Unfolding nature "in silico" : overcoming practical and metodological limitations of species distribution models

Abstract : The existence of a causal relationship between the spatial distribution of living organisms and their environment, in particular climate, has been long recognized and is the central principle of biogeography. In turn, this recognition has led scientists to the idea of using the climatic, topographic, edaphic and biotic characteristics of the environment to predict its potential suitability for a given species or biological community. In this thesis, my objective is to contribute to the development of methodological improvements in the field of species distribution modeling. More precisely, the objectives are to propose solutions to overcome limitations of species distribution models when applied to conservation biology issues, or when .used as an assessment tool of the potential impacts of global change. The first objective of my thesis is to contribute to evidence the potential of species distribution models for conservation-related applications. I present a methodology to generate pseudo-absences in order to overcome the frequent lack of reliable absence data. I also demonstrate, both theoretically (simulation-based) and practically (field-based), how species distribution models can be successfully used to model and sample rare species. Overall, the results of this first part of the thesis demonstrate the strong potential of species distribution models as a tool for practical applications in conservation biology. The second objective this thesis is to contribute to improve .projections of potential climate change impacts on species distributions, and in particular for mountain flora. I develop and a dynamic model, MIGCLIM, that allows the implementation of dispersal limitations into classic species distribution models and present an application of this model to two virtual species. Given that accounting for dispersal limitations requires information on seed dispersal, distances, a general methodology to classify species into broad dispersal types is also developed. Finally, the M~GCLIM model is applied to a large number of species in a study area of the western Swiss Alps. Overall, the results indicate that while dispersal limitations can have an important impact on the outcome of future projections of species distributions under climate change scenarios, estimating species threat levels (e.g. species extinction rates) for a mountainous areas of limited size (i.e. regional scale) can also be successfully achieved when considering dispersal as unlimited (i.e. ignoring dispersal limitations, which is easier from a practical point of view). Finally, I present the largest fine scale assessment of potential climate change impacts on mountain vegetation that has been carried-out to date. This assessment involves vegetation from 12 study areas distributed across all major western and central European mountain ranges. The results highlight that some mountain ranges (the Pyrenees and the Austrian Alps) are expected to be more affected by climate change than others (Norway and the Scottish Highlands). The results I obtain in this study also indicate that the threat levels projected by fine scale models are less severe than those derived from coarse scale models. This result suggests that some species could persist in small refugias that are not detected by coarse scale models. Résumé : L'existence d'une relation causale entre la répartition des espèces animales et végétales et leur environnement, en particulier le climat, a été mis en évidence depuis longtemps et est un des principes centraux en biogéographie. Ce lien a naturellement conduit à l'idée d'utiliser les caractéristiques climatiques, topographiques, édaphiques et biotiques de l'environnement afin d'en prédire la qualité pour une espèce ou une communauté. Dans ce travail de thèse, mon objectif est de contribuer au développement d'améliorations méthodologiques dans le domaine de la modélisation de la distribution d'espèces dans le paysage. Plus précisément, les objectifs sont de proposer des solutions afin de surmonter certaines limitations des modèles de distribution d'espèces dans des applications pratiques de biologie de la conservation ou dans leur utilisation pour évaluer l'impact potentiel des changements climatiques sur l'environnement. Le premier objectif majeur de mon travail est de contribuer à démontrer le potentiel des modèles de distribution d'espèces pour des applications pratiques en biologie de la conservation. Je propose une méthode pour générer des pseudo-absences qui permet de surmonter le problème récurent du manque de données d'absences fiables. Je démontre aussi, de manière théorique (par simulation) et pratique (par échantillonnage de terrain), comment les modèles de distribution d'espèces peuvent être utilisés pour modéliser et améliorer l'échantillonnage des espèces rares. Ces résultats démontrent le potentiel des modèles de distribution d'espèces comme outils pour des applications de biologie de la conservation. Le deuxième objectif majeur de ce travail est de contribuer à améliorer les projections d'impacts potentiels des changements climatiques sur la flore, en particulier dans les zones de montagnes. Je développe un modèle dynamique de distribution appelé MigClim qui permet de tenir compte des limitations de dispersion dans les projections futures de distribution potentielle d'espèces, et teste son application sur deux espèces virtuelles. Vu que le fait de prendre en compte les limitations dues à la dispersion demande des données supplémentaires importantes (p.ex. la distance de dispersion des graines), ce travail propose aussi une méthode de classification simplifiée des espèces végétales dans de grands "types de disperseurs", ce qui permet ainsi de d'obtenir de bonnes approximations de distances de dispersions pour un grand nombre d'espèces. Finalement, j'applique aussi le modèle MIGCLIM à un grand nombre d'espèces de plantes dans une zone d'études des pré-Alpes vaudoises. Les résultats montrent que les limitations de dispersion peuvent avoir un impact considérable sur la distribution potentielle d'espèces prédites sous des scénarios de changements climatiques. Cependant, quand les modèles sont utilisés pour évaluer les taux d'extinction d'espèces dans des zones de montages de taille limitée (évaluation régionale), il est aussi possible d'obtenir de bonnes approximations en considérant la dispersion des espèces comme illimitée, ce qui est nettement plus simple d'un point dé vue pratique. Pour terminer je présente la plus grande évaluation à fine échelle d'impact potentiel des changements climatiques sur la flore des montagnes conduite à ce jour. Cette évaluation englobe 12 zones d'études réparties sur toutes les chaines de montages principales d'Europe occidentale et centrale. Les résultats montrent que certaines chaines de montagnes (les Pyrénées et les Alpes Autrichiennes) sont projetées comme plus sensibles aux changements climatiques que d'autres (les Alpes Scandinaves et les Highlands d'Ecosse). Les résultats obtenus montrent aussi que les modèles à échelle fine projettent des impacts de changement climatiques (p. ex. taux d'extinction d'espèces) moins sévères que les modèles à échelle large. Cela laisse supposer que les modèles a échelle fine sont capables de modéliser des micro-niches climatiques non-détectées par les modèles à échelle large.

