New species of Miradiscops (Gastropoda: Scolodontidae) from Martinique

Only 17 endemic land snail species are known so far on the Lesser Antillean island of Martinique, most of which are macrogastropods that are easily visible, and thus, easily collectable. On the other hand, species of microgastropods remain undersampled and overlooked. Based on recently collected shells from Mount Vauclin, we describe a new species of Scolodontidae, Miradiscops madinina sp. nov. from Martinique. This is the first recorded incidence of Miradiscops stricto sensu from the volcanic arc of the Lesser Antilles, as well as the second species of Scolodontidae recorded from Martinique. This emphasises the importance of Mount Vauclin as a home to endemic invertebrates on the island and the need for collection efforts that includes soil and leaf litter sampling

Biogeographic comparisons of herbivore attack, growth and impact of Japanese knotweed between Japan and France

International audienceTo shed light on the process of how exotic species become invasive, it is necessary to study them both in their native and non-native ranges. Our intent was to measure differences in herbivory, plant growth and the impact on other species in Fallopia japonica in its native and non-native ranges. We performed a cross-range full descriptive, field study in Japan (native range) and France (non-native range). We assessed DNA ploidy levels, the presence of phytophagous enemies, the amount of leaf damage, several growth parameters and the co-occurrence of Fallopia japonica with other plant species of herbaceous communities.Invasive Fallopia japonica plants were all octoploid, a ploidy level we did not encounter in the native range, where plants were all tetraploid. Octoploids in France harboured far less phytophagous enemies, suffered much lower levels of herbivory, grew larger and had a much stronger impact on plant communities than tetraploid conspecifics in the native range in Japan. Our data confirm that Fallopia japonica performs better-plant vigour and dominance in the her-baceous community-in its non-native than its native range. Because we could not find octoploids in the native range, we cannot separate the effects of differences in ploidy from other biogeographic factors. To go further, common garden experiments would now be needed to disentangle the proper role of each factor, taking into account the ploidy levels of plants in their native and non-native ranges. Synthesis. As the process by which invasive plants successfully invade ecosystems in their non-native range is probably multifactorial in most cases, examining several components-plant growth, herbivory load, impact on recipient systems-of plant invasions through biogeographic comparisons is important. Our study contributes towards filling this gap in the research, and it is hoped that this method will spread in invasion ecology, making such an approach more common

Anthropogenic extinction of Pacific land snails: a case study of Rurutu, French Polynesia, with description of eight new species of endodontids (Pulmonata).

Faunistic surveys are fundamental in the conservation of land mollusks, particularly as a means of achieving accurate estimates of species richness and levels of extinction of endangered taxa. The family Endodontidae comprises one of the most diverse groups of indigenous land snails of Pacific Islands. Due to anthropogenic degradation of their habitats, most members of the family are now extinct or severely endangered. In Rurutu, French Polynesia, 11 species of Endodontidae were previously described (10 endemics), but only 1 is known to have been extant during the first half of the 20th Century. Extensive collections made in Rurutu in 2003 recovered only empty shells of these 11 species, as well as of an additional 8 endemic species of endodontids not known to previous investigators: Australdonta oheatora sp. nov., A. anneae sp. nov., A. sibleti sp. nov., A. florencei sp. nov., A. pakalolo sp. nov., A. teaae sp. nov., Minidonta boucheti sp. nov. and M. bieleri sp. nov. The radiation of endodontids in Rurutu was thus much larger than previously envisaged. However, we hypothesize that all species of the family are now extinct in the island

Radiation and decline of endodontid land snails in Makatea, French Polynesia.

The family Endodontidae Pilsbry, 1895 comprised one of the most diverse groups of indigenous land snails of Pacific Islands. However, due to anthropogenic degradation of their habitats and predation by or competition with introduced species, most members of the family are now extinct or severely endangered. Based on limited and sporadic collections, the endodontid fauna of the raised coral island of Makatea in the western Tuamotu Archipelago was known to consist of four valid species, Mautodontha (Mautodontha) daedalea (Gould, 1846), Kleokyphus callimus Solem, 1976, K. hypsus Solem, 1976 and Pseudolibera lillianae Solem, 1976, the last three of which were endemic. To these, we add 18 new species based on a reappraisal of museum collections and analysis of abundant new material collected in 2005: M. (M.) domaneschii, M. (M.) virginiae, M. (M.) harperae, M. (Garrettoconcha) aurora, M. (G.) occidentalis, M. (G.) temaoensis, M. (G.) makateaensis, M. (G.) passosi, M. (G.) spelunca, K. cowiei, P. solemi, P. matthieui, P. cookei, P. aubertdelaruei, P. extincta, P. paraminderae, P. elieporoii, and P. parva. The recently collected material also revealed new information on the morphology, intraspecific variation and distribution of the four previously known species, which are here revised and re-described. With 22 recognized taxa, the radiation of endodontids in Makatea is second in species richness only to that of Rapa Iti in the Austral Islands, from where 24 endodontids have been described. Despite intensive field work in Makatea in 2005, only M. (M.) daedalea was found alive. All other Makatean endodontids were represented solely by empty and worn shells and are probably extinct.

