SpeciesGeoCoder: Fast categorisation of species occurrences for analyses of biodiversity, biogeography, ecology and evolution

Abstract

Understanding the patterns and processes underlying the uneven distribution of biodiversity across space and time constitutes a major scientific challenge in evolutionary biology. With rapidly accumulating species occurrence data, there is an increasing need for making the process of coding species into operational units for biogeographic and evolutionary analyses faster, automated, transparent and reproducible. Here we present SpeciesGeoCoder, a free software package written in Python and R, that allows for easy coding of species into user-defined areas. These areas may be of any size and be purely geographical (i.e., polygons) such as political units, conservation areas, biomes, islands, biodiversity hotspots, and areas of endemism, but may also include altitudinal ranges. This flexibility allows scoring species into complex categories, such as those encountered in topographically and ecologically heterogeneous landscapes. In addition, SpeciesGeoCoder can be used to facilitate sorting and cleaning of occurrence data. The various outputs of SpeciesGeoCoder include quantitative biodiversity statistics, global and local distribution maps, and NEXUS files that can be directly used in many phylogeny-based applications for ancestral state reconstruction, investigations on biome evolution, and diversification rate analyses. Our simulations indicate that even datasets containing hundreds of millions of records can be analysed in relatively short time using a regular desktop computer. We exemplify the use of our program through two contrasting examples: i) inferring historical dispersal of birds across the Isthmus of Panama, separating lowland vs. montane species and optimising the results onto a species-level, dated phylogeny; and ii) exploring seasonal variations in the occurrence of 10 GPS-tracked individuals of moose (Alces alces) over one year in northern Sweden. These analyses show that SpeciesGeoCoder allows an easy, flexible and fast categorisation of species distribution data for various analyses in ecology and evolution, with potential use at different spatial, taxonomic and temporal scales.