Constitutive and Plastic Gene Expression Variation Associated with Desiccation Resistance Differences in the Drosophila americana Species Group

Abstract

Stress response mechanisms are ubiquitous and important for adaptation to heterogenous environments and could be based on constitutive or plastic responses to environmental stressors. Here we quantify constitutive and plastic gene expression differences under ambient and desiccation stress treatments, in males and females of three species of Drosophila known to differ in desiccation resistance. Drosophila novamexicana survives desiccation trials significantly longer than the two subspecies of Drosophila americana, consistent with its natural species range in the desert southwest USA. We found that desiccation stress reduces global expression differences between species-likely because many general stress response mechanisms are shared among species-but that all species showed plastic expression changes at hundreds of loci during desiccation. Nonetheless, D. novamexicana had the fewest genes with significant plastic expression changes, despite having the highest desiccation resistance. Of the genes that were significantly differentially expressed between species-either within each treatment (>200 loci), constitutively regardless of treatment (36 loci), or with different species-specific plasticity (26 loci)-GO analysis did not find significant enrichment of any major gene pathways or broader functions associated with desiccation stress. Taken together, these data indicate that if gene expression changes contribute to differential desiccation resistance between species, these differences are likely shaped by a relatively small set of influential genes rather than broad genome-wide differentiation in stress response mechanisms. Finally, among the set of genes with the greatest between-species plasticity, we identified an interesting set of immune-response genes with consistent but opposing reaction norms between sexes, whose potential functional role in sex-specific mechanisms of desiccation resistance remains to be determined.

Keywords: Drosophila; RNA-seq; desiccation.

Figure 1

Variation in desiccation resistance between species and sexes, in minutes survived under acute desiccation (n = 5 for all identities) (means = black bars; quartiles = boxes). Original data is from Davis and Moyle 2019 [26]. ANOVA shows that species (F(2) = 10.16; p = 0.00027) but not sexes (F(1) = 0.66; p = 0.42) significantly differ in desiccation resistance.

Figure 2

Numbers of genes that are shared versus species-specific in their plastic gene expression responses to desiccation stress (log₂ fold change or greater), within males (top) and females (bottom). Total number of plastic genes for each species indicated in parentheses. Arrows indicate whether gene expression is elevated (up) or reduced (down) in the desiccation treatment, relative to the control/ambient treatment.

Figure 3

Pairwise species comparisons of (log₂ fold) gene expression differences between ambient (non-desiccating) and desiccation conditions, for males (top) and females (bottom). Each point shows the expression change for one gene for each pair of species; diagonal lines are y=x and represent the expectation if species share an identical plastic response to desiccation stress. Points that lie far from this line indicate genes that have greater differences in plastic expression patterns between species.

Figure 4

Top 20 genes by greatest between-species variance in fold-change for males (top) and females (bottom). Six genes: Uro, Def, DptB, YOgnVI05360, YOgnVI05361, and YOgnVI04823 are shared between males and females, and all but Uro show opposing patterns between the sexes. Functional information about these genes is given in Table 2 and Table 3.