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SIMIL: an r (CRAN) scripts collection for computing genetic structure similarities based on structure 2 outputs
Author(s) -
NADIR ALVAREZ,
NILS ARRIGO,
CONSORTIUM INTRABIODIV
Publication year - 2008
Publication title -
molecular ecology resources
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 2.96
H-Index - 136
eISSN - 1755-0998
pISSN - 1755-098X
DOI - 10.1111/j.1755-0998.2007.02076.x
Subject(s) - biology , genetic structure , weighting , similarity (geometry) , scripting language , population structure , sampling (signal processing) , statistics , bayesian probability , evolutionary biology , phylogeography , phylogenetic tree , population , computational biology , genetics , genetic variation , computer science , mathematics , gene , artificial intelligence , image (mathematics) , computer vision , operating system , medicine , demography , radiology , filter (signal processing) , sociology
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 .