Genetic differentiation in the soil-feeding termite Cubitermes sp. affinis subarquatus: occurrence of cryptic species revealed by nuclear and mitochondrial markers

BACKGROUND: Soil-feeding termites are particularly interesting models for studying the effects of fragmentation, a natural or anthropic phenomenon described as promoting genetic differentiation. However, studying the link between fragmentation and genetics requires a method for identifying species unambiguously, especially when morphological diagnostic characters are lacking. In humivorous termites, which contribute to the fertility of tropical soils, molecular taxonomy and phylogenetic relationships are rarely studied, though mitochondrial and nuclear molecular markers are widely used in studies of pest termites. Here, we attempt to clarify the taxonomy of soil-feeding colonies collected throughout the naturally fragmented Lopé Reserve area (Gabon) and morphologically affiliated to Cubitermes sp. affinis subarquatus. The mitochondrial gene of cytochrome oxidase II (COII), the second nuclear rDNA internal transcribed spacer (ITS2) and five microsatellites were analyzed in 19 colonies. RESULTS: Bayesian Inference, Maximum Likelihood and Maximum Parsimony phylogenetic analyses, which were applied to the COII and ITS2 sequences, and Neighbor-Joining reconstructions, applied to the microsatellite data, reveal four major lineages in the Cubitermes sp. affinis subarquatus colonies. The concordant genealogical pattern of these unlinked markers strongly supports the existence of four cryptic species. Three are sympatric in the Reserve and are probably able to disperse within a mosaic of forests of variable ages and savannahs. One is limited to a very restricted gallery forest patch located in the North, outside the Reserve. CONCLUSION: Our survey highlights the value of combined mitochondrial and nuclear markers for exploring unknown groups such as soil-feeding termites, and their relevance for resolving the taxonomy of organisms with ambiguous morphological diagnostic characters

Distinguer/Expliciter. L’ontologie du Web comme ontologie

Distinguishing/ Making Explicit. Web Ontology as Ontology of Operations. By taking seriously the “ empirical metaphysics” contained in the architecture of the Web, our goal is to grasp the kind of entities it came to distinguish. Yet, such distinctions are not understood as classical philosophical distinctions. Indeed, the work accomplished by the Web architects belongs to engineering. For that reason, we outline a processually-based approach to ontology. It embeds the very operations of distinction and explicitation through which ontological types are made to emerge. We then relate this first sketch to a variety of examples picked up from the first part, dealing with folksonomies, computer ontologies and the very principles behind the architecture of the Web. Therefrom, we take into account the plurality of the modes of access on the Web on a broader scale in order to extend our previous developments on the ontological dynamics though which new distinctions are made explicit. A model is laid down which draws from Robert Stalnaker’s two-dimensional semantics, generalized on a multi-dimensional level and reshaped so as to escape the exclusive focus on the notion of truth.Prenant au sérieux la «métaphysique empirique » de l’architecture du Web, nous entendons saisir les entités qu’elle distingue. Il ne s’agit donc pas de reconduire ainsi des distinctions classiques. Le travail réalisé par les architectes du Web ressortit à l’ingénierie. Pour cette raison, nous posons les linéaments d’une approche processuelle de l’ontologie, intégrant en son sein les opérations de distinction et d’explicitation qui conduisent à faire émerger des types ontologiques. Cette réflexion est rapportée à plusieurs exemples abordés au cours de la première partie, des folksonomies aux ontologies informatiques, en passant par les principes architecturaux du Web. Enfin, nous prenons en compte la pluralité des modalités d’accès afin d’étendre à l’échelle du Web tout entier la réflexion sur la dynamique ontologique au cours de laquelle surgissent de nouvelles distinctions. Un pour rendre compte de la sémantique des URI est suggéré qui s’appuie sur la sémantique bi-dimensionnelle de Robert Stalnaker, étendue à la multi-dimensionnalité et repensée dans une optique dégagée de son ancrage exclusif dans la question du vrai.Monnin Alexandre, Livet Pierre. Distinguer/Expliciter. L’ontologie du Web comme ontologie. In: Intellectica. Revue de l'Association pour la Recherche Cognitive, n°61, 2014/1. Philosophie du Web et Ingénierie des Connaissances. pp. 59-104

Distinguer/Expliciter. L'ontologie du Web comme ontologie "d'opérations"

