Table 1.

Number of differentially methylated regions broken down by context and type.

Comparison	Context	Typea	DMR	Sweep DMRb	Interacting DMRc	Interacting DMRs in sweepsd
Teosinte vs. Landrace	CG	Hypo in landrace	287	80 (27.8%, P = 0.001)*	96 (33.4%, P = 0.001)*	18 (18.7%, P = 0.02)*
		Hyper in landrace	144	36 (25%, P = 0.001)*	61 (42.3%, P = 0.001)*	6 (9.8%, P = 6.5 × 10−4)*
	CHG	Hypo in landrace	438	121 (27.6%, P = 0.001)*	115 (26.2%, P = 0.001)*	22 (19.1%, P = 0.024)*
		Hyper in landrace	150	45 (30%, P = 0.002)*	39 (26%, P = 0.001)*	8 (20.5%, P = 0.19)
Landrace vs. Maize	CG	Hypo in maize	143	29 (20.2%, P = 0.078)*	45 (31.4%, P = 0.01)*	9 (20%, P = 1)
		Hyper in maize	28	13 (46.4%, P = 0.001)	3 (10.7%, P = 0.47)	1 (33.3%, P = 1)
	CHG	Hypo in maize	158	36 (22.7%, P = 0.027)*	46 (29.1%, P = 0.001)*	10 (21.7%, P = 1)
		Hyper in maize	30	13 (43.3%, P = 0.001)*	5 (16.6%, P = 0.12)	1 (20%, P = 0.5)
Teosinte vs. Maize	CG	Hypo in maize	998	281 (28.1%, P = 0.001)*	396 (39.6%, P = 0.001)*	67 (16.9%, P = 2.4 × 10−10)*
		Hyper in maize	544	147 (27%, P = 0.001)*	259 (47.6%, P = 0.001)*	32 (12.3%, P = 4.2 × 10−13)*
	CHG	Hypo in maize	1,855	490 (26.4%, P = 0.001)*	594 (32%, P = 0.001)*	104 (17.5%, P = 3.3 × 10−9)*
		Hyper in maize	503	159 (3x1.6%, P = 0.001)*	124 (24.6%, P = 0.001)*	19 (15.3%, P = 1.1 × 10−5)*

^aHypo and hyper indicate hypomethylated and hypermethylated regions in a given population.

^bNumber of DMR overlapped with selective sweeps (Sweep DMR/total DMR). Statistical significance was determined using one-sided permutation test (*P < 0.05).

^cNumber of DMR involved in interactive loops (Interacting DMR/total DMR). Statistical significance was determined using one-sided permutation test (*P < 0.05).

^dNumber of interacting DMR overlapped with selective sweeps (Interacting DMRs in sweeps/total interacting DMR, χ²-test, *P < 0.05).