Table 3. Nucleotide diversity (π) on SD-Mal and SD+ chromosomes.
| π ( ± st. dev.) | p-value | ||||||
|---|---|---|---|---|---|---|---|
| Chr. | Region | SD+ | SD-Mal | SD+ × f | SD-Mal vs. SD+ | SD-Mal vs. SD+*f | |
| 1 | 2L | Distal to Sd-RanGAP |
1.03E-02 | 1.03E-02 | 1.52E-04 | 0.5727 | 0.00E + 00 |
| (±3.01E-03) | (±3.09E-03) | (±4.43E-05) | |||||
| 2 | 2L | Proximal to Sd-RanGAP |
4.44E-03 | 9.39E-05 | 6.52E-05 | 5.84E-90 | 0.0027 |
| (±2.75E-03) | (±1.66E-04) | (±4.04E-05) | |||||
| 3 | 2R | In(2R)Mal | 8.94E-03 | 7.97E-05 | 1.31E-04 | 0.00E + 00 | 1.42E-33 |
| (±2.95E-03) | (±1.18E-04) | (±4.33E-05) | |||||
| 4 | 2L-2R | SD-Mal supergene | 6.42E-03 | 7.98E-05 | 9.43E-05 | 0.00E + 00 | 2.60E-06 |
| (±4.03E-03) | (±1.32E-04) | (±5.92E-05) | |||||
Average nucleotide diversity (π) per site and empirical standard deviation estimated in 10-kb windows along chromosome 2, for SD+, SD-Mal, and SD+ scaled by the estimated frequency of SD-Mal chromosomes (SD+× f, where f = 1.47%). Outside of the linked region (row 1), πSD-Mal ~ πSD+. Inside of the linked region (rows 2–4), πSD-Mal < πSD+; even after scaling πSD+ by the frequency of SD-Mal in the population, πSD-Mal < πSD+× f. Due to non-independence of SNPs in non-recombining regions, we also estimated variance in π based on Charlesworth and Charlesworth, 2010; which is 5.30E-05 for In(2R)Mal and 6.27E-05 for the entire SD-Mal supergene. p-values reported by paired t-test between 10-kb windows.