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POPMAPS: An R package to estimate ancestry probability surfaces

Metadata Updated: October 28, 2023

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.

  See 'Related External Resources, Type: Source Code' below for direct access to the POPMAPS R software package.

Access & Use Information

Public: This dataset is intended for public access and use. License: No license information was provided. If this work was prepared by an officer or employee of the United States government as part of that person's official duties it is considered a U.S. Government Work.

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Dates

Metadata Created Date June 1, 2023
Metadata Updated Date October 28, 2023

Metadata Source

Harvested from DOI EDI

Additional Metadata

Resource Type Dataset
Metadata Created Date June 1, 2023
Metadata Updated Date October 28, 2023
Publisher U.S. Geological Survey
Maintainer
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Identifier USGS:627e7b24d34e3bef0c9a2cc2
Data Last Modified 20220715
Category geospatial
Public Access Level public
Bureau Code 010:12
Metadata Context https://project-open-data.cio.gov/v1.1/schema/catalog.jsonld
Metadata Catalog ID https://datainventory.doi.gov/data.json
Schema Version https://project-open-data.cio.gov/v1.1/schema
Catalog Describedby https://project-open-data.cio.gov/v1.1/schema/catalog.json
Harvest Object Id 7b2a87db-074e-4e65-a5ef-5213ab65bfde
Harvest Source Id 52bfcc16-6e15-478f-809a-b1bc76f1aeda
Harvest Source Title DOI EDI
Metadata Type geospatial
Old Spatial -180.0,90.0,180.0,90.0
Publisher Hierarchy White House > U.S. Department of the Interior > U.S. Geological Survey
Source Datajson Identifier True
Source Hash 7e3eb81614bd0f6dbb6bdf10c4cedc22a5ca7ad7be78f4d7bd2c7daf652f980f
Source Schema Version 1.1
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