Modified home range kernel density estimators that take environmental interactions into account

International audienceBackground: Kernel density estimation (KDE) is a major tool in the movement ecologist toolbox that is used to delineate where geo-tracked animals spend their time. Because KDE bandwidth optimizers are sensitive to temporal autocorrelation, statistically-robust alternatives have been advocated, first, data-thinning procedures, and more recently, autocorrelated kernel density estimation (AKDE). These yield asymptotically consistent, but very smoothed distributions, which may feature biologically unrealistic aspects such as spilling beyond impassable borders.Method: I introduce a semi-parametric variant of AKDE designed to extrapolate more realistic home range shapes by incorporating movement mechanisms into the bandwidth optimizer and into the base kernels. I implement a first approximative version based on the step selection framework. This method allows accommodating land cover selection, permeability of linear features, and attraction for select landscape features when delineating home ranges.Results: In a plains zebra (Equus quagga), the reluctance to cross a railway, the avoidance of dense woodland, and the preference for grassland when foraging created significant differences between the estimated home range contours by the new and by previous methods.Conclusion: There is a tradeoff to find between fully parametric density estimators, which can be very realistic but need to be provided with a good model and adequate environmental data, and non-parametric density estimators, which are more widely applicable and asymptotically consistent, but whose details are bandwidth-limited. The proposed semi-parametric approach attempts to strike this balance, but I outline a few areas of future improvement. I expect the approach to find its use in studies that compare extrapolated resource availability and interpolated resource use, in order to discover the movement mechanisms that we need to improve the extrapolations

Departures from the energy-biodiversity relationship in south african passerines: are the legacies of past climates mediated by behavioral constraints on dispersal?

Legacies of paleoclimates in contemporary biodiversity patterns have mostly been investigated with global datasets, or with weakly dispersive organisms, and as a consequence been interpreted in terms of geographical or physical constraints. If paleoclimatic legacies also occurred at the regional scale in the distributions of vagile organisms within biomes, they would rather suggest behavioral constraints on dispersal, i.e., philopatric syndromes. We examined 1) the residuals of the regression between contemporary energy and passerine species richness in South African biomes and 2) phylogenetic dispersion of passerine assemblages, using occupancy models and quarter-degree resolution citizen science data. We found a northeast to southwest gradient within mesic biomes congruent with the location of Quaternary mesic refugia, overall suggesting that as distance from refugia increased, more clades were lacking from local assemblages. A similar but weaker pattern was detected in the arid Karoo Biomes. In mobile organisms such as birds, behavioral constraints on dispersal appear strong enough to influence species distributions thousands of years after historical range contractions

Le patrimoine maritime culturel : de l'inventaire à l'action (exemple des espaces côtiers bretons)

http://www.meshs.fr/documents/pdf/publications/actes/colloque_littoral/Marie.pdfInternational audienceSeaside is an attractive territory, which is in perpetual evolution. However, the last evolutions have changed very quickly the coastal zone and raised the question of the identities, which are cultural creation. This paper deals with cultural maritime heritage, with example from the Breton coastal area. It takes part into the Integrated Coastal Zone Management (ICZM). The research team of the “Observatoire du Patrimoine Maritime Culturel” set up a method of inventory of this specific heritage to make proposals of management geographically differentiated, to insert them into the public policies at different scales.Le patrimoine maritime culturel est un élément primordial et souvent oublié du développement durable des littoraux. Il existe pourtant, au sein de nos sociétés en mutation, un « risque culturel » de se couper du passé et par la même de perspectives d'avenir. Pour répondre à la nécessaire prise en compte des héritages maritimes – témoins de la diversité dans le temps et dans l'espace des relations Homme/mer –, un projet de recherche pluridisciplinaire et appliqué a été mis en place en appui des politiques publiques. Dans ce cadre, la question fondamentale est de réussir à passer du diagnostic à l'action, du simple inventaire des héritages maritimes à des propositions d'aménagement du territoire dans une démarche concertée avec les acteurs du littoral. L'objectif n'est pas de figer les territoires littoraux mais de les faire vivre. Il s'agit tout d'abord de cerner les éléments pris en compte. Dans un but d'accompagnement des mutations à l'œuvre actuellement sur les littoraux, ont été retenus comme éléments potentiels d'un patrimoine maritime culturel à mettre en valeur les éléments bâtis terrestres (phares, forteresses, conserveries, habitat de pêcheur, villas balnéaires...), les ouvrages maritimes (quais, digues...) et les éléments flottants (bateaux, pontons). Neuf champs patrimoniaux ont pu ainsi être définis. Les recherches sur le terrain et aux archives ont permis de réaliser une base de données géoréférencées dans laquelle chaque élément est présenté en trois volets : l'histoire, les caractéristiques techniques et juridiques, l'usage et le devenir. La spatialisation du territoire permet de donner une vue hiérarchisée de la distribution et de l'organisation spatiale de ces héritages maritimes. Des formes bien individualisées d'organisation de l'espace, en particulier celle des petits fronts portuaires, sont également mises en évidence afin de définir des types de risques et de proposer des types d'aménagement adaptés. L'étude a été réalisée dès le début en relation étroite avec les acteurs des littoraux à différentes échelles : locale, régionale, nationale. En effet, le patrimoine maritime culturel, comme tout patrimoine, est une construction sociale et culturelle développée en fonction d'un projet porté par la société ou les sociétés concernées. Aussi, des partenariats sont noués et des actions de sensibilisation sont menées en direction des divers publics. Il existe néanmoins des freins importants à la mise en place d'actions de valorisation du patrimoine maritime culturel. L'implication des élus et aménageurs n'est pas toujours à la hauteur des exigences en raison de leur manque d'intérêt pour le sujet. Les enjeux économiques à court terme, liés à la pression immobilière exercée actuellement sur les littoraux, s'opposent souvent à une politique de « développement culturel durable ». Les outils juridiques ne sont pas toujours adaptés. Quoi qu'il en soit, toute action de valorisation du patrimoine maritime culturel ne peut réussir que si elle est menée conjointement avec une politique de reconnaissance de son intérêt aux niveaux régional, national, voire aujourd'hui européen

