TABLE 2

Maximum-likelihood analysis of variation in the dN/dS ratio (= ω) across branches and across sites

ModelParameter estimatesNo. of parametersCandidate sites for positive selection
Lineage models (Yang 1998)
    One ratioω = 0.33−1564.3715NA
    Two ratioωT3 = 1.19, ωBackground = 0.20−1550.8516NA
    Three ratioωT3 Rat = 1.38, ωT3 Pero = 1.04, ωBackground = 0.20−1550.7517NA
Branch-site models (foreground branch: HBA-T3Rat)
    Null Aω0-b = ω0-f = 0.03, (p0 = 0.54)−1517.8217NA
ω1-b = ω1-f = 1.00, (p1 = 0.25)
ω2A-b = 0.03, ω2A-f = 1.00, (p2A = 0.14)
ω2B-b = 1.00, ω2B-f = 1.00, (p2B = 0.07)
    Aω0-b = ω0-f = 0.03, (p0 = 0.62)−1511.541819(AB1) Gly →
ω1-b = ω1-f = 1.00, (p1 = 0.29)Asn**
ω2A-b = 0.03, ω2A-f = 19.62, (p2A = 0.06)24(B5) Tyr → Ile**
ω2B-b = 1.00, ω2B-f = 19.62, (p2B = 0.03)29(B10) Leu → Ile*
38(C3) Thr → Ser*
39(C4) Thr → Ser*
48(CD6) Val → Thr**
50(CD8) Pro → Glu*
Branch-site models (foreground branch: HBA-T3Pero)
    Null Aω0-b = ω0-f = 0.03, (p0 = 0.56)−1519.3617NA
ω1-b = ω1-f = 1.00, (p1 = 0.29)
ω2A-b = 0.03, ω2A-f = 1.00, (p2A = 0.09)
ω2B-b = 1.00, ω2B-f = 1.00, (p2B = 0.05)
    Aω0-b = ω0-f = 0.03, (p0 = 0.62)−1512.791832(B13) Met → Asp**
ω1-b = ω1-f = 1.00, (p1 = 0.32)36(C1) Phe → Pro**
ω2A-b = 0.03, ω2A-f = , (p2A = 0.04)58(E7) His → Gln*
ω2B-b = 1.00, ω2B-f = , (p2B = 0.02)
  • Maximum-likelihood estimates of ω that are indicative of positive selection are in italics. **P > 0.95, *0.95 > P > 0.75.