Table 4.
Codon Model Based Test of Positive and Purifying Selection across the Three Stem Cell Classes and Their Corresponding Control Genes
| Statistic | Both Stem Cell | Both Stem Cell Control | Germline Stem Cell | Germline Stem Cell Control | Neural Stem Cell | Neural Stem Cell Control |
|---|---|---|---|---|---|---|
| PAML Model 0 | ||||||
| ω | 0.032 (0.023, 0.041) | 0.036 (0.027, 0.043) | 0.033 (0.026, 0.042) | 0.041 (0.036, 0.045) | 0.03 (0.022, 0.043) | 0.034 (0.030, 0.040) |
| PAML Model 8 | ||||||
| ω+ | 49 (0.096%) | 116 (0.110%) | 109 (0.090%) | 213 (0.084%) | 47 (0.086%) | 113 (0.084%) |
| HYPHY FUBAR | ||||||
| ω+ | 17 (0.033%) | 27 (0.026%) | 36 (0.030%) | 89 (0.035%) | 24 (0.044%) | 51 (0.038%) |
| ω− | 40,688 (80.0%) | 84,593 (80.2%) | 94,762 (78.6%) | 200,475 (79.2%) | 42,157 (77.5%) | 106,005 (79.1%) |
| Total Codons | 50,869 | 105,449 | 120,558 | 253,087 | 54,412 | 134,081 |
Note.—ω, median ratio of nonsynonymous divergence to synonymous divergence with 95% bootstrap confidence interval in parenthesis; ω+, number of sites with significant evidence (posterior probability ≥ 0.9) of positive selection and its proportions are indicated in parenthesis; ω−, number of sites with significant evidence (posterior probability ≥ 0.9) of purifying selection and its proportions are indicated in parenthesis.