Africa-wide analysis of genetic diversity across the <i>rp1</i> pyrethroid resistance locus.

<p><b>A)</b> Genetic diversity (pi) across the 120kb <i>rp1</i> in Cameroon (orange), Malawi (blue), and Mozambique (green). <b>B)</b> Phylogeny of the ‘BAC25’ fragment (located 25kb along the BAC sequence and 9kb upstream of the <i>CYP6P9a</i> gene), which shows the most extreme difference in diversity between Cameroon (orange) and southern populations Malawi (blue) and Mozambique (green), which form a single clade. <b>C)</b> Phylogeny of the <i>CYP6P9a</i> gene sampled from throughout Africa, showing clear geographical divergence between southern Africa (Malawi and Mozambique; 100% bootstrap support), East Africa (Uganda; 87% bootstrap support) and West/Central Africa (Ghana, Benin, Cameroon; 78% bootstrap support). <b>D)</b> Haplotype network for Non-synonymous nucleotide variants in <i>CYP6P9a</i>. Light blue = haplotype shared between Malawi and Mozambique (MAL/MOZ); pink = haplotype shared between Benin, Cameroon and Ghana (BN/CAM/GH); teal = Benin (BN); red = Ghana (GH); orange = Cameroon (CAM); green = Mozambique (MOZ); blue = Malawi (MAL); purple = Uganda (UG). The size of the shapes is proportional to the frequency of the haplotype and numbers on each branch show the mutational steps separating haplotypes.