Transcriptome of Tribolium castaneum selection lines (control-, drought-, heat-, heat/drought-adapted) under different climatic conditions

We studied plastic and evolutionary responses in gene expression of Tribolium castaneum after beetles' exposure to new environments that differed from ancestral control conditions in temperature, humidity or both. Using experimental evolution with ten replicated lines per condition, we were able to demonstrate adaptation (higher offspring number compared to control lines) after 20 generations. We measured whole-transcriptome gene expression with RNA-seq to infer evolutionary and plastic changes. We found more evidence for changes in mean expression (shift in the intercept of reaction norms) in adapted lines than for changes in plasticity (shifts in slopes). Plasticity was mainly preserved in selected lines and was responsible for a large part of the phenotypic divergence in expression between ancestral and new conditions. However, we found that genes with the largest evolutionary changes in expression also evolved reduced plasticity and often showed expression levels closer to the ancestral stage. Results obtained in the three different conditions were similar, suggesting that restoration of ancestral expression levels during adaptation is a general evolutionary pattern. With a larger sample in the most stressful condition, we were able to detect a positive correlation between proportion of genes with reversion of the ancestral plastic response and mean fitness per selection line. Overall design: We used the Tribolium castaneum Cro1 strain collected from a wild population in 2010 and adapted to lab standard conditions (33°C, 70% relative humidity) for more than 20 generations. Beetles were kept in 24h darkness on organic wheat flour mixed with 10% organic baker's yeast. We sterilized flour and yeast by heating them for 12h at 80°C before use. To test for adaptation to new environmental conditions we used replicate lines and exposed them to three treatments and Control conditions. The conditions in the treatments were: Dry : 33°C and 30% relative humidity; Hot : 37°C and 70% r. h.; Hot-Dry: 37°C and 30% r. h. To generate replicate lines, we used 120 individuals (60 females and 60 males in the pupal stage from our Cro1 stock population) and placed them into a vial containing 80g medium. After seven to ten days, in which the pupae became adults, mated and laid eggs, adult beetles were removed by sieving the medium. We waited until the next generation (eggs/larvae in the medium) had reached the pupal stage and again collected 120 pupae per line to establish the next generation. Selection lines could adapt to treatment conditions for 20 generations. Before testing for adaptation, all lines stayed for one generation in control condition. Sequenced individuals were transferred to the respective condition in the egg stage and developed completely in treatment conditions. We sequenced adult reproducing females from different replicate lines under different conditions (seven Control-lines, four Dry-lines, five Hot-lines, seven Hot-Dry lines). For each selection line we used individuals from control conditions as well as individuals from treatment conditions to infer evolutionary changes (difference between Control- and Dry/Hot/Hot-Dry lines within the same condition) and plastic changes (difference between individuals from the same selection line under control and treatment conditions).