TABLE 3.
Frequencies of sequence variants at golden probe loci
| Allele frequency
|
||||||||
|---|---|---|---|---|---|---|---|---|
| Tropical
|
Temperate
|
|||||||
| Gene | Type | Chromosome | Mb | FL | QLD | ME | TAS | Alleles |
| cp309 | Intron | 3L | 15.0 | 0.63 | 0.53 | 0.06 | 0.13 | G → A |
| CG13466 | Intron | 3L | 14.9 | 0.44 | 0.57 | 0.07 | 0.15 | AG → TT |
| Gr93c | Coding | 3R | 17.7 | 0.63 | 0.75 | 0.25 | 0.25 | GT → TA |
| pointed1 | Intron | 3R | 19.2 | 0.73 | 0.71 | 0.38 | 0.23 | 13-bp insertion |
| fas1 | Intergenic | 3R | 12.5 | 0.75 | 0.71 | 0.54 | 0.36 | C → T (22 bp away from probe) |
| CG32606 | Intergenic | X | 13.8 | 0.25 | 0.18 | 0.06 | 0.00 | TTA → GCG |
| pointed2 | Intron | 3R | 19.2 | 0.2/0.5/0.3 | 0.4/0.4/0.2 | 0.6/0/0.4 | 0.8/0.2/0 | GCTG → AGCG → AGCA |
| spn-D | Intergenic | 3R | 23.0 | 0.1/0/0.9 | 0.1/0.2/0.7 | 0.2/0.4/0.4 | 0.4/0.4/0.2 | ATAA → -CGT → -TGT |
| CG2989 | Coding | X | 1.9 | 0.4/0.1/0.5 | 0.4/0.2/0.4 | 0.3/0/0.7 | 0.9/0/0.1 | ATCC → TTCC → ACTA |
| foraging | Intron | 2L | 3.6 | 0.25 | 0.89 | 0.44 | 0.22 | 3-bp deletion |
The “alleles” column shows the SNP, SNPs, or indels that overlap the probe, with three alleles present at some sites. Because these probes are our most significant, it is not suprising that most of them overlap multiple SNPs or indels. FL, Florida; QLD, Queensland; ME, Maine; TAS, Tasmania.