Abstract
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.
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