Table 1 Estimates of nucleotide substitution rate and time to the most recent common ancestor for turnip mosaic virus.

From: The Timescale of Emergence and Spread of Turnip Mosaic Potyvirus

Parameter

Protein-coding region

Major ORF

HC-Pro*

P3*

NIb*

a. All sites

Sequence length (nt)

9432

927

873

855

Sampling date range

1968–2012

1968–2014

1968–2014

1968–2014

TMRCAb (years)

  All isolates

1201 (468–2150)c (n = 106)

951 (326–1291) (n = 329)

758 (274–1548) (n = 369)

1080 (318–1605) (n = 351)

  basal-B group

321 (173–520) (n = 21)

163 (79–308) (n = 102)

174 (81–345) (n = 105)

190 (86–361) (n = 81)

    basal-B1 subgroup

252 (160–356) (n = 5)

NDd (n = 12)

ND (n = 12)

ND (n = 12)

    basal-B2 subgroup

235 (154–345) (n = 15)

114 (59–268) (n = 93)

129 (75–299) (n = 93)

141 (75–300) (n = 68)

  Iranian group

178 (95–233) (n = 20)

162 (69–305) (n = 35)

142 (62–295) (n = 35)

173 (81–314) (n = 35)

    Iranian 1 subgroup

102 (49–175) (n = 6)

90 (33–140) (n = 7)

87 (37–125) (n = 7)

89 (35–146) (n = 7)

    Iranian 2 subgroup

140 (75–207) (n = 14)

101 (45–158) (n = 28)

111 (42–183) (n = 98)

124 (57–191) (n = 28)

  basal-BR group

228 (141–344) (n = 8)

167 (46–267) (n = 15)

ND (n = 17)

ND (n = 19)

  Asian BR group

234 (145–337) (n = 7)

198 (57–279) (n = 45)

125 (47–261) (n = 69)

129 (61–244) (n = 59)

  world-B group

321 (204–479) (n = 46)

181 (59–293) (n = 130)

135 (50–192) (n = 139)

153 (80–279) (n = 153)

    world-B1 subgroup

ND (n = 3)

ND (n = 6)

ND (n = 6)

ND (n = 5)

    world-B2 subgroup

ND (n = 5)

154 (40–222) (n = 39)

86 (42–176) (n = 21)

107 (62–192) (n = 27)

    world-B3 subgroup

152 (70–205) (n = 37)

121 (32–189) (n = 83)

72 (31–119) (n = 110)

87 (36–127) (n = 120)

Substitution rate (nt/site/year)

  All isolates

8.89 × 10−4 (6.87 × 10−4–1.30 × 10−3)

1.41 × 10−3 (1.09 × 10−3–1.78 × 10−3)

1.46 × 10−3 (1.25 × 10−3–1.87 × 10−3)

1.37 × 10−3 (1.04 × 10−3–1.73 × 10−3)

  basal-B group

8.14 × 10−4 (6.70 × 10−4–1.25 × 10−3)

1.27 × 10−3 (9.02 × 10−4–2.13 × 10−3)

1.63 × 10−3 (8.29 × 10−4–3.24 × 10−3)

9.26 × 10−4 (7.91 × 10−4–2.51 × 10−3)

    basal-B1 subgroup

9.23 × 10−4 (7.90 × 10−4–1.58 × 10−3)

ND

ND

ND

    basal-B2 subgroup

7.53 × 10−4 (5.20 × 10−4–9.62 × 10−3)

1.58 × 10−3 (8.56 × 10−4–3.41 × 10−3)

1.39 × 10−3 (9.11 × 10−4–2.46 × 10−3)

1.25 × 10−3 (9.01 × 10−4–2.03 × 10−3)

  Iranian group

8.20 × 10−4 (6.84 × 10−4–1.53 × 10−3)

1.19 × 10−3 (6.23 × 10−4–2.34 × 10−3)

1.28 × 10−3 (7.22 × 10−4–3.01 × 10−3)

1.38 × 10−3 (8.01 × 10−4–3.12 × 10−3)

