Detecting loci under selection in a hierarchically structured population

By Laurent Excoffier, T. Hofer, Matthieu Foll. Heredity, 2009

808 citations recorded by the source corpus.

View Paper: https://www.semanticscholar.org/paper/cb915863ec55e2d6e98fd408d035b950f830736f

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In Genetics

Citations in the corpus

Arlequin suite ver 3.5: a new series of programs to perform population genetics analyses under Linux and Windows (2010, methodology): “…Arlequin ver 3.5 a procedure to detect loci under selection from genome scans that contrast patterns of genetic diversity within and between populations, extending the FDIST approach of Beaumont & Nichols (1996) to the case where populations are hierarchically structured (see Excofﬁer et al. 2009).”
Phylogeography unplugged: comparative surveys in the genomic era (2014, background): “…phylogenomic approaches are allowing broad evaluation of which loci are under selection, thus permitting the evaluation of the importance of reproductive and ecological factors in speciation (Excoffier et al. 2009, Gagnaire et al. 2011, Bird et al. 2012, Deagle et al. 2012, Pespeni et al. 2012).”
Finding the Genomic Basis of Local Adaptation: Pitfalls, Practical Solutions, and Future Directions (2016, neutral): “For example, some loci display false signatures of selection as a result of range expansion due to a phenomenon known as allele sur ﬁ ng (Cur-rat et al. 2006; Travis et al. 2007; Excof ﬁ er et al. 2009 a ).”
A new FST‐based method to uncover local adaptation using environmental variables (2015, background): “, 2004) and hierarchical population structure (Excoffier et al., 2009).”
Pcadapt: An R Package to Perform Genome Scans for Selection Based on Principal Component Analysis (2016, neutral): “Statistical tests based on FST that do not account for hierarchical structure, when it occurs, generate a large excess of false-positive loci (Excoffier et al. 2009; Bierne et al. 2013).”
Patterns of phenotypic plasticity and local adaptation in the wide elevation range of the alpine plant Arabis alpina (2018, background): “We did so because of the particular hierarchical structure of our data, which the F-model has difficulty to account for (Excoffier et al., 2009, but see Foll et al., 2014).”
A framework for incorporating evolutionary genomics into biodiversity conservation and management (2015, neutral): “tions about demographic history [164-166], although this”
Robust Identification of Local Adaptation from Allele Frequencies (2012, background): “…history of populations can lead to a high rate of false-positive and negatives when searching for the signal of 1 Copyright 2013. local adaptation due to the unaccounted sources of variance and non-independence among populations (Robertson, 1975; Excoffier et al., 2009; Bonhomme et al., 2010).”
Likelihood-Free Inference of Population Structure and Local Adaptation in a Bayesian Hierarchical Model (2010, background): “…we expect that very highly heterozygous loci will have reduced FST, potentially leading to false positives for balancing selection (Beaumont 2008; Excoffier et al. 2009), but the amount that FST is reduced for a given level of heterozygosity depends on the number of demes in the…”
Ecological genomics meets community-level modelling of biodiversity: mapping the genomic landscape of current and future environmental adaptation. (2015, methodology): “Other computational approaches based on FST outliers (Foll & Gaggiotti 2008; Excoffier et al. 2009), or gene–environment associations (Joost et al.”
A practical guide to environmental association analysis in landscape genomics (2015, background): “Corrections for neutral genetic structure are important in EAA, because neutral genetic structure can mimic patterns expected under non-neutral processes (Excoffier & Ray 2008; Excoffier et al. 2009; but see Vilhjalmsson & Nordborg 2013).”
Population Genomics of Parallel Adaptation in Threespine Stickleback using Sequenced RAD Tags (2010, background): “3 Mb on LG I [103] (but see reanalysis by [28]).”