pygenoscape: a Python package for spatial interpolation and visualization of genetic distance landscapes.

Area of Science:

• Population genetics
• Phylogeography
• Bioinformatics

Background:

• Traditional methods for spatial genetic structure analysis often rely on discrete population models.
• These models can obscure continuous geographic patterns and genetic turnover.
• There is a need for tools that represent spatial genetic data continuously.

Purpose of the Study:

• To introduce pygenoscape, an open-source Python package.
• To enable the transformation of genetic distance data into continuous spatial representations.
• To facilitate the visualization of genetic turnover and spatial genetic structure.

Main Methods:

• The pygenoscape package accepts pairwise genetic distance matrices or aligned nucleotide sequences.
• It integrates distance embedding, geographic projection, and spatial interpolation.
• A reproducible command-line workflow with interactive visualization is provided.

Main Results:

• pygenoscape successfully represented spatial genetic patterns in empirical data (Bombus terrestris, Hydroides dianthus).
• The tool recovered known spatial genetic structures, including isolation-by-distance and barriers.
• Results were consistent with previous population genetic analyses.

Conclusions:

• pygenoscape offers a novel approach to visualize spatial genetic data.
• The package enhances the study of population genetics and phylogeography by revealing continuous patterns.
• It provides a valuable, accessible tool for researchers in the field.