TABLE 2.
Basic features of the 41 sequenced probes chosen from the nested ANOVA and of six random probes
| Gene name | Rank | FDR | No. of FDs | Fragment (bp) | Recombination Rate (cM/Mb) | Chromosome | Probe location | Site type | Synonymous/nonsynonymous | Ancestral allele | Derived allele |
|---|---|---|---|---|---|---|---|---|---|---|---|
| period | 2 | 0.0000016 | <1 | 222 | 1.84 | X | 2,579,880–2,579,904 | 5′ UTR | — | SNP: A | T(ref.); Indel: (15bp. insertion in N.A.) |
| 235.468 | 4 | 0.0000124 | <1 | 194 | 3.46 | X | 15,156,739–15,156,763 | Intergenic | — | A….GG | A…..GC > G……TC(ref.) |
| 5097.1107 | 20 | 0.0000222 | <1 | 107 | 2.82 | X | 7,322,927–7,322,951 | Intergenic | — | A.G | A.A(ref. N.A.) or T.G(Africa) |
| fred | 74 | 0.0000744 | <1 | 51 | 2.76 | 2L | 3,921,381–3,921,405 | Intron | — | C…G(ref.) | A…G > A….T |
| Cyp6a22 | 75 | 0.0000756 | <1 | 158 | 1.46 | 2R | 10,760,407–10,760,431 | Intron | — | TA..T | AC..T(ref. N.A.) or TA..Cor AA..C(Africa) |
| 1857.837 | 107 | 0.0001210 | <1 | 153 | 3.17 | X | 20,876,262–20,876,286 | Intergenic | — | T | C(ref.) |
| FucT6 | 108 | 0.0001345 | <1 | 158 | 3.32 | X | 11,602,351–11,602,375 | CDS | Syn | G…G | A…C(ref.) |
| CG2694 | 224 | 0.0003093 | <1 | 100 | 1.85 | X | 2,608,335–2,608,359 | CDS | Syn | T(ref.) | C |
| couch potato | 245 | 0.0003394 | <1 | 183 | 0.88 | 3R | 13,790,151–13,790,175 | Intron | — | T(ref.) | A |
| Atapalpha | 246 | 0.0003387 | <1 | 69 | 1.25 | 3R | 16,781,505–16,781,529 | Intron | — | G | T(ref.) |
| CG15293 | 257 | 0.0003581 | <1 | 174 | 3.52 | 2L | 14,108,392–14,108,416 | CDS | NonS | GAGGG..GGG | TGAAC..GAA(ref.) |
| E2f | 442 | 0.0008782 | <1 | 103 | 1.32 | 3R | 17,461,287–17,461,311 | Intron | — | C(ref.) | T |
| 2555.2470 | 574 | 0.0011381 | <1 | 159 | 3.36 | X | 18,578,377–18,578,401 | Intergenic | — | T | C(ref.) |
| CG14998 | 672 | 0.0014177 | <1 | 142 | 3.03 | 3L | 4,126,308–4,126,332 | CDS | NonS | G | A(ref.) |
| Tak1 | 699 | 0.0014919 | 1 | 122 | 3.22 | X | 20,388,005–20,388,029 | CDS | NonS | GCC | CTT(ref.) |
| 2375.2501 | 908 | 0.0022309 | 2 | 183 | 0 | X | 1,229,872–1,229,896 | Intergenic | — | C…G | A…G or C…T > G…T(ref.) |
| Nmdar2 | 919 | 0.0022462 | 2 | 167 | 0 | X | 1,394,893–1,394,917 | Intron | — | Indel: CAT^GG | CAT..[114 bp deletion]..GG(ref.) |
| Btk29A | 1,201 | 0.0030002 | 4 | 152 | 3.44 | 2L | 8,271,429–8,271,453 | Intron | — | C….C | T…C(ref.) or C…A |
| 75.618 | 1,263 | 0.0031734 | 4 | 195 | 3.45 | X | 14,440,737–14,440,761 | Intergenic | — | G | A(ref.) |
| Eip75B | 1,890 | 0.0056572 | 11 | 137 | 2.73 | 3L | 17,985,031–17,985,055 | Intron | — | T(ref.) | G |
| CG32635 | 2,105 | 0.0066248 | 14 | 152 | 3.42 | X | 13,389,886–13,389,910 | CDS | NonS | T | A(ref.) |
| CG7728 | 2,119 | 0.0067023 | 14 | 109 | 2.83 | 3L | 17,011,993–17,012,017 | CDS | Syn | G(ref.) | A |
| CG11106 | 2,250 | 0.0073320 | 16 | 88 | 3.28 | X | 11,096,487–11,096,511 | CDS | NonS | T | G(ref.) |
