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AFLPsim: an R package to simulate and detect dominant markers under selection in hybridizing populations.

Abstract

BACKGROUND

In spite of a large diversity of approaches to investigate loci under selection from a population genetic perspective, very few programs have been specifically designed to date to test selection in hybrids using dominant markers. In addition, simulators of dominant markers are very scarce and they do not usually take into account hybridization.

RESULTS

Here, we present a new, multifunctional, R package for dominant genetic markers, AFLPsim. This package can simulate dominant markers in hybridizing populations and implements genome scan methods for detecting outlier dominant loci in hybrids. In addition, it includes tools for further manipulating the results, plotting them and other tasks. We describe and tabulate the major functions implemented in AFLPsim. In addition, we provide some demonstration of its use and we perform a comparative study with other software. Finally, we conclude by briefly describing the input and output formats.

CONCLUSIONS

The R package AFLPsim application provides several useful tools in the context of hybridization studies. It can simulate dominant markers in hybridizing populations and predict their demographic evolution. In addition, we implement a new genome scan method for detecting outlier dominant loci in hybrids, which shows a rather high sensitivity and is very conservative in comparison with Gagnaire et al.'s, Bayescan and introgress. The application is downloadable at http://cran.r-project.org/web/packages/AFLPsim/.

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  • Authors+Show Affiliations

    ,

    Departamento de Biología Vegetal y Ecología, Universidad de Sevilla, Ap-1095, 41080 Sevilla, Spain ; Department of Systematic and Evolutionary Botany, University of Vienna, Rennweg 14, Vienna, 1030 Austria.

    Departamento de Biología Vegetal y Ecología, Universidad de Sevilla, Ap-1095, 41080 Sevilla, Spain.

    Source

    Plant methods 10: 2014 pg 40

    Pub Type(s)

    Journal Article

    Language

    eng

    PubMed ID

    25926861

    Citation

    TY - JOUR T1 - AFLPsim: an R package to simulate and detect dominant markers under selection in hybridizing populations. AU - Balao,Francisco, AU - García-Castaño,Juan Luis, Y1 - 2014/12/13/ PY - 2014///ecollection PY - 2014/7/24/received PY - 2014/11/24/accepted PY - 2014/12/13/epublish PY - 2015/5/1/entrez PY - 2014/1/1/pubmed PY - 2014/1/1/medline KW - Demographic simulation KW - Dominant markers KW - Genome scan KW - Hybridization KW - Outlier loci KW - R package SP - 40 EP - 40 JF - Plant methods JO - Plant Methods VL - 10 N2 - BACKGROUND: In spite of a large diversity of approaches to investigate loci under selection from a population genetic perspective, very few programs have been specifically designed to date to test selection in hybrids using dominant markers. In addition, simulators of dominant markers are very scarce and they do not usually take into account hybridization. RESULTS: Here, we present a new, multifunctional, R package for dominant genetic markers, AFLPsim. This package can simulate dominant markers in hybridizing populations and implements genome scan methods for detecting outlier dominant loci in hybrids. In addition, it includes tools for further manipulating the results, plotting them and other tasks. We describe and tabulate the major functions implemented in AFLPsim. In addition, we provide some demonstration of its use and we perform a comparative study with other software. Finally, we conclude by briefly describing the input and output formats. CONCLUSIONS: The R package AFLPsim application provides several useful tools in the context of hybridization studies. It can simulate dominant markers in hybridizing populations and predict their demographic evolution. In addition, we implement a new genome scan method for detecting outlier dominant loci in hybrids, which shows a rather high sensitivity and is very conservative in comparison with Gagnaire et al.'s, Bayescan and introgress. The application is downloadable at http://cran.r-project.org/web/packages/AFLPsim/. SN - 1746-4811 UR - https://www.unboundmedicine.com/medline/citation/25926861/AFLPsim:_an_R_package_to_simulate_and_detect_dominant_markers_under_selection_in_hybridizing_populations_ L2 - http://www.plantmethods.com/content/10//40 ER -