Code used in McCullough et al. in review "Rapidly Radiating Clade of ‘Great Speciators’ Harbors Rampant Incomplete Lineage Sorting and Low Levels of Gene Flow (Aves: Todiramphus kingfishers)"
This repository has code for data processing and most analyses. See Dryad repository (link to include here when generated) for supplementary information and datasets.
We created a dataset will all samples (n=63) and seven different subsets for PCAs/ADMIXTURE etc. Some analyses were run on the UNM Center for Advanced Research computing, which requires a slurm submission script to the cluster and used a conda environment that had stacks, bwa, and samtools installed. Other code was run in R. Color editing for PCAs/admixture plots was done by hand in Adobe Illustrator.
01_align: folder with a slurm that aligns demultiplexed reads to Mariana Kingfisher reference genome and generation of bam files using SAMtools
02_stacks: Stacks to build catalog of RAD loci and creation of VCF files for all samples and the 7 subsets. Includes a folder of the different population maps to use to create subsets
03_SNPfiltr: R code for SNPFiltr for the full dataset and subsets. Use the population maps from step #2. The bottom of this file has instructions to get a whitelist of RAD loci to use for SVDquartets
04_Splitstree: code to convert vcf into distance matrix to be used as input into splitstree
05_PCAs: code, used in conjunction with downloaded vcf files from dryad, to produce the PCAs.
06_genetic-stats: code to produce Figure 2C.
07_ADMIXTURE: slurm scripts and R code used to generate ADMIXTURE plots