| CG2898 | 2,546 | 0.0087331 | 22 | 159 | 3.2 | X | 10,269,933–10,269,957 | CDS | NonS | G….G | C…G > C…A(ref.) |
| sphinx1 | 2,649 | 0.0093497 | 25 | 147 | 3.19 | 3L | 7,431,854–7,431,876 | CDS | Syn | G…T(ref.) | A…G |
| feo | 2,830 | 0.0103741 | 29 | 183 | 3.24 | X | 10,747,118–10,747,142 | CDS | Syn | C | T(ref.) |
| Cad96Cb | 3,971 | 0.0165277 | 66 | 93 | 1.64 | 3R | 21,051,158–21,051,182 | CDS | Syn | G | A(ref.) |
| Shaker | 6,638 | 0.0319373 | 212 | 200 | 3.4 | X | 17,847,304–17,847,328 | CDS | — | — | — |
| Spn | 6,876 | 0.0335110 | 230 | 88 | 2.91 | 3L | 2,540,498–2,540,522 | Intron | — | C…G(ref.) | A…G or C…C |
| ligand | 8,725 | 0.0438968 | 383 | 170 | 0 | 2R | 3,959,855–3,959,879 | CDS | — | — | — |
| Gr28b | 8,761 | 0.0441712 | 387 | 108 | 3.36 | 2L | 7,456,562–7,456,586 | Intron | — | A…C | G…T(ref.) |
| Pxd | 9,154 | 0.0463209 | 424 | 97 | 0.75 | 3R | 12,847,742–12,847,766 | Intron | — | T | C(ref.) |
| CG12115 | 10,331 | 0.0523437 | 541 | 132 | 3.06 | X | 9,083,537–9,083,561 | CDS | Syn | G….G | A…Gor G….T(ref.) > A….T |
| CG11261 | 11,819 | 0.0604584 | 715 | 145 | 3.13 | 3L | 13,003,921–13,003,945 | CDS | NonS | T | C(ref.) |
| CG15764 | 17,016 | 0.0873993 | 1487 | 117 | 2.55 | X | 5,763,338–5,763,362 | CDS | — | TorC | T(ref.)orC |
| CG15894 | 19,306 | 0.0974121 | 1881 | 260 | 2.63 | X | 6,214,894–6,214,918 | CDS | NonS | GG | CA(ref.) |
| Ob50b | 24,055 | 0.1181299 | 2842 | 99 | 1.38 | 2R | 10,259,477–10,259,501 | CDS | NonS | T..A..G..G | G..T..C..A(ref.) |
| pathetic | 32,325 | 0.1499259 | 4846 | 111 | 3.21 | 3L | 9,488,908–9,488,932 | CDS | Syn | G..A | A..G(ref.) |
| ham | 50,670 | 0.2063295 | 10455 | 134 | 0 | 2L | 18,765,080–18,765,104 | CDS | NonS | A(ref.) | T |
| CG33213 | >57,763 | >0.224 | >12944 | 174 | 1.81 | 3R | 23,744,914–23,744,938 | CDS | Syn | G | A(ref.) |
| CG1745 | >57,763 | >0.224 | >12944 | 132 | 3.3 | X | 11,350,112–11,350,136 | CDS | Syn | A…Cor G…G | A….Cor G…G(ref.) |
| Flo-2 | Random | NA | NA | 190 | 3.46 | X | 14,802,654–14,802,844 | Intron | — | A | T(ref.) |
| sgg | Random | NA | NA | 245 | 1.84 | X | 2,542,804–2,543,048 | Intron | — | AA(ref.) | CC |
| CG3655 | Random | NA | NA | 311 | 0 | X | 1,018,839–1,019,436 | Intron | — | G..A..G | A..G..T(ref.) |
| chb | Random | NA | NA | 260 | 0 | 3L | 21,170,325–21,170,584 | Intron | — | T | G(ref.) |
| intergene | Random | NA | NA | 190 | 2.1 | 2L | 1,302,500–1,302,648 | Intergenic | — | G(ref.) | A |
| Trp1 | Random | NA | NA | 149 | 0.38 | 2R | 5,647,602–5,647,724 | Intron | — | A | G(ref.) |
CDS, (protein) coding site: the change is synonymous (Syn) or nonsynonymous (NonS). The polarity of the single feature polymorphism is determined on the basis of the sequence of D. simulans/D. sechelia (presumed ancestral state). The D. melanogaster reference sequence (ref.) is shown. Two sequenced probes (in Shaker and ligand loci) were false discoveries (see above). Probe within the locus CG15764 was polymorphic, but with very low FST values (see Table S2 for details).