Canalization of gene expression is a major signature of regulatory cold adaptation in temperate Drosophila melanogaster

Abstract

Background: Transcriptome analysis may provide means to investigate the underlying genetic causes of shared and divergent phenotypes in different populations and help to identify potential targets of adaptive evolution. Applying RNA sequencing to whole male Drosophila melanogaster from the ancestral tropical African environment and a very recently colonized cold-temperate European environment at both standard laboratory conditions and following a cold shock, we seek to uncover the transcriptional basis of cold adaptation.

Results: In both the ancestral and the derived populations, the predominant characteristic of the cold shock response is the swift and massive upregulation of heat shock proteins and other chaperones. Although we find ~25 % of the genome to be differentially expressed following a cold shock, only relatively few genes (n = 16) are up- or down-regulated in a population-specific way. Intriguingly, 14 of these 16 genes show a greater degree of differential expression in the African population. Likewise, there is an excess of genes with particularly strong cold-induced changes in expression in Africa on a genome-wide scale.

Conclusions: The analysis of the transcriptional cold shock response most prominently reveals an upregulation of components of a general stress response, which is conserved over many taxa and triggered by a plethora of stressors. Despite the overall response being fairly similar in both populations, there is a definite excess of genes with a strong cold-induced fold-change in Africa. This is consistent with a detrimental deregulation or an overshooting stress response. Thus, the canalization of European gene expression might be responsible for the increased cold tolerance of European flies.

Keywords: Adaptation; Canalization; Cold tolerance; Transcriptomics.

Fig. 1

CCRT for the eight focal strains. Chill coma recovery time (CCRT) was determined following a 7 h cold shock in an ice-water bath. Depicted values are averaged over both sexes and a multitude of independent experiments. Strains originate from Umea, Sweden (SU07, SU08, SU58), Leiden, the Netherlands (E14), Siavonga, Zambia (ZI197, ZI216, ZI418), and Lake Kariba, Zimbabwe (A157)

Fig. 2

Transcriptome overview: PCA. PCA was calculated using the built-in methods provided by DESeq2 [42] for variance stabilizing transformation of read counts and PCA on the 500 genes with the highest overall expression variance. Note that samples are clearly separated according to continent and condition with the exception of RT and CS samples, which cluster tightly together in both populations such that symbols partly overlap

Fig. 3

Genome-wide L2FC per population. Using DESeq2 [42] the log2 fold-change (L2FC) in expression between rec90 and RT was calculated for 13803 genes with sufficient read count in both populations separately for African and European flies. Genes were then grouped into distinct bins according to their L2FC. Bin size is 0.2. The area where the African and European histograms overlap is depicted in dark red. a All genes, b genes with an absolute L2FC > 0.6

Fig. 4

Amount of highly plastic genes per strain. Genewise L2FC between rec90 and RT was calculated for each strain after normalization of raw counts using the TPM method [43, 44]. All genes with zero read count in one sample were excluded resulting in 12617 genes in total. Depicted are only genes with an absolute L2FC > 1 with no respect to up- or down-regulation