Edler D et al. (2017), Infomap Bioregions: Interactive Mapping of Biog...

ECB-ART-44940

Syst Biol 2017 Mar 01;662:197-204. doi: 10.1093/sysbio/syw087.

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Infomap Bioregions: Interactive Mapping of Biogeographical Regions from Species Distributions.

Edler D , Guedes T , Zizka A , Rosvall M , Antonelli A .

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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 data sets 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. [Biogeography; bioregionalization; conservation; mapping].

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Species referenced: Echinodermata
Genes referenced: LOC100893907 LOC115919910 LOC115925415 LOC583082 ROCK

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	Fig. 1. Step-by-step illustration of how Infomap Bioregions generates bioregions from species distribution data. Infomap Bioregions: a) inputs comma-separated values for point occurrences, b) adaptively bins species records into discrete geographical grid cells such that the data density determines the spatial resolution, c) extracts a bipartite network between species and grid cells, d) clusters the bipartite network with the Infomap clustering algorithm, e) visualizes the grid cell clusters as bioregions on a zoomable map, f) exports the geographical map in svg or png format, the tables of top occurring and top indicative species for each bioregion in csv format, the species presence/absence matrix for the bioregions in NEXUS format and the geographical information of the bioregions in shapefile or GeoJSON format.
	Figure 2. Bioregion map of the world’s amphibians generated with Infomap Bioregions, using the IUCN species range maps. White areas have insufficient data and were excluded from the analysis. The inset shows a zoom-in of Central America, the West Indies, and northwestern South America, depicting many small bioregions that reflect high turnover of species assemblages and narrow-range distributions characteristic for the region. Table 1 shows information about labeled bioregions.
	Figure 3. Bioregion map and phylogenetic tree of world mammals with ancestral range reconstruction, generated with Infomap Bioregions. a) Phylogenetic tree of 5747 mammals computed from Faurby and Svenning (2015), fully zoomable on the online application. Ancestral ranges were reconstructed under Fitch parsimony. Pie charts depict most parsimonious ancestral ranges at nodes, and current distributions for extant species. Branch lines are scaled to the number of terminals subtending each branch, in order to improve visualization of the overall tree structure. b) Magnified part of the tree, highlighting the rock-wallabies (genus Petrogale) which are currently distributed across several bioregions in Australia. This analysis suggests that all rock-wallabies, including the yellow-footed rock-wallaby (Petrogale xanthopus), which is the most indicative species of the southeast bioregion (i), originated from a common ancestor in northern Australia. c) Bioregion map of world mammals using species point occurrences from GBIF. White areas have insufficient data and were excluded from the analysis. Colors are used consistently across the subfigures. Table 2 shows information about labeled bioregions.
	Figure 4. Comparison between Infomap bioregions and WWF ecoregions using the Mapcurves algorithm (Hargrove et al. 2006). a) Infomap bioregions for the amphibian data set; b) Infomap bioregions for the mammalian data set; c) WWF ecoregions from Olson et al. (2001); d) Mapcurves as a measure for the GOF for the Infomap bioregions with respect to the WWF ecoregions. The graph shows the percentage of bioregions with a GOF score better than the corresponding value on the horizontal axis (zero to one). A perfect fit for all bioregions would be indicated by a horizontal line at the top; e) GOF map of the Infomap bioregions for amphibians and the total GOF score; f) GOF map of the Infomap bioregions for mammals and the total GOF score. The fit of the bioregions to the WWF ecoregions is generally very good, with the exception of several very small bioregions identified by Infomap Bioregions.

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