Fig.1

Populations are distinct at each developmental stage. A Hierarchical clustering of transcriptomes from stage 2 (labels ending with _2) and stage 5 (labels ending with _5) embryos, from 8 lines of D. melanogaster, four from Raleigh (RAL, orange) and four from Zambia (ZI, blue), with closely related species D. simulans (Sim, in green text) as an outgroup. Samples cluster first by stage, then by species, then by population. B PCA shows that these same samples separate first by stage (PC1, which explains a large proportion of the variance at 79.2%), then by population (PC2, 11.4% of the variance), though more distinctly at stage 2 than stage 5