A spatial modelling framework for assessing climate change impacts on freshwater ecosystems: Response of brown trout (Salmo trutta L.) biomass to warming water temperature

Mountain regions worldwide are particularly sensitive to on-going climate change. Specifically in the Alps in Switzerland, the temperature has increased twice as fast than in the rest of the Northern hemisphere. Water temperature closely follows the annual air temperature cycle, severely impacting streams and freshwater ecosystems. In the last 20 years, brown trout (Salmo trutta L) catch has declined by approximately 40-50% in many rivers in Switzerland. Increasing water temperature has been suggested as one of the most likely cause of this decline. Temperature has a direct effect on trout population dynamics through developmental and disease control but can also indirectly impact dynamics via food-web interactions such as resource availability. We developed a spatially explicit modelling framework that allows spatial and temporal projections of trout biomass using the Aare river catchment as a model system, in order to assess the spatial and seasonal patterns of trout biomass variation. Given that biomass has a seasonal variation depending on trout life history stage, we developed seasonal biomass variation models for three periods of the year (Autumn-Winter, Spring and Summer). Because stream water temperature is a critical parameter for brown trout development, we first calibrated a model to predict water temperature as a function of air temperature to be able to further apply climate change scenarios. We then built a model of trout biomass variation by linking water temperature to trout biomass measurements collected by electro-fishing in 21 stations from 2009 to 2011. The different modelling components of our framework had overall a good predictive ability and we could show a seasonal effect of water temperature affecting trout biomass variation. Our statistical framework uses a minimum set of input variables that make it easily transferable to other study areas or fish species but could be improved by including effects of the biotic environment and the evolution of demographical parameters over time. However, our framework still remains informative to spatially highlight where potential changes of water temperature could affect trout biomass. (C) 2015 Elsevier B.V. All rights reserved.-

Overcoming limitations of modelling rare species by using ensembles of small models

1. Species distribution models (SDMs) have become a standard tool in ecology and applied conservation biology. Modelling rare and threatened species is particularly important for conservation purposes. However, modelling rare species is difficult because the combination of few occurrences and many predictor variables easily leads to model overfitting. A new strategy using ensembles of small models was recently developed in an attempt to overcome this limitation of rare species modelling and has been tested successfully for only a single species so far. Here, we aim to test the approach more comprehensively on a large number of species including a transferability assessment. 2. For each species numerous small (here bivariate) models were calibrated, evaluated and averaged to an ensemble weighted by AUC scores. These 'ensembles of small models' (ESMs) were compared to standard Species Distribution Models (SDMs) using three commonly used modelling techniques (GLM, GBM, Maxent) and their ensemble prediction. We tested 107 rare and under-sampled plant species of conservation concern in Switzerland. 3. We show that ESMs performed significantly better than standard SDMs. The rarer the species, the more pronounced the effects were. ESMs were also superior to standard SDMs and their ensemble when they were independently evaluated using a transferability assessment. 4. By averaging simple small models to an ensemble, ESMs avoid overfitting without losing explanatory power through reducing the number of predictor variables. They further improve the reliability of species distribution models, especially for rare species, and thus help to overcome limitations of modelling rare species.

Determining shoal membership using affinity propagation

We propose using the affinity propagation (AP) clustering algorithm for detecting multiple disjoint shoals, and we present an extension of AP, denoted by STAP, that can be applied to shoals that fusion and fission across time. STAP incorporates into AP a soft temporal constraint that takes cluster dynamics into account, encouraging partitions obtained at successive time steps to be consistent with each other. We explore how STAP performs under different settings of its parameters (strength of the temporal constraint, preferences, and distance metric) by applying the algorithm to simulated sequences of collective coordinated motion. We study the validity of STAP by comparing its results to partitioning of the same data obtained from human observers in a controlled experiment. We observe that, under specific circumstances, AP yields partitions that agree quite closely with the ones made by human observers. We conclude that using the STAP algorithm with appropriate parameter settings is an appealing approach for detecting shoal fusion-fission dynamics.

A subalpine rangeland bird community before and after fire: prescribed burning in the Eastern Pyrenees

High mountain rangelands host important populations of threatened bird species, but can be affected by extensive changes in land use. I studied the breeding bird community of two shrubland plots at 1,850–2,100 m a.s.l. in the Pyrenees. Breeding territories were mapped for four years, before and after the prescribed burning, the aim of which was to increase the grazing value of the study area. The most abundant species (reaching ≥3 breeding pairs/10 ha in at least one plot and one year) were Dunnock Prunella modularis, Dartford Warbler Sylvia undata, Stonechat Saxicola torquatus, Rock Bunting Emberiza cia and Ortolan Bunting E. hortulana. The open-shrubland plot contained a similar number of breeding species (10 vs.9), but a lower overall density (23 vs. 28 breeding pairs/10 ha) than the dense-shrubland plot. Most breeding species alsooccurred in winter. After fire, the number of bird species, overall density and conservation value (an index that takes into account all species’ densities and their categories of conservation concern in Europe) decreased, but tended to recover afterwards. These results may help understand the composition and dynamics of bird assemblages in managed mountain areas

