For all researches, please visit our "Peer-reviewed publications" page.
De Pooter D, Appeltans W, Bailly N, Bristol S, Deneudt K, Eliezer M et al. (2017)
Toward a new data standard for combined marine biological and environmental datasets - expanding OBIS beyond species occurrences
Biodiversity Data Journal 5 e10989.
The Ocean Biogeographic Information System (OBIS) is the world’s most comprehensive online, open-access database of marine species distributions. OBIS grows with millions of new species observations every year. Contributions come from a network of hundreds of institutions, projects and individuals with common goals: to build a scientific knowledge base that is open to the public for scientific discovery and exploration and to detect trends and changes that inform society as essential elements in conservation management and sustainable development. Until now, OBIS has focused solely on the collection of biogeographic data (the presence of marine species in space and time) and operated with optimized data flows, quality control procedures and data standards specifically targeted to these data. Based on requirements from the growing OBIS community to manage datasets that combine biological, physical and chemical measurements, the OBIS-ENV-DATA pilot project was launched to develop a proposed standard and guidelines to make sure these combined datasets can stay together and are not, as is often the case, split and sent to different repositories. The proposal in this paper allows for the management of sampling methodology, animal tracking and telemetry data, biological measurements (e.g., body length, percent live cover, ...) as well as environmental measurements such as nutrient concentrations, sediment characteristics or other abiotic parameters measured during sampling to characterize the environment from which biogeographic data was collected. The recommended practice builds on the Darwin Core Archive (DwC-A) standard and on practices adopted by the Global Biodiversity Information Facility (GBIF). It consists of a DwC Event Core in combination with a DwC Occurrence Extension and a proposed enhancement to the DwC MeasurementOrFact Extension. This new structure enables the linkage of measurements or facts - quantitative and qualitative properties - to both sampling events and species occurrences, and includes additional fields for property standardization. We also embrace the use of the new parentEventID DwC term, which enables the creation of a sampling event hierarchy. We believe that the adoption of this recommended practice as a new data standard for managing and sharing biological and associated environmental datasets by IODE and the wider international scientific community would be key to improving the effectiveness of the knowledge base, and will enhance integration and management of critical data needed to understand ecological and biological processes in the ocean, and on land.
Keywords: Darwin Core Archive, data standardisation, ecosystem data, environmental data, oceanographic data, sample event, species occurrence, telemetry data
Calderón L, Campagna L, Wilke T, Lormee H, Eraud C, Dunn J et al. (2016)
Genomic evidence of demographic fluctuations and lack of genetic structure across flyways in a long distance migrant, the European turtle dove
BMC Evolutionary Biology 16(1) 237.
Understanding how past climatic oscillations have affected organismic evolution will help predict the impact that current climate change has on living organisms. The European turtle dove, Streptopelia turtur, is a warm-temperature adapted species and a long distance migrant that uses multiple flyways to move between Europe and Africa. Despite being abundant, it is categorized as vulnerable because of a long-term demographic decline. We studied the demographic history and population genetic structure of the European turtle dove using genomic data and mitochondrial DNA sequences from individuals sampled across Europe, and performing paleoclimatic niche modelling simulations. Overall our data suggest that this species is panmictic across Europe, and is not genetically structured across flyways. We found the genetic signatures of demographic fluctuations, inferring an effective population size (Ne) expansion that occurred between the late Pleistocene and early Holocene, followed by a decrease in the Ne that started between the mid Holocene and the present. Our niche modelling analyses suggest that the variations in the Ne are coincident with recent changes in the availability of suitable habitat. We argue that the European turtle dove is prone to undergo demographic fluctuations, a trait that makes it sensitive to anthropogenic impacts, especially when its numbers are decreasing. Also, considering the lack of genetic structure, we suggest all populations across Europe are equally relevant for conservation.
Keywords: Climate change, Conservation, Demography, Genomics, Migratory birds, Paleoclimatic, Population genetic structure, niche modelling
Coro G, Magliozzi C, Vanden Berghe E, Bailly N, Ellenbroek A, Pagano P (2016)
Ecological Modelling 323 61-76.
