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Table 3 Site model parameter estimates generated by the CodeML analyses for the eight dlx paralogs

From: Sequence analyses of the distal-less homeoboxgene family in East African cichlid fishes reveal signatures of positive selection

Locus Parameter estimates under different models
M0 (one ratio) M1a (neutral) M2a (selection) M3 (discrete) M7 (ß) M8 (ß & ω) M8a (ß & ωs = 1)
dlx1a ω = 0.111 p 0  = 0.940, ω 0  = 0 p 0  = 0.980, ω 0  = 0 p 0  = 0.640, ω 0  = 0 p = 0.005, q = 0.049 p = 0.005, q = 22.651 p = 1.333, q = 24.671
p 1  = 0.060, ω 1  = 1 p 1  = 0, ω 1  = 1 p 1  = 0.340, ω 1  = 0 p 0  = 0.980 p 0  = 0.936
p 2 = 0.020, ω 2 = 12.580 p 2 = 0.020, ω 2 = 12.580 p 1 = 0.020, ω= 12.580 p 1  = 0.065, ω = 1
dlx2a ω = 0.457 p 0  = 0.833, ω 0  = 0 p 0  = 0.879, ω 0  = 0 p 0  = 0, ω 0  = 0 p = 0.005, q = 0.011 p = 0.005, q = 0.046 p = 0.005, q = 12.618
p 1  = 0.167, ω 1  = 1 p 1  = 0.110, ω 1  = 1 p 1  = 0.986, ω 1  = 0.081 p 0  = 0.989 p 0  = 0.833
p 2 = 0.010, ω 2 = 18.903 p 2 = 0.014, ω 2 = 16.629 p 1 = 0.011, ω= 18.053 p 1  = 0.167, ω = 1
dlx3a ω = 0.320 p 0  = 0.758, ω 0  = 0 p 0  = 0.921, ω 0  = 0 p 0  = 0.877, ω 0  = 0 p = 0.005, q = 0.017 p = 0.015, q = 0.088 p = 0.005, q = 13.826
p 1  = 0.242, ω 1  = 1 p 1  = 0.034, ω 1  = 1 p 1 = 0.120, ω 1 = 2.099 p 0  = 0.032 p 0  = 0.758
p 2 = 0.045, ω 2 = 4.451 p 2 = 0.003, ω 2 = 11.657 p 1 = 0.032, ω= 5.096 p 1  = 0.242, ω = 1
dlx3b ω = 0.047 p 0  = 1, ω 0  = 0.047 p 0  = 1, ω 0  = 0.047 p 0  = 0.243, ω 0  = 0.047 p = 4.896, q = 99.00 p = 4.895, q = 99.00 p = 4.895, q = 99.00
p 1  = 1E-5, ω 1  = 1 p 1  = 0, ω 1  = 1 p 1  = 0.262, ω 1  = 0.047 p 0  = 1 p 0  = 1
p 2  = 0, ω 2  = 1 p 2  = 0.495, ω 2  = 0.047 p 1  = 1E-5, ω = 1 p 1  = 1E-5, ω = 1
dlx4a ω = 0.050 p 0  = 1, ω 0  = 0.050 p 0  = 1, ω 0  = 0.050 p 0  = 0.216, ω 0  = 0.050 p = 5.267, q = 99.00 p = 5.266, q = 99.00 p = 0.137, q = 2.305
p 1  = 1E-5, ω 1  = 1 p 1  = 0, ω 1  = 1 p 1  = 0.384, ω 1  = 0.050 p 0  = 1 p 0  = 1
p 2  = 0, ω 2  = 1 p 2  = 0.400, ω 2  = 0.050 p 1  = 1E-5, ω = 1 p 1  = 1E-5, ω = 1
dlx4b ω = 0.259 p 0  = 0.872, ω 0  = 0 p 0  = 0.993, ω 0  = 0.090 p 0  = 0, ω 0  = 0 p = 0.005, q = 0.042 p = 9.871, q = 99.00 p = 0.005, q = 30.817
p 1  = 0.128, ω 1  = 1 p 1  = 0, ω 1  = 1 p 1  = 0.993, ω 1  = 0.090 p 0  = 0.993 p 0  = 0.872
p 2 = 0.007, ω 2 = 12.858 p 2 = 0.007, ω 2 = 12.858 p 1 = 0.007, ω= 12.859 p 1  = 0.128, ω = 1
dlx5a ω = 1E-4 p 0  = 1, ω 0  = 0 p 0  = 1, ω 0  = 0 p 0  = 0.424, ω 0  = 0 p = 0.005, q = 1.294 p = 0.005, q = 99.00 p = 0.005, q = 44.274
p 1  = 1E-5, ω 1  = 1 p 1  = 0, ω 1  = 1 p 1  = 0.420, ω 1  = 0 p 0  = 1 p 0  = 1
p 2  = 0, ω 2  = 1 p 2  = 0.156, ω 2  = 0 p 1  = 1E-5, ω = 1 p 1  = 1E-5, ω = 1
dlx6a ω = 0.029 p 0  = 0.967, ω 0  = 0 p 0  = 0.992, ω 0  = 0 p 0  = 0.899, ω 0  = 0 p = 0.066, q = 1.696 p = 0.005, q = 2.390 p = 0.005, q = 1.672
p 1  = 0.033, ω 1  = 1 p 1  = 0, ω 1  = 1 p 1  = 0.093, ω 1  = 0 p 0  = 0.992 p 0  = 0.967
p 2 = 0.008, ω 2 = 6.336 p 2 = 0.008, ω 2 = 6.336 p 1 = 0.008, ω= 6.336 p 1  = 0.033, ω = 1
  1. Note: p0-2 are the proportions of sites assigned to an ω category or to a beta distribution with p and q as parameters. ω ratios greater than one and their corresponding proportions are depicted in bold.