Distance sampling of duikers in the rainforest: Dealing with transect avoidance

International audienceBushmeat is a major source of protein and income in tropical regions but is often over-harvested. A better monitoring of bushmeat stocks could help achieve sustainability. We used a combination of simulations and transect survey data collected from blue duikers (Philantomba monticola) in the Lomako wildlife reserve, Democratic Republic of the Congo, to investigate the use of transect-based distance sampling to monitor bushmeat stocks. The comparison of dung piles and direct observations of duikers evidenced that animals avoided both the transects in the absence of observers, and the observers themselves. This type of behavioural response appeared common in a literature survey. It causes a negative bias in the estimates of population densities from the standard distance sampling methodology. This negative bias would lead to over-pessimistic predictions of population viability, especially if the behavioural response is more intense in the locations where the animals are hunted. In turn, this would lead to excessively conservative management recommendations. To correct for the effect of the behavioural response of the animals to either the transects or the observers, we recommend recording both the forward and perpendicular distances to the observers (2D distance sampling), not just the perpendicular distance. We also recommend multiple-observer protocols. As a cautionary note, we also demonstrate a scenario where the intensity of the behavioural response is too high to reliably estimate the abundance of the population. As a perspective, we outline the general principles of a local stakeholder-based program combining distance sampling with less intensive types of ecological indicators to monitor wildlife populations

An analysis of the fishmeal industry: From wild fisheries to international fishmeal and fish oil markets

Because of the stagnation of commercial landings, the development of aquaculture activities is expected to rise during the next decades to match the growing demand for fisheries goods. Overall, it is often expected that the aquaculture sector could reduce to a certain extent the pressure applied over wild stocks. However, this development is likely to be limited by the availability of key aquaculture inputs, namely fishmeal and fish oil. Aquaculture is indeed one of the primary users of fishmeal and fish oils products, together, with the poultry and pigs industries (respectively around 45% and 80% of the total consumption). The availability of these inputs mainly depends on the pelagic stocks, which are already strongly or over exploited. Thus, the fishmeal industry is expected to play a key role in the future interactions between the aquaculture and the fisheries industries. In particular, the optimization of pelagic resources use is crucial to support further development of aquaculture, as well as the understanding of global input and output flows related to the reduction sector. Reduction technologies are characterised by a number of conversion ratios. Yet, these ratios are in general poorly documented. Based on an analysis of fish production and trade databases, this paper provides some information on the performances of the reduction industries around the world, and on the raw materials used by these industries

3D individual based model for simultaneous growth and interaction of L. Monocytogenes and lactic acid bacteria

International audienceBy interacting with pathogens, lactic acid bacteria (LAB) are able to contribute to food safety. By means of their lactic acid production which induces pH decrease, LAB influence the growth of pathogens. The aim of this study is to model and simulate lactic acid production, pH evolution, according to carbohydrate concentration in media, temperature, water activity and ratio of both population

The challenges of estimating the distribution of flight heights from telemetry or altimetry data

