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Table 1 Likelihood values and parameter estimates for 45 S gene sequences from the whole epidemic of SARS from 2002 to 2004.

From: Adaptive evolution of the spike gene of SARS coronavirus: changes in positively selected sites in different epidemic groups

Model code lnL dN/dS Estimates of parameters l Positively selected sites
M0 (one-ratio) -5818.14 0.64 ω = 0.64 51.91 None
M3 (discrete) -5792.19 0.69 p0 = 0.43340, p1 = 0.50712 (p2 = 0.05948), ω0 = 0.12, ω1 = 0.13, ω2 = 9.68 (13.28) 75T 239S 244T 311G 479R 609L 613E 743R 765V 778D 1148L 1163E
M1a (NearlyNeutral) -5807.78 0.36 p0 = 0.63944 (p1 = 0.36056) 31.25 Not allowed
M2a (PositiveSelection) -5792.16 0.69 p0 = 0.78594, p1 = 0.16251 (p2 = 0.05155), ω2 = 10.29 (9.21) 75T 239S 244T 311G 479R 609L 613E 743R 765V 778D 1148L 1163E
M7 (beta) -5807.92 0.40 p = 0.00568, q = 0.00856 31.51 Not allowed
M8 (beta&v) -5792.16 0.69 p0 = 0.94614 (p1 = 0.05386)
p = 0.05787, q = 0.30879, ω = 10.11
(9.21) 75T 239S 244T 311G 479R 609L 613E 743R 765V 778D 1148L 1163E
  1. The values in parentheses represent the significant level of 0.01 with a χ2distribution at d.f. = 4 (M0 vs. M3) or 2 (M1a vs. M2a and M7 vs. M8). The amino acid sequence of strain PC4-13 was used as the sequence reference, and positive selected sites were identified with posterior probability p ≥ 0.9. In boldface, p ≥ 0.95.