Changing landscapes of Switzerland: assessing effects of historic and future land uses and land covers on the occurrence of selected butterfly species

Summary Landscapes are continuously changing. Natural forces of change such as heavy rainfall and fires can exert lasting influences on their physical form. However, changes related to human activities have often shaped landscapes more distinctly. In Western Europe, especially modern agricultural practices and the expanse of overbuilt land have left their marks in the landscapes since the middle of the 20th century. In the recent years men realised that mare and more changes that were formerly attributed to natural forces might indirectly be the result of their own action. Perhaps the most striking landscape change indirectly driven by human activity we can witness in these days is the large withdrawal of Alpine glaciers. Together with the landscapes also habitats of animal and plant species have undergone vast and sometimes rapid changes that have been hold responsible for the ongoing loss of biodiversity. Thereby, still little knowledge is available about probable effects of the rate of landscape change on species persistence and disappearance. Therefore, the development and speed of land use/land cover in the Swiss communes between the 1950s and 1990s were reconstructed using 10 parameters from agriculture and housing censuses, and were further correlated with changes in butterfly species occurrences. Cluster analyses were used to detect spatial patterns of change on broad spatial scales. Thereby, clusters of communes showing similar changes or transformation rates were identified for single decades and put into a temporally dynamic sequence. The obtained picture on the changes showed a prevalent replacement of non-intensive agriculture by intensive practices, a strong spreading of urban communes around city centres, and transitions towards larger farm sizes in the mountainous areas. Increasing transformation rates toward more intensive agricultural managements were especially found until the 1970s, whereas afterwards the trends were commonly negative. However, transformation rates representing the development of residential buildings showed positive courses at any time. The analyses concerning the butterfly species showed that grassland species reacted sensitively to the density of livestock in the communes. This might indicate the augmented use of dry grasslands as cattle pastures that show altered plant species compositions. Furthermore, these species also decreased in communes where farms with an agricultural area >5ha have disappeared. The species of the wetland habitats were favoured in communes with smaller fractions of agricultural areas and lower densities of large farms (>10ha) but did not show any correlation to transformation rates. It was concluded from these analyses that transformation rates might influence species disappearance to a certain extent but that states of the environmental predictors might generally outweigh the importance of the corresponding rates. Information on the current distribution of species is evident for nature conservation. Planning authorities that define priority areas for species protection or examine and authorise construction projects need to know about the spatial distribution of species. Hence, models that simulate the potential spatial distribution of species have become important decision tools. The underlying statistical analyses such as the widely used generalised linear models (GLM) often rely on binary species presence-absence data. However, often only species presence data have been colleted, especially for vagrant, rare or cryptic species such as butterflies or reptiles. Modellers have thus introduced randomly selected absence data to design distribution models. Yet, selecting false absence data might bias the model results. Therefore, we investigated several strategies to select more reliable absence data to model the distribution of butterfly species based on historical distribution data. The results showed that better models were obtained when historical data from longer time periods were considered. Furthermore, model performance was additionally increased when long-term data of species that show similar habitat requirements as the modelled species were used. This successful methodological approach was further applied to assess consequences of future landscape changes on the occurrence of butterfly species inhabiting dry grasslands or wetlands. These habitat types have been subjected to strong deterioration in the recent decades, what makes their protection a future mission. Four spatially explicit scenarios that described (i) ongoing land use changes as observed between 1985 and 1997, (ii) liberalised agricultural markets, and (iii) slightly and (iv) strongly lowered agricultural production provided probable directions of landscape change. Current species-environment relationships were derived from a statistical model and used to predict future occurrence probabilities in six major biogeographical regions in Switzerland, comprising the Jura Mountains, the Plateau, the Northern and Southern Alps, as well as the Western and Eastern Central Alps. The main results were that dry grasslands species profited from lowered agricultural production, whereas overgrowth of open areas in the liberalisation scenario might impair species occurrence. The wetland species mostly responded with decreases in their occurrence probabilities in the scenarios, due to a loss of their preferred habitat. Further analyses about factors currently influencing species occurrences confirmed anthropogenic causes such as urbanisation, abandonment of open land, and agricultural intensification. Hence, landscape planning should pay more attention to these forces in areas currently inhabited by these butterfly species to enable sustainable species persistence. In this thesis historical data were intensively used to reconstruct past developments and to make them useful for current investigations. Yet, the availability of historical data and the analyses on broader spatial scales has often limited the explanatory power of the conducted analyses. Meaningful descriptors of former habitat characteristics and abundant species distribution data are generally sparse, especially for fine scale analyses. However, this situation can be ameliorated by broadening the extent of the study site and the used grain size, as was done in this thesis by considering the whole of Switzerland with its communes. Nevertheless, current monitoring projects and data recording techniques are promising data sources that might allow more detailed analyses about effects of long-term species reactions on landscape changes in the near future. This work, however, also showed the value of historical species distribution data as for example their potential to locate still unknown species occurrences. The results might therefore contribute to further research activities that investigate current and future species distributions considering the immense richness of historical distribution data. Résumé Les paysages changent continuellement. Des farces naturelles comme des pluies violentes ou des feux peuvent avoir une influence durable sur la forme du paysage. Cependant, les changements