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landgenreport: a new r function to simplify landscape genetic analysis using resistance surface layers.
Bernd Gruber1, Aaron T Adamack1
1Institute for Applied Ecology, University of Canberra, Canberra, Canberra, ACT, 2601, Australia.
Molecular Ecology Resources
|February 4, 2015
Summary
The popgenreport R package now integrates landscape genetic analysis (LGA) in one framework, simplifying the study of landscape features on gene flow using resistance surfaces.
Area of Science:
- Ecology
- Genetics
- Bioinformatics
Background:
- Landscape genetic analysis (LGA) is valuable for understanding gene flow but often requires multiple software packages.
- Data for LGA, including genotyped individuals and landscape resistance layers, is increasingly available.
Purpose of the Study:
- To introduce new functions in the R package popgenreport for streamlined landscape genetic analysis.
- To provide a single, integrated framework for performing LGA, addressing the fragmentation of existing tools.
Main Methods:
- The popgenreport package utilizes spatially referenced genetic data and landscape resistance layers.
- It generates pairwise genetic, cost, and Euclidean distance matrices.
- Statistical tests assess the contribution of landscape resistance to population structure.
Main Results:
- The new functions enable a complete LGA within a single R package framework.
- Outputs include pairwise distance matrices and statistical test results.
- Customizable options for cost path and genetic distance measures are available.
Conclusions:
- The popgenreport package simplifies LGA, making it more accessible.
- This integrated approach facilitates the detection of landscape feature effects on gene flow.
- The package is available on CRAN with comprehensive tutorials.
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