Data from Koch and Guillaume 2020 Molecular Ecology: Restoring ancestral phenotypes is a general pattern in gene expression evolution during adaptation to new environments in Tribolium castaneum
Creators: name: Koch, Eva
name: Guillaume, Frédéric
Publisher: name: Zenodo
Year: 2020
Subjects: Tribolium castaneum
Fitness
Adaptation
Gene expression

description: Fitness data of <em>Tribolium castaneum</em> (red flour beetle) selection lines under four different climate conditions and analysis of gene expression profiles (available at GEO, accession GSE156256). We were interested to test for adaptation, i.e. whether native selection lines showed higher offspring numbers relative to control lines in the respective treatments and to examine underlying changes in gene expression using whole transcriptome data. <strong>Abstract</strong><br> We studied plastic and evolutionary responses in gene expression of <em>Tribolium castaneum</em> 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 of selection lines in their native treatment compared to control lines) after 20 generations. We measured whole-transcriptome gene expression with RNA-seq in a subset of these individuals to infer evolutionary and plastic changes. In all treatments we detected significant plastic as well as evolutionary changes in gene expression.Plasticity was mainly preserved in adapted 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. <strong>Method</strong> We used the <em>Tribolium castaneum</em> 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. In generation 15 we produced additional mixed lines to prevent loss of genetic diversity by gene drift and inbreeding, which might impede adaptation: We mixed the six replicate lines of each selection regime in equal proportions (20 individuals from each replicate line) four times, resulting in four mixed lines with 120 individuals each. Before testing for adaptation, all lines stayed for one generation in control condition. Individuals used for the fitness assay were transferred to the respective condition in the egg stage and developed completely in treatment conditions. We then assessed their performance in each condition. A virgin male and a virgin female of the same selection line from the same condition but from different families were placed into a 15 mL tube with 1 g medium. After four days, the mating pair was removed. A subset of the females was transferred to 1 mL Eppendorf tubes (one individual per tube), immediately frozen in liquid nitrogen and stored at -80°C to use them for gene expression measurements. 9 g medium was added to the mating tube. After four weeks (in Control and Hot) or five weeks (Dry and Hot-Dry), all offspring had reached the adult stage and were counted. We used the number of adult offspring as fitness estimate for females. Gene expression was measured using RNA-seq. We extracted mRNA from the whole body of reproducing females. Sequencing data and read counts are available from GEO (accession GSE156256). <strong>Files</strong> This data publication contains the following data and script files FitnessData.txt : Data from fitness assay during a transplant experiment after experimental evolution<br> Selection-line ID; linetype (mixed/normal, see Methods); Selection: condition, in which the selection-line spent 20 generations (CT: Control; D: Dry; Hot; HD: Hot-Dry); Treatment: condition, in which offspring number was measured; family: each selection line consisted of several families; offspring: number of adult offspring that a female could produce within four days of egg-laying Samples_Transpl_2018.txt : List of sequenced samples<br> Sample IDs of those individuals that were sequenced; Selection: condition, in which the selection-line spent 20 generations (CT: Control; D: Dry; Hot; HD: Hot-Dry); Treatment: condition, in which the individual grew up and reproduced; group: combination of selection regime and treatment; batch: sequencing run Counts.txt: Raw read counts<br> Read counts obtained from RNA-seq for a subset of individuals used in the fitness assay. RNA-seq data is available at GEO (accession GSE156256). Fitness_analysis.R :Fitness analysis to test for adaptation:<br> We compared offspring number of native selection lines and control lines within treatment conditions ExpressionAnalysis_D.R ; ExpressionAnalysis_H.R; ExpressionAnalysis_HD.R:<br> Gene expression analysis (for each treatment separately)<br> We identified differentially expressed genes accounting for non-independence between samples from the same selection line. We tested for differences between expression levels between Control-lines and selection-lines within control and treatment conditions (=evolutionary change); responses to treatments (=plasticity), i.e. differences between individuals from the same selection line under different conditions; differences in plasticity between lines from different selection regimes; we explored differences between plastic and evolutionary changes following an approach proposed by Ho and Zhang (Nature Communications, 9(1), 1–11.doi:10.1038/s41467-017-02724-5)