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  • Evaluation of redundancy analysis to identify signatures of local adaptation.

    Author(s) : Capblancq, T.Luu, K.Blum, M. G. B.Bazin, E.

    Author Affiliation : CNRS, LECA UMR 5553, Univ. Grenoble Alpes, Grenoble, France.

    Author Email : thibaut.capblancq@univ-grenoble-alpes.fr

    Journal article : Molecular Ecology Resources 2018 Vol.18 No.6 pp.1223-1233

    Abstract : Ordination is a common tool in ecology that aims at representing complex biological information in a reduced space. In landscape genetics, ordination methods such as principal component analysisprincipal component analysisSubject Category: Techniques, Methodologies and Equipment
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    (PCA) have been used to detect adaptive variation based on genomic data. Taking advantage of environmental data in addition to genotype data, redundancy analysis (RDA) is another ordination approach that is useful to detect adaptive variation. This study aims at proposing a test statistic based on RDA to search for loci under selection. We compare redundancy analysis to pcadapt, which is a nonconstrained ordination method, and to a latent factor mixed model (LFMM), which is a univariate genotype-environment association method. Individual-based simulations identify evolutionary scenarios where RDA genome scans have a greater statistical power than genome scans based on PCA. By constraining the analysis with environmental variables, RDA performs better than PCA in identifying adaptive variation when selection gradients are weakly correlated with population structure. In addition, we show that if RDA and LFMM have a similar power to identify genetic markersgenetic markersSubject Category: Miscellaneous
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    associated with environmental variables, the RDA-based procedure has the advantage to identify the main selective gradients as a combination of environmental variables. To give a concrete illustration of RDA in population genomicsgenomicsSubject Category: Disciplines, Occupations and Industries
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    , we apply this method to the detection of outliers and selective gradients on an SNP data set of Populus trichocarpa (Geraldes et al., 2013). The RDA-based approach identifies the main selective gradient contrasting southern and coastal populations to northern and continental populations in the north-western American coast.

    ISSN : 1755-098X

    DOI : 10.1111/1755-0998.12906

    Record Number : 20193345291

    Publisher : Wiley

    Location of publication : Oxford

    Country of publication : UK

    Language of text : English

    Indexing terms for this abstract:

    Organism descriptor(s) : Populus balsamifera subsp. trichocarpapopulus balsamifera subsp. trichocarpaSubject Category: Organism Names
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    Descriptor(s) : adaptationadaptationSubject Category: Natural Processes
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    , environmental factorsenvironmental factorsSubject Category: Properties
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    , genesgenesSubject Category: Miscellaneous
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    , genetic markersgenetic markersSubject Category: Miscellaneous
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    , genomesgenomesSubject Category: Miscellaneous
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    , genomicsgenomicsSubject Category: Disciplines, Occupations and Industries
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    , nucleotide sequencesnucleotide sequencesSubject Category: Chemicals and Chemical Groups
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    , principal component analysisprincipal component analysisSubject Category: Techniques, Methodologies and Equipment
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    , statistical analysisstatistical analysisSubject Category: Techniques, Methodologies and Equipment
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    Identifier(s) : DNA sequences, statistical methods

    Broader term(s) : Populus balsamiferapopulus balsamiferaSubject Category: Organism Names
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    , PopuluspopulusSubject Category: Organism Names
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    , SalicaceaesalicaceaeSubject Category: Organism Names
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    , MalpighialesmalpighialesSubject Category: Organism Names
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    , eudicotseudicotsSubject Category: Organism Names
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    , angiospermsangiospermsSubject Category: Organism Names
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    , SpermatophytaspermatophytaSubject Category: Organism Names
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    , plantsplantsSubject Category: Organism Names
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    , eukaryoteseukaryotesSubject Category: Organism Names
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