Estimating absence locations of a species is important in conservation biology and conservation planning. For instance, using reliable absence as much as presence information, species distribution models can enhance their performance and produce more accurate predictions of the distribution of a species. Unfortunately, estimating reliable absence locations is difficult and often requires a deep knowledge of the species’ distribution and of its abiotic and biotic environmental preferences and tolerance. In this paper, we propose a methodology to reconstruct reliable absence information from presence-only information, and the conditions that those presence-only data have to meet to make this possible. Large species occurrence data collections (otherwise called occurrence datasets) contain high quality and expert-reviewed species observation records from scientific surveys. These surveys can be used to retrieve species presence locations, but they also record places where the species in their target list were not observed. Although these absences could be simply due to sampling variation, it is possible to intersect many of these reports to estimate true absence locations, i.e. those due to habitat unsuitability or geographical hindrances. In this paper, we present a method to generate reliable absence locations of this type for marine species, using scientific surveys reports contained in the Ocean Biogeographic Information System (OBIS), an authoritative species occurrence dataset. Our method spatially aggregates information from surveys focussing on the same target species. It detects absence locations for a given species as those locations in which repeated surveys (that included the species of interest in their target list) reported information only on other species. We qualitatively demonstrate the reliability of our method using distribution records of the Atlantic cod as a case study. Additionally, we quantitatively estimate its performance using another authoritative large species occurrence dataset, the Global Biodiversity Information Facility (GBIF). We also demonstrate that our approach has higher accuracy and presents complementary behaviour with respect to another method using environmental envelopes. Our process can support species distribution models (as well as other types of models, e.g. climate change models) by providing reliable data to presence/absence approaches. It can manage regional as well as global scale scenarios and runs within a collaborative e-Infrastructure (D4Science) that publishes it as-a-Service, allowing biologists to reproduce, repeat and share experimental results.
Keywords: Absence locations, Ecological niche modelling, Marine biodiversity, Occurrence data, Scientific surveys, Species distribution maps
Katsanevakis S, Tempera F, Teixeira H (2016)
Diversity and Distributions.
Aim To develop a standardized, quantitative method for mapping cumulative impacts of invasive alien species on marine ecosystems. Location The methodology is applied in the Mediterranean Sea but is widely applicable. Methods A conservative additive model was developed to account for the Cumulative IMPacts of invasive ALien species (CIMPAL) on marine ecosystems. According to this model, cumulative impact scores are estimated on the basis of the distributions of invasive species and ecosystems, and both the reported magnitude of ecological impacts and the strength of such evidence. In the Mediterranean Sea case study, the magnitude of impact was estimated for every combination of 60 invasive species and 13 habitats, for every 10 × 10 km cell of the basin. Invasive species were ranked based on their contribution to the cumulative impact score across the Mediterranean. Results The CIMPAL index showed strong spatial heterogeneity. Spatial patterns varied depending on the pathway of initial introduction of the invasive species in the Mediterranean Sea. Species introduced by shipping gave the highest impact scores and impacted a much larger area than those introduced by aquaculture and the Suez Canal. Overall, invasive macroalgae had the highest impact among all taxonomic groups. These results represent the current best estimate of the spatial variation in impacts of invasive alien species on ecosystems, in the Mediterranean Sea. Main Conclusions A framework for mapping cumulative impacts of invasive alien species was developed. The application of this framework in the Mediterranean Sea provided a baseline that can be built upon with future improved information. Such analysis allows the identification of hotspots of highly impacted areas, and prioritization of sites, pathways and species for management actions.
Keywords: CIMPAL, biological invasions, cumulative impacts, indicators, invasive alien species, pathways
Badieritakis E, Thanopoulos R, Fantinou A, Emmanouel N (2015)
A qualitative and quantitative study of thrips (Thysanoptera) on alfalfa and records of thrips species on cultivated and wild Medicago species of Greece
Foliage and litter samples of twelve Medicago species (medics) (Fabaceae) were collected for the study of Thysanoptera from mainland and insular Greece between 2007-2013. The species composition, population dynamics and spatial distribution of thrips were also evaluated based on two similarly managed experimental plots, except the number of cuttings, within an alfalfa hay field in Kopais Valley (Central Greece) between 2007-2008. Nine thrips species were recorded from nine medics, two of which (Pseudodendrothrips mori and Sericothrips bicornis) are new to the Greek fauna. Eight species of Thysanoptera were recorded on alfalfa and five species in the rest of the medics, among which Medicago strasseri is an endemic shrub of Crete. Data regarding the quantitative part of the study demonstrated that Frankliniella occidentalis, which was the most abundant thrips species in both plots, presented a seasonal pattern of population fluctuation and also tended to aggregate. The mean population density of this species significantly differed between the above-mentioned plots, but no such a difference was estimated for the larvae of Thripidae.
