Table 4. Results of selection analyses per branches.

Region	Branch	Subregion	ORF	Covariation
R1	PVYN strain	116–124	P1	121
		160–165
		205–214		214
		240–245		241
	PVYO strain	116–124		121
		208–214		214
	PVY-MN	151–157
		209–214		214
	NC57	199–209
		213–223		214
		264–269
	Z16	585–591	HC-Pro
R2	Z16	757–763	P3	761
	NC57	931–949		936, 939, 943, 946, 947
	Chile3	1053–1060
		1094–1100		1094
	Gpost	1436–1442	CI
R3	SON41	2247–2250	NIa-Pro
	NC57	2370–2378	NIb	2373
	PVY-MN	2859–2865	CP

For each region under study, branches showing positive selection, location of amino acid subregions involved and ORFs are indicated. For terminal branches, the name of the corresponding isolate is shown, whereas for internal branches the strain subjected to the selection event is indicated. Covarying positions detected in the previous analyses falling into the subregions providing a positive selection signature are shown in the last column. (P<0.0001 for all subregions).