TABLE 4.
Base composition evolution among near-telomeric X chromosome loci in the D. melanogaster subgroup
|
yak
|
teiyak
|
ore
|
ereore
|
||||||
|---|---|---|---|---|---|---|---|---|---|
| bp | WS | SW | WS | SW | WS | SW | WS | SW | |
| CG2995 | |||||||||
| Int | 278 | 0.1 | 6.4 | 2.0 | 6.3 | 1.8 | 0.2 | 5.0 | 3.4 |
| Sil | 1458 | 5.6 | 11.2 | 4.2 | 17.5 | 6.1 | 7.4 | 4.2 | 6.9 |
| Rep | 0.0 | 4.0 | 2.0 | 1.0 | 0.0 | 2.0 | 1.0 | 0.0 | |
| cin | |||||||||
| Int | 224 | 4.5 | 6.1 | 4.0 | 2.3 | 4.8 | 0.1 | 2.2 | 7.9 |
| Sil | 1347 | 5.6 | 2.3 | 6.5 | 11.6 | 5.9 | 5.9 | 8.2 | 12.8 |
| Rep | 1.0 | 3.6 | 0.0 | 3.7 | 3.0 | 3.6 | 5.2 | 4.0 | |
| y | |||||||||
| Int | |||||||||
| Sil | 1323 | 3.2 | 0.4 | 23.6 | 4.1 | 43.0 | 1.5 | 10.4 | 4.8 |
| Rep | 0.0 | 1.0 | 0.0 | 0.9 | 2.0 | 0.4 | 0.0 | 1.6 | |
| sc | |||||||||
| Int | |||||||||
| Sil | 996 | 2.1 | 4.8 | 3.2 | 2.7 | 16.3 | 1.1 | 4.9 | 1.8 |
| Rep | 1.0 | 1.8 | 0.0 | 0.0 | 2.0 | 0.0 | 1.6 | 0.0 | |
| l(1)sc | |||||||||
| Int | |||||||||
| Sil | 765 | 3.9 | 0.9 | 9.0 | 2.4 | 20.9 | 0.0 | 2.7 | 0.0 |
| Rep | 0.0 | 0.0 | 1.0 | 2.0 | 3.0 | 0.0 | 1.0 | 0.0 | |
| ase | |||||||||
| Int | |||||||||
| Sil | 969 | 4.0 | 3.2 | 7.7 | 2.2 | 31.2 | 3.0 | 6.6 | 0.8 |
| Rep | 1.8 | 0.0 | 2.0 | 1.0 | 11.0 | 1.0 | 2.2 | 0.2 | |
| l(1)1Bb | |||||||||
| Int | 438 | 18.6 | 10.7 | 14.5 | 6.4 | 15.1 | 7.8 | 17.1 | 18.4 |
| Sil | 1839 | 15.7 | 6.7 | 26.7 | 2.2 | 22.3 | 2.1 | 7.5 | 6.4 |
| Rep | 1.0 | 0.0 | 0.1 | 1.0 | 2.0 | 0.3 | 1.4 | 9.8 | |
| EG:171D11.2 | |||||||||
| Int | 295 | 6.1 | 2.0 | 15.2 | 3.8 | 5.6 | 4.1 | 4.6 | 6.5 |
| Sil | 1401 | 12.7 | 3.7 | 26.9 | 4.1 | 17.7 | 0.7 | 7.1 | 7.3 |
| Rep | 2.0 | 0.0 | 1.4 | 3.0 | 2.3 | 2.0 | 1.0 | 2.9 | |
| l(1)1Bi | |||||||||
| Int | 165 | 4.9 | 1.6 | 4.9 | 4.7 | 2.9 | 2.8 | 8.2 | 6.7 |
| Sil | 1734 | 21.5 | 4.7 | 29.2 | 1.9 | 8.8 | 7.0 | 4.4 | 13.3 |
| Rep | 2.5 | 1.0 | 10.4 | 3.0 | 9.4 | 11.2 | 2.9 | 1.3 | |
| Su(wa) | |||||||||
| Int | 257 | 4.0 | 6.3 | 10.0 | 0.4 | 4.1 | 6.9 | 4.0 | 6.8 |
| Sil | 1545 | 14.7 | 5.1 | 23.7 | 2.1 | 2.8 | 7.7 | 6.5 | 11.9 |
| Rep | 4.5 | 1.0 | 5.1 | 3.0 | 2.0 | 3.0 | 3.0 | 6.8 | |
| CG11403 | |||||||||
