Landscape Stewardship Collective is sharing the public alpha release of POPMAPS2, a maintained successor to POPMAPS: Population Management using Ancestry Probability Surfaces.
POPMAPS was developed to help translate empirical genetic data into spatially explicit ancestry probability surfaces. In practice, those surfaces can help researchers and land managers see where genetic variation changes across a landscape, where population boundaries are likely to occur, and where uncertainty remains high because the available data do not strongly support a single assignment.
Why this matters
Many restoration and conservation decisions depend on understanding genetic variation across space. Seed sourcing, rare plant recovery, translocation planning, and long-term monitoring all benefit from tools that connect population genomic data with geography in a transparent, repeatable way.
POPMAPS2 keeps the original POPMAPS ancestry-surface workflow while adding modern package infrastructure, documentation, tests, spatial-performance improvements, parameter tuning, candidate-surface comparison, and updated map outputs. The goal is to make the workflow easier to validate, easier to explain, and easier to apply carefully in real management contexts.
What POPMAPS2 currently supports
The current public alpha supports geographic interpolation, conductance and cost-distance surfaces, suitability and resistance inputs, leave-one-out and spatial-block validation, candidate-surface comparison, and modern map figures for ancestry probability, hard boundaries, and ancestry axes.
Just as important, POPMAPS2 is intentionally scoped. It does not infer population structure, fit species distribution models, run EEMS or FEEMS, optimize resistance surfaces, or replace biological interpretation. Those analyses happen upstream. POPMAPS2 then helps translate their outputs into ancestry surfaces that can be evaluated, compared, and interpreted.
What public alpha means
The package is installable, tested, documented, and usable for validation work, but it is not on CRAN yet and the public API may still change before the software manuscript and CRAN submission. Users who need reproducible analyses should use tagged releases, because the main branch may move quickly as validation, performance work, and figure workflows continue.
We are especially interested in careful use cases where POPMAPS2 can support transparent decision-making without treating any automated output as a final answer. Management decisions should still be grounded in biological interpretation, validation results, uncertainty, and local expertise.
View POPMAPS2 documentation View source code
The original POPMAPS workflow is described in Massatti and Winkler's 2022 Methods in Ecology and Evolution paper, Spatially explicit management of genetic diversity using ancestry probability surfaces.