Todennäköisyyspohjaisen kaapelipaloriskianalyysimenetelmän kehittäminen ydinvoimalaitokselle

Ydinenergian tuottamisessa turvallisuus on tärkeää. Todennäköisyyspohjaisella riskianalyysillä voidaan arvioida turvallisuusvaatimusten täyttymistä eri tilanteissa. Tässä diplomityössä tarkastellaan todennäköisyyspohjaisen riskianalyysin käyttöä ydinvoimalaitoksen kaapelipalojen vaikutusten arvioinnissa. Työn tarkoituksena on omalta osaltaan edistää ydinvoimalaitosten kaapelipaloturvallisuuden parantamista. Työssä esitellään todennäköisyyspohjaisen riskianalyysin ja todennäköisyyspohjaisen paloanalyysin periaatteet sekä nykyiset kaapelipaloanalyysimenetelmät. Olemassa olevien menetelmien pohjalta kehitettiin menetelmä Olkiluoto 1 ja 2 laitosyksiköiden kaapelipaloturvallisuuden arviointiin. Työssä tarkastellaan myös maailmalla sattuneita kaapelipaloja sekä ydinvoimalaitosten palosimulointiin kehitettyä ohjelmistoa. Työssä kehitetty kaapelipaloanalyysi jakautuu kahteen päävaiheeseen: virtapiirien vika-analyysiin ja virtapiirivikojen todennäköisyysanalyysiin. Virtapiirien vika-analyysi käsittää kaapeleiden vikamoodien, virtapiirien vikaantumisluokkien sekä vikaantumisten vaikutuksien määrittämisen. Virtapiirivikojen todennäköisyysanalyysissä määritetään puolestaan vikaantumistodennäköisyydet kaapelipalokokeiden tulosten pohjalta. Kehitettyä analyysimenetelmää sovellettiin esimerkinomaisesti Olkiluoto 1 ja 2 laitosyksiköiden kahdelle eri huonetilalle. Tuloksena saatiin turvallisuudelle tärkeiden järjestelmien virtapiirien vikaantumismallit sekä niiden todennäköisyydet. Tulosten perusteella voidaan todeta, että työssä kehitetty kaapelipaloanalyysimenetelmä toimi hyvin. Tulevaisuudessa menetelmää on tarkoitus hyödyntää Olkiluoto 1 ja 2 -laitosyksiköiden kaapelipaloturvallisuuden arvioinnissa.

Combining niche modelling and landscape genetics to study local adaptation: A novel approach illustrated using alpine plants

Understanding the factors that shape adaptive genetic variation across species niches has become of paramount importance in evolutionary ecology, especially to understand how adaptation to changing climate affects the geographic range of species. The distribution of adaptive alleles in the ecological niche is determined by the emergence of novel mutations, their fitness consequences and gene flow that connects populations across species niches. Striking demographical differences and source sink dynamics of populations between the centre and the margin of the niche can play a major role in the emergence and spread of adaptive alleles. Although some theoretical predictions have long been proposed, the origin and distribution of adaptive alleles within species niches remain untested. In this paper, we propose and discuss a novel empirical approach that combines landscape genetics with species niche modelling, to test whether alleles that confer local adaptation are more likely to occur in either marginal or central populations of species niches. We illustrate this new approach by using a published data set of 21 alpine plant species genotyped with a total of 2483 amplified fragment length polymorphisms (AFLP), distributed over more than 1733 sampling sites across the Alps. Based on the assumption that alleles that were statistically associated with environmental variables were adaptive, we found that adaptive alleles in the margin of a species niche were also present in the niche centre, which suggests that adaptation originates in the niche centre. These findings corroborate models of species range evolution, in which the centre of the niche contributes to the emergence of novel adaptive alleles, which diffuse towards niche margins and facilitate niche and range expansion through subsequent local adaptation. Although these results need to be confirmed via fitness measurements in natural populations and functionally characterised genetic sequences, this study provides a first step towards understanding how adaptive genetic variation emerges and shapes species niches and geographic ranges along environmental gradients.

