landgenreport: A new R function to simplify landscape genetic analysis using resistance surface layers

Bernd GRUBER, Aaron ADAMACK

    Research output: Contribution to journalArticle

    15 Citations (Scopus)

    Abstract

    We describe functions recently added to the r package popgenreport that can be used to perform a landscape genetic analysis (LGA) based on landscape resistance surfaces, which aims to detect the effect of landscape features on gene flow. These functions for the first time implement a LGA in a single framework. Although the approach has been shown to be a valuable tool to study gene flow in landscapes, it has not been widely used to date, despite the type of data being widely available. In part, this is likely due to the necessity to use several software packages to perform landscape genetic analyses. To apply LGA functions, two types of data sets are required: a data set with spatially referenced and genotyped individuals, and a resistance layer representing the effect of the landscape. The function outputs three pairwise distance matrices from these data: a genetic distance matrix, a cost distance matrix and a Euclidean distance matrix. Statistical tests are performed to test whether the cost matrix contributes to the understanding of the observed population structure. A full report on the analysis and outputs in the form of plots and tables of all intermediate steps of the LGA is produced. It is possible to customize the LGA to allow for different cost path approaches and measures of genetic distances. The package is written in the r language and is available through the Comprehensive r Archive. Comprehensive tutorials and information on how to install and use the package are provided at the authors' website (www.popgenreport.org).
    Original languageEnglish
    Pages (from-to)1172-1178
    Number of pages7
    JournalMolecular Ecology Resources
    Volume15
    Issue number5
    DOIs
    Publication statusPublished - 2015

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    genetic analysis
    genetic techniques and protocols
    surface layer
    Gene Flow
    Costs and Cost Analysis
    matrix
    Language
    Software
    gene flow
    genetic distance
    Population
    cost
    Datasets
    population structure
    statistical analysis
    software

    Cite this

    @article{2672d175c48b490eb1752591a2df3c91,
    title = "landgenreport: A new R function to simplify landscape genetic analysis using resistance surface layers",
    abstract = "We describe functions recently added to the r package popgenreport that can be used to perform a landscape genetic analysis (LGA) based on landscape resistance surfaces, which aims to detect the effect of landscape features on gene flow. These functions for the first time implement a LGA in a single framework. Although the approach has been shown to be a valuable tool to study gene flow in landscapes, it has not been widely used to date, despite the type of data being widely available. In part, this is likely due to the necessity to use several software packages to perform landscape genetic analyses. To apply LGA functions, two types of data sets are required: a data set with spatially referenced and genotyped individuals, and a resistance layer representing the effect of the landscape. The function outputs three pairwise distance matrices from these data: a genetic distance matrix, a cost distance matrix and a Euclidean distance matrix. Statistical tests are performed to test whether the cost matrix contributes to the understanding of the observed population structure. A full report on the analysis and outputs in the form of plots and tables of all intermediate steps of the LGA is produced. It is possible to customize the LGA to allow for different cost path approaches and measures of genetic distances. The package is written in the r language and is available through the Comprehensive r Archive. Comprehensive tutorials and information on how to install and use the package are provided at the authors' website (www.popgenreport.org).",
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    landgenreport: A new R function to simplify landscape genetic analysis using resistance surface layers. / GRUBER, Bernd; ADAMACK, Aaron.

    In: Molecular Ecology Resources, Vol. 15, No. 5, 2015, p. 1172-1178.

    Research output: Contribution to journalArticle

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    AU - ADAMACK, Aaron

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    AB - We describe functions recently added to the r package popgenreport that can be used to perform a landscape genetic analysis (LGA) based on landscape resistance surfaces, which aims to detect the effect of landscape features on gene flow. These functions for the first time implement a LGA in a single framework. Although the approach has been shown to be a valuable tool to study gene flow in landscapes, it has not been widely used to date, despite the type of data being widely available. In part, this is likely due to the necessity to use several software packages to perform landscape genetic analyses. To apply LGA functions, two types of data sets are required: a data set with spatially referenced and genotyped individuals, and a resistance layer representing the effect of the landscape. The function outputs three pairwise distance matrices from these data: a genetic distance matrix, a cost distance matrix and a Euclidean distance matrix. Statistical tests are performed to test whether the cost matrix contributes to the understanding of the observed population structure. A full report on the analysis and outputs in the form of plots and tables of all intermediate steps of the LGA is produced. It is possible to customize the LGA to allow for different cost path approaches and measures of genetic distances. The package is written in the r language and is available through the Comprehensive r Archive. Comprehensive tutorials and information on how to install and use the package are provided at the authors' website (www.popgenreport.org).

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