AbstractBackgroundGlobal positioning systems (GPS) and altimeters are increasingly used to monitor vertical space use by aerial species, a key aspect of their ecological niche, that we need to know to manage our own use of the airspace, and to protect those species. However, there are various sources of error in flight height data (“height” above ground, as opposed to “altitude” above a reference like the sea level). First the altitude is measured with a vertical error from the devices themselves. Then there is error in the ground elevation below the tracked animals, which translates into error in flight height computed as the difference between altitude and ground elevation. Finally, there is error in the horizontal position of the animals, which translates into error in the predicted ground elevation below the animals. We used controlled field trials, simulations, and the reanalysis of raptor case studies with state-space models to illustrate the effect of improper error management.ResultsErrors of a magnitude of 20 m appear in benign conditions for barometric altimeters and GPS vertical positioning (expected to be larger in more challenging context). These errors distort the shape of the distribution of flight heights, inflate the variance in flight height, bias behavioural state assignments, correlations with environmental covariates, and airspace management recommendations. Improper data filters such as removing all negative flight height records introduce several biases in the remaining dataset, and preclude the opportunity to leverage unambiguous errors to help with model fitting. Analyses that ignore the variance around the mean flight height, e.g., those based on linear models of flight height, and those that ignore the variance inflation caused by telemetry errors, lead to incorrect inferences.ConclusionThe state-space modelling framework, now in widespread use by ecologists and increasingly often automatically implemented within on-board GPS data processing algorithms, makes it possible to fit flight models directly to the output of GPS devices, with minimal data pre-selection, and to analyse the full distribution of flight heights, not just the mean. In addition to basic research about aerial niches, behaviour quantification, and environmental interactions, we highlight the applied relevance of our recommendations for airspace management and the conservation of aerial wildlife.</jats:sec

Positive relationships between association strength and phenotypic similarity characterize the assembly of mixed-species bird flocks worldwide

Competition theory predicts that local communities should consist of species that are more dissimilar than expected by chance. We find a strikingly different pattern in a multicontinent data set (55 presence-absence matrices from 24 locations) on the composition of mixed-species bird flocks, which are important sub-units of local bird communities the world over. By using null models and randomization tests followed by meta-analysis, we find the association strengths of species in flocks to be strongly related to similarity in body size and foraging behavior and higher for congeneric compared with noncongeneric species pairs. Given the local spatial scales of our individual analyses, differences in the habitat preferences of species are unlikely to have caused these association patterns; the patterns observed are most likely the outcome of species interactions. Extending group-living and social-information-use theory to a heterospecific context, we discuss potential behavioral mechanisms that lead to positive interactions among similar species in flocks, as well as ways in which competition costs are reduced. Our findings highlight the need to consider positive interactions along with competition when seeking to explain community assembly

Satellite Tagging and Biopsy Sampling of Killer Whales at Subantarctic Marion Island: Effectiveness, Immediate Reactions and Long-Term Responses

Remote tissue biopsy sampling and satellite tagging are becoming widely used in large marine vertebrate studies because they allow the collection of a diverse suite of otherwise difficult-to-obtain data which are critical in understanding the ecology of these species and to their conservation and management. Researchers must carefully consider their methods not only from an animal welfare perspective, but also to ensure the scientific rigour and validity of their results. We report methods for shore-based, remote biopsy sampling and satellite tagging of killer whales Orcinus orca at Subantarctic Marion Island. The performance of these methods is critically assessed using 1) the attachment duration of low-impact minimally percutaneous satellite tags; 2) the immediate behavioural reactions of animals to biopsy sampling and satellite tagging; 3) the effect of researcher experience on biopsy sampling and satellite tagging; and 4) the mid- (1 month) and long- (24 month) term behavioural consequences. To study mid- and long-term behavioural changes we used multievent capture-recapture models that accommodate imperfect detection and individual heterogeneity. We made 72 biopsy sampling attempts (resulting in 32 tissue samples) and 37 satellite tagging attempts (deploying 19 tags). Biopsy sampling success rates were low (43%), but tagging rates were high with improved tag designs (86%). The improved tags remained attached for 26±14 days (mean ± SD). Individuals most often showed no reaction when attempts missed (66%) and a slight reaction-defined as a slight flinch, slight shake, short acceleration, or immediate dive-when hit (54%). Severe immediate reactions were never observed. Hit or miss and age-sex class were important predictors of the reaction, but the method (tag or biopsy) was unimportant. Multievent trap-dependence modelling revealed considerable variation in individual sighting patterns; however, there were no significant mid- or long-term changes following biopsy sampling or tagging