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SpeciesGeoCoder: Fast Categorization of Species Occurrences for Analyses of Biodiversity, Biogeography, Ecology, and Evolution.

Artikel i vetenskaplig tidskrift
Författare Mats H. Töpel
Alexander Zizka
Maria Fernanda Calió
Ruud Scharn
Daniele Silvestro
Alexandre Antonelli
Publicerad i Systematic Biology
Volym 66
Nummer/häfte 2
Sidor 145-151
ISSN 1063-5157
Publiceringsår 2017
Publicerad vid Institutionen för marina vetenskaper
Institutionen för biologi och miljövetenskap
Sidor 145-151
Språk en
Länkar dx.doi.org/10.1093/sysbio/syw064
Ämneskategorier Bioinformatik och systembiologi, Evolutionsbiologi, Biologisk systematik, Informatik, Bioinformatik (beräkningsbiologi)


Understanding the patterns and processes underlying the uneven distribution of biodiversity across space constitutes a major scientific challenge in systematic biology and biogeography, which largely relies on effectively mapping and making sense of rapidly increasing species occurrence data. There is thus an urgent need for making the process of coding species into spatial units faster, automated, transparent, and reproducible. Here we present SpeciesGeoCoder, an open-source software package written in Python and R, that allows for easy coding of species into user-defined operational units. These units may be of any size and be purely spatial (i.e., polygons) such as countries and states, conservation areas, biomes, islands, biodiversity hotspots, and areas of endemism, but may also include elevation 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 obtained from online databases, and for testing the impact of incorrect identification of specimens on the spatial coding of species. The various outputs of SpeciesGeoCoder include quantitative biodiversity statistics, global and local distribution maps, and files that can be used directly in many phylogeny-based applications for ancestral range reconstruction, investigations of biome evolution, and other comparative methods. Our simulations indicate that even datasets containing hundreds of millions of records can be analyzed in relatively short time using a standard computer. We exemplify the use of SpeciesGeoCoder by inferring the historical dispersal of birds across the Isthmus of Panama, showing that lowland species crossed the Isthmus about twice as frequently as montane species with a marked increase in the number of dispersals during the last 10 million years. [ancestral area reconstruction; biodiversity patterns; ecology; evolution; point in polygon; species distribution data.].

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