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dc.contributor.author Lotterhos, Katie E
dc.date.accessioned 2019-04-12T20:36:18Z
dc.date.available 2019-04-12T20:36:18Z
dc.date.issued 2019-04-10
dc.identifier doi:10.5061/dryad.rj0kj10
dc.identifier.citation Lotterhos KE (2019) The Effect of Neutral Recombination Variation on Genome Scans for Selection. G3: Genes - Genomes - Genetics.
dc.identifier.uri http://hdl.handle.net/10255/dryad.211683
dc.description Recently, there has been an increasing interest in identifying the role that regions of low recombination or inversion play in adaptation of species to local environments. Many examples of groups of adapted genes located within inversions are arising in the literature, in part inspired by theory that predicts the evolution of these so-called “supergenes.” We still, however, have a poor understanding of how genomic heterogeneity, such as varying rates of recombination, may confound signals of selection. Here, I evaluate the effect of neutral inversions and recombination variation on genome scans for selection, including tests for selective sweeps, differentiation outlier tests, and association tests. There is considerable variation among methods in their performance, with some methods being unaffected and some showing elevated false positive signals within a neutral inversion or region of low recombination. In some cases the false positive signal can be dampened or removed, if it is possible to use a quasi-independent set of SNPs to parameterize the model before performing the test. These results will be helpful to those seeking to understand the importance of regions of low recombination in adaptation.
dc.relation.haspart doi:10.5061/dryad.rj0kj10/1
dc.relation.isreferencedby doi:10.1534/g3.119.400088
dc.subject principal components
dc.subject adaptation
dc.subject population structure
dc.subject linkage disequilibrium
dc.title Data from: The effect of neutral recombination variation on genome scans for selection
dc.type Article
dc.contributor.correspondingAuthor Lotterhos, Katie E
prism.publicationName G3: Genes - Genomes - Genetics
dryad.fundingEntity 1655701@National Science Foundation (United States)

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Description This zip file contains all scripts and simulation outputs from SLiM, including raw tree files. See the GitHub repository https://github.com/TestTheTests/TTT_RecombinationGenomeScans for more information, and filtered vcf files used for all analyses.
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