This repository contains all analyses for the following publication: Warner, M.R., Qiu, L., Holmes, M.J., Mikheyev, A.S. & Linksvayer, T.A. 2019. The convergent evolution of caste in ants and honey bees is based on a shared core of ancient reproductive genes and many plastic genes. In press, Nature Communications. Preprint: https://doi.org/10.1101/454645
Prior to running scripts dealing with figures (src/analysis_R/submission_figures.R), multiple separate analyses need to be done**:
- differential expression (src/analysis_R/DEanalysis.R)
- phylostratigraphy (src/evolution/snakefile_blastPS)
- Aligning drosophila data (src/Drosophila_data/snakefile_calcExpression) and calculate sex-bias (src/Drosophila_data/dmel_sex.R)
- Aligning Jasper et al honey bee tissue data (src/jasper_data/snakefile_calcExpression) and calculate tau (src/jasper_data/jasper_tissue.R)
- Plaid clustering (src/analysis_R/plaid.R)
- evolutionary rate analyses (src/evolution)
**This list is detailed and implemented in the file complete.snake
Evolutionary data can be found here: https://www.dropbox.com/s/ug1jsyv5zm5xy2g/evolution_data.tar.gz?dl=0. Download, unpack, and put the evolution/ directory in data/.
Software required: