Table 3.
Sites predicted to be under differential positive selection using the Bayesian ratio of omegas (ω1/ω2) test, the fixed effects likelihood comparison of selective pressures (FEL-CSP), and FEL-Clade tests
| S-RNase Region (codon positions) | ||||||
|---|---|---|---|---|---|---|
| Test | HVa (1-38) | HVb (44-62) | C3 (63-68) | V1 (69-84) | C4 (85-93) | V2 (94-131) |
| ωp/ωsα Physalis codons |
7,8, 10, 11, 13,14, 15, 26, 33 |
44, 46, 49 52, 53, 56 (0.97), 59 62 |
- - - - |
69, 71, 84 | 87 (0.98) |
9, 101, 104, 110, 111, 112, 119 (0.96), 120 (0.96), 123, 124 (0.97), 125 127 (0.95), 129, 131 |
| FEL CSPb Physalis codons |
8, 9,13, 24, 26 (0.08), 31 |
46, 53 | - | 84 | 87 |
96, 99, 116, 125 127, 129, 131 |
| FEL Clade A Physalis codons |
3, 6, 9, 10, 13 |
46, 56 | - | 87, 89, 90 | 96, 99, 110, 121 | |
| FEL Clade C Physalis codons |
9, 14, 24 | 44, 57 | - | 92 | 97, 127, 129 | |
| FEL Clade Sc Solanum codons |
21, 22, 23, 29 30, 32, 34, 35, 38 |
60 | Clade A as forground - |
77 | 103, 106, 109 | |
| FEL Clade Sc Solanum codons |
23, 31 | 47, 48, 50 | Clade C as forground - |
80 | 124 | |
Bold indicates sites predicted to be under stronger selection in Physalis than in Solanum by both ωp/ωs and FEL CSP tests. FEL-Clade tests comparing clades A and C show mostly different sites under selection as well as several different sites selected in Solanum depending on the foreground Physalis clade present.
a) For the ω1/ω2 test codons had a posterior probability score ≥ 0.99 unless otherwise indicated in parentheses.
b) For the FEL test all sites listed had a p-value ≤ 0.05 except site 26.
c) The FEL Clade Tests had either Clade A or Clade C as the foreground with all other Physalis alleles removed from the alignment and phylogeny.