Table 4

Branch-Site models and tests of selection
Branch model Parameter estimates lnL p
Site class 0 1 2a 2b
Harvey M2 H0 pn 0.712 0.044 0.230 0.014 −1939.35 0.65
back ω 0.046 1.000 0.046 1.000
fore ω 0.046 1.000 1.000 1.000
M2 H1 pn 0.744 0.046 0.197 0.012 −1939.25
back ω 0.047 1.000 0.047 1.000
fore ω 0.047 1.000 1.440 1.440
Ibericus M2 H0 pn 0.866 0.040 0.090 0.004 −1945.76 0.29
back ω 0.055 1.000 0.055 1.000
fore ω 0.055 1.000 1.000 1.000
M2 H1 pn 0.897 0.042 0.058 0.003 −1945.51
back ω 0.055 1.000 0.055 1.000
fore ω 0.055 1.000 2.437 2.437
Harvey M3 H1 pn 0.587 0.249 0.115 0.049 −1916.07 0.0005
back ω 0.003 0.221 0.004 0.221
fore ω 0.003 0.221 1.497 1.497
Ibericus M3 H1 pn 0.622 0.357 0.013 0.008 −1925.01 0.017
back ω 0.004 0.198 0.004 0.198
fore ω 0.004 0.198 2.549 2.549
Clade B M3 H1 pn 0.605 0.356 0.025 0.015 −1921.68 0.33
back ω 0.002 0.169 0.002 0.169
fore ω 0.002 0.169 0.694 0.694

Branch refers to the branch allowed to have a dN/dS distribution independent of the rest of the tree; Model refers to the Nsites value in codeml; M2 is the branch-site test of positive selection; M3 is the test of divergent selection pressure. For M2:H0 the foreground ω (branch tested) is fixed at 1; (omega = 1; fix_omega = 1); for M2:H1 ω is estimated from the data (omega = 0); for M3:H0 all branches have the same distribution of ω (see Table  4, “M3” for values); for M3:H1 the branch values are estimated independently from the data. Other parameter values were codon frequency =3, and for M3, ncat = 3. dN/dS and pn is the proportion of codons with ratio ωn; κ is the transition:transversion ratio; LnL is the log likelihood, p is the result of χ2 test; bold indicates test that were statistically significant.

Gribble and Mark Welch

Gribble and Mark Welch BMC Evolutionary Biology 2012 12:134   doi:10.1186/1471-2148-12-134

Open Data