ReadMe.txt

This repository contains code and data sufficient to reproduce the analyses & results within the manuscript "Fluctuating selection facilitates the discovery of broadly effective but difficult to reach adaptive outcomes in yeast."

This project consisted of (1) a 500 generation experimental evolution experiment within which the proportions of evolving barcoded yeast strains were monitored over 50 days (Subdirectory: Evoluitonary_Dynamics), and (2) a series of competition based fitness assays designed to measure the fitness of ancestral and evolved yeast strains relative to a common ancestor (Subdirectory: Fitness_Assays). The manuscript referenced above focuses on the data and analyses associated with the Fitness_Assays portion of this repository. Details follow. 

Data parsing, processing, and analyses were conducted in three steps: (1) convert raw fastq files to counts matrices, (2) join counts data with experiment and methodological metadata, and (3) conduct analyses, produce figures & tables. Each step has a corresponding subdirectory within the Fitness_Assays subdirectory. R notebooks within are fully commented and include headers describing the file purpose, inputs, and outputs. 

Final dataframes for main analyses are found within the file Fitness_Assays/2_CountstoAnalysis/Formatted_Data/FitAssayData.Rdata. Upon loading this file three tables will be available for exploration and analysis "my", "myrc", and "myrcw". Each table contains metadata and fitness information with the same source but different formats for summarization. Table "my" has 1 row per [assay environment]X[replicate]X[barcode ID], table "myrc" is further summarized to 1 row per [assay environment]X[barcode ID] and table "myrcw" is the most summarized to 1 row per [barcode ID]. These three levels of data summarization are provided for convienience of analysis and plotting. Raw counts tables (converted directly from FastQ originals) are available at the following location: Outputs/Collected_Data_&_Metadata/Fitness_Assays/...