POPMAPS: An R package to estimate ancestry probability surfaces

This software code was developed to estimate the probability that individuals found at a geographic location will belong to the same genetic cluster as individuals at the nearest empirical sampling location for which ancestry is known. POPMAPS includes 5 main functions to calculate and visualize these results (see Table 1 for functions and arguments). Population assignment coefficients and a raster surface must be estimated prior to using POPMAPS functions (see Fig. 1a and b). With these data in hand, users can run a jackknife function to choose an optimal parameter combination that reconstructs empirical data best (Figs. 2 and S2). Pertinent parameters include 1) how many empirical sampling localities should be used to estimate ancestry coefficients and 2) what is the influence of empirical sites on ancestry coefficient estimation as distance increases (Fig. 2). After choosing these parameters, a user can estimate the entire ancestry probability surface (Fig. 1c and d, Fig. 3). This package can be used to estimate ancestry coefficients from empirical genetic data across a user-defined geospatial layer. Estimated ancestry coefficients are used to calculate ancestry probabilities, which together with 'hard population boundaries,' compose an ancestry probability surface. Within a hard boundary, the ancestry probability informs a user of the confidence that they can have of genetic identity matching the principal population if they were to find individuals of the focal organism at a location. Confidence can be modified across the ancestry probability surface by changing parameters influencing the contribution of empirical data to the estimation of ancestry coefficients. This information may be valuable to inform decision-making for organisms having management needs.