attribués aux activités humaines ont souvent modelé les paysages plus profondément. Depuis les années 1950 surtout, les pratiques agricoles modernes ou l'expansion des surfaces d'habitat et d'infrastructure ont caractérisé le développement du paysage en Europe de l'Ouest. Ces dernières années, l'homme a commencé à réaliser que beaucoup de changements «naturels » pourraient indirectement résulter de ses propres activités. Le changement de paysage le plus apparent dont nous sommes témoins de nos jours est probablement l'immense retraite des glaciers alpins. Avec les paysages, les habitats des animaux et des plantes ont aussi été exposés à des changements vastes et quelquefois rapides, tenus pour coresponsable de la continuelle diminution de la biodiversité. Cependant, nous savons peu des effets probables de la rapidité des changements du paysage sur la persistance et la disparition des espèces. Le développement et la rapidité du changement de l'utilisation et de la couverture du sol dans les communes suisses entre les années 50 et 90 ont donc été reconstruits au moyen de 10 variables issues des recensements agricoles et résidentiels et ont été corrélés avec des changements de présence des papillons diurnes. Des analyses de groupes (Cluster analyses) ont été utilisées pour détecter des arrangements spatiaux de changements à l'échelle de la Suisse. Des communes avec des changements ou rapidités comparables ont été délimitées pour des décennies séparées et ont été placées en séquence temporelle, en rendrent une certaine dynamique du changement. Les résultats ont montré un remplacement répandu d'une agriculture extensive des pratiques intensives, une forte expansion des faubourgs urbains autour des grandes cités et des transitions vers de plus grandes surfaces d'exploitation dans les Alpes. Dans le cas des exploitations agricoles, des taux de changement croissants ont été observés jusqu'aux années 70, alors que la tendance a généralement été inversée dans les années suivantes. Par contre, la vitesse de construction des nouvelles maisons a montré des courbes positives pendant les 50 années. Les analyses sur la réaction des papillons diurnes ont montré que les espèces des prairies sèches supportaient une grande densité de bétail. Il est possible que dans ces communes beaucoup des prairies sèches aient été fertilisées et utilisées comme pâturages, qui ont une autre composition floristique. De plus, les espèces ont diminué dans les communes caractérisées par une rapide perte des fermes avec une surface cultivable supérieure à 5 ha. Les espèces des marais ont été favorisées dans des communes avec peu de surface cultivable et peu de grandes fermes, mais n'ont pas réagi aux taux de changement. Il en a donc été conclu que la rapidité des changements pourrait expliquer les disparitions d'espèces dans certains cas, mais que les variables prédictives qui expriment des états pourraient être des descripteurs plus importants. Des informations sur la distribution récente des espèces sont importantes par rapport aux mesures pour la conservation de la nature. Pour des autorités occupées à définir des zones de protection prioritaires ou à autoriser des projets de construction, ces informations sont indispensables. Les modèles de distribution spatiale d'espèces sont donc devenus des moyens de décision importants. Les méthodes statistiques courantes comme les modèles linéaires généralisés (GLM) demandent des données de présence et d'absence des espèces. Cependant, souvent seules les données de présence sont disponibles, surtout pour les animaux migrants, rares ou cryptiques comme des papillons ou des reptiles. C'est pourquoi certains modélisateurs ont choisi des absences au hasard, avec le risque d'influencer le résultat en choisissant des fausses absences. Nous avons établi plusieurs stratégies, basées sur des données de distribution historique des papillons diurnes, pour sélectionner des absences plus fiables. Les résultats ont démontré que de meilleurs modèles pouvaient être obtenus lorsque les données proviennent des périodes de temps plus longues. En plus, la performance des modèles a pu être augmentée en considérant des données de distribution à long terme d'espèces qui occupent des habitats similaires à ceux de l'espèce cible. Vu le succès de cette stratégie, elle a été utilisée pour évaluer les effets potentiels des changements de paysage futurs sur la distribution des papillons des prairies sèches et marais, deux habitats qui ont souffert de graves détériorations. Quatre scénarios spatialement explicites, décrivant (i) l'extrapolation des changements de l'utilisation de sol tels qu'observés entre 1985 et 1997, (ii) la libéralisation des marchés agricoles, et une production agricole (iii) légèrement amoindrie et (iv) fortement diminuée, ont été utilisés pour générer des directions de changement probables. Les relations actuelles entre la distribution des espèces et l'environnement ont été déterminées par le biais des modèles statistiques et ont été utilisées pour calculer des probabilités de présence selon les scénarios dans six régions biogéographiques majeures de la Suisse, comportant le Jura, le Plateau, les Alpes du Nord, du Sud, centrales orientales et centrales occidentales. Les résultats principaux ont montré que les espèces des prairies sèches pourraient profiter d'une diminution de la production agricole, mais qu'elles pourraient aussi disparaître à cause de l'embroussaillement des terres ouvertes dû à la libéralisation des marchés agricoles. La probabilité de présence des espèces de marais a décrû à cause d'une perte générale des habitats favorables. De plus, les analyses ont confirmé que des causes humaines comme l'urbanisation, l'abandon des terres ouvertes et l'intensification de l'agriculture affectent actuellement ces espèces. Ainsi ces forces devraient être mieux prises en compte lors de planifications paysagères, pour que ces papillons diurnes puissent survivre dans leurs habitats actuels. Dans ce travail de thèse, des données historiques ont été intensivement utilisées pour reconstruire des développements anciens et pour les rendre utiles à des recherches contemporaines. Cependant, la disponibilité des données historiques et les analyses à grande échelle ont souvent limité le pouvoir explicatif des analyses. Des descripteurs pertinents pour caractériser les habitats anciens et des données suffisantes sur la distribution des espèces sont généralement rares, spécialement pour des analyses à des échelles fores. Cette situation peut être améliorée en augmentant l'étendue du site d'étude et la résolution, comme il a été fait dans cette thèse en considérant toute la Suisse avec ses communes. Cependant, les récents projets de surveillance et les techniques de collecte de données sont des sources prometteuses, qui pourraient permettre des analyses plus détaillés sur les réactions à long terme des espèces aux changements de paysage dans le futur. Ce travail a aussi montré la valeur des anciennes données de distribution, par exemple leur potentiel pour aider à localiser des' présences d'espèces encore inconnues. Les résultats peuvent contribuer à des activités de recherche à venir, qui étudieraient les distributions récentes ou futures d'espèces en considérant l'immense richesse des données de distribution historiques.

