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 (ASKLFPDTVEEY)

321

FR

-

326

FR

-

356

FRS

-

^a F = 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).

^c Excludes codons 217–282 that are expressed in different frames in rep and repA.

Harkins et al. Virology Journal 2009 6:104   doi:10.1186/1743-422X-6-104