Experimental evidence indicating that mastreviruses probably did not co-diverge with their hosts

Table 2 Site-by-site signals of positive and negative selection acting on movement protein (mp), coat protein (cp) and replication associated protein (rep) gene codons during the SSRV evolution experiment

Gene	Codon	Method^a	Selection^b	Motif/domain (site underlined where relevant)
mp	21	R	+
	63	R	+	C-terminal boundary of hydrophobic domain
cp	3	R	-	DNA Binding domain
	67	R	-	DNA Binding domain
	69	R	-	DNA Binding domain
	85	FR	-	DNA Binding domain
	105	FR	-	DNA Binding domain
	122	FR	-
	136	R	-
	157	FRS	-
	180	R	-
	201	R	-
	217	R	-
	219	R	-
rep ^b	7	FR	-
	28	FR	-	RCR motif I (FLTYPHC)
	30	FR	+
	133	FR	-
	147	FR	-
	155	FR	-
	158	FR	-
	185	FRS	-	Rep-Rep oligomerisation domain (ASKLFPD TVEEY)
	321	FR	-
	326	FR	-
	356	FRS	-

^aF = Fixed effects likelihood method; R = Relative effects likelihood method; S = Single likelihood ancestor counting method.
^b+ = evidence of positive selection (p-value < 0.1); - = evidence of negative selection (p-value < 0.1).
^cExcludes codons 217–282 that are expressed in different frames in rep and repA.

ISSN: 1743-422X