Appendix 1—table 3. Numbers of truly and falsely predicted concordantly evolving pairs of sites for the simulated data with positively and negatively epistatically interacting sites.

The evolution of the population of genotypes with twenty independently evolving pairs of epistatically interacting sites was simulated by MimicrEE2. Ten pairs of sites were evolving under recurrent positive epistasis and other ten pairs were evolving under magnitude negative epistasis. The four different detection models were applied and for each model the number of true (#TP) and false (#FP) predictions are shown for estimated FDR≤10%.

Model		#FP	#TP
consider alleles	shuffle mutations in fgr. only	5	10
	shuffle mutations both in bgr. and fgr.	55	6
ignore alleles	shuffle mutations in fgr. only	22	8
	shuffle mutations both in bgr. and fgr.	250	7