Supplementary Data chapter 4 Genotypic linkage disequilibrium locus by locus for "Target site (knockdown resistance) gene mutations and population genetic structure of Aedes aegypti in Saudi Arabia"
The linkage disequilibrium (LD) tests were estimated among all possible pairs of the 17 loci in each population for a total of 13 populations using GENEPOP v4.2 (Rousset 2008) (Dememorisation: 10,000; batches: 100; and iterations per batch: 10,000). In Excel calculator v1.2 (Gaetano 2013), LD significance levels for multiple testing were corrected using the Holm-Bonferroni sequential correction to adjust the p-value to minimize type I error.
Only the pair of loci AG1 and AG3 showed significant linkage disequilibrium after the Holm-Bonferroni sequential correction, and were consistently correlated across all mosquito populations in Saudi Arabia. Although AG1 and AG3 showed linkage across the population in Saudi Arabia, these two loci were reported with no physical linkage in previous studies (Slotman et al. 2007, Rasheed et al. 2013). Furthermore, Brown et al. (2011), removed the two loci (AG1 and AG3) with no impact on the results (Brown et al. 2011). Interestingly, this significant linkage was also observed in Thailand but not Ugandan samples (Additional file 1: Table S4); thus, we decided to keep both loci.