TABLE 2.

Definitions of each metric used to assess a selection detection method's accuracy with the simulated data

Accuracy metric	Definition	Equationa
True discovery rate	The proportion of all simulated loci identified as outliers that were actually under selection (i.e., QTL loci)	$\frac{\text{Osel}}{\text{Osel}+\text{Onet}}$
True positive rate	The proportion of loci under selection (i.e., QTL loci) correctly identified as an outlier	$\frac{\text{Osel}}{\text{Totalsel}}$
False positive rate	The number of neutral loci incorrectly identified as under selection (false positive outliers) divided by the number of retained polymorphic neutral SNPs	$\frac{\text{Onet}}{\text{Totalnet}}$
False discovery rate	The proportion of outlier SNPs that were false positives (i.e., simulated neutral loci) (Lotterhos & Whitlock, 2014)	$\frac{\text{Onet}}{\text{Osel}+\text{Onet}}$
False negative rate	The proportion of polymorphic QTLs that were not identified as outliers (and thus not identified as under selection)	$\frac{\text{Totalsel}‐\text{Osel}}{\text{Totalsel}}$

^a Osel, outer loci truly under selection; Onet, false positive neutral outlier loci; Totalsel, total number of polymorphic loci under selection; Totalnet, total number of polymorphic neutral loci.