Broad-scale adaptive genetic variation in alpine plants is driven by temperature and precipitation.

Identifying adaptive genetic variation is a challenging task, in particular in non-model species for which genomic information is still limited or absent. Here, we studied distribution patterns of amplified fragment length polymorphisms (AFLPs) in response to environmental variation, in 13 alpine plant species consistently sampled across the entire European Alps. Multiple linear regressions were performed between AFLP allele frequencies per site as dependent variables and two categories of independent variables, namely Moran's eigenvector map MEM variables (to account for spatial and unaccounted environmental variation, and historical demographic processes) and environmental variables. These associations allowed the identification of 153 loci of ecological relevance. Univariate regressions between allele frequency and each environmental factor further showed that loci of ecological relevance were mainly correlated with MEM variables. We found that precipitation and temperature were the best environmental predictors, whereas topographic factors were rarely involved in environmental associations. Climatic factors, subject to rapid variation as a result of the current global warming, are known to strongly influence the fate of alpine plants. Our study shows, for the first time for a large number of species, that the same environmental variables are drivers of plant adaptation at the scale of a whole biome, here the European Alps.

Cytochrome b haplotype divergences in West European Apodemus

Sequencing of the cytochrome b mitochondrial gene (732 base pairs) in samples of Apodemus sylvaticus from Central Europe (eastern France, Switzerland, southern Germany and western Austria) revealed significant molecular variation not reflected in previous morphological and genetic studies of this species. A comparison with the sequences (150 bp) of 54 specimens available from GenBank (NCBI) showed that two problematic individuals originating from southern Germany have to be assigned to A. fulvipectus, a species not yet known in western Europe. A. sylvaticus specimens (n = 14) sampled north of the Alps exhibited a maximum intraspecific sequence divergence of about 5.1%, whereas the maximum divergence is much Lower in A. flavicollis (1%, n = 5) and in A. alpicola (0.5%, n = 4), although the samples originate from a similar geographic range of about 350 km. We also found a high rate of erroneously assigned specimens in GenBank, which indicates that the discrimination of Apodemus species remains a problem and requires further investigations.