    Iranian 1 subgroup

9.31 × 10−4 (7.14 × 10−4–1.41 × 10−3)

1.32 × 10−3 (7.58 × 10−4–2.22 × 10−3)

1.44 × 10−3 (1.08 × 10−3–2.56 × 10−3)

1.26 × 10−3 (9.08 × 10−4–2.58 × 10−3)

    Iranian 2 subgroup

9.32 × 10−4 (7.11 × 10−4–1.48 × 10−3)

1.22 × 10−3 (7.31 × 10−4–2.51 × 10−3)

1.15 × 10−3 (8.97 × 10−4–2.67 × 10−3)

1.08 × 10−3 (9.22 × 10−4–2.18 × 10−3)

  basal-BR group

1.65 × 10−3 (8.98 × 10−4–2.03 × 10−3)

2.08 × 10−3 (8.14 × 10−4–3.54 × 10−3)

ND

ND

  Asian BR group

1.33 × 10−3 (9.04 × 10−4–1.78 × 10−3)

1.16 × 10−3 (5.99 × 10−4–1.98 × 10−3)

1.55 × 10−3 (8.62 × 10−4–2.94 × 10−3)

1.29 × 10−3 (8.07 × 10−4–3.05 × 10−3)

  world-B group

1.10 × 10−3 (7.99 × 10−4–1.77 × 10−3)

1.68 × 10−3 (7.02 × 10−4–3.25 × 10−3)

1.02 × 10−3 (5.96 × 10−4–2.81 × 10−3)

9.22 × 10−4 (4.93 × 10−4–2.15 × 10−3)

    world-B1 subgroup

ND

ND

ND

ND

  world-B2 subgroup

ND

1.35 × 10−3 (5.08 × 10−4–2.10 × 10−3)

9.16 × 10−4 (3.87 × 10−4–1.84 × 10−3)

7.45 × 10−4 (3.27 × 10−4–1.44 × 10−3)

    world-B3 subgroup

9.20 × 10−4 (5.24 × 10−4–1.69 × 10−3)

2.02 × 10−3 (9.77 × 10−4–3.05 × 10−3)

2.51 × 10−3 (1.25 × 10−3–2.97 × 10−3)

1.79 × 10−3 (1.02 × 10−3–3.69 × 10−3)

dN/dSe

0.062

0.022

0.126

0.026

No. of variable sitesf

4653/9432 (49%)

421/927 (45%)

556/873 (64%)

428/855 (50%)

b. Synonymous sites

Sequence length (nt)

6078

525

300

519

Sampling date range

1968–2012

1968–2014

1968–2014

1968–2014

TMRCA (years)

  All isolates

1570 (521–3430)

1059 (549–1401)

1134 (646–1867)

1178 (635–1791)

  basal-B group

389 (200–676)

276 (181–472)

254 (136–421)

271 (140–463)

    basal-B1 subgroup

ND

ND

ND

ND

    basal-B2 subgroup

321 (210–434)

252 (169–439)

220 (116–379)

238 (139–442)

  Iranian group

247 (155–338)

152 (69–229)

172 (63–267)

139 (57–206)

    Iranian 1 subgroup

130 (69–202)

79 (36–178)

107 (55–169)

105 (47–151)

    Iranian 2 subgroup

144 (83–217)

122 (56–202)

129 (54–213)

114 (48–205)

  basal-BR group

269 (184–363)

204 (110–374)

ND

ND

  Asian BR group

ND

276 (174–445)

222 (129–403)

199 (100–324)

  world-B group

373 (235–507)

232 (119–392)

205 (93–381)

220 (102–389)

    world-B1 subgroup

ND

ND

ND

ND

    world-B2 subgroup

ND

190 (88–324)

158 (75–252)

181 (81–297)

    world-B3 subgroup

195 (106–297)

138 (79–241)

124 (75–199)

111 (63–174)

Substitution rate (nt/site/year)

  All isolates

8.22 × 10−4 (6.25 × 10−4–1.56 × 10−3)

1.45 × 10−3 (1.13 × 10−3–1.81 × 10−3)

1.65 × 10−3 (1.29 × 10−3–2.01 × 10−3)