Progress in front propagation research

We review the progress in the field of front propagation in recent years. We survey many physical, biophysical and cross-disciplinary applications, including reduced-variable models of combustion flames, Reid's paradox of rapid forest range expansions, the European colonization of North America during the 19th century, the Neolithic transition in Europe from 13 000 to 5000 years ago, the description of subsistence boundaries, the formation of cultural boundaries, the spread of genetic mutations, theory and experiments on virus infections, models of cancer tumors, etc. Recent theoretical advances are unified in a single framework, encompassing very diverse systems such as those with biased random walks, distributed delays, sequential reaction and dispersion, cohabitation models, age structure and systems with several interacting species. Directions for future progress are outlined

Study and modelling of the effect of herbicides pulse exposure on freshwater microalgae

De plus en plus de substances chimiques sont émises et détectées dans l'environnement.Parmi ces substances, on trouve les herbicides qui sont utilisés en agriculture pour luttercontre la présence des mauvaises herbes. Après leur application sur les sols, les herbicidespeuvent être entrainés par les eaux de pluie jusque dans les ruisseaux et les rivières. Lesconcentrations de ces substances varient donc de manière importante dans les systèmesaquatiques en période de pluie ou en période de temps sec. Des pics élevés de concentrationssont suivis de période de concentrations très faibles ou nulles. Les herbicides présents dans lescours d'eau peuvent engendrer des effets toxiques sur les algues et les plantes aquatiques. Orles tests classiques d'écotoxicologie effectués en laboratoire sont réalisés en exposant lesespèces vivantes à des polluants de manière continue. Ils ne permettent donc pas d'évaluer leseffets des concentrations fluctuantes comme celles des herbicides. Le but de cette thèse estd'étudier et de modéliser les effets des concentrations fluctuantes d'herbicide sur les espècesde microalgues vertes Scenedesmus vacuolatus et Pseudokirchneriella subcapitata. Desexpériences en laboratoire ont également été effectuées dans le but de valider le modèle.Quatre herbicides ont été testés. Il s'agit de l'atrazine (utilisé jusqu'à récemment pour lemaïs), du diuron (utilisé dans la vigne), de l'isoproturon (utilisé pour les céréales) et du Smétolachlore(utilisé pour le maïs). Les résultats de ce travail de thèse indiquent que les effetsdes concentrations fluctuantes d'herbicide peuvent être modélisés sur des algues d'eau douce.Le modèle est relativement simple pour les inhibiteurs de la photosynthèse tels que l'atrazine,le diuron ou l'isoproturon. Il nécessite la connaissance de deux paramètres, le taux decroissance de l'algue sans polluant et la courbe dose-réponse pour chaque substance.Cependant, des expériences supplémentaires doivent être réalisées si la substance étudiéeinduit un délai de l'effet et du rétablissement ou si une algue est cultivée avec une autre alguedans le même milieu de croissance. Le modèle pourrait également être adapté pour tenircompte des mélanges de substances. Appliqué pour prédire les effets sur les algues descénarios réels, le modèle montre que les longs pics de concentrations jouent le rôle le plusimportant. Il est donc crucial de les mesurer lors du monitoring des cours d'eau. D'autre part,une évaluation du risque effectuée avec ce modèle montre que l'impact des pics deconcentrations sur les espèces les plus sensibles est total. Cela met en évidence, une fois deplus, l'importance de tenir compte de ces concentrations fluctuantes dans l'évaluation durisque environnemental des herbicides, mais également des autres polluants.

Is response to fire influenced by dietary specialization and mobility? A comparative study with multiple animal assemblages

Fire is a major agent involved in landscape transformation and an indirect cause of changes in species composition. Responses to fire may vary greatly depending on life histories and functional traits of species. We have examined the taxonomic and functional responses to fire of eight taxonomic animal groups displaying a gradient of dietary and mobility patterns: Gastropoda, Heteroptera, Formicidae, Coleoptera, Araneae, Orthoptera, Reptilia and Aves. The fieldwork was conducted in a Mediterranean protected area on 3 sites (one unburnt and two burnt with different postfire management practices) with five replicates per site. We collected information from 4606 specimens from 274 animal species. Similarity in species composition and abundance between areas was measured by the Bray-Curtis index and ANOSIM, and comparisons between animal and plant responses by Mantel tests. We analyze whether groups with the highest percentage of omnivorous species, these species being more generalist in their dietary habits, show weak responses to fire (i.e. more similarity between burnt and unburnt areas), and independent responses to changes in vegetation. We also explore how mobility, i.e. dispersal ability, influences responses to fire. Our results demonstrate that differences in species composition and abundance between burnt and unburnt areas differed among groups. We found a tendency towards presenting lower differences between areas for groups with higher percentages of omnivorous species. Moreover, taxa with a higher percentage of omnivorous species had significantly more independent responses of changes in vegetation. High- (e.g. Aves) and low-mobility (e.g. Gastropoda) groups had the strongest responses to fire (higher R scores of the ANOSIM); however, we failed to find a significant general pattern with all the groups according to their mobility. Our results partially support the idea that functional traits underlie the response of organisms to environmental changes caused by fire.

