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

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 scarc...

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Autores principales: Balao, Francisco, García-Castaño, Juan Luis
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2014
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4413549/
https://www.ncbi.nlm.nih.gov/pubmed/25926861
http://dx.doi.org/10.1186/1746-4811-10-40
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author Balao, Francisco
García-Castaño, Juan Luis
author_facet Balao, Francisco
García-Castaño, Juan Luis
author_sort Balao, Francisco
collection PubMed
description 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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spelling pubmed-44135492015-04-30 AFLPsim: an R package to simulate and detect dominant markers under selection in hybridizing populations Balao, Francisco García-Castaño, Juan Luis Plant Methods Software 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/. BioMed Central 2014-12-13 /pmc/articles/PMC4413549/ /pubmed/25926861 http://dx.doi.org/10.1186/1746-4811-10-40 Text en © Balao and García-Castaño; licensee BioMed Central. 2014 This article is published under license to BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.
spellingShingle Software
Balao, Francisco
García-Castaño, Juan Luis
AFLPsim: an R package to simulate and detect dominant markers under selection in hybridizing populations
title AFLPsim: an R package to simulate and detect dominant markers under selection in hybridizing populations
title_full AFLPsim: an R package to simulate and detect dominant markers under selection in hybridizing populations
title_fullStr AFLPsim: an R package to simulate and detect dominant markers under selection in hybridizing populations
title_full_unstemmed AFLPsim: an R package to simulate and detect dominant markers under selection in hybridizing populations
title_short AFLPsim: an R package to simulate and detect dominant markers under selection in hybridizing populations
title_sort aflpsim: an r package to simulate and detect dominant markers under selection in hybridizing populations
topic Software
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4413549/
https://www.ncbi.nlm.nih.gov/pubmed/25926861
http://dx.doi.org/10.1186/1746-4811-10-40
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