Table 2.

Results obtained from tests of selection on the mitochondrial genome of the Atlantic salmon

Locus	Position	Type of selection	MEME		FUBAR		TreeSAAP (Category)
			ω+	P	dN-dS	Post. P
ND1	3878:C/T	-			−9.924	0.997
	3926:C/T	-			−5.068	0.920
	3989:A/G	-			−8.576	0.995
	4424:C/T	-			−4.683	0.913
	4517:G/A	-			−4.613	0.993
	4568:C/T	-			−4.683	0.918
	4578:G/A	+	>100	0.175	3.793	0.918	Alpha-helical tendencies (6)
	4718:C/T	-			−5.153	0.902
ND2	5161:A/G	-			−5.017	0.923
	5290:A/G	-			−4.086	0.914
	5341:T/C	+	>100	0.564	−0.328	0.569	Alpha-helical tendencies (6)
	5365:C/T	-			−7.495	0.991
	5416:A/G	-			−6.931	0.987
	5768:G/A	+	>100	0.216	0.855	0.805	Alpha-helical tendencies (6)
	5812:C/A	-			−3.339	0.902
COX1	6970:C/T	-			−6.446	0.987
	7021:A/G	-			−4.431	0.906
	7039:A/G	-			−4.428	0.905
	7483:G/A	-			−7.016	0.997
	7684:T/C	-			−6.419	0.983
COX2	8492:T/C	-			−4.749	0.888
ATP6	9281:A/G	-			−3.654	0.902
	9314:T/C	-			−2.981	0.891
	9356:C/T	-			−2.984	0.893
	9551:A/G	-			−1.253	0.928
ND3	10963:C/A	+	>100	0.423	2.706	0.901	Equil const ion COOH (8)
	10879:T/C	-			−6.959	0.996
ND4	11489:A/G	-			−3.031	0.979
	11693:C/T	-			−9.421	0.989
	11762:T/C	-			−8.488	0.994
	11891:G/A	-			−1.439	0.915
	11906:C/T	-			−4.551	0.912
	11937:A/G	+	>100	0.006	7.564	0.972	Power to be at C-terminal (6)
	12167:A/G	-			−6.616	0.982
ND5	14405:T/C	-			−4.071	0.900
	14570:C/T	-			−4.718	0.923
CYTB	16178:A/G	-			−9.805	0.996
	16361:G/A	-			−2.654	0.950

Type of selection: positive (+) or negative (−). Sites in bold correspond to those identified by the three different methods as being under selection, those in italics are sites identified by two different methods. Thresholds for each method: MEME P < 0.1, FUBAR p > 0.9 & amino acid change categories 6–8