DOI: 10.5061/dryad.rbnzs7hqs
title: Evidence for ancient selective sweeps followed by differentiation among three species of Sphyrapicus sapsuckers

description: Scripts and metadata associated with publication Evidence for ancient
 selective sweeps followed by differentiation among three species of
 Sphyrapicus sapsuckers. Scripts detail the steps taken to process, align,
 and QC raw WGS reads, calculate differentiation statistics, and generate
 figures (maps, PCAs, Manhattan plots, scatter plots, phylogenetic trees,
 Genotype x Individual plots). Metadata for samples used in the analyses
 includes sample IDs, museum voucher IDs (where applicable), species,
 collection date and location, and sample sex. 
description: # Evidence for Ancient Selective Sweeps Followed by Differentiation Among
 Three Species of *Sphyrapicus* Sapsuckers — Dryad README ## General
 Information **1. Title of Dataset:**\ *Evidence for ancient selective
 sweeps followed by differentiation among three species of Sphyrapicus
 sapsuckers* dataset **2. Author Information:** * **Name:** Libby Natola
 and Darren Irwin * **Institution:** University of British Columbia *
 **ORCID:** [0000-0001-7576-2825](https://orcid.org/0000-0001-7576-2825) *
 **Email:** libby.natola at gmail.com **3. Description of Dataset:**\ This
 README details files and analyses used in *Genomic divergence and
 speciation in red-naped, red-breasted, and yellow-bellied sapsuckers* for
 *Journal of Evolutionary Biology* 2025. **4. Date and Geographic Location
 of Data Collection:**\ Data were collected by Libby Natola from 2019–2022
 at the University of British Columbia. --- ## Sharing/Access Information
 ### 1. Licenses/Restrictions Placed on Data CC0 1.0 Universal --- ## File
 List ### Genomic Data Filtering and Processing: 1.
 `WGS_processing_only_clean.txt` — Scripts to process datasets. Analyses
 run on UBC's ARC Sockeye HPC cluster. 2. `sample_info.txt` — Sample
 metadata. 3. `pseudochromosomes.fasta.gz` — Red-breasted Sapsucker
 (*Sphyrapicus ruber*) PacBio assembly mapped to Golden-fronted Woodpecker
 (*Melanerpes aurifrons*) from Wiley and Miller 2020. 4.
 `IrwinLabGenomicsAnalysisScript.jl` — Julia to R script. 5.
 `IrwinLabGenomicsTransferJuliaToR.R` — Converts Julia output files into
 R-readable files. 6. `plotGenomeFstDxyPi.processing.txt` — Runs and loops
 the Julia and Julia-to-R scripts. 7. `calculate_summary_stats.txt` —
 Summary statistics script. ### Analyses/Figures: 1. `WGS_sample_map.R` — R
 script for map generation (run locally). Generates intermediate figure
 files for **Figure 1** in text, finalized in Inkscape. 2.
 `PCA_manhattan.R` — Scripts for PCA and Manhattan plots (run on HPC,
 interactively in RStudio Server with Conda WGS environment). Generates
 intermediate figure files for **Figures 3 and 4**, finalized in Inkscape.
 3. `genomics_R_functions_auto_vs_Z.R` — R source script for
 `Autosomal_Z_comparisons.R`. 4. `Autosomal_Z_comparisons.R` — Scripts for
 autosome vs. Z chromosome comparisons, Fst × πB plots, Welch's tests,
 phylogenetic tree, **Table 1** in text. Generates intermediate figure
 files for **Figures 5, 6,** and **Supplemental Figure S2**, finalized in
 Inkscape. 5. `Sphyrapicus_genomics_Feb2025_Zchrom_GBI.jl` — Script for
 genotype-by-individual plots. Generates intermediate figure files
 finalized for **Figure 7** in text in Inkscape. 6.
 `genomics_R_functions_differentiation-stats.R` — R source script for
 `plotGenomeFstDxyPi2.R` 7. `plotGenomeFstDxyPi2.R` — R script for rolling
 Fst, πB, πW plots (run on HPC). Generates intermediate figure files for
 **Supplemental Figure S1**, finalized in Inkscape.