Fig. 6.

Results in terms of MCC scores of the three correlation-aware statistical methods (x axis) on the pPLN base scenario with an effect size of $3$, a BM model of evolution on the maximum likelihood tree (Stern and Crandall 2018a), with the observed “sight” groups, and intraspecies variation accounting for $40\text{\%}$ (light orange line), $20\text{\%}$ (dark purple line), or $0\text{\%}$ (black line) of the total variance). The counts were normalized using ${\log }_2(\text{TPM})$ values. Boxplots are based on $50$ replicates.