Table 1.
Testing adaptive diversification in D. simulans using D. melanogaster, D. simulans and D. sechellia sequence comparisons.
| Gene | Map | ℓM0 | ℓM1 | 2Δℓa | ℓM2 | 2Δℓb | ℓ(ω = 1) | ℓ(ω) | 2Δℓc |
|---|---|---|---|---|---|---|---|---|---|
| CG9936 | 78A | -12873.9 | -12868.2 | 11.5 | -12873.7 | 0.5 | -12843.5 | -12843.5 | 0.0 |
| CG10510 | 78C | -2045.6 | -2041.3 | 8.5 | -2042.67 | 5.9 | -2041.6 | -2041.7 | 0.2 |
| CG9389 | 78C | -2837.7 | -2834.6 | 6.2 | -2835.8 | 3.8 | -2826.2 | -2829.4 | 6.3 |
| CG32436 | 78C | -7261.6 | -7230.0 | 63.2 | -7259.4 | 4.5 | -7218.2 | -7218.2 | 0.0 |
| CG7405 | 78F | -1422.1 | -1415.9 | 12.4 | -1421.7 | 0.8 | -1422.1 | -1422.1 | 0.0 |
| CG7478 | 79A | -1288.0 | -1283.4 | 9.1 | -1283.4 | 9.1 | -1276.9 | -1281.2 | 8.5 |
| CG31542 | 83A | -898. 2 | -892.0 | 12.3 | -893.4 | 9.6 | -873.4 | -887.2 | 27.6 |
| CG1041 | 83E | -2402.3 | -2394.8 | 15.1 | -2399.3 | 5.9 | -2386.2 | -2382.2 | 0.0 |
| CG15179 | 84A | -890.0 | -889.2 | 1.7 | NA | NA | -878.3 | -888.5 | 20.5 |
| CG1030 | 84A | -1954.5 | -1946.0 | 16.9 | -1953.7 | 1.6 | -1936.7 | -1936.7 | 0.0 |
| CG1984 | 84B | -2081.0 | -2074.0 | 14.0 | -2074.3 | 13.3 | -1992.6 | -2014.7 | 44.2 |
| CG7362d | 88D | -2209.9 | -2209.1 | 1.4 | NA | NA | -2199.2 | -2202.4 | 6.3 |
| CG6125 | 88F | -3268.6 | -3259.0 | 19.2 | -3268.3 | 0.6 | -3246.1 | -3246.1 | 0.0 |
| CG3158 | 89A | -4968.6 | -4960.7 | 15.7 | -4961.8 | 13.6 | -4775.0 | -4911.8 | 273.6 |
| CG14891d | 89B | -2687.7 | -2685.4 | 4.7 | NA | NA | -2688.1 | -2691.4 | 6.5 |
| CG31287 | 89B | -1220.8 | -1220.5 | 0.6 | NA | NA | -1203.8 | -1216.2 | 24.8 |
| CG6963 | 89B | -2061.3 | -2057.8 | 7.0 | -2060.1 | 2.5 | -2053.4 | -2053.4 | 0.0 |
| CG31232e | 91A | -664.5 | -659.8 | 9.5 | -661.7 | 5.5 | -643.1 | -643.1 | 0.0 |
| CG14307e | 91A | -4285.9 | -4278.2 | 15.4 | -4279.2 | 13.4 | -4066.8 | -4175.1 | 216.5 |
| CG6255 | 92A | -2099.4 | -2088.3 | 22.1 | -2088.4 | 21.9 | -1966.6 | -2039.2 | 145.3 |
| CG4836 | 92B | -6245.6 | -6229.6 | 32.1 | -6245.5 | 0.2 | -6190.0 | -6204.6 | 29.1 |
| CG12249 | 92B | -3301.2 | -3297.0 | 8.4 | -3298.2 | 6.0 | -3301.2 | -3301.2 | 0.0 |
aThe test statistics compares the likelihood (ℓ) of the free-ratios model (ℓM1) to the likelihood of a model that assumes constant ratios along branches (ℓM0). The test statistics follows a chi-square distribution with two degrees of freedom. Significant values (P < 0.05) are bolded.
bThe test statistics compares the likelihood (ℓ) of a model allowing for an ω estimate along the D. simulans branch and a different ω estimate for the background branches (ℓM2) to the likelihood of a model that assumes constant ratios along branches (ℓM0). The test statistics follows a chi-square distribution with one degree of freedom. Significant values (P < 0.05) are bolded.
cThe test statistics compares the likelihood (ℓ) of a branch-site model with the same model but fixing the foreground ω to 1. The test statistics follows a chi-square distribution with one degree of freedom. Significant values (P < 0.05) are bolded.
dComparisons are D. melanogaster -- D. simulans -- D. mauritiana.
eVariable results depending on the D. melanogaster open reading frame used in the analysis (See Additional file 1).