Keywords: Greece, Medicago, Thysanoptera, population dynamics, spatial distribution
Crowl A, Visger C, Mansion G, Hand R, Wu H, Kamari G et al. (2015)
Evolution and biogeography of the endemic Roucela complex (Campanulaceae: Campanula) in the Eastern Mediterranean
Ecology and Evolution.
At the intersection of geological activity, climatic fluctuations, and human pressure, the Mediterranean Basin – a hotspot of biodiversity – provides an ideal setting for studying endemism, evolution, and biogeography. Here, we focus on the Roucela complex (Campanula subgenus Roucela), a group of 13 bellflower species found primarily in the eastern Mediterranean Basin. Plastid and low-copy nuclear markers were employed to reconstruct evolutionary relationships and estimate divergence times within the Roucela complex using both concatenation and species tree analyses. Niche modeling, ancestral range estimation, and diversification analyses were conducted to provide further insights into patterns of endemism and diversification through time. Diversification of the Roucela clade appears to have been primarily the result of vicariance driven by the breakup of an ancient landmass. We found geologic events such as the formation of the mid-Aegean trench and the Messinian Salinity Crisis to be historically important in the evolutionary history of this group. Contrary to numerous past studies, the onset of the Mediterranean climate has not promoted diversification in the Roucela complex and, in fact, may be negatively affecting these species. This study highlights the diversity and complexity of historical processes driving plant evolution in the Mediterranean Basin.
Keywords: Aegean Archipelago, Campanulaceae, Mediterranean, Roucela clade, continental islands, drabifolia complex, endemism
Creemers R, Denoël M, Campos J, Vences M, Crochet P, Gonçalves J et al. (2014)
Amphibia-Reptilia 35(1) 1-31.
A precise knowledge of the spatial distribution of taxa is essential for decision-making processes in land management and biodiversity conservation, both for present and under future global change scenarios. This is a key base for several scientific disciplines (e.g. macro-ecology, biogeography, evolutionary biology, spatial planning, or environmental impact assessment) that rely on species distribution maps. An atlas summarizing the distribution of European amphibians and reptiles with 50 × 50 km resolution maps based on ca. 85 000 grid records was published by the Societas Europaea Herpetologica (SEH) in 1997. Since then, more detailed species distribution maps covering large parts of Europe became available, while taxonomic progress has led to a plethora of taxonomic changes including new species descriptions. To account for these progresses, we compiled information from different data sources: published in books and websites, ongoing national atlases, personal data kindly provided to the SEH, the 1997 European Atlas, and the Global Biodiversity Information Facility (GBIF). Databases were homogenised, deleting all information except species names and coordinates, projected to the same coordinate system (WGS84) and transformed into a 50 × 50 km grid. The newly compiled database comprises more than 384 000 grid and locality records distributed across 40 countries. We calculated species richness maps as well as maps of Corrected Weighted Endemism and defined species distribution types (i.e. groups of species with similar distribution patterns) by hierarchical cluster analysis using Jaccard’s index as association measure. Our analysis serves as a preliminary step towards an interactive, dynamic and online distributed database system (NA2RE system) of the current spatial distribution of European amphibians and reptiles. The NA2RE system will serve as well to monitor potential temporal changes in their distributions. Grid maps of all species are made available along with this paper as a tool for decision-making and conservation-related studies and actions. We also identify taxonomic and geographic gaps of knowledge that need to be filled, and we highlight the need to add temporal and altitudinal data for all records, to allow tracking potential species distribution changes as well as detailed modelling of the impacts of land use and climate change on European amphibians and reptiles.
Keywords: European herpetofauna, IUCN red list, biogeography, conservation, distribution atlas, distribution types, endemism, species richness
Katsanevakis S, Coll M, Piroddi C, Steenbeek J, Ben Rais Lasram F, Zenetos A et al. (2014)
Frontiers in Marine Science 1 32.
