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Figures
- Fig. 1.
Conceptual illustration of the ‘during-winter’ and ‘after-winter’ hypotheses for apple versus hawthorn fly race divergence in gene expression and the experimental design. (A,B) Transcripts regulating earlier diapause termination in apple relative to hawthorn flies could be differentially regulated between populations during winter (‘during-winter’ hypothesis; A), or only after exposure to warmer temperatures necessary to begin post-diapause development (‘after-winter’ hypothesis; B). Green and pink represent up- and down-regulation of transcripts in apple relative to hawthorn flies and not absolute values, so the key feature is when the shifts in transcription levels occur between the host races, i.e. the fork in up- and down-regulation can be seen prior to 0 h in the during-winter hypothesis and extends afterward, whereas it is initiated only after the 0 h time point in the after-winter hypothesis. Note that both positive and negative values of this relative measure may reflect up- or down-regulation of transcripts in one population compared with the other. Solid and dashed lines in the upper panel denote accelerating and constant differences between populations following the temperature shift. (C) Experimental design: upon pupariation, apple and haw fly pupae were exposed to common, simulated overwinter conditions, then sampled for RNAseq at three time points – one at the end of winter (0 h), one 24 h after the end of winter, and one 48 h after transfer to warmer conditions.
- Fig. 2.
Venn diagram depicting the number of transcripts differentially expressed at different time points in apple versus hawthorn flies. Significant differential expression (false discovery rate, FDR<0.05, as determined from linear models) was identified in three pairwise comparisons as inferred from generalized linear models of transcript counts including parameters for sampling time point and host race but no interaction; two comparisons between sampling time points (0 h versus 24 h and 24 h versus 48 h; Fig. 1) and one comparison between the apple and hawthorn host races (populations). Overlapping regions represent sets of transcripts that were differentially expressed in two or more comparisons.
- Fig. 3.
Network diagram of all transcripts significantly differentially expressed between host races connected to core wnt and insulin signaling pathway genes by at least one edge. Differential expression was determined by a significant host effect in the generalized linear model (FDR<0.05) and a non-significant host×time point interaction. Edges represent the existence of one or more gene–gene interactions in the Drosophila Interactions Database (DroID). Gene names are from the Drosophila melanogaster annotation v6.10 referenced in supplement S1.2.
- Fig. 4.
Time series of transcript abundance relative to expression at the first sampling point (0 h) for transcripts consistent with a pattern of post-winter suppression. (A) Ribosome biogenesis. (B) Nucleotide binding. Values are estimates of log2 (expression at time point/expression at 0 h) obtained via post hoc contrasts of GLM parameters. These include transcripts from two functional categories that were enriched in the set of all transcripts that were oppositely differentially expressed (up-regulated at 24 h but down-regulated at 48 h, or vice versa) between (1) 0 and 24 h and (2) 24 and 48 h.
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