Fig. 4
Analysis of chromosome V and the major region of introgression. a. Genetic differentiation (FST) measured in 10 kbp windows throughout chromosome V is presented between MHco3(ISE) parent and both MHco3/10.BC4.IVM.P4 (light) and MHco3/4.BC4.IVM.P4 (dark) representing the final time point of the crosses. Inset presents the smoothed FST distribution of the two comparisons. Published candidate genes in or near the introgression region (grey vertical lines), as well as the original Hcms8a20 microsatellite marker that Redman et al. (2012) linked to ivermectin resistance (black vertical line), are presented. b. Comparison of Tajima’s D per chromosome between MHco3(ISE) parent (blue), MHco10(CAVR) (left panels) or MHco4(WRS) (right panels) and passage 3 (MHco3/10.BC4.IVM.P3 or MHco3/4.BC4.IVM.P3; orange) and passage 4 (MHco3/10.BC4.IVM.P4 or MHco3/4.BC4.IVM.P4; yellow) of the crosses (top panels). Tajima’s D was calculated using npstat in 100 kbp windows spanning the genome. To emphasise the difference between the susceptible MHco3(ISE) and resistant passages 3 and 4 samples, we calculated the variance in the mean value of Tajima’s D between samples, which is presented as red smoothed line (bottom panel). The null expectation is that variance between these samples will be low in regions of the genome not under selection. c. Inferred likelihoods from the multi-locus population genetic model. The mean likelihood of the best fitting single-locus model at each locus position is shown by the solid black line; the light blue interval around this line shows the 5–95% confidence interval for this statistic calculated by a bootstrapping process. The position of the maximum likelihood value is shown by the vertical black dotted line; a confidence interval for this position, calculated from the bootstrapping values, is shaded in grey. The mean likelihood of the best fitting constrained two-locus model is shown by the black dashed line; the value shown represents the best value of the model given that one of the selected loci is at the given position