Data from: Recurrent selection explains parallel evolution of genomic regions of high relative but low absolute differentiation in a ring species

Irwin DE, Alcaide M, Delmore KE, Irwin JH, Owens GL

Date Published: August 1, 2016

DOI: http://dx.doi.org/10.5061/dryad.t951d

 

Files in this package

Content in the Dryad Digital Repository is offered "as is." By downloading files, you agree to the Dryad Terms of Service. To the extent possible under law, the authors have waived all copyright and related or neighboring rights to this data. CC0 (opens a new window) Open Data (opens a new window)

Title Greenish Warbler consensus genome v1.0
Description Contains a consensus greenish warbler genome assembly, based on a consensus of genome assemblies of three greenish warbler (Phylloscopus trochiloides) individuals (viridanus TL2; trochiloides LN10; and plumbeitarsus BK2). The file contains sequences for 31 chromosomes and chromosome fragments, based on mapping of greenish warbler contigs to the zebra finch genome assembly (version 3.2.4; Warren et al. 2010). The file is in standard Fasta format. It needs to be un-compressed first by running the command: gunzip Phylloscopus_trochiloides.Greenish_warbler.3sample.consensus.wrapped.toplevel.fa.gz The three whole-genome shotgun assemblies have been deposited at DDBJ/ENA/GenBank under the accessions LXPA00000000 (viridanus), LXOZ00000000 (trochiloides), and LXOY00000000 (plumbeitarsus).
Download Phylloscopus_trochiloides.Greenish_warbler...fa.gz (269.1 Mb)
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Title Greenish Warbler VCF files: invariant and SNPs
Description This folder contains 31 files in the VCF format. Each contains genotypic information for a single chromosome (or chromosome fragment) for all individuals in the two GBS (genotype by sequencing) plates in the study. The files have names corresponding to "GW_Lane5plusLiz.GWref.genotypes.allSites.chr*.infoSites.vcf"; the * represents the chromosome name. All sites, both variant and invariant, where there was a total of more than 10 sequencing reads among all individuals were included. The chromosomes refer to those in the Zebra Finch assembly (version 3.2.4; Warren et al. 2010). For details of how these VCF files were produced and how they were then used, see the associated paper (Irwin et al., in review, Molecular Ecology) and this file in this same Dryad package: "GW_islands_of_diff_processing_scripts.txt"
Download GW_infoSites_vcf_chromosome_files.tar.gz (1.331 Gb)
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Title Greenish Warbler genotypes: 45-sample analysis
Description This folder contains genotypic information used in the 45-sample analysis comparing the taxa viridanus, trochiloides, and plumbeitarsus (15 individuals each). For each chromosome, there is a file containing the genotypes (ending in "012NA"), a file containing the list of individuals (ending in "012.indv"), and a file containing the list of positions on the chromosome (ending in "012.pos"). For details of how these files were produced see the file "GW_islands_of_diff_processing_scripts.txt", also provided in this Dryad package. These files are ready to be used for subsequent analysis and presentation in the R scripts supplied in this package. The metadata file ("GW_Lane5_plus_Liz.45samples.Fst_groups.txt"; also in this package) will be needed in the R processing.
Download GW_45samples_012NA_files.tar.gz (39.26 Mb)
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Title Genotypes: outgroup analysis
Description This folder contains genotypic information used in the 9-sample analysis comparing greenish warbler and outgroup taxa (1 individual for each of 9 taxa). For each chromosome, there is a file containing the genotypes (ending in "012NA"), a file containing the list of individuals (ending in "012.indv"), and a file containing the list of positions on the chromosome (ending in "012.pos"). For details of how these files were produced see the file "GW_islands_of_diff_processing_scripts.txt", also provided in this Dryad package. These files are ready to be used for subsequent analysis and presentation in the R scripts supplied in this package. The metadata file ("GW_Lane5_plus_Liz.nine-taxa.Fst_groups.txt"; also in this package) will be needed in the R processing.
Download GW_nine_taxa_012NA_files.tar.gz (25.78 Mb)
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Title metadata for the 45-sample analysis
Description This file is required for conducting the 45-sample analysis using the R script provided in this package. The file provides the names of each individual, the location code, the "group" (used for coloring points in various plots) and "Fst_group" (used for defining groups in the Fst analysis), and the "plot_order" (not used in the present paper).
Download GW_Lane5_plus_Liz.45samples.Fst_groups.txt (1.437 Kb)
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Title metadata for the outgroup analysis