1.36 × 10−3 (9.91 × 10−4–1.72 × 10−3)

  basal-B group

8.55 × 10−4 (4.23 × 10−4–3.26 × 10−3)

1.23 × 10−3 (6.14 × 10−4–3.92 × 10−3)

1.71 × 10−3 (5.29 × 10−4–3.14 × 10−3)

1.62 × 10−3 (6.23 × 10−4–2.94 × 10−3)

    basal-B1 subgroup

ND

ND

ND

ND

    basal-B2 subgroup

7.21 × 10−4 (3.93 × 10−4–1.31 × 10−3)

9.13 × 10−4 (2.60 × 10−4–1.75 × 10−3)

1.12 × 10−3 (3.12 × 10−4–2.22 × 10−3)

1.23 × 10−3 (2.64 × 10−4–2.15 × 10−3)

  Iranian group

1.02 × 10−3 (6.94 × 10−4–2.14 × 10−3)

1.21 × 10−3 (6.21 × 10−4–4.11 × 10−3)

2.35 × 10−3 (4.65 × 10−4–4.25 × 10−3)

1.79 × 10−3 (3.11 × 10−4–4.01 × 10−3)

b. Synonymous sites

    Iranian 1 subgroup

9.24 × 10−4 (5.22 × 10−4–2.23 × 10−3)

1.28 × 10−3 (4.02 × 10−4–3.21 × 10−3)

2.08 × 10−3 (3.55 × 10−4–3.58 × 10−3)

1.62 × 10−3 (3.99 × 10−4–5.07 × 10−3)

    Iranian 2 subgroup

8.10 × 10−4 (4.31 × 10−4–1.67 × 10−3)

1.41 × 10−3 (2.47 × 10−4–3.31 × 10−3)

2.35 × 10−3 (2.47 × 10−4–3.59 × 10−3)

1.45 × 10−3 (6.21 × 10−4–3.61 × 10−3)

  basal-BR group

1.54 × 10−3 (7.13 × 10−4–3.24 × 10−3)

2.66 × 10−3 (1.10 × 10−3–3.48 × 10−3)

ND

ND

  Asian BR group

ND

1.38 × 10−3 (1.92 × 10−4–3.01 × 10−3)

1.89 × 10−3 (2.76 × 10−4–3.87 × 10−3)

1.58 × 10−3 (3.05 × 10−4–4.02 × 10−3)

  world-B group

1.25 × 10−3 (9.01 × 10−4–2.25 × 10−3)

1.65 × 10−3 (9.75 × 10−4–3.21 × 10−3)

9.15 × 10−4 (6.25 × 10−4–1.49 × 10−3)

1.05 × 10−3 (8.24 × 10−4–2.11 × 10−3)

    world-B1 subgroup

ND

ND

ND

ND

    world-B2 subgroup

ND

9.89 × 10−4 (3.74 × 10−4–1.48 × 10−3)

8.56 × 10−4 (3.02 × 10−4–1.35 × 10−3)

9.03 × 10−4 (2.74 × 10−4–1.57 × 10−3)

    world-B3 subgroup

8.16 × 10−4 (4.24 × 10−4–1.53 × 10−3)

2.47 × 10−3 (1.62 × 10−3–3.08 × 10−3)

3.41 × 10−3 (1.12 × 10−3–3.77 × 10−3)

2.59 × 10−3 (1.12 × 10−3–3.58 × 10−3)

No. of variable sites

2095/6078 (34%)

195/525 (37%)

110/300 (37%)

191/519 (37%)

  1. aComplete major ORF (open reading frame) (polyprotein), HC-Pro* (partial helper-component proteinase), P3* (partial protein 3) and NIb* (partial nuclear inclusion b) regions.
  2. bTime to the most recent common ancestor (years before 2012).
  3. c95% credibility intervals in parentheses.
  4. dNot determined. The data set did not pass the date-randomization test.
  5. eNon-synonymous (dN) and synonymous (dS) substitution (dN/dS) ratios were calculated for four proteins.
  6. fThe number of variable sites/total sites.
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