SIMIL: an R (CRAN) scripts collection for computing genetic structure similarities based on STRUCTURE 2 outputs

Details

Serval ID
serval:BIB_3A355C6C5336
Type
Article: article from journal or magazin.
Collection
Publications
Title
SIMIL: an R (CRAN) scripts collection for computing genetic structure similarities based on STRUCTURE 2 outputs
Journal
Molecular Ecology Resources
Author(s)
Alvarez N., Arrigo N.
Working group(s)
Consortium Intrabiodiv
ISSN
1471-8278
Publication state
Published
Issued date
2008
Peer-reviewed
Oui
Volume
8
Number
4
Pages
757-762
Language
english
Abstract
The emergence of comparative phylogeography requires tools that allow comparing quantitatively the genetic structures between species. Whereas numerous methods have been developed to compare trees inferred from two species, comparison methods involving population structures issued from Bayesian inferences or maximum likelihood criterion have been poorly investigated. Here, we present a method implemented in an R (CRAN) scripts collection, SIMIL, based on the mean absolute differences computed from STRUCTURE 2 outputs. The scripts collection is illustrated by the computation of unweighted and weighted genetic-structure-similarity (GSS) indices in three alpine plants. Different weighting procedures - taking into account the level of overlap between the species sampling areas - are compared among the different species pairs and among the different numbers of gene pools considered in STRUCTURE.
Keywords
comparative phylogeography, genetic structure, mean absolute difference, R (CRAN), similarity index, STRUCTURE
Web of science
Create date
18/04/2010 12:27
Last modification date
20/08/2019 14:29
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