Description This file is required for conducting the 9-sample analysis using the R script provided in this package. The file provides the names of each individual, the location code, the "group" (used for coloring points in various plots) and "Fst_group" (used for defining groups in the Fst analysis), and the "plot_order" (not used in the present paper).
Download GW_Lane5_plus_Liz.nine_taxa.Fst_groups.txt (328 bytes)
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Title main R analysis script
Description This file contains the main R scripts used to conduct the analysis and produce the figures. It uses as input the "012NA" files (and associated files) produced as described in the "GW_islands_of_diff_processing_scripts.txt" file. Note that two metadata files (also contained in this Dryad package) are also needed. Also crucial is a file of R functions ("genomics_R_functions.R") written especially for this analysis, but designed to work more generally; these functions are called by this script file.
Download GW_GBS_R_analysis_script_for_Dryad.R (34.28 Kb)
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Title custom R functions file
Description This R file contains functions written by Darren Irwin for the analysis of Greenish Warbler GBS variation, but are designed to work more broadly for any dataset in similar input format. To reproduce the analysis in the paper, the main R script file ("GW_GBS_R_analysis_script_for_Dryad.R") should be run; it calls functions in the present file.
Download genomics_R_functions.R (96.41 Kb)
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Title SiteStats and WindowStats R files
Description This folder contains files containing locus-based statistics ("SiteStats") and window-based statistics (WindowStats) for each chromosome. These files can be produced by the R script (in this package), and they can also be used by that script (whether the script saves and/or loads SiteStats and WindowStats files can be adjusted in that script using the setting for "calculate_or_load_stats" and the related settings below that). Producing these files can take days of processing time; I have included them here so you can produce most of the figures in the paper, by running the R script below the heading "GENOME-WIDE plots". That script will call the appropriate files (as long as you have designated a path/folder structure that matches the R script). Files are included for both the "45-sample" analysis and the "nine_taxa.one_per_taxon" analysis.
Download SitesStats_and_WindowStats_files_GW_archiv...ar.gz (350.4 Mb)
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Title SNPs only across the whole-genome
Description This folder contains genotypic information for variant sites across the whole genome, among all greenish warbler individuals in the study. This information was used to produce Figure S1. The folder contains a file containing the genotypes (ending in "012NA"), a file containing the list of individuals (ending in "012.indv"), and a file containing the list of positions on the chromosome (ending in "012.pos"). For details of how these files were produced see the file "GW_islands_of_diff_processing_scripts.txt", also provided in this Dryad package. These files are ready to be used for subsequent analysis and presentation in the R scripts supplied in this package. The metadata file ("GW_Lane5_plus_Liz.GW_only.adults_only.Fst_groups.txt"; also in this package) will be needed in the R processing.
Download GW.SNPs_only.whole-genome_archived.tar.gz (16.18 Mb)
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Title metadata for Figure S1 (whole-genome PCA)
Description This file contains metadata for greenish warbler individuals used in the whole-genome PCA analysis (Figure S1). The R script in this package uses this information to color points in the PCA.
Download GW_Lane5_plus_Liz.GW_only.adults_only.Fst...ps.txt (4.527 Kb)
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Title scripts: converting GBS reads to genotypes
Description This text file contains scripts and notes for the steps used in converting raw Illumina GBS sequencing reads to individual genotypes (at both variant and invariant sites) across the genome. The resulting genotype files (in "012NA" format) were then used as input into R, for the rest of the analysis and production of figures.
Download GW_islands_of_diff_processing_scripts.txt (37.67 Kb)
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When using this data, please cite the original publication:

Irwin DE, Alcaide M, Delmore KE, Irwin JH, Owens GL (2016) Recurrent selection explains parallel evolution of genomic regions of high relative but low absolute differentiation in a ring species. Molecular Ecology 25(18): 4488-4507. http://dx.doi.org/10.1111/mec.13792

Additionally, please cite the Dryad data package:

Irwin DE, Alcaide M, Delmore KE, Irwin JH, Owens GL (2016) Data from: Recurrent selection explains parallel evolution of genomic regions of high relative but low absolute differentiation in a ring species. Dryad Digital Repository. http://dx.doi.org/10.5061/dryad.t951d
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