Fig. 2

Differential expression within and between populations (Higher number of differential expression within Zambia. Larger magnitude of changes within Raleigh at Stage 5) A Percent of genes differentially expressed within and between the Zambia and Raleigh populations at stage 2 and stage 5. More differences are found within populations (blue, orange) than between populations (pink). B Proportion of transcripts which have variation in transcript levels in only one population (orange or blue) or have differentially expression within both populations (green) at stage 2 and stage 5. C To control for the number of comparisons within and between lines, we also examined pairwise differences between lines at each stage (stage 2 top, stage 5 bottom). When compared in this way, at both stages, the distributions of DE genes within the Zambia population and between the Zambia and Raleigh populations are similar, with fewer DE genes within the Raleigh lines. D Distributions of the magnitudes of differences in expression in DE genes, which shows that the magnitude of changes between differentially expressed genes is greater within the Raleigh population at stage 5 than the Zambia population at this stage