Evidence for ancient selective sweeps followed by differentiation among three species of Sphyrapicus sapsuckers
Data files
Aug 19, 2025 version files 329.36 MB
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Autosomal_Z_comparisons.R
44.97 KB
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calculate_summary_stats.txt
22.26 KB
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genomics_R_functions_auto_vs_Z.R
120.50 KB
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genomics_R_functions_differentiation-stats.R
119.68 KB
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IrwinLabGenomicsAnalysisScript.jl
18.36 KB
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IrwinLabGenomicsTransferJuliaToR.R
2.77 KB
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PCA_manhattan.R
12.61 KB
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plotGenomeFstDxyPi.processing.txt
14.86 KB
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plotGenomeFstDxyPi2.R
12.48 KB
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pseudochromosomes.fasta.gz
328.89 MB
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README.md
2.94 KB
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sample_info.txt
5.53 KB
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Sphyrapicus_genomics_Feb2025_Zchrom_GBI.jl
30.92 KB
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WGS_processing_only_clean.txt
57.38 KB
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WGS_sample_map.R
6.23 KB
Abstract
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.
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
- 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:
WGS_processing_only_clean.txt— Scripts to process datasets. Analyses run on UBC's ARC Sockeye HPC cluster.sample_info.txt— Sample metadata.pseudochromosomes.fasta.gz— Red-breasted Sapsucker (Sphyrapicus ruber) PacBio assembly mapped to Golden-fronted Woodpecker (Melanerpes aurifrons) from Wiley and Miller 2020.IrwinLabGenomicsAnalysisScript.jl— Julia to R script.IrwinLabGenomicsTransferJuliaToR.R— Converts Julia output files into R-readable files.plotGenomeFstDxyPi.processing.txt— Runs and loops the Julia and Julia-to-R scripts.calculate_summary_stats.txt— Summary statistics script.
Analyses/Figures:
WGS_sample_map.R— R script for map generation (run locally). Generates intermediate figure files for Figure 1 in text, finalized in Inkscape.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.genomics_R_functions_auto_vs_Z.R— R source script forAutosomal_Z_comparisons.R.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.Sphyrapicus_genomics_Feb2025_Zchrom_GBI.jl— Script for genotype-by-individual plots. Generates intermediate figure files finalized for Figure 7 in text in Inkscape.genomics_R_functions_differentiation-stats.R— R source script forplotGenomeFstDxyPi2.RplotGenomeFstDxyPi2.R— R script for rolling Fst, πB, πW plots (run on HPC). Generates intermediate figure files for Supplemental Figure S1, finalized in Inkscape.