R code for differential gene expression and enrichment analyses

The information about the magnitude of differences in thermal plasticity both between and within populations, as well as identification of the underlying molecular mechanisms are key to understanding the evolution of thermal plasticity. In particular, genes underlying variation in the physiological response to temperature can provide raw material for selection acting on plastic traits. Using RNAseq, we investigate the transcriptional response to temperature in males and females from bulb mite populations selected for the increased frequency of one of two discrete male morphs (fighter- and scrambler-selected populations) that differ in relative fitness depending on temperature. We show that different mechanisms underlie the divergence in thermal response between fighter- and scrambler-selected populations at decreased vs. increased temperatures. Temperature decrease to 18°C was associated with higher transcriptomic plasticity of males with more elaborate armaments, as indicated by a sign..., The data originate from RNAseq on bulb mite populations selected for the increased or decreased frequency of the fighter morph. Gene expression was measured in both sexes in mites developing at three different temperatures (18, 23, and 28°C)., , # R code for differential gene expression and enrichment analyses

[https://doi.org/10.5061/dryad.2jm63xsxt](https://doi.org/10.5061/dryad.2jm63xsxt)

This is the code together with input files (raw read counts together with metadata) used to analyse gene expression data. 

Description of the metadata file:

* S and F in Morph stand for scrambler and fighter-selected population, respectively.
* F and M in Sex stand for female and male, respectively.
* Temperature is given in degrees Celcius.

## Sharing/Access information

Raw sequencing reads for the analyses can be downloaded from:

* [http://www.ncbi.nlm.nih.gov/bioproject/868706](http://www.ncbi.nlm.nih.gov/bioproject/868706)