Animal modelling for inherited central vision loss.

Disease-causing variants of a large number of genes trigger inherited retinal degeneration leading to photoreceptor loss. Because cones are essential for daylight and central vision such as reading, mobility, and face recognition, this review focuses on a variety of animal models for cone diseases. The pertinence of using these models to reveal genotype/phenotype correlations and to evaluate new therapeutic strategies is discussed. Interestingly, several large animal models recapitulate human diseases and can serve as a strong base from which to study the biology of disease and to assess the scale-up of new therapies. Examples of innovative approaches will be presented such as lentiviral-based transgenesis in pigs and adeno-associated virus (AAV)-gene transfer into the monkey eye to investigate the neural circuitry plasticity of the visual system. The models reported herein permit the exploration of common mechanisms that exist between different species and the identification and highlighting of pathways that may be specific to primates, including humans.

Modelling the consequences of a reduction in alcohol consumption among patients with alcohol dependence based on real-life observational data.

BACKGROUND: Most available pharmacotherapies for alcohol-dependent patients target abstinence; however, reduced alcohol consumption may be a more realistic goal. Using randomized clinical trial (RCT) data, a previous microsimulation model evaluated the clinical relevance of reduced consumption in terms of avoided alcohol-attributable events. Using real-life observational data, the current analysis aimed to adapt the model and confirm previous findings about the clinical relevance of reduced alcohol consumption. METHODS: Based on the prospective observational CONTROL study, evaluating daily alcohol consumption among alcohol-dependent patients, the model predicted the probability of drinking any alcohol during a given day. Predicted daily alcohol consumption was simulated in a hypothetical sample of 200,000 patients observed over a year. Individual total alcohol consumption (TAC) and number of heavy drinking days (HDD) were derived. Using published risk equations, probabilities of alcohol-attributable adverse health events (e.g., hospitalizations or death) corresponding to simulated consumptions were computed, and aggregated for categories of patients defined by HDDs and TAC (expressed per 100,000 patient-years). Sensitivity analyses tested model robustness. RESULTS: Shifting from >220 HDDs per year to 120-140 HDDs and shifting from 36,000-39,000 g TAC per year (120-130 g/day) to 15,000-18,000 g TAC per year (50-60 g/day) impacted substantially on the incidence of events (14,588 and 6148 events avoided per 100,000 patient-years, respectively). Results were robust to sensitivity analyses. CONCLUSIONS: This study corroborates the previous microsimulation modeling approach and, using real-life data, confirms RCT-based findings that reduced alcohol consumption is a relevant objective for consideration in alcohol dependence management to improve public health.

Modelling body mass index and endometrial cancer risk in a pooled-analysis of three case-control studies.

OBJECTIVE: To quantify the relation between body mass index (BMI) and endometrial cancer risk, and to describe the shape of such a relation. DESIGN: Pooled analysis of three hospital-based case-control studies. SETTING: Italy and Switzerland. POPULATION: A total of 1449 women with endometrial cancer and 3811 controls. METHODS: Multivariate odds ratios (OR) and 95% confidence intervals (95% CI) were obtained from logistic regression models. The shape of the relation was determined using a class of flexible regression models. MAIN OUTCOME MEASURE: The relation of BMI with endometrial cancer. RESULTS: Compared with women with BMI 18.5 to <25 kg/m(2) , the odds ratio was 5.73 (95% CI 4.28-7.68) for women with a BMI ≥35 kg/m(2) . The odds ratios were 1.10 (95% CI 1.09-1.12) and 1.63 (95% CI 1.52-1.75) respectively for an increment of BMI of 1 and 5 units. The relation was stronger in never-users of oral contraceptives (OR 3.35, 95% CI 2.78-4.03, for BMI ≥30 versus <25 kg/m(2) ) than in users (OR 1.22, 95% CI 0.56-2.67), and in women with diabetes (OR 8.10, 95% CI 4.10-16.01, for BMI ≥30 versus <25 kg/m(2) ) than in those without diabetes (OR 2.95, 95% CI 2.44-3.56). The relation was best fitted by a cubic model, although after the exclusion of the 5% upper and lower tails, it was best fitted by a linear model. CONCLUSIONS: The results of this study confirm a role of elevated BMI in the aetiology of endometrial cancer and suggest that the risk in obese women increases in a cubic nonlinear fashion. The relation was stronger in never-users of oral contraceptives and in women with diabetes. TWEETABLE ABSTRACT: Risk of endometrial cancer increases with elevated body weight in a cubic nonlinear fashion.