Table 2.
Results from tests of selection on PPC2.
| Model | ⍵ 1 | lnL | np 2 | Significance 3 |
|---|---|---|---|---|
| M0 | ⍵ = 0.126 | −27536.821 | 44 | na |
| Branch | ⍵b = 0.126,⍵f = 0.115 | −27536.753 | 45 | LR = 0.136, P = 0.71 |
| Sites, M1a (nearly neutral) | ⍵1 = 0.07 (p1 = 0.82), ⍵2 = 1 (p2 = 0.18) | −26777.829 | 45 | na |
| sites, M2a (positive selection) | ⍵1 = 0.07 (p1 = 0.82), ⍵2 = 1 (p2 = 0.09), ⍵3 = 1 (p3 = 0.09) | −26777.829 | 47 | LR = 0 |
| MA null | 0[⍵b = 0.065, ⍵f = 0.065, p = 0.82], 1[⍵b = 1, ⍵f = 1, p = 0.18], 2a[⍵b = 0.07, ⍵f = 1, p = 0], 2b[⍵b = 1, ⍵f = 1, p = 0] | −26777.829 | 46 | na |
| MA | 0[⍵b = 0.065, ⍵f = 0.065, p = 0.82], 1[⍵b = 1, ⍵f = 1, p = 0.18], 2a[⍵b = 0.07, ⍵f = 1, p = 0], 2b[⍵b = 1, ⍵f = 1, p = 0] | −26777.829 | 47 | LR = 0 |
| M2a_rel (null for clade‐sites C tests) | ⍵1 = 0.02 (p1 = 0.59), ⍵2 = 1 (p2 = 0.09), ⍵3 = 0.23 (p3 = 0.33) | −26537.435 | 47 | na |
| Clade‐sites C | 0[⍵b = 0.01, ⍵f = 0.01, p = 0.55], 1[⍵b = 1, ⍵f = 1, p = 0.09], 2[⍵b = 0.18, ⍵f = 0.52, p = 0.36] | −26508.092 | 48 | LR = 58.68, P < 0.001 |
1
Values reported for background, foreground, in which foreground is the branch of interest in the Agavoideae; for sites models, three classes of omegas and proportion of sites in each class are reported; for branch × sites models, foreground and background values for omega are reported plus proportion of sites in each site class (0, 1, 2a and 2b).
2
Number of parameters.
3
Based on a likelihood ratio test that is χ2 distributed. na, null models that were not tested against any other null.