Table 2.
Results from selection tests in highland (N = 48) and lowland (N = 48) forms
| Locus | Length | S | Number of sequenced exons | Cumulative length of exons | Nonsynonymous mutations | Synonymous mutations | Number of alleles | π | ϴw | Tajima’s D | MK test |
|---|---|---|---|---|---|---|---|---|---|---|---|
| Highland polymorphic form only | |||||||||||
| Agouti (complete) | 3522 | 12 | 3 | 417 | 1 | 0 | 16 | 0.000218* | 0.000664 | −1.79** | — |
| Agouti cis 2 | 346 | 1 | 0 | 0 | 0 | 0 | 2 | 0.000061 | 0.000565 | −1.04 | — |
| Agouti cis 4 | 228 | 1 | 0 | 0 | 0 | 0 | 2 | 0.000874 | 0.000676 | 0.34 | — |
| Agouti cis 6 | 267 | 1 | 0 | 0 | 0 | 0 | 2 | 0.000682 | 0.000739 | −0.09 | — |
| Corin | 702 | 2 | 2 | 239 | 0 | 0 | 2 | 0.00146** | 0.00056 | 2.46** | — |
| DCT | 512 | 3 | 1 | 301 | 1 | 1 | 4 | 0.000904 | 0.00115 | −0.39 | NS |
| POMC | 379 | 7 | 1 | 379 | 5 | 2 | 9 | 0.002123 | 0.00364 | −0.99 | NS |
| SLC | 652 | 5 | 3 | 256 | 0 | 2 | 8 | 0.000828 | 0.001797 | −1.22 | NS |
| TYR | 767 | 2 | 1 | 767 | 2 | 0 | 3 | 0.000233 | 0.00051 | −0.85 | NS |
| TYRP1 | 589 | 1 | 1 | 382 | 1 | 0 | 2 | 0.00086* | 0.00035 | 1.78*** | NS |
| Lowland forms | |||||||||||
| Agouti (partial) | 960 | 12 | 0 | 0 | 0 | 0 | 12 | 0.00079 | 0.00243 | −1.80* | — |
| Agouti cis 2 | 346 | 0 | 0 | 0 | 0 | 0 | 1 | — | — | — | — |
| Agouti cis 4 | 228 | 1 | 0 | 0 | 0 | 0 | 2 | 0.00144 | 0.00068 | 1.3 | — |
| Agouti cis 6 | 267 | 1 | 0 | 0 | 0 | 0 | 2 | 0.00053 | 0.00074 | −0.32 | — |
| Corin | 702 | 3 | 2 | 239 | 0 | 0 | 4 | 0.0006 | 0.00083 | −0.5 | — |
| DCT | 512 | 10 | 1 | 301 | 2 | 4 | 10 | 0.00144* | 0.0038 | −1.60* | NS |
| POMC | 379 | 10 | 1 | 379 | 8 | 2 | 17 | 0.00307 | 0.00518 | −1.05 | NS |
| SLC | 652 | 6 | 3 | 256 | 1 | 2 | 10 | 0.00107 | 0.00183 | −0.95 | NS |
| TYR | 767 | 4 | 1 | 767 | 2 | 2 | 5 | 0.00014** | 0.00102 | −1.73** | NS |
| TYRP1 | 589 | 1 | 1 | 382 | 1 | 0 | 2 | 0.0001 | 0.00036 | −0.9 | NS |
S, Number of segregating sites; π: Nei & Li’s nucleotide diversity; ϴw: Watterson’s theta; NS: non-significant. Selection was assessed with Tajima’s D and positive selection was assessed in coding regions with a McDonald–Kreitman (MK) test. Significance levels: *P < 0.05, **; P < 0.01, ***; P < 0.001. Significant values after Bonferroni correction for multiple testing are indicated in bold.