Table 1.
DNA polymorphism in the 13-kb where the CH phenotype is mapped (see Fig. 1)
| Phenotype (geographic origin) | D. melanogaster lines | Positions of the polymorphic sites
|
||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 4012 | 6500 | 9512 | 550-bp
region surrounding 10294
|
11009 | 630-bp
region surrounding 12552
|
|||||||||||
| 10294 | 10387 | 10416 | 10597 | 10730 | 12441 | 12452 | 12515 | 12552 | 12641 | 12748 | ||||||
| D. simulans | C | C | T | + | T | CA | G | G | D | GT | + | C | G | |||
| D. mauritiana | C | T | T | + | CA | G | G | D | GT | + | C | G | ||||
| D. sechellia | C | T | T | + | T | CA | G | G | D | GT | + | C | G | |||
| Low 5,9-HD (Cosmopolitan) | Oregon-R | T | T | – | A | – | A | AG | – | T | – | I | AA | D | – | T |
| closs3, NY | – | T | – | A | – | A | AG | – | T | – | I | AA | D | – | T/– | |
| CAM110, NC | – | T | A/– | A | – | A | AG | – | G | – | I | AA | D | – | – | |
| French V3-1 | – | G | – | A | – | A | AG | – | G | – | I | AA | D | – | – | |
| Yep11, Australia | – | T/G | A/– | A | – | A | AG | – | G | – | I | AA | D | – | – | |
| cu kar | T | T | – | A | – | A | AG | – | G | – | I | AA | D | – | – | |
| TWN24, Taiwan | – | T | – | A | – | A | AG | – | G | – | I | AA | D | – | – | |
| QD12, Japan | T | G | – | A | – | A | AG | – | G | – | I | AA | D | – | – | |
| QL4, China | – | T | – | A | – | A | AG | – | G | – | I | AA | D | – | – | |
| Taishan, China | – | T | – | A | – | A | AG | – | G | – | I | AA | D | – | – | |
| Low 5,9-HD (African/ Caribbean) | LA20, Zambia | – | T | – | A | – | A | AG | – | G | – | I | AA | D | – | – |
| OK17, Botswana | T | T | – | A | – | A | AG | – | G | – | I | AA | D | – | – | |
| ZH27, Zimbabwe | T | G | – | A | – | A | AG | – | G | – | I | AA | D | – | – | |
| Intermediate (Cosmopolitan) | Hg, CA | – | T/G | A/– | A/– | – | A | AG | – | G | – | I | AA | D/– | – | – |
| GF60, IN | – | G | A/– | A/– | – | A | AG | – | G | – | I | AA | D/– | – | – | |
| High 5,9-HD (African/ Caribbean) | ZS53, Zimbabwe | – | G | A | – | – | A | AG | – | T | – | I | AA | – | – | – |
| ZS2, Zimbabwe | – | G | – | – | – | – | AG | – | G | – | I | AA | – | – | – | |
| Caribbean A, St. Croix | – | G | A | – | D | A | AG | – | G | A | I | AA | +′ | – | – | |
| Caribbean B, St. Croix | – | G | A | – | – | – | AG | – | G | – | I | AA | – | – | – | |
| Caribbean C, St. Croix | – | G | A | – | – | – | AG | – | G | – | I | AA | – | – | – | |
| Caribbean D, Dominican Republic | – | G | A | – | – | A | AG | – | G | A | I | AA | +′ | – | – | |
| Caribbean E, Cuba | T | T | – | – | – | – | AG | A | G | – | I | AA | – | T | – | |
| Caribbean F, Dominican Republic | – | G | A | – | D | – | – | – | G | – | – | – | – | – | – | |
| High 5,9-HD (Cosmopolitan) | Iso-1 | – | T | – | – | – | – | AG | A | G | – | I | AA | – | T | – |
Sequences are grouped by the CH phenotype of the chromosome and their geographic origin (in parentheses) as indicated in the left column. The collection site of each line is indicated in the second column (NY = New York state, NC = North Carolina, CA = California, and IN = Indiana; Iso-1 is a North American strain used in the Drosophila genome project). The two sites (10294 and 12552) that show a complete association with the CH phenotype are highlighted in bold. To avoid cluttering the table, singletons in these two stretches are omitted; these sites are site 10385 in Caribbean D, site 10649, 12634, 12900 in Caribbean F, site 12542 in OK17, and site 12685 in QL4. These singletons are used in the analysis of Table 3. Inferred derived nucleotides are italicized and the ancestral state is indicated by –. D, deletion; + or +′ nondeletion (+ and +′ differ by 1 bp).