Integration of Web APIs and Linked Data Using SPARQL Micro-Services - Application to Biodiversity Use Cases

International audienceIn recent years, Web APIs have become a de facto standard for exchanging machine-readable data on the Web. Despite this success, however, they often fail in making resource descriptions interoperable due to the fact that they rely on proprietary vocabularies that lack formal semantics.The Linked Data principles similarly seek the massive publication of data on the Web, yet with the specific goal of ensuring semantic interoperability.Given their complementary goals, it is commonly admitted that cross-fertilization could stem from the automatic combination of Linked Data and Web APIs. Towards this goal, in this paper we leverage the micro-service architectural principles to define a SPARQL Micro-Service architecture, aimed at querying Web APIs using SPARQL. A SPARQL micro-service is a lightweight SPARQL endpoint that provides access to a small, resource-centric, virtual graph. In this context, we argue that full SPARQL Query expressiveness can be supported efficiently without jeopardizing servers availability.Furthermore, we demonstrate how this architecture can be used to dynamically assign dereferenceable URIs to Web API resources that do not have URIs beforehand, thus literally “bringing” Web APIs into the Web of Data. We believe that the emergence of an ecosystem of SPARQL micro-services published by independent providers would enable Linked Data-based applications to easily glean pieces of data from a wealth of distributed, scalable, and reliable services. We describe a working prototype implementation and we finally illustrate the use of SPARQL micro-services in the context of two real-life use cases related to the biodiversity domain, developed in collaboration with the French National Museum of Natural History

Unleash the Potential of your Website! 180,000 webpages from the French Natural History Museum marked up with Bioschemas/Schema.org biodiversity types

International audienceThe challenge of finding, retrieving and making sense of biodiversity data is being tackled by many different approaches. Projects like the Global Biodiversity Information Facility (GBIF) or Encyclopedia of Life (EoL) adopt an integrative approach where they republish, in a uniform manner, records aggregated from multiple data sources. With this centralized, siloed approach, such projects stand as powerful one-stop shops, but tend to reduce the visibility of other data sources that are not (yet) aggregated. At the other end of the spectrum, the Web of Data promotes the building of a global, distributed knowledge graph consisting of datasets published by independent institutions according to the Linked Open Data principles (Heath and Bizer 2011), such as Wikidata or DBpedia. Beyond these "sophisticated" infrastructures, websites remain the most common way of publishing and sharing scientific data at low cost. Thanks to web search engines, everyone can discover webpages. Yet, the summaries provided in results lists are often insufficiently informative to decide whether a web page is relevant with respect to some research interests, such that integrating data published by a wealth of websites is hardly possible. A strategy around this issue lies in annotating websites with structured, semantic metadata such as the Schema.org vocabulary (Guha et al. 2015). Webpages typically embed Schema.org annotations in the form of markup data (written in the RDFa or JSON-LD formats), which search engines harvest and exploit to improve ranking and provide more informative summarization.Bioschemas is a community effort working to extend Schema.org to support markup for Life Sciences websites (Michel and The Bioschemas Community 2018, Garcia et al. 2017). Bioschemas primarily re-uses existing terms from Schema.org, occasionally re-uses terms from third-party vocabularies, and when necessary proposes new terms to be endorsed by Schema.org. As of today, Bioschemas's biodiversity group has proposed the Taxon type*1 to support the annotation of any webpage denoting taxa, TaxonName to support more specifically the annotation of taxonomic names registries, and guidelines describing how to leverage existing vocabularies such as Darwin Core terms.To proceed further, the biodiversity community must now demonstrate its interest in having these terms endorsed by Schema.org: (1) through a critical mass of live markup deployments, and (2) by the development of applications capable of exploiting this markup data.Therefore, as a first step, the French National Museum of Natural History has marked up its natural heritage inventory website: over 180,000 webpages describing the species inventoried in French territories have been annotated with the Taxon and TaxonName types in the form of JSON-LD scripts (see example scripts). As an example, one can check the source of the Delphinus delphis page.In this presentation, by demonstrating that marking up existing webpages can be very inexpensive, we wish to encourage the biodiversity community to adopt this practice, engage in the discussion about biodiversity-related markup, and possibly propose new terms related e.g. to traits or collections. We believe that generalizing the use of such markup by the many websites reporting checklists, museum collections, occurrences, life traits etc. shall be a major step towards the generalized adoption of FAIR*2 principles (Wilkinson 2016), shall dramatically improve information discovery using search engines, and shall be a key accelerator for the development of novel, web-scale, biodiversity data integration scenarios

A Model to Represent Nomenclatural and Taxonomic Information as Linked Data. Application to the French Taxonomic Register, TAXREF

International audienceTaxonomic registers are key tools to help us comprehend the diversity of nature. Publishing such registers in the Web of Data, following the standards and best practices of Linked Open Data (LOD), is a way of integrating multiple data sources into a world-scale, biological knowledge base. In this paper, we present an ongoing work aimed at the publication of TAXREF, the French national taxonomic register, on the Web of Data. Far beyond the mere translation of the TAXREF database into LOD standards, we show that the key point of this endeavor is the design of a model capable of capturing the two coexisting yet distinct realities underlying taxonomic registers, namely the nomenclature (the rules for naming biological entities) and the taxonomy (the description and characterization of these biological entities). We first analyze different modelling choices made to represent some international taxonomic registers as LOD, and we underline the issues that arise from these differences. Then, we propose a model aimed to tackle these issues. This model separates nomenclature from taxonomy, it is flexible enough to accommodate the ever-changing scientific consensus on taxonomy, and it adheres to the philosophy underpinning the Semantic Web standards. Finally, using the example of TAXREF, we show that the model enables interlinking with third-party LOD data sets, may they represent nomenclatural or taxonomic information

TAXREF-LD: A Reference Thesaurus for Biodiversity on the Web of Linked Data

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