MIGCLIM: Predicting plant distribution and dispersal in a changing climate

Many studies have forecasted the possible impact of climate change on plant distribution using models based on ecological niche theory. In their basic implementation, niche-based models do not constrain predictions by dispersal limitations. Hence, most niche-based modelling studies published so far have assumed dispersal to be either unlimited or null. However, depending on the rate of climatic change, the landscape fragmentation and the dispersal capabilities of individual species, these assumptions are likely to prove inaccurate, leading to under- or overestimation of future species distributions and yielding large uncertainty between these two extremes. As a result, the concepts of "potentially suitable" and "potentially colonisable" habitat are expected to differ significantly. To quantify to what extent these two concepts can differ, we developed MIGCLIM, a model simulating plant dispersal under climate change and landscape fragmentation scenarios. MIGCLIM implements various parameters, such as dispersal distance, increase in reproductive potential over time, barriers to dispersal or long distance dispersal. Several simulations were run for two virtual species in a study area of the western Swiss Alps, by varying dispersal distance and other parameters. Each simulation covered the hundred-year period 2001-2100 and three different IPCC-based temperature warming scenarios were considered. Our results indicate that: (i) using realistic parameter values, the future potential distributions generated using MIGCLIM can differ significantly (up to more than 95% decrease in colonized surface) from those that ignore dispersal; (ii) this divergence increases both with increasing climate warming and over longer time periods; (iii) the uncertainty associated with the warming scenario can be nearly as large as the one related to dispersal parameters; (iv) accounting for dispersal, even roughly, can importantly reduce uncertainty in projections.

Microsatellite variation reveals low genetic subdivision in a chromosome race of Sorex araneus (Mammalia, Insectivora)

Two hundred and forty-five individuals of the common shrew (Sorex araneus, Insectivora, Mammalia) from 24 sampling localities situated in four different valleys of the western European Alps were genotyped for six microsatellite loci. Allelic variability ranged from 3 to 32 different alleles at a single locus and the average gene diversity over all loci was 0.69. An analysis for F and R statistics revealed weak genetic population subdivision (Fst = 0.032; Rst = 0.016). This suggests considerable gene flow and little phylogeographic structure within and between valleys. We tested whether a stepwise mutation model (SMM) better explained variation at the microsatellite loci than an infinite allele model (IAM). No trend in favor of either model was detected.

Limited genetic diversity and high differentiation among the remnant adder (Vipera berus) populations in the Swiss and French Jura Mountains

Although the adder (Vipera berus) has a large distribution area, this species is particularly threatened in Western Europe due to high habitat fragmentation and human persecution. We developed 13 new microsatellite markers in order to evaluate population structure and genetic diversity in the Swiss and French Jura Mountains, where the species is limited to only a few scattered populations. We found that V. berus exhibits a considerable genetic differentiation among populations (global F-ST = 0.269), even if these are not geographically isolated. Moreover, the genetic diversity within populations in the Jura Mountains and in the less perturbed Swiss Alps is significantly lower than in other French populations, possibly due to post-glacial recolonisation processes. Finally, in order to minimize losses of genetic diversities within isolated populations, suggestions for the conservation of this species in fragmented habitats are proposed.

Paleoenvironmental evolution of the Helvetic shallow-water carbonate platform near the Barremian-Aptian boundary, and its relationship with paleoceanographic and paleoclimatic change in the Tethys