Human activities, such as shipping, aquaculture, and the opening of the Suez Canal, have led to the introduction of nearly 1,000 alien species into the Mediterranean Sea. We investigated how human activities, by providing pathways for the introduction of alien species, may shape the biodiversity patterns in the Mediterranean Sea. Richness of Red Sea species introduced through the Suez Canal (Lessepsian species) is very high along the eastern Mediterranean coastline, reaching a maximum of 129 species per 100 km2, and declines towards the north and west. The distribution of species introduced by shipping is strikingly different, with several hotspot areas occurring throughout the Mediterranean basin. Two main hotspots for aquaculture-introduced species are observed (the Thau and Venice lagoons). Certain taxonomic groups were mostly introduced through specific pathways – fish through the Suez Canal, macrophytes by aquaculture, and invertebrates through the Suez Canal and by shipping. Hence, the local taxonomic identity of the alien species was greatly dependent on the dominant maritime activities/interventions and the related pathways of introduction. The composition of alien species differs among Mediterranean ecoregions; such differences are greater for Lessepsian and aquaculture-introduced species. The spatial pattern of native species biodiversity differs from that of alien species: the overall richness of native species declines from the north-western to the south-eastern regions, while the opposite trend is observed for alien species. The biodiversity of the Mediterranean Sea is changing, and further research is needed to better understand how the new biodiversity patterns shaped by human activities will affect the Mediterranean food webs, ecosystem functioning, and the provision of ecosystem services.
Keywords: Lessepsian migrants, alien species, aquaculture, biodiversity patterns, biological invasions, pathways, shipping
Kougioumoutzis K, Tiniakou A (2014)
Ecological factors driving plant species diversity in the South Aegean Volcanic Arc and other central Aegean islands
Plant Ecology & Diversity 1-14.
Background: The South Aegean Volcanic Arc (SAVA), one of the most notable geological structures of the Mediterranean Sea, is floristically well known. Nevertheless, the factors that contribute to shaping the plant species richness of the SAVA remain unclear. Aims: To investigate the factors that affect plant species richness and identify plant diversity hotspots in the SAVA and other central Aegean islands. Methods: We used stepwise multiple regression to test the relationship between a number of environmental factors and plant species richness in the SAVA, as well as the residuals from the species–area linear regressions of native, Greek and Cycladian endemic taxa as indicators of relative species richness. Results: The area was confirmed to be the most powerful single explanatory variable of island species richness, while geodiversity, maximum elevation and mean annual precipitation explained a large proportion of variance for almost all the species richness measures. Anafi, Amorgos and Folegandros were found to be endemic plant diversity hotspots. Conclusions: We have demonstrated that geodiversity is an important factor in shaping plant species diversity in the Cyclades, while mean annual precipitation, human population density and maximum elevation were significant predictors of the Greek endemics present in the Cyclades. Finally, Anafi was found to be a plant diversity hotspot in the South Aegean Sea.
Keywords: Aegean archipelago, South Aegean Volcanic Arc, endemism, environmental diversity, geodiversity, human impact, island species–area relationship, species richness
Kougioumoutzis K, Tiniakou A, Georgiou O, Georgiadis T (2014)
Edinburgh Journal of Botany 71(02) 135-160.
The island of Kimolos, located in the western Kiklades in Greece, constitutes together with Milos, Polyaegos, Anafi and the Santorini island group the central part of the South Aegean Volcanic Arc. The flora of Kimolos consists of 443 taxa, 70 of which are under a statute of protection, 30 are Greek endemics and 225 are reported here for the first time. We show that Kimolos has the highest percentage of Greek endemics in the South Aegean Volcanic Arc. The known distribution of the endemics Sedum eriocarpum subsp. eriocarpum and Anthemis rigida subsp. liguliflora is expanded, being reported for the first time for the phytogeographical region of the Kiklades. The floristic cross-correlation between Kimolos and other parts of the South Aegean Volcanic Arc by means of Sørensen’s index revealed that its phytogeographical affinities are somewhat stronger to Anafi than to neighbouring Milos.
Keywords: biodiversity, endemism, phytogeography, volcanic flora