Data and code for Greenway et al. (2020)

This repository includes data and code associated with Greenway et al.: "Convergent evolution of conserved mitochondrial pathways underlies repeated adaptation to extreme environments". A pre-print of this paper can be found on bioRxiv.

Biochemical and physiologial analyses

Four datasets were associated with biochemical and physiological analyses:

• Measurements of COX activity
• Measurements of SQR activity
• Measurements of mitochondrial H2S concentrations
• Measurements of mitochondrial respiration

All data were analyzed and visualized in R. Executable code is available as an R Markdown File. Alternatively analyses and outputs can be previewed as HTML.

Comparative genomic analyses of Poecilia mexiana

• Scripts for local ancestry analysis and the calculation of FST

Comparative transcriptomic analyses of Poeciliidae

• Comparative transcriptomics included analysis of gene expression variation and analysis of molecular evolution. Scripts for the entire analytical pipeline--from mapping to analysis in EVE and PAML--can be found here
• Two auxiliary python scripts associated with comparative transcriptomic analysis can be found in the "transcriptomics" folder.