Abstract:During my doctoral research, I focused on deciphering the interactions between sea-level and climate change during the Late Barremian-Early Aptian, their expression in the Tethys basin and in the Helvetic carbonate platform. The research highlights are summarized here in three points: In the Helvetic Alps, the transition between the Lower Schrattenkalk (Upper Barremian) and the Rawil Member (Lowermost Aptian) is characterized by a change from a predominantly photozoan to a heterozoan carbonate-producing system, which coincides in time with a general increase in detrital and nutrient input. The clay mineral record shows the appearance of kaolinite within the Rawil Member, whereas this mineral is absent from the uppermost Lower and lowermost Upper Schrattenkalk Members. This indicates the installation of a warmer and more humid climate during this time period. A negative peak in 513C is recorded at the top of the Lower Schrattenkalk Member, and correlates with the well-known negative excursion of -l%o occurring in other basins and dated as latest Barremian, thus confirming a latest Barremian and earliest Aptian age for the Lower Schrattenkalk and Rawil Members, respectively. Furthermore, a sequence stratigraphie framework has been defined for the Rawil Member, based on both the ecology of faunal and floral assemblages, and their palaeoenvironmental interpretation, as well as on the stacking pattern of limestone beds observed during field prospection. The presence of a sequence boundary is postulated near the top of the Lower Schrattenkalk Member, which is correlated with the earliest Aptian SbAl defined in Vercors (France). The SbAl is characterized by a maximum of proximal assemblages and by the disappearance of several benthic foraminiferal species. Within the Rawil Member itself, the stacking pattern and microfacies trends are interpreted to represent the TST of the first Aptian sequence. With regards to the pelagic setting in the Tethyan realm, I investigated the Gorgo a Cerbara section (central Italy). There, thin organic-rich layers occur episodically in pelagic carbonates of the upper Barremian portion of the Maiolica Formation. They are associated with high Corg:Ptot ratios, which indicate the presence of intermittent dysoxic to anoxic conditions. Coarse correlations are also observed between TOC, Ρ and biogenic silica contents, indicating links between Ρ availability, productivity, and organic matter preservation. The corresponding 813Ccarb and δ180 records remain, however, quite stable, indicating that these brief periods of enhanced TOC preservation did not have sufficient impact on the marine carbon household to deviate 6,3C records, and are probably not the consequence of major climate change. On the other hand, organic-rich layers become more frequent around the Barremian-Aptian boundary in both pelagic and hemi-pelagic environments (Gorgo a Cerbara and La Bédoule, France), which are correlated with negative excursions in 6l3Ccarb and 613Corg records. During the earliest Aptian, at Gorgo a Cerbara, the frequency of organic-rich intervals progressively increases and redox-sensitive trace-element enrichments become more frequent, until the highest TOC-enriched level just below the "Livello Selli", indicator of Oceanic Anoxic Event la (OAEla). The latter is associated with the well-known negative spike in 613Ccarb and S,3Corg records, a diminution in the δ,80 record interpreted as the consequence of a wanning interval, an important peak in Ρ accumulation and high Cor::Ptot ratios indicating the prevalence of anoxic conditions. The Selli Level (OAEla) documents a general cooling phase and coincides with maximum RSTE enrichments as well as high Corg:Ptot ratios, which confirm the importance of anoxic conditions during OAE1 a at this site.During the Early Aptian, environmental change on the platform is expressed by orbitolinids proliferation that may be induced by both climate change and sea-level rise. In the basin, the successive black shales horizons from the Late Barremian until the OAE la are interpreted as the progressive impact of palaeoenvironmental change probably linked to the formation of the Ontong- Java plate-basalt plateau.RésuméCe travail de thèse a permis d'investiguer les interactions entre les variations du niveau marin et les changements climatiques sur la plate-forme helvétique ainsi qu'en domaine pélagique à la limite Barrémien-Aptien (Crétacé).Dans les Alpes helvétiques, la limite Barrémien-Aptien est marquée par la transition du Schrattenkalk inférieur, caractérisé par des carbonates photozaires, au Membre de Rawil caractérisé par des carbonates héterozoaires. Cette transition est marquée par une arrivée massive d'éléments détritiques et un apport de nutriments ayant entraîné la prolifération de foraminifères agglutinés tels que les orbitolines. L'analyse des minéraux argileux indique l'apparition de la kaolinite durant le Membre de Rawil, interprétée comme l'installation d'un climat plus chaud et humide. Un pic négatif en 513C est enregistré au sommet du Schrattenkalk inférieur correspond à l'excursion négative de -1%0 bien connue en domaine pélagique et datée comme Barrémien terminal. Cette corrélation apporte un contrôle chronostratigraphique supplémentaire permettant de dater le Schrattenkalk inférieur du Barrémien sup. et le Membre de Rawil de l'Aptien inf. D'autre part, une étude stratigraphique, basée sur des observations de terrain et sur l'interprétation d'assemblages floristiques et faunistiques en terme de paléoenvironnement a permis de mettre en évidence une limite de séquence au sommet du Schrattenkalk inf., corrélable avec la SbAl définie dans le Vercors. Durant la mise en place du Membre de Rawil, l'évolution des microfaciès est interprétée comme le « Transgressive System Tract » de la première séquence aptienne.En domaine pélagique, de minces couches riches en matière organique (MO) apparaissent dès le Barrémien sup. dans la coupe de Gorgo a Cerbara (Italie). Elles sont associées à un ratio C:P élevé indiquant des conditions épisodiquement dysoxiques à anoxiques. De plus, une corrélation nette entre Carbone Organique Total (TOC), phosphore (P) et silice biogénique est observée correspondant à un lien entre Ρ disponible, productivité et préservation de la MO. Pourtant, dans le même temps, le ÔI3C et le δ1βΟ restent constants indiquant des conditions environnementales stables et un cycle du carbone non perturbé par la préservation de MO qui ne serait pas la conséquence d'un changement climatique global mais juste d'un effet local.Ala limite Barrémien-Aptien, en domaine hémi-pélagique (La Bédoule, France) et pélagique (Gorgo a Cerbara), les couches riches en MO sont plus fréquentes et plus épaisses, elles se sont déposées en même temps qu'un pic négatif en 513CCARB et ô13Coib probablement dû à un épisode volcanique. A l'Aptien inf. le TOC des niveaux riches en MO augmente progressivement en même temps que la teneur en éléments traces jusqu'au dernier enrichissement avant l'événement anoxique océanique la (OAE la) correspondant au « niveau critique inf. », indiquant des conditions anoxiques moins restreintes. Celui-ci est également caractérisé par le fameux pic négatif en Ô13C (C3), une diminution du δ180 interprétée comme un réchauffement, par un pic en Ρ et un ratio C:P élevé. L'OAE 1 a, quant à lui, enregistre un refroidissement et coïncide avec le maximum en éléments traces ainsi qu'un fort ratio C:P mettant en valeur l'importance des conditions anoxiques pendant 1ΌΑΕ la dans cette coupe alors qu'aucune perturbation n'est enregistrés à La Bédoule probablement à cause de conditions paléogéographiques locales.Durant l'Aptien inf., les changements environnementaux sur la plate-forme se marquent par la prolifération d'orbitolines due à un changement climatique et une hausse du niveau marin. En domaine profond, la succession de niveaux riches en MO du Barrémien sup. jusqu'à l'OAE la documente l'impact progressif de changements paléoenvironnementaux, probablement liés à la formation du plateau d'Ontong Java à l'ouest de l'océan Pacifique.

