TABLE 2.
Lineage-specific silent changes for X chromosome loci in the D. melanogaster subgroup
| Lineage | Sil tot | up | pu | dup,pu | G | Gene dir | WSR P |
|---|---|---|---|---|---|---|---|
| mel | |||||||
| Near telomeric | 234.4 | 44.6 | 128.9 | −0.49 | 42.6*** | 1/13 | 0.0008** |
| Nontelomeric | 229.1 | 28.2 | 151.1 | −0.69 | 92.3*** | 0/9 | 0.0039** |
| sim | |||||||
| Near telomeric | 187.9 | 43.2 | 90.2 | −0.35 | 16.9*** | 2/12 | 0.0006** |
| Nontelomeric | 143.7 | 54.9 | 54.4 | 0.00 | 0.0 | 4/5 | 0.73 |
| tei | |||||||
| Near telomeric | 161.6 | 67.8 | 50.9 | 0.14 | 2.4 | 9/4 | 0.39 |
| Nontelomeric | 121.0 | 62.9 | 31.3 | 0.34 | 10.8** | 7/2 | 0.020* |
| yak | |||||||
| Near telomeric | 228.3 | 104.6 | 72.5 | 0.18 | 5.8* | 11/3 | 0.17 |
| yak-TRIMCU | 174.9 | 97.0 | 39.6 | 0.42 | 24.8*** | 11/0 | |
| Nontelomeric | 222.5 | 48.3 | 126.4 | −0.45 | 36.1*** | 1/8 | 0.0078* |
| teiyak | |||||||
| Near telomeric | 317.8 | 170.4 | 68.8 | 0.42 | 44.5*** | 9/5 | 0.042* |
| teiyak-TRIMCU | 231.2 | 145.2 | 26.2 | 0.69 | 90.7*** | 8/1 | |
| Nontelomeric | 173.4 | 74.5 | 48.0 | 0.22 | 5.8* | 6/3 | 0.20 |
| ere | |||||||
| Near telomeric | 189.1 | 53.6 | 82.4 | −0.21 | 6.1* | 3/11 | 0.050* |
| Nontelomeric | 176.1 | 77.5 | 48.7 | 0.23 | 6.6* | 4/5 | 0.50 |
| ore | |||||||
| Near telomeric | 302.4 | 179.4 | 63.6 | 0.48 | 57.4*** | 9/5 | 0.10 |
| ore-TRIMCU | 173.9 | 138.9 | 8.0 | 0.89 | 140.9*** | 6/0 | |
| Nontelomeric | 181.5 | 42.5 | 107.8 | −0.43 | 29.2*** | 0/9 | 0.0039** |
| ereore | |||||||
| Near telomeric | 205.5 | 66.0 | 95.1 | −0.18 | 5.3* | 4/10 | 0.10 |
| ereore-TRIMCU | 33.6 | 20.0 | 4.7 | 0.62 | 10.0** | 4/0 | |
| Nontelomeric | 188.6 | 42.9 | 105.3 | −0.42 | 27.0*** | 0/9 | 0.0039** |
Total counts of the preferred (up), unpreferred (pu), and total silent (Sil tot) changes across genes on the near-telomeric (6391 codons) and nontelomeric loci (4906 codons) for each lineage and on the near-telomeric regions of increasing MCU (TRIMCU) in yak, teiyak, ore, and ereore are shown. TRIMCU are defined as yak (cin-futsch, 5006 codons), teiyak (y-CG11403, 4101 codons), ore (y-EG:171D11.2, 2431 codons), and ereore (y-ase, 1351 codons). dup,pu, (up − pu)/(up + pu), indicates degrees of deviation from equal numbers of up and pu changes. The G-values of goodness-of-fit tests for the expected equal numbers of up and pu changes at equilibrium are shown. Gene dir represents the number of genes that show positive/negative dup,pu. Probabilities of Wilcoxon signed-rank test (WSR) are given except for TRIMCU. *P < 0.05, **P < 0.005, ***P < 0.0005. Abbreviations for lineages: mel, D. melanogaster; sim, D. simulans; tei, D. teissieri; yak, D. yakuba; teiyak, D. teissieri–D. yakuba; ere, D. erecta; ore, D. orena; and ereore, D. erecta–D. orena.