Beyond similarity: A network approach for identifying and delimiting biogeographical regions

Biogeographical regions (geographically distinct assemblages of species and communities) constitute a cornerstone for ecology, biogeography, evolution and conservation biology. Species turnover measures are often used to quantify biodiversity patterns, but algorithms based on similarity and clustering are highly sensitive to common biases and intricacies of species distribution data. Here we apply a community detection approach from network theory that incorporates complex, higher order presence-absence patterns. We demonstrate the performance of the method by applying it to all amphibian species in the world (c. 6,100 species), all vascular plant species of the USA (c. 17,600), and a hypothetical dataset containing a zone of biotic transition. In comparison with current methods, our approach tackles the challenges posed by transition zones and succeeds in identifying a larger number of commonly recognised biogeographical regions. This method constitutes an important advance towards objective, data derived identification and delimitation of the world's biogeographical regions.Comment: 5 figures and 1 supporting figur

Synergies of planning for forests and planning for Natura 2000: Evidences and prospects from northern Italy

Improvements in the management of Natura 2000 sites are essential to achieve the targets set out by the Habitats and Birds Directives of the European Union. A current focus is on the development of management plans, which are fundamental instruments in the implementation of conservation measures. This study explores the viability of using existing forest plans to assist in this purpose. As case study, we consider the regulatory framework of the Veneto Region, northern Italy. We collected quantitative and qualitative data on forest plans at the regional and at three sub-regional spatial scales: local, district, and biogeographical. Forest plans cover about 54% of the terrestrial area of Natura 2000 sites in Veneto, and 75% of Sites of Community Importance in the Alpine biogeographical region. At the local scale of analysis, metrics from forest plans represent a valuable historical record which can be used to interpret the current state and future trends, especially for forests with long management records. These data can be used to assess biodiversity indicators for the monitoring of Natura 2000 forest and non-forest habitats, in compliance with Article 17 of the Habitats Directive. Moreover, the heterogeneous stand conditions which are promoted by some forest management approaches can improve the conservation efforts for some habitats and species. The scale of local forest plans are typically the most appropriate for implementing habitat management strategies. From this study, we conclude that management authorities should take advantage of the wide spatial coverage and distribution of existing forest plans, especially in mountain areas inside and outside the Natura 2000 network, for the successful conservation of European Union habitats and species

Infomap Bioregions: Interactive mapping of biogeographical regions from species distributions

Biogeographical regions (bioregions) reveal how different sets of species are spatially grouped and therefore are important units for conservation, historical biogeography, ecology and evolution. Several methods have been developed to identify bioregions based on species distribution data rather than expert opinion. One approach successfully applies network theory to simplify and highlight the underlying structure in species distributions. However, this method lacks tools for simple and efficient analysis. Here we present Infomap Bioregions, an interactive web application that inputs species distribution data and generates bioregion maps. Species distributions may be provided as georeferenced point occurrences or range maps, and can be of local, regional or global scale. The application uses a novel adaptive resolution method to make best use of often incomplete species distribution data. The results can be downloaded as vector graphics, shapefiles or in table format. We validate the tool by processing large datasets of publicly available species distribution data of the world's amphibians using species ranges, and mammals using point occurrences. We then calculate the fit between the inferred bioregions and WWF ecoregions. As examples of applications, researchers can reconstruct ancestral ranges in historical biogeography or identify indicator species for targeted conservation.Comment: 8 pages, 4 figures, 2, tables, for interactive application, http://bioregions.mapequation.or

Biodiversity hotspots on the Dutch Continental Shelf: a marine strategy framework directive perspective

This report presenst hotspots of biodiversity for benthos, fish, birds, marine mammals and habitats on the Dutch Continental Shelf. These hotspots are based on a spatial application of biodiversity metrics developed in this study for the GES(Good Environmental Status)-descriptor 1 ‘Biological diversity is maintained’ of the Marine Strategy Framework Directive (MSFD) (EU 2008). The choice of the biodiversity metrics is based on the proposed indicators of biodiversity in the Commission Decision (EU 2010). The purpose of this study is to provide insight in possibilities for spatial protection measures in the framework of the MSFD. This report feeds information and ideas into further work for the MSFD in the Netherlands. IMARES has compiled this report for the Dutch Ministry of Economic Affairs, Agriculture and Innovation (Ministry of EL&I) and the Ministry of Infrastructure and the Environment (I&M)

Comparison of three modelling approaches of potential natural forest habitats in Bavaria, Germany

In the context of the EU Habitats Directive, which contains the obligation of environmental monitoring, nature conservation authorities face a growing demand for effective and competitive methods to survey protected habitats. Therefore the presented research study compared three modelling approaches (rule-based method with applied Bavarian woodland types, multivariate technique of cluster analysis, and a fuzzy logic approach) for the purpose of detecting potential habitat types. The results can be combined with earth observation data of different geometric resolution (ASTER, SPOT5, aerial photographs or very high resolution satellite data) in order to determine actual forest habitat types. This was carried out at two test sites, situated in the pre-alpine area in Bavaria (southern Germany). The results were subsequently compared to the terrestrial mapped habitat areas of the NATURA 2000 management plans. First results show that these techniques are a valuable support in mapping and monitoring NATURA 2000 forest habitats

Modeling the ecology and evolution of biodiversity: Biogeographical cradles, museums, and graves

Individual processes shaping geographical patterns of biodiversity are increasingly understood, but their complex interactions on broad spatial and temporal scales remain beyond the reach of analytical models and traditional experiments. To meet this challenge, we built a spatially explicit, mechanistic simulation model implementing adaptation, range shifts, fragmentation, speciation, dispersal, competition, and extinction, driven by modeled climates of the past 800,000 years in South America. Experimental topographic smoothing confirmed the impact of climate heterogeneity on diversification. The simulations identified regions and episodes of speciation (cradles), persistence (museums), and extinction (graves). Although the simulations had no target pattern and were not parameterized with empirical data, emerging richness maps closely resembled contemporary maps for major taxa, confirming powerful roles for evolution and diversification driven by topography and climate

Australian Sphingidae – DNA Barcodes Challenge Current Species Boundaries and Distributions

© 2014 Rougerie et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. The attached file is the published version of the article

FlatNJ: A novel network-based approach to visualize evolutionary and biogeographical relationships

Split networks are a type of phylogenetic network that allow visualization of conflict in evolutionary data. We present a new method for constructing such networks called FlatNetJoining (FlatNJ). A key feature of FlatNJ is that it produces networks that can be drawn in the plane in which labels may appear inside of the network. For complex data sets that involve, for example, non-neutral molecular markers, this can allow additional detail to be visualized as compared to previous methods such as split decomposition and NeighborNet. We illustrate the application of FlatNJ by applying it to whole HIV genome sequences, where recombination has taken place, fluorescent proteins in corals, where ancestral sequences are present, and mitochondrial DNA sequences from gall wasps, where biogeographical relationships are of interest. We find that the networks generated by FlatNJ can facilitate the study of genetic variation in the underlying molecular sequence data and, in particular, may help to investigate processes such as intra-locus recombination. FlatNJ has been implemented in Java and is freely available at www.uea.ac.uk/computing/software/flatnj