The number of highly differentiated sites between each pair of treatments.

For each pair of treatments, we performed CMH tests on each site using the five replicate populations from each treatment. For the Cad vs Salt comparison here we used only the five replicate populations for each treatment; for the main analysis discussed in the text we also included the ancestral populations of each treatment (AC and AS). We did five different ways of pairings for the tests. The q-value was calculated from the p-value for each pairing in the CMH test and then transformed by the “BY” method. Then we used q-value cutoff equals 10−5 to pick up the significant sites that pass this cutoff for all five ways of pairings. For the Salt-Cad pairs in the Table, 93.8% of the significant sites (90661) are found in the β-sites (123291) and for Temp-Spatial, it is just 13.7% of them (488). For Salt-Temp, Salt-Spatial, Cad-Temp, Cad-Spatial pairs, there are 71.8%, 82.8%, 64.3% and 78.2% of their own significant sites found in the β-sites (six Salt-six Cad) respectively.