-site Associated DNA (RAD) sequencing found support for genetic drift as the dominant evolutionary mech- anism driving population divergence among island fox populations. In particular, pop- ulations had exceptionally low genetic variation, small Ne (range = 2.1–89.7; median = 19.4), and significant genetic signatures of bottlenecks. Moreover, islands with the lowest genetic variation (and, by inference, the strongest historical genetic drift) were most genetically differentiated from mainland grey foxes, and vice versa, indicating genetic drift drives genome-wide divergence. Nonetheless, outlier tests identified 3.6–6.6% of loci as high FST outliers, suggesting that despite strong genetic drift, divergent selection contributes to population divergence. Patterns of similarity among populations based on high FST outliers mirrored patterns based on morphology, providing additional evidence that outliers reflect adaptive divergence. Extremely low genetic variation and small Ne in some island fox populations, particularly on San Nicolas Island, suggest that they may be vulnerable to fixation of deleterious alleles, decreased fitness and reduced adaptive potential

Modelling the impact of toxic and disturbance stress on white-tailed eagle (Haliaeetus albicilla) populations

Several studies have related breeding success and survival of sea eagles to toxic or non-toxic stress separately. In the present investigation, we analysed single and combined impacts of both toxic and disturbance stress on populations of white-tailed eagle (Haliaeetus albicilla), using an analytical single-species model. Chemical and eco(toxico)logical data reported from laboratory and field studies were used to parameterise and validate the model. The model was applied to assess the impact of ∑PCB, DDE and disturbance stress on the white-tailed eagle population in The Netherlands. Disturbance stress was incorporated through a 1.6% reduction in survival and a 10–50% reduction in reproduction. ∑PCB contamination from 1950 up to 1987 was found to be too high to allow the return of white-tailed eagle as a breeding species in that period. ∑PCB and population trends simulated for 2006–2050 suggest that future population growth is still reduced. Disturbance stress resulted in a reduced population development. The combination of both toxic and disturbance stress varied from a slower population development to a catastrophical reduction in population size, where the main cause was attributed to the reduction in reproduction of 50%. Application of the model was restricted by the current lack of quantitative dose–response relationships between non-toxic stress and survival and reproduction. Nevertheless, the model provides a first step towards integrating and quantifying the impacts of multiple stressors on white-tailed eagle populations