Cytological locations are given on the basis of D. melanogaster cytology (FlyBase Consortium 2003). The marker type is m, microsatellite; s, SNP; id, insertion/deletion. The PCR protocol for all microsatellites is 1 cycle 95°, 5 min; 5 cycles 95°, 45 sec, 68°, 5 min, 72°, 1 min, decreasing the T_A each cycle by 2°; 4 cycles 95°, 45 sec, 58°, 2 min, 72°, 1 min, decreasing the T_A each cycle by 2°; 27 cycles 95°, 45 sec, 50°, 2 min, 72°, 1 min; and 1 cycle 72° 5 min. The PCR protocol for all other markers is 1 cycle 94°, 5 min; 30 cycles 94°, 1 min, T_A°, 45 sec, 72° 1 min; 1 cycle 72°, 5 min; where T_A is listed. Primers are listed from the 5′ end. Microsatellite markers were run on a 6% polyacrylamide gel and imaged with a LICOR Gene Readir 4200 DNA analyzer. PCR fragments containing SNPs were digested with a restriction endonuclease and then run on a 3% agarose gel and manually genotyped. T_A, annealing temperature; NA, not applicable.