This repository contains the scripts and parameter files used for the genomic analysis of the Primula cusickiana species complex. The article describing these analyses is published with Systematic Botany and can be found here.
The ipyrad directory contains 3 folders, each corresponding to a unique run of the ipyrad software pipeline. Directories contain the relevant params files used for each run, as well as relevant outfiles (although not all output files are included, as this is unecessary and would require too much space).
The PreliminaryRuns directory contains the ipyrad barcode and parameters files used for initial exploratory run (titled "UniqueReps"), along with output files. ComplexWide holds the same files for the final run including all complex member samples, and MaguireOnly contains the relevant ipyrad files for the run examining only maguirei samples.
In addition, ComplexWide and MaguireiOnly include folders which contain the files used for FST calculations (using VCFtools).
The ComplexWide folder also contains the JuneSubset.nex file, which was passed into the software SplitsTree to generate the split network diagram shown in the manuscript.
The R directory contains the R script used in data analysis. This includes the plotting code for STRUCTURE plots (in structure) and DAPC (in DAPC). Code used to generate Jaccard distribution of samples is included in the JaccardDistances.R script.
Additionally included are R scripts used in intial data exploration.
The Mapping directory includes the Python script and .csv file used to generate the map of samples with the cluster membership at STRUCTURE output K=7. Credit goes to Dr. Carol Rowe for compiling this Python script!
The structure directory contains folders holding the mainparams and extraparams files for two STRUCTURE runs: the complex wide analysis, and the analysis looking at strictly maguirei samples. Additionally, output files (.str, .stru, .vcf, and .nex) are included, as well as the BASH script used to run STRUCTURE.
For any questions regarding these scripts, please contact Austin Koontz (either through GitHub or via email). Other scripts/parameter files used in the analysis of this dataset can be made available upon request. Raw data has been uploaded to the NCBI short-read archive (SRA), accession number PRJNA705310.