Fig. 3.

Results in terms of MCC (top), FDR (middle), and TPR (bottom) scores of the five selected statistical methods (x axis) on the pPLN base scenario, that has an effect size of $3$, a BM model of evolution with added intraspecies variation accounting for $20\text{\%}$ of the total variance, on the maximum likelihood tree (Stern and Crandall 2018a), with the observed “sight” groups (dark purple line, see fig. 1). The “alt” (light orange line) and “block” (black line) groups were also tested, with the same parameters. For the FDR, the black dashed line represents the nominal rate of $5\text{\%}$ used to call positives. When required, the counts were normalized using ${\log }_2(\text{TPM})$ values. Boxplots are based on $50$ replicates.