Table 2.

Significant DMRs identified in comparisons of lake and river sites.

Comparison		1 Window DMR	≥2 Window DMR
Between sites within habitat	Lake 1 v. Lake 2	21	6
	River 2 v. River 1	8	4
Between habitats for each combination	Lake 1 v. River 1	138	26
	Lake 1 v. River 2	288	51
	Lake 2 v. River 1	253	57
	Lake 2 v. River 2	292	63

The p-value thresholds for all analyses were 1e-05. A large majority of DMRs appear to be habitat specific and associated with adaptive phenotypic differences.