| Int | 108 | 2.1 | 5.0 | 4.1 | 3.1 | 1.0 | 1.0 | 0.0 | 1.0 |
| Sil | 1731 | 18.0 | 9.9 | 24.6 | 6.2 | 10.6 | 11.3 | 4.8 | 14.2 |
| Rep | 5.5 | 2.4 | 5.5 | 1.0 | 0.0 | 5.9 | 3.2 | 2.5 | |
| futsch | |||||||||
| Int | 367 | 5.0 | 6.0 | 7.8 | 7.2 | 8.7 | 6.2 | 2.4 | 3.4 |
| Sil | 1368 | 9.9 | 5.3 | 8.9 | 4.6 | 5.8 | 5.4 | 3.8 | 7.2 |
| Rep | 1.0 | 0.0 | 0.0 | 1.0 | 0.0 | 0.0 | 1.0 | 0.0 | |
| sta | |||||||||
| Int | 187 | 1.0 | 1.0 | 1.1 | 1.0 | 1.0 | 3.0 | 0.1 | 4.0 |
| Sil | 810 | 4.0 | 8.0 | 1.9 | 7.4 | 1.6 | 7.0 | 1.8 | 6.9 |
| Rep | 0.0 | 6.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | |
| dor | |||||||||
| Int | 103 | 1.0 | 2.0 | 2.6 | 2.4 | 3.9 | 3.3 | 1.2 | 2.5 |
| Sil | 1671 | 1.2 | 17.6 | 7.2 | 6.3 | 10.5 | 7.6 | 4.1 | 6.6 |
| Rep | 0.7 | 1.0 | 0.2 | 1.7 | 1.0 | 5.0 | 1.5 | 1.3 | |
| Sum | |||||||||
| Int | 2422 | 47.1 | 47.0 | 66.1 | 37.5 | 49.1 | 35.4 | 44.8 | 60.5 |
| Sil | 18957 | 122.0 | 83.7 | 203.4 | 75.4 | 203.3 | 67.6 | 77.0 | 100.7 |
| Rep | 21.0 | 21.8 | 27.7 | 22.2 | 37.7 | 34.4 | 24.8 | 30.3 | |
| TRIMCU | |||||||||
| Int | 45.1 | 37.6 | 48.6 | 18.3 | 20.7 | 12.0 | 0.0 | 0.0 | |
| Sil | 111.2 | 46.9 | 174.6 | 27.9 | 151.3 | 8.5 | 24.6 | 7.4 | |
| Rep | 20.3 | 10.8 | 25.4 | 14.9 | 22.3 | 3.7 | 4.7 | 1.7 | |
| Non-TRIMCU | |||||||||
| Int | 2.1 | 9.4 | 17.5 | 19.1 | 28.4 | 23.4 | 44.8 | 60.5 | |
| Sil | 10.8 | 36.8 | 28.8 | 47.4 | 52.0 | 59.1 | 52.4 | 93.3 | |
| Rep | 0.7 | 11.0 | 2.2 | 7.4 | 15.4 | 30.7 | 20.1 | 28.5 | |
Counts of AT → GC (WS) and GC → AT (WS) changes at intronic (Int), silent (Sil), and replacement (Rep) sites for each near-telomeric gene in four D. melanogaster subgroup species are shown. WS and SW changes from the loci located at the near-telomeric regions of increasing major codon usage (TRIMCU) are pooled. Total numbers of WS and SW changes for the near-telomeric loci outside TRIMCU regions (non-TRIMCU) are also shown. Definitions of TRIMCU regions and abbreviations for lineages are given in Table 2. Data from the D. melanogaster, D. simulans, D. teissieri, and D. erecta lineages are given in supplemental Table S5 at http://www.genetics.org/supplemental/.