From: Molecular evolution of psbA gene in ferns: unraveling selective pressure and co-evolutionary pattern
Models | Ts/Tv | np | â„“ | Estimated value of parameters | Positively selected codons** |
---|---|---|---|---|---|
Dataset one* | Â | Â | Â | Â | Â |
M0: One ratio | 4.38 | 22 | -3906.05 | ω = 0.0184 | None |
M1a: Near neutral | 4.55 | 23 | -3858.84 | p0 = 97.14%, ω0 = 0.00618; p1 = 2.86%, ω1 = 1 | Not allowed |
M2a: Positive | 4.55 | 25 | -3858.83 | p0 = 97.14%, ω0 = 0.00618; p1 = 2.86%, ω1 = 1; p2 = 0%, ω2 = 79.26 | 91 L (97.2%) |
M3: Discrete | 4.60 | 26 | -3854.64 | p0 = 96.31%, ω0 = 0.00488; p1 = 3.39%, ω1 = 0.5646; p2 = 0.3%, ω2 = 3.9847 | 91 L (99.8%) |
M7: β | 4.48 | 23 | -3865.36 | p = 0.0267, q = 0.614 | Not allowed |
M8: β &ω > 1 | 4.53 | 25 | -3857.78 | p0 =97.84%, p = 0.01575, q = 0.46508; p1 = 2.15%, ω = 1.08788 | 91 L (99.7%) |
Dataset two* | Â | Â | Â | Â | Â |
M0: One ratio | 5.97 | 29 | -3093.72 | ω = 0.02403 | None |
M1a: Near neutral | 6.07 | 30 | -3061.96 | p0 = 96.57%, ω0 = 0.00127; p1 = 3.43%, ω1 = 1 | Not allowed |
M2a: Positive | 5.80 | 32 | -3061.96 | p0 = 96.57%, ω0 = 0.00127; p1 = 3.43%, ω1 = 1; p2 = 0, ω2 = 34.2681 | 347E (58.3%) |
M3: Discrete | 5.71 | 33 | -3060.47 | p0 = 46.14%, ω0 = 0; p1 = 49.52%, ω1 = 0; p2 = 4.31%, ω2 = 0.61912 | None |
M7: β | 5.75 | 30 | -3064.99 | p = 0.00981, q = 0.19983 | Not allowed |
M8: β &ω > 1 | 5.80 | 32 | -3061.93 | p0 =96.61%, p = 0.01744, q = 2.58197; p1 = 3.38%, ω = 1 | 347E (81.6%), 349P (61.5%), 353 G (54.4%) |
Dataset three* | Â | Â | Â | Â | Â |
M0: One ratio | 4.66 | 47 | -5742.02 | ω = 0.01934 | None |
M1a: Near neutral | 4.87 | 48 | -5654.74 | p0 = 96.39%, ω0 = 0.00538; p1 = 3.6%, ω1 = 1 | Not allowed |
M2a: Positive | 4.18 | 50 | -5656.81 | p0 = 96.47%, ω0 = 0.0054; p1 = 3.55%, ω1 = 1; p2 = 0, ω2 = 4.46 | 71 L (72.4%), 91 L (78.0%) |
M3: Discrete | 4.90 | 51 | -5637.73 | p0 = 90.54%, ω0 = 0; p1 = 8.51%, ω1 = 0.5308; p2 = 0.943%, ω2 = 1.71 | 71 L (96.1%), 91 L (97.1%), 351 V (81.3%) |
M7: β | 4.78 | 48 | -5648.93 | p = 0.03078, q = 0.63009 | Not allowed |
M8: β &ω > 1 | 5.09 | 50 | -5641.45 | p0 =98.21%, p = 0.01555, q = 0.36594; p1 = 1.78%, ω = 1.19067 | 71 L (96.4%), 91 L(97.2%), 351 V (84.9%) |