International audienceThis paper purports to be an ontological inquiry about ontologies. By taking seriously the “empirical metaphysics” contained in the architecture of the Web, our goal is to grasp the kind of entities it came to distinguish. A necessary step in order to contextualize computer ontologies with regards to their technical surrounding and its architectural constrains. Yet, such distinctions are not understood as classically analytic or synthetic a priori ones. Indeed, the work accomplished by the Web architects belongs to engineering. For that reason, we outline a processually-based approach to ontology, no longer dualistic but rather triadic. It embeds the very operations of distinction and explicitation through which ontological types are made to emerge. We then relate this first sketch to a variety of examples picked up from the first part, dealing with folksonomies, computer ontologies and the very principles behind the architecture of the Web. Therefrom, , we take into account the plurality of the modes of access on the Web on a broader scale in order to extend our previous developments on the ontological dynamics though new distinctions are made explicit. A model is laid down which draws from Robert Stalnaker’s two-dimensional semantics, in its generalized multi-dimensional version, reshaped in order to escape its being focused on the notion of truth.Prenant au sérieux la « métaphysique empirique » de l’architecture du Web, nous entendons saisir les entités qu’elle distingue. Il ne s’agit donc pas de reconduire ainsi des distinctions classiques. Le travail réalisé par les architectes du Web ressortit à l’ingénierie. Pour cette raison, nous posons les linéaments d’une approche processuelle de l’ontologie, intégrant en son sein les opérations de distinction et d’explicitation qui conduisent à faire émerger des types ontologiques. Cette réflexion est rapportée à plusieurs exemples abordés au cours de la première partie, des folksonomies aux ontologies informatiques, en passant par les principes architecturaux du Web. Enfin, nous prenons en compte la pluralité des modalités d’accès afin d’étendre à l’échelle du Web tout entier la réflexion sur la dynamique ontologique au cours de laquelle surgissent de nouvelles distinctions. Un pour rendre compte de la sémantique des URI est suggéré qui s’appuie sur la sémantique bi-dimensionnelle de Robert Stalnaker, étendue à la multi-dimensionnalité et repensée dans une optique dégagée de son ancrage exclusif dans la question du vrai

Modélisation des systèmes physiques de production pour l'évaluation des coûts des activités

Notre étude s'intéresse à l'utilisation et l'exploitation des concepts de ressource et d'activité. Ces notions sont utilisées communément par les ingénieurs et les gestionnaires dans le but d'améliorer les performances des systèmes de production ou de le mesurer financièrement. Malheureusement, l'exploitation pratique de ces concepts se heurte à une difficulté commune aux deux domaines : quantifier les activités. De plus, l'absence de langage commun entre ingénieur et gestionnaire nuie à la liaison entre la vue activité des ingénieurs (vision micro) et la vue coût des gestionnaires (vision macro). Notre travail a contribué, dans un premier temps, à concevoir selon les canons de la modélisation d'entreprise, un modèle de référence qui constituait un chaînon manquant de la fonction lexicologique d'un langage commun. Les manques constatés sur l'existence de démarche concrète exploitant un modèle de référence pour évaluer un système ont abouti à notre seconde contribution : une démarche d'instanciation de notre modèle de référence en un modèle particulier. Enfin, notre objectif étant la quantification des activités, la troisième contribution porte sur une démarche de mesure du modèle particulier, intégrable aux méthodes de conception et d 'évaluation à base d'activités. Nous avons montré diverses applications possibles reposant sur la combinaison des modèles et démarches présentés.Our study concerns the use and exploitation of the resource and activity concepts used in design of a production system. These two concepts are used by engineers and managers in order to improve efficiency of production systems or to measure its financial performance. Unfortunately, the convenient exploitation of these two concepts is confronted to a common difficulty of the both fields : quantify activities. Moreover, because of the absence of common language between engineers and managers, it isn't possible to link the engineer's activity view (micro view) and the manager's cost view (macro view). These both views are however essential to quantify activities. Our work proposes a reference model based on the rules of enterprise modeling. This one constitutes the missing link for a common language and the bridge between a generic model and a particular model. Then we propose an instantiation approach to transform the reference model in a particular model. Finally, in order to quantify the activities, we propose a measure approach of the particular model, which can for example be integrated to activities based costing methods. We illustrate our approach with an industrial example.STRASBOURG-Sc. et Techniques (674822102) / SudocSudocFranceF

Evaluer un système de production à l'aide d'un modèle de référence basé sur l'activity based costing

International audienceLa maîtrise de l'évaluation des coûts de production est devenue une nécessité pour les entreprises contemporaines. Depuis plusieurs décennies, la méthode ABC (Activity Based Casting) propose une solution pour répartir les coûts indirects de production à l'aide du concept d'inducteur de coût. Cependant la méthode ABC ne propose pas de critères généraux pour identifier les inducteurs de coût pertinents. Un nouveau principe de résolution basé sur l'utilisation d'un modèle de référence est proposé dans cet article dans le cas particulier des systèmes de production. Ce modèle tient compte simultanément de l'ensemble des inducteurs de coût sans pour autant complexifier l'utilisation de la méthode ABC. Une application industrielle illustre l'utilisation et l'intérêt de ce modèle

Genetic differentiation in the soil-feeding termite <it>Cubitermes </it>sp. <it>affinis subarquatus</it>: occurrence of cryptic species revealed by nuclear and mitochondrial markers

