SDMtoolbox 2.0: the next generation Python-based GIS toolkit for landscape genetic, biogeographic and species distribution model analyses

TLDR

SDMtoolbox 2.0 is a Python‑based GIS toolkit for spatial studies in ecology, evolution, and genetics, offering universal pre‑ and post‑processing tools compatible with any modeling software. Its goal is to automate complex, repetitive spatial analyses through an intuitive GUI and to enable careful parameterization of species distribution models to maximize discriminatory power while minimizing overfitting. The toolkit processes occurrence and environmental data, directly interfaces with MaxEnt, and includes 79 ArcGIS scripts for macroecology, landscape genetics, evolutionary studies, plus batch conversion tools for GIS data types. The release lets researchers use the latest ArcGIS and MaxEnt versions, cuts development time, and provides functions for biodiversity quantification, least‑cost path and corridor generation, spatial randomization assessment, and enforcement of dispersal limits in future‑climate SDMs.

Abstract

SDMtoolbox 2.0 is a software package for spatial studies of ecology, evolution, and genetics. The release of SDMtoolbox 2.0 allows researchers to use the most current ArcGIS software and MaxEnt software, and reduces the amount of time that would be spent developing common solutions. The central aim of this software is to automate complicated and repetitive spatial analyses in an intuitive graphical user interface. One core tenant facilitates careful parameterization of species distribution models (SDMs) to maximize each model’s discriminatory ability and minimize overfitting. This includes carefully processing of occurrence data, environmental data, and model parameterization. This program directly interfaces with MaxEnt, one of the most powerful and widely used species distribution modeling software programs, although SDMtoolbox 2.0 is not limited to species distribution modeling or restricted to modeling in MaxEnt. Many of the SDM pre- and post-processing tools have ‘universal’ analogs for use with any modeling software. The current version contains a total of 79 scripts that harness the power of ArcGIS for macroecology, landscape genetics, and evolutionary studies. For example, these tools allow for biodiversity quantification (such as species richness or corrected weighted endemism), generation of least-cost paths and corridors among shared haplotypes, assessment of the significance of spatial randomizations, and enforcement of dispersal limitations of SDMs projected into future climates—to only name a few functions contained in SDMtoolbox 2.0. Lastly, dozens of generalized tools exists for batch processing and conversion of GIS data types or formats, which are broadly useful to any ArcMap user.