Toarcian radiolaria from Mt. Mangart (Slovenian-Italian border) and their paleoecological implications

Diverse and well-preserved Toarcian radiolarians have been recovered from a succession of organic-rich shale with intercalations of siliceous limestone. The succession is located at the Slovenian-Italian border in the Julian Alps and was deposited on a subsided block pertaining to the south Tethyan passive continental margin. Twenty spumellarian and 17 nassellarian genera were found in total. Thirty-six taxa were identified to species level and one new species, Bistarkum mangartense n. sp., is described. The assemblages show a high predominance of spumellarians over nassellarians. Spongy spumellarians, especially Orbiculiforma ?, are markedly abundant. Pantanelliidae are generally rare but reach a pronounced peak of 13% in one stratigraphic level. Among nassellarians, Parahsuum is the most abundant but members belonging to Syringocapsidae are scarce to absent. In addition to paleolatitude and water column depth, ecological conditions accompanying the early Toarcian global anoxic event may have to a considerable extent determined the specific taxonomic composition of these radiolarian faunas. (C) 2003 Elsevier B.V. All rights reserved.

Improving the prediction of plant species distribution and community composition by adding edaphic to topo-climatic variables

Questions Soil properties have been widely shown to influence plant growth and distribution. However, the degree to which edaphic variables can improve models based on topo-climatic variables is still unclear. In this study, we tested the roles of seven edaphic variables, namely (1) pH; (2) the content of nitrogen and of (3) phosphorus; (4) silt; (5) sand; (6) clay and (7) carbon-to-nitrogen ratio, as predictors of species distribution models in an edaphically heterogeneous landscape. We also tested how the respective influence of these variables in the models is linked to different ecological and functional species characteristics. Location The Western Alps, Switzerland. Methods With four different modelling techniques, we built models for 115 plant species using topo-climatic variables alone and then topo-climatic variables plus each of the seven edaphic variables, one at a time. We evaluated the contribution of each edaphic variable by assessing the change in predictive power of the model. In a second step, we evaluated the importance of the two edaphic variables that yielded the largest increase in predictive power in one final set of models for each species. Third, we explored the change in predictive power and the importance of variables across plant functional groups. Finally, we assessed the influence of the edaphic predictors on the prediction of community composition by stacking the models for all species and comparing the predicted communities with the observed community. Results Among the set of edaphic variables studied, pH and nitrogen content showed the highest contributions to improvement of the predictive power of the models, as well as the predictions of community composition. When considering all topo-climatic and edaphic variables together, pH was the second most important variable after degree-days. The changes in model results caused by edaphic predictors were dependent on species characteristics. The predictions for the species that have a low specific leaf area, and acidophilic preferences, tolerating low soil pH and high humus content, showed the largest improvement by the addition of pH and nitrogen in the model. Conclusions pH was an important predictor variable for explaining species distribution and community composition of the mountain plants considered in our study. pH allowed more precise predictions for acidophilic species. This variable should not be neglected in the construction of species distribution models in areas with contrasting edaphic conditions.

Stratigraphic, sedimentological and palaeoenvironmental constraints on the rise of the Urgonian platform in the western Swiss Jura

Urgonian-type carbonates are a characteristic feature of many late Early Cretaceous shallow-marine, tropical and subtropical environments. The presence of typical photozoan carbonate-producing communities including corals and rudists indicates the prevalence of warm, transparent and presumably oligotrophic conditions in a period otherwise characterized by the high density of globally occurring anoxic episodes. Of particular interest, therefore, is the exploration of relationships between Urgonian platform growth and palaeoceanographic change. In the French and Swiss Jura Mountains, the onset and evolution of the Urgonian platform have been controversially dated, and a correlation with other, better dated, successions is correspondingly difficult. It is for this reason that the stratigraphy and sedimentology of a series of recently exposed sections (Eclepens, Vaumarcus and Neuchatel) and, in addition, the section of the Gorges de l'Areuse were analysed. Calcareous nannofossil biostratigraphy, the evolution of phosphorus contents of bulk rock, a sequence-stratigraphic interpretation and a correlation of drowning unconformities with better dated sections in the Helvetic Alps were used to constrain the age of the Urgonian platform. The sum of the data and field observations suggests the following evolution: during the Hauterivian, important outward and upward growth of a bioclastic and oolitic carbonate platform is documented in two sequences, separated by a phase of platform drowning during the late Early Hauterivian. Following these two phases of platform growth, a second drowning phase occurred during the latest Hauterivian and Early Barremian, which was accompanied by significant platform erosion and sediment reworking. The Late Barremian witnessed the renewed installation of a carbonate platform, which initiated with a phase of oolite production, and which progressively evolved into a typical Urgonian carbonate platform colonized by corals and rudists. This phase terminated at the latest in the middle Early Aptian, due to a further drowning event. The evolution of this particular platform segment is compatible with that of more distal and well-dated segments of the same northern Tethyan platform preserved in the Helvetic zone of the Alps and in the northern subalpine chains (Chartreuse and Vercors).

Phylogenetic relatedness and proboscis length contribute to structuring bumblebee communities in the extremes of abiotic and biotic gradients

Aim To improve our understanding of how biological communities assemble, we investigated changes in bumblebee communities in space along an elevation gradient. We assessed how much deterministic abiotic and biotic factors shape community assembly. We focused on proboscis length (influencing the species' dietary regime) and phylogenetic relatedness to investigate if competition and environmental filtering occur in more and less productive climates, respectively. Location Western Swiss Alps. Methods We recorded bumblebee species in 149 plots along a 1800-m wide elevation gradient. We contrasted two major clades of bumblebees, a short-tongued and a long-tongued clade. We calculated the phylogenetic and proboscis-length diversity of the bumblebee communities and compared these observed data with a random distribution to detect clustering likely to be caused by environmental filtering or overdispersion likely to be caused by competition. We compared the prevalence of clustered and overdispersed communities along the gradients of plant species richness (biotic) and temperature (abiotic). Results Under colder conditions, where plant species richness is lower and floral resources are scarcer, the clade with shorter proboscides prevails over the clade with longer proboscides, and communities are functionally and phylogenetic clustered. Under warmer conditions, we found phylogenetic but not functional overdispersion in communities. Main conclusions We show for the first time a strong correlation between phylogenetic relatedness, proboscis length and species distribution along temperature and plant richness gradients shaping bumblebee communities. The low temperatures and low levels of plant species richness limit the dispersal of the species from the long-tongued clade, which have more specialized diets, into high-elevation areas. Competition under warmer conditions may produce communities composed of less closely related species that share distinct ecological preferences. Our empirical results corroborate theoretical expectation as well as experiments on the prevalence of deterministic processes in the most severe and most productive parts of environmental gradients.

Climate oscillations and species interactions: large-scale congruence but regional differences in the phylogeographic structures of an alpine plant and its monophagous insect

Aim. To predict the fate of alpine interactions involving specialized species, using a monophagous beetle and its host-plant as a case study. Location. The Alps. Methods. We investigated genetic structuring of the herbivorous beetle Oreina gloriosa and its specific host-plant Peucedanum ostruthium. We used genome fingerprinting (in the insect and the plant) and sequence data (in the insect) to compare the distribution of the main gene pools in the two associated species and to estimate divergence time in the insect, a proxy for the temporal origin of the interaction. We quantified the similarity in spatial genetic structures by performing a Procrustes analysis, a tool from the shape theory. Finally, we simulated recolonization of an empty space analogous to the deglaciated Alps just after ice retreat by two lineages from two species showing unbalanced dependence, to examine how timing of the recolonization process, as well as dispersal capacities of associated species, could explain the observed pattern. Results. Contrasting with expectations based on their asymmetrical dependence, patterns in the beetle and plant were congruent at a large scale. Exceptions occurred at a regional scale in areas of admixture, matching known suture zones in Alpine plants. Simulations using a lattice-based model suggested these empirical patterns arose during or soon after recolonization, long after the estimated origin of the interaction c. 0.5 million years ago. Main conclusions. Species-specific interactions are scarce in alpine habitats because glacial cycles have limited opportunities for coevolution. Their fate, however, remains uncertain under climate change. Here we show that whereas most dispersal routes are paralleled at large scale, regional incongruence implies that the destinies of the species might differ under changing climate. This may be a consequence of the host-dependence of the beetle that locally limits the establishment of dispersing insects.

Ambient seismic noise monitoring of a clay landslide: Toward failure prediction

Given that clay-rich landslides may become mobilized, leading to rapid mass movements (earthflows and debris flows), they pose critical problems in risk management worldwide. The most widely proposed mechanism leading to such flow-like movements is the increase in water pore pressure in the sliding mass, generating partial or complete liquefaction. This solid-to-liquid transition results in a dramatic reduction of mechanical rigidity in the liquefied zones, which could be detected by monitoring shear wave velocity variations. With this purpose in mind, the ambient seismic noise correlation technique has been applied to measure the variation in the seismic surface wave velocity in the Pont Bourquin landslide (Swiss Alps). This small but active composite earthslide-earthflow was equipped with continuously recording seismic sensors during spring and summer 2010. An earthslide of a few thousand cubic meters was triggered in mid-August 2010, after a rainy period. This article shows that the seismic velocity of the sliding material, measured from daily noise correlograms, decreased continuously and rapidly for several days prior to the catastrophic event. From a spectral analysis of the velocity decrease, it was possible to determine the location of the change at the base of the sliding layer. These results demonstrate that ambient seismic noise can be used to detect rigidity variations before failure and could potentially be used to predict landslides.