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

Methoda

Selectionb

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

-


repb

7

FR

-

28

FR

-

RCR motif I (FLTYPH

    C
)

30

FR

+

133

FR

-

147

FR

-

155

FR

-

158

FR

-

185

FRS

-

Rep-Rep oligomerisation domain (ASKLFP

    D
TVEEY)

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

Open Data