Abstract Background Soil-feeding termites are particularly interesting models for studying the effects of fragmentation, a natural or anthropic phenomenon described as promoting genetic differentiation. However, studying the link between fragmentation and genetics requires a method for identifying species unambiguously, especially when morphological diagnostic characters are lacking. In humivorous termites, which contribute to the fertility of tropical soils, molecular taxonomy and phylogenetic relationships are rarely studied, though mitochondrial and nuclear molecular markers are widely used in studies of pest termites. Here, we attempt to clarify the taxonomy of soil-feeding colonies collected throughout the naturally fragmented Lopé Reserve area (Gabon) and morphologically affiliated to Cubitermes sp. affinis subarquatus. The mitochondrial gene of cytochrome oxidase II (COII), the second nuclear rDNA internal transcribed spacer (ITS2) and five microsatellites were analyzed in 19 colonies. Results Bayesian Inference, Maximum Likelihood and Maximum Parsimony phylogenetic analyses, which were applied to the COII and ITS2 sequences, and Neighbor-Joining reconstructions, applied to the microsatellite data, reveal four major lineages in the Cubitermes sp. affinis subarquatus colonies. The concordant genealogical pattern of these unlinked markers strongly supports the existence of four cryptic species. Three are sympatric in the Reserve and are probably able to disperse within a mosaic of forests of variable ages and savannahs. One is limited to a very restricted gallery forest patch located in the North, outside the Reserve. Conclusion Our survey highlights the value of combined mitochondrial and nuclear markers for exploring unknown groups such as soil-feeding termites, and their relevance for resolving the taxonomy of organisms with ambiguous morphological diagnostic characters.</p

Positive Effect of Ecological Restoration with Fabaceous Species on Microbial Activities of Former Guyanese Mining Sites

Understanding ecological trajectories after mine site rehabilitation is essential to develop relevant protocols adapted for gold mining sites. This study describes the influence of a range of mine site rehabilitation and revegetation protocols on soil physicochemical parameters and microbial activities related to carbon, nitrogen and phosphorus cycles. We sampled soil from six rehabilitated mining sites in French Guiana with different plant cover (herbaceous, Cyperaceous, monoculture of Clitoria racemosa and Acacia mangium and association of C. racemosa and A. mangium). We measured the mineralization potential of organic matter by estimating the mineralization of carbon, nitrogen and phosphorus and the microbial catabolic diversity balance. The results showed an improvement in the quality of organic matter on revegetated sites with tree cover. On restored sites with fabaceous species, the microbial biomass is three times higher than non-restored sites, improving the rates of organic matter mineralization and restoring the catabolic diversity to the level of natural Guyanese soils. These results confirm that the establishment of fabaceous species under controlled conditions significantly improves the restoration of microbial communities in mining soils

Isolation of polymorphic microsatellite markers in Aporrectodea icterica (Savigny 1826)

International audienceEarthworms play a major role in soil dynamics acting as modifiers of properties and soil characteristics. Although population genetics is a promising approach to get a better understanding of their ecology, the use of molecular tools in earthworm studies is still scarce. Here, we developed and analyzed seven microsatellite loci for Aporrectodea icterica, a common endogeic species of most temperate natural and agricultural soils, with the aim to investigate its dispersal capacity in further researches. Although sequences of a fragment of the mitochondrial gene cytochrome oxidase subunit I (COI) showed the existence of two mitochondrial lineages within the species, with a mean divergence between them of 10%, microsatellite data proved that these two COI lineages are interbreeding and form part of a single species

Influence of Ecological Restoration on Mercury Mobility and Microbial Activities on Former Guyanese Mining Sites

As rehabilitation efforts in Guyana are recent, there is little information on the effect of different ecological rehabilitation protocols for Guyana's mining sites on biogeochemical cycles and mercury mobility. This study was conducted to assess the impact of different ecological restoration protocols on soil quality with the use of soil microbial indicators and by estimating the mercury mobility. We sampled soil from six rehabilitated mining sites in French Guyana with different ecological restoration procedures. We carried out measurements of enzymatic activities and an analysis of mercury environmental speciation to assess its potential toxicity according to a mobility gradient. The results obtained in this study show that the rehabilitation of mining sites has been carried out in a heterogeneous manner and soil quality is very variable, even in nearby sites. Sites that have been rehabilitated with fabaceous species have positive soil quality indicators. In addition, the results highlight a change in mercury mobility that is 82.1% correlated after co-inertia analysis with soil texture properties, which also confirms a direct effect of rehabilitation on mercury mobility. The non-restored sites had a much higher potential of mercury mobility and toxicity than the sites where ecological restoration was successful. These results highlight the positive effect of controlled rehabilitation and ecological restoration on microbiological activities and the potential toxicity of mercury