Table 3. Population genetic diversity statistics for the invariant genes tested for evidence of positive selection.
| Gene | Trait | Panel | L | l | S | π | θ | Sig. |
| ACTIN-RELATED PROTEIN 7 | Pleiotropic effects on | W | 549 | 48.67 | 2 | 0.01761 | 0.01585 | ns |
| plant development | P | - | - | - | - | - | - | |
| I | 549 | 48.67 | 0 | 0 | 0 | ns | ||
| BLIND | Branching | W | 383 | 12.17 | 0 | 0 | 0 | ns |
| P | - | - | - | - | - | - | ||
| I | 383 | 12.17 | 0 | 0 | 0 | ns | ||
| CHALCONE SYNTHASE | Plant growth; regulation | W | 310 | 40.81 | 0 | 0 | 0 | ns |
| of auxin | P | - | - | - | - | - | - | |
| I | 310 | 40.67 | 0 | 0 | 0 | ns | ||
| CONSTANS | Flowering | W | 483 | 114.17 | 9 | 0.03213 | 0.02787 | ns |
| P | - | - | - | - | - | - | ||
| I | 483 | 114.11 | 4 | 0.00518 | 0.00919 | ns | ||
| CYTOKININ OXIDASE/ | Plant growth | W | 375 | 88.67 | 3 | 0.01015 | 0.0136 | ns |
| DEHYDROGENASE 1 | P | - | - | - | - | - | - | |
| I | 375 | 88.67 | 0 | 0 | 0 | ns | ||
| ELONGATION FACTOR | Plant growth | W | 380 | 37.98 | 2 | 0.00943 | 0.01587 | ns |
| BINDING SITE 1B | P | - | - | - | - | - | - | |
| I | 380 | 38 | 0 | 0 | 0 | ns | ||
| FASCIATED | Fruit development | W | 435 | 43.17 | 0 | 0.02978 | 0.0268 | ns |
| P | - | - | - | - | - | - | ||
| I | 435 | 43.17 | 0 | 0 | 0 | ns | ||
| GLABRA 2 | Seed development | W | 639 | 88.31 | 7 | 0.028370.02493 | 0.02493 | ns |
| P | - | - | - | - | - | - | ||
| I | 639 | 89 | 4 | 0.0124 | 0.01204 | ns | ||
| GLABRA2-EXPRESSION | Cell fate/division affecting | W | 625 | 90.04 | 0 | 0 | 0 | ns |
| MODULATOR | plant development | P | - | - | - | - | - | - |
| I | 625 | 90.58 | 0 | 0 | 0 | ns | ||
| HEADING DATE 6 | Flowering | W | 737 | 38.67 | 0 | 0 | 0 | ns |
| P | - | - | - | - | - | - | ||
| I | 737 | 38.67 | 0 | 0 | 0 | ns | ||
| INOSITOL POLYPHOSPHATE | Branching | W | 367 | 86.11 | 11 | 0.02669 | 0.0385 | ns |
| 6-/3-KINASE 2B | P | - | - | - | - | - | - | |
| I | 367 | 85.98 | 2 | 0.00391 | 0.00598 | ns | ||
| ISOPENTENYLTRANSFERASE 5 | Plant growth | W | 486 | 116.52 | 1 | 0.00107 | 0.00108 | * |
| P | N/A | N/A | N/A | N/A | N/A | N/A | ||
| I | 486 | 116.50 | 0 | 0 | 0 | ** | ||
| LATERAL SUPPRESSOR | Branching | W | 532 | 103.67 | 7 | 0.02244 | 0.02035 | ns |
| P | 532 | 103.67 | 0 | 0 | 0 | * | ||
| I | 532 | 103.67 | 0 | 0 | 0 | ** | ||
| LOW PHOSPHATE ROOT | Root growth/development | W | 413 | 97.75 | 10 | 0.02774 | 0.03391 | ns |
| P | 413 | 98.06 | 11 | 0.01868 | 0.03715 | ns | ||
| I | 413 | 98 | 0 | 0 | 0 | *** | ||
| MORE AXILLARY GROWTH 2 | Branching | W | 468 | 86.5 | 1 | 0.00165 | 0.00364 | * |
| P | 468 | 86.44 | 4 | 0.00774 | 0.01532 | ns | ||
| I | 468 | 86.5 | 0 | 0 | 0 | ** | ||
| MORE AXILLARY GROWTH 4 | Branching | W | 104 | 0 | - | - | - | - |
| P | - | - | - | - | - | - | ||
| I | 104 | 0 | - | - | - | - | ||
| METHYL-CPG BINDING 9 | Branching | W | 227 | 52.25 | 11 | 0.05391 | 0.06345 | ns |
| P | - | - | - | - | - | - | ||
| I | 225 | 52.37 | 4 | 0.0202 | 0.0202 | ns | ||
| PHENYLALANINE | Plant growth | W | 473 | 105.54 | 12 | 0.02178 | 0.03427 | ns |
| AMMONIA-LYASE 1 | P | 473 | 105.5 | 1 | 0.00158 | 0.00314 | ns | |
| I | 473 | 105.5 | 0 | 0 | 0 | * | ||
| PHYTOCHROME A | Flowering | W | 447 | 46.5 | 2 | 0.02085 | 0.01424 | ns |
| P | - | - | - | - | - | - | ||
| I | 447 | 46.5 | 0 | 0 | 0 | ns | ||
| PHYTOCHROME B | Flowering | W | 683 | 166.83 | 13 | 0.02648 | 0.02639 | ns |
| P | 683 | 166.83 | 5 | 0.00908 | 0.00992 | ns | ||
| I | 683 | 166.83 | 0 | 0 | 0 | ** | ||
| PHYTOCHROME E | Flowering | W | 457 | 103.48 | 14 | 0.0379 | 0.04254 | ns |
| P | - | - | - | - | - | - | ||
| I | 457 | 103.42 | 5 | 0.01029 | 0.01267 | ns | ||
| PIN-FORMED 1 | Root/shoot development | W | 411 | 101.92 | 11 | 0.02743 | 0.03253 | ns |
| P | - | - | - | - | - | - | ||
| I | 411 | 101.93 | 2 | 0.0063 | 0.00504 | ns | ||
| PHOTOPERIOD -H1 | Flowering | W | 246 | 50.31 | 3 | 0.017560.01797 | 0.01797 | ns |
| P | - | - | - | - | - | - | ||
| I | 246 | 50.33 | 1 | 0.00841 | 0.00511 | ns | ||
| RGA-LIKE 2 | Germination | W | 377 | 89.5 | 31 | 0.11417 | 0.12297 | ns |
| P | 377 | 89.06 | 13 | 0.07069 | 0.04834 | ns | ||
| I | 377 | 88.83 | 0 | 0 | 0 | *** |
Panel, W = wild, P = primitive, I = improved; L = alignment length in basepairs; l = number of synonymous sites; S = number of segregating synonymous sites; π = nucleotide diversity for synonymous sites; θ = Waterson's theta for synonymous sites; Sig. = ML-HKA significance: ns = not significant, P<0.001 = ***, P<0.01 = **, P<0.05 = *. Bold genes are those that showed significant evidence of selection. Note: we were unable to successfully sequence the IPT5 gene in P.