Table 1.
Overview of CODEML and CODEMLSITES programs statistics upon the evolutionary analyses in upland cotton RGAs
| RGAs PGGs | Number of clustered RGAs sequenses (composition of clusters) | CODEML analysis | CODEMLSITES analysis | |||||
|---|---|---|---|---|---|---|---|---|
| Proportion of branches under positive selection | Positive selection acting on anchestral (A) and (or) terminal (T) branches | Highest omega values in branches of the evolutionaty trees | Statistical significance (P) | Total number of sitesa | Positively selected sites | Positively selected sitesb | ||
| Gh_RGA-1 | 62 (Gh_GB, Gh_EM, Gh_LA) | 6.8 | A/T | ∞ | <0.01 | 447 | 6 | 2I, 7Y, 9A, 12H, 16R, 17L |
| Gh_RGA-2 | 38 (Gh_GB, Gh_EM, Gh_LA) | 29.7 | A/T | ∞ | < 0.9 | 252 | ||
| Gh_RGA-3 | 5 (Gh_GB) | 12.5 | T | 288.1 | <0.05 | 258 | 2 | 25L, 39Y |
| Gh_RGA-4 | 6 (Gh_GB, Gh_EM) | 10 | A | ∞ | <0.05 | 486 | 3 | 34Q, 42H, 44D |
| Gh_RGA-5 | 13 (Gh_GB) | 12.5 | A/T | ∞ | <0.001 | 510 | 9 | 17S, 31 K, 40 V, 104L, 117A, 121G, 138L, 168F, 169A |
| Gh_RGA-6 | 13 (Gh_GB) | 16.7 | T | 1.88 | <0.01 | 237 | 15 | 2E, 3 K, 8 K, 28D, 30C, 42P, 45E, 50 N, 54E, 55I, 58G, 62 N, 69 V,70A, 72 N |
| Gh_RGA-7 | 5 (Gh_GB) | 42.9 | T | 3.52 | <0.01 | 507 | 6 | 48L, 52D, 99 V, 116E, 152P, 154P |
| Gh_RGA-8 | 19 (Gh_GB) | 13.9 | T | ∞ | <0.9 | 495 | 1 | 8L |
| Gh_RGA-9 | 2 (Gh_EM | NT | ||||||
| Gh_RGA-10 | 2 (Gh_GB) | NT | ||||||
Likelihood ratio test among M8 and M7 models
aLengths are refereing to the alignments feeding the CODEMLSITES program
bPosterior Bayesian probabilities >0.95 are shown in lightface, and >0.99 values are shown in boldface