Table 1.
Results from tests of selection on PPC1.
| Branch | Model | ⍵ 1 | lnL | np 2 | Significance 3 |
|---|---|---|---|---|---|
| na | M0 | ⍵ = 0.077 | −52767.838 | 110 | na |
| PPC1‐A | Branch | ⍵b = 0.078, ⍵f = 0.013 | −52762.554 | 111 | LR = 10.57, P = 0.001 |
| PPC1‐B | Branch | ⍵b = 0.077, ⍵f = 0.065 | −52767.705 | 111 | LR = 0.265, P = 0.608 |
| na | Sites, M1a (nearly neutral) | ⍵1 = 0.059 (p1 = 0.92), ⍵2 = 1 (p2 = 0.08) | −52185.176 | 111 | na |
| na | Sites, M2a (positive selection) | ⍵1 = 0.059 (p1 = 0.92), ⍵2 = 1 (p2 = 0.05), ⍵3 = 1 (p3 = 0.03) | −52185.176 | 113 | LR = 0 |
| PPC1‐A | MA null | 0[⍵b = 0.059, ⍵f = 0.059, p = 0.92], 1[⍵b = 1, ⍵f = 1, p = 0.08], 2a[⍵b = 0.059, ⍵f = 1, p = 0], 2b[⍵b = 1, ⍵f = 1, p = 0] | −52185.176 | 112 | na |
| PPC1‐A | MA | 0[⍵b = 0.059, ⍵f = 0.059, p = 0.92], 1[⍵b = 1, ⍵f = 1, p = 0.08], 2a[⍵b = 0.059, ⍵f = 39.8, p = 0.002], 2b[⍵b = 1, ⍵f = 1, p = 0] | −52185.176 | 113 | LR = 0 |
| PPC1‐B | MA null | 0[⍵b = 0.059, ⍵f = 0.059, p = 0.92], 1[⍵b = 1, ⍵f = 1, p = 0.08], 2a[⍵b = 0.059, ⍵f = 1, p = 0], 2b[⍵b = 1, ⍵f = 1, p = 0] | −52185.176 | 112 | na |
| PPC1‐B | MA | 0[⍵b = 0.059, ⍵f = 0.059, p = 0.92], 1[⍵b = 1, ⍵f = 1, p = 0.08], 2a[⍵b = 0.059, ⍵f = 39.8, p = 0.002], 2b[⍵b = 1, ⍵f = 39.8, p = 0.0002] | −52182.449 | 113 | LR = 5.45, P = 0.019 |
| na | M2a_rel (null for clade‐sites C tests) | ⍵1 = 0.02 (p1 = 0.72), ⍵2 = 1 (p2 = 0.02), ⍵3 = 0.22 (p3 = 0.26) | −51414.294 | 113 | na |
| PPC1‐A | Clade‐sites C | 0[⍵b = 0.02, ⍵f = 0.02, p = 0.72], 1[⍵b = 1, ⍵f = 1, p = 0.016], 2[⍵b = 0.23, ⍵f = 0.27, p = 0.26] | −51413.361 | 114 | LR = 1.87, P = 0.17 |
| PPC1‐B | Clade‐sites C | 0[⍵b = 0.02, ⍵f = 0.02, p = 0.71], 1[⍵b = 1, ⍵f = 1, p = 0.02], 2[⍵b = 0.21, ⍵f = 0.44, p = 0.27] | −51392.506 | 114 | LR = 43.58, 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 (p) in each class are reported; for branch × sites models, foreground and background values for omega are reported plus a proportion of sites in each site class (0, 1, 2a and 2b).
2
Number of parameters.
3
Based on a likelihood ratio test which is χ2 distributed. na, null models that were not tested against any other null.