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Table 2 Phylogenetic analysis by ML estimation for SARS S gene sequences from different epidemic groups.

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

Epidemic phases Model code lnL dN/dS Estimates of parameters 2Δl Positive selection
02–04 interspecies epidemic group M0 (one-ratio) -5339.90 0.64 ω = 0.64 40.23 Yes
  M3 (discrete) -5319.78 0.77 p0 = 0.00000, = p1 = 0.99407 (p2 = 0.00593), ω0 = 0.00, ω1 = 0.38, ω2 = 66.02 (13.28)  
  M1a (NearlyNeutral) -5334.74 0.35 p0 = 0.65391 (p1 = 0.34609) 29.92 Yes
  M2a (PositiveSelection) -5319.78 0.77 p0 = 0.99407, p1 = 0.00000 (p2 = 0.00593), ω2 = 66.01 (9.21)  
  M7 (beta) -5336.08 0.30 p = 0.01702, q = 0.03977 32.23 Yes
  M8 (beta&v) -5319.97 0.80 p0 = 0.99405 (p1 = 0.00595), p0 = 0.01217, q = 0.01714 ω = 67.24 (9.21)  
03-early-mid epidemic group M0 (one-ratio) -5194.47 0.94 ω = 0.94 24.25 Yes
  M3 (discrete) -5182.34 1.10 p0 = 0.05053, p1 = 0.92251 (p2 = 0.02696), ω0 = ω1 = 0.00, ω2 = 40.88 (13.28)  
  M1a (NearlyNeutral) -5192.6 9 0.45 p0 = 0.54981 (p1 = 0.45019) 20.70 Yes
  M2a (PositiveSelection) -5182.34 1.10 p0 = 0.97303, p1 = 0.00000 (p2 = 0.02696), ω2 = 40.88 (9.21)  
  M7 (beta) -5192.73 0.40 p = 0.00510, q = 0.00776 20.78 Yes
  M8 (beta&v) -5182.34 1.10 p0 = 0.97303 (p1 = 0.02697), p = 0.00500, q = 1.39962, ω = 40.87 (9.21)  
03-late epidemic group M0 (one-ratio) -5121.66 0.26 ω = 0.26 NA No
  M3 (discrete) -5121.66 0.26 p0 = 0.43056, p1 = 0.37490 (p2 = 0.19455), ω0 = 0.25, ω1 = 0.26, ω2 = 0.26 (13.28)  
  M1a (NearlyNeutral) -5121.66 0.26 p0 = 1.00000 (p1 = 0.00000) NA No
  M2a (PositiveSelection) -5121.66 0.26 p0 = 1.00000, p1 = 0. 00000 (p2 = 0.00000), ω0 = 0.26, ω1 = ω2 = 1.00 (9.21)  
  M7 (beta) -5121.66 0.25 p = 33.88884, q = 99.00000 NA No
  M8 (beta&v) -5121.68 0.26 p0 = 1.00000 (p1 = 0.00000), p = 0.64576, q = 1.83663, ω = 2.08 (9.21)  
  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). NA, not applicable.
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BMC Microbiology

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