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introgress: a software package for mapping components of isolation in hybrids.

Abstract

A new software package (introgress) provides functions for analysing introgression of genotypes between divergent, hybridizing lineages, including estimating genomic clines from multi-locus genotype data and testing for deviations from neutral expectations. The software works with co-dominant, dominant and haploid marker data, and does not require fixed allelic differences between parental populations for the sampled genetic markers. Permutation and parametric procedures generate neutral expectations for introgression and provide a basis for significance tests of observed genomic clines. The software also implements maximum likelihood estimates of hybrid index from genotypic data and a number of graphical analyses. The package is an extension of the R statistical software, is written in the R language and is freely available through the Comprehensive R Archive Network (CRAN; http://cran.r-project.org/). In this study, we describe introgress and demonstrate its use with a sample data set.

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    Source

    Molecular ecology resources 10:2 2010 Mar pg 378-84

    Pub Type(s)

    Journal Article

    Language

    eng

    PubMed ID

    21565033

    Citation

    TY - JOUR T1 - introgress: a software package for mapping components of isolation in hybrids. AU - Gompert,Zachariah, AU - Alex Buerkle,C, Y1 - 2009/06/10/ PY - 2009/6/10/aheadofprint PY - 2011/5/14/entrez PY - 2010/3/1/pubmed PY - 2010/3/1/medline SP - 378 EP - 84 JF - Molecular ecology resources JO - Mol Ecol Resour VL - 10 IS - 2 N2 - A new software package (introgress) provides functions for analysing introgression of genotypes between divergent, hybridizing lineages, including estimating genomic clines from multi-locus genotype data and testing for deviations from neutral expectations. The software works with co-dominant, dominant and haploid marker data, and does not require fixed allelic differences between parental populations for the sampled genetic markers. Permutation and parametric procedures generate neutral expectations for introgression and provide a basis for significance tests of observed genomic clines. The software also implements maximum likelihood estimates of hybrid index from genotypic data and a number of graphical analyses. The package is an extension of the R statistical software, is written in the R language and is freely available through the Comprehensive R Archive Network (CRAN; http://cran.r-project.org/). In this study, we describe introgress and demonstrate its use with a sample data set. SN - 1755-0998 UR - https://www.unboundmedicine.com/medline/citation/21565033/introgress:_a_software_package_for_mapping_components_of_isolation_in_hybrids_ L2 - http://openurl.ebscohost.com/linksvc/linking.aspx?genre=article&sid=PubMed&issn=1755-098X&title=Mol Ecol Resour&volume=10&issue=2&spage=378&atitle=introgress: a software package for mapping components of isolation in hybrids.&aulast=Gompert&date=2010 ER -