Configuration files and code used in assembling UCE data for comparative river island phylogeography project. Most pipelines based on the Phyluce pipeline, with some modifications from seq_cap_pop
Remaining files are for data manipulation and PGLS / ANOVA analyses
Zenodo archive:
Folders:
DAPC: scripts used for Discriminant Analysis of Principle Components (DAPC) for each species
seqcap_pop: scripts used for calling SNPs using the seqcap_pop pipeline: https://github.com/mgharvey/seqcap_pop
Scripts:
PopGenome.R: Fst and Dxy calculations with the R package PopGenome
PopGenome.DAPC_assignments.R: Fst and Dxy calculations with the R package PopGenome, but with samples assigned to genetic clusters from DAPC
calculate_average_dxy_fst.py: calculate Fst and Dxy metrics from alignments, averaging across all pairwise comparisons
calculate_average_dxy_fst_all_species.sh: run the calculate_average_dxy_fst.py script for all species
gene_trees-all_species.sh: estimate UCE gene trees in RAxML
calculate_mtdna_tree_depth.R and calculate_uce_gene_tree_depth.R: calculate average branch lengths of mitochondrial and UCE gene trees
dendropy_popgenstats.py: calculate population genetic metrics in DendroPy
distruct_structure_all_species.sh: run Distruct for visualizing STRUCTURE results
genepop_ibd.R: calculate isolation-by-distance slopes with the R package genepop and process results: genepop_ibd_process_results.R
heterozygosity_outliers.R: detect extreme heterozygosity outliers for removal from dataset
pgls_caper.R: run PGLS analysis in R package caper (old)
phylANOVA.R: format input data and run phylogenetic ANOVA and PGLS analyses. Most analyses and plotting are included in this file.
sensitivity_analysis.R: process some heterozygosity data in sensitivity analysis
heterozygosity_per_pop.R: calculate heterozygosity for each population from DAPC