Table 1.

Pairwise φ-ST values of MSL and NML comparing methylation-sensitive and methylation-insensitive differentiation among (a) the EAHB morphological groups and (b) the sampling site, with outgroups denoted as distinct from the sites

Cloneset A	Cloneset B	MSL	P (MSL)	NML	P (NML)
a
Nakabululu	Nfuuka	0.002	0.343	0.004	0.352
Musakala	Nakitembe	0.001	0.390	− 0.019	0.902
Nakitembe	Nfuuka	0.023	0.061	0.016	0.196
Mbidde	Nfuuka	0.017	0.079	0.046	< 0.001
Musakala	Nfuuka	0.026	0.048	0.013	0.204
Mbidde	Nakabululu	0.022	0.076	0.008	0.241
Nakabululu	Nakitembe	0.017	0.120	0.003	0.370
Musakala	Nakabululu	0.023	0.091	0.001	0.430
Mbidde	Musakala	0.035	0.049	0.011	0.200
Mbidde	Nakitembe	0.034	0.033	0.017	0.149
O1 (Unknown)	O2 (Dessert)	0.662	0.327	0.539	0.338
O1 (Unknown)	O3 (Plantain)	0.611	0.262	0.594	0.247
O1 (Unknown)	Nfuuka	0.050	0.278	0.260	0.151
O1 (Unknown)	Nakitembe	0.089	0.196	− 0.077	0.199
O1 (Unknown)	Nakabululu	0.087	0.210	0.342	0.215
O1 (Unknown)	Mbidde	0.031	0.403	0.235	0.346
O1 (Unknown)	Musakala	0.122	0.371	0.184	0.251
O2 (Dessert)	O3 (Plantain)	0.656	0.102	0.626	0.102
O3 (Plantain)	Nfuuka	0.560	< 0.001	0.878	< 0.001
O3 (Plantain)	Nakitembe	0.522	0.002	0.761	0.001
O3 (Plantain)	Nakabululu	0.561	< 0.001	0.873	< 0.001
O3 (Plantain)	Mbidde	0.546	< 0.001	0.854	< 0.001
O3 (Plantain)	Musakala	0.611	0.001	0.841	0.002
O2 (Dessert)	Nfuuka	0.403	0.004	0.887	0.003
O2 (Dessert)	Nakitembe	0.353	0.008	0.765	0.009
O2 (Dessert)	Nakabululu	0.398	0.006	0.885	0.005
O2 (Dessert)	Mbidde	0.382	0.005	0.864	0.005
O2 (Dessert)	Musakala	0.376	0.008	0.852	0.008
b
Kenya	O2 (Dessert)	0.555	< 0.001	0.856	< 0.001
O3 (Plantain)	Kenya	0.402	< 0.001	0.858	0.001
Kenya	Uganda	0.195	< 0.001	0.016	0.013
O2 (Dessert)	O3 (Plantain)	0.656	0.102	0.626	0.102
Uganda	O2 (Dessert)	0.595	< 0.001	0.866	< 0.001
O3 (Plantain)	Uganda	0.450	< 0.001	0.870	< 0.001