Data from: Evaluating the use of ABBA-BABA statistics to locate introgressed loci

Martin SH, Davey JW, Jiggins CD

Date Published: October 21, 2014

DOI: http://dx.doi.org/10.5061/dryad.j1rm6

 

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 README
Downloaded 147 times
Description General summary of scripts and commands used in this study.
Download README.md (6.491 Kb)
Details View File Details
Title Figure_1.R
Downloaded 28 times
Description Script to generate plots in Figure 1 B and C.
Download Figure_1.R (2.748 Kb)
Details View File Details
Title compare_f_estimators.r
Downloaded 42 times
Description Script to generate Figures 2 and S1.
Download compare_f_estimators.r (17.99 Kb)
Details View File Details
Title Figures_3_S3.R
Downloaded 24 times
Description Script to generate Figures 3 and S3. Requires data files such as Heliconius_autosome_windows_5kb.csv and Heliconius_Zchromosome_windows_5kb.csv. These names are hard-coded into this script, so editing is required to load different files.
Download Figures_3_S3.R (6.421 Kb)
Details View File Details
Title Figure_4.R
Downloaded 13 times
Description Script to generate Figure 4. Requires as input files such as model_files_win10000_s0.01_l5000_r50.alternate_models.dxy.summary.sg.tsv, generated using run_model_combinations.py, shared_ancestry_simulator.R and generate_summary_statistics.R.
Download Figure_4.R (7.315 Kb)
Details View File Details
Title Figure_5.R
Downloaded 12 times
Description Script to generate Figure 5. Requirees as input files such as model_files_win10000_s0.01_l5000_r50.alternate_models.dxy.summary.sg.tsv, generated using run_model_combinations.py shared_ancestry_simulator.R and generate_summary_statistics.R.
Download Figure_5.R (3.767 Kb)
Details View File Details
Title egglib_sliding_windows.py
Downloaded 190 times
Description Python script to calculate ABBA BABA statistics, as well as pi and dXY from heliconius whole-genome data. It makes use of the EGGLIB library. Input was a "calls" format file, provided in Martin et al. 2013. Window size is specified with the -w flag, sliding increment with the -i flag and minimum number of sites with the -m flag. The latter is a hard cutoff, and windows with fewer sites are discarded. There is also a soft cutoff between 0 and 1, specified with --minimumExploitableData. The script will output a column called sitesOverMinExD. At a value of 0.5, this would report the number of sites in the window that had genotype calls for at least 50% of the individuals. To analyse autosomes and Z-linked scaffolds separately, the --include and --exclude flags were used, along with the file Hmel1-1_Zupdated_Zscafs.txt, which provides names of all Z-linked scaffolds provided in Martin et al. 2013. For the Z chromosome analysis, ploidy was specified using the --ploidy flag, because there were two females in the dataset of Martin et al. 2013.
Download egglib_sliding_windows.py (27.41 Kb)
Details View File Details
Title Hmel1-1_Zupdated_Zscafs.txt
Downloaded 23 times
Description List of Z-liniked scaffolds, used when running egglib_sliding_windows.py.
Download Hmel1-1_Zupdated_Zscafs.txt (996 bytes)
Details View File Details
Title run_model_combinations.py
Downloaded 20 times
Description Script to generate YAML files for use by shared_ancestry_simulator.R. These can be generated as follows: ./run_model_combinations.py -m Model_parameter_list.csv -w 10000 -t 30 -s 0.01 -l 5000 -r 5 ./run_model_combinations.py -m Model_parameter_list.csv -w 10000 -t 30 -s 0.01 -l 5000 -r 50
Download run_model_combinations.py (5.974 Kb)
Details View File Details
Title Model_parameter_list.csv
Downloaded 14 times
Description Parameter list used by run_model_combinations.py to generate the YAML files used by shared_ancestry_simulator.R.
Download Model_parameter_list.csv (14.73 Kb)
Details View File Details
Title shared_ancestry_simulator.R
Downloaded 30 times
Description A single combined model can be generated like this: ./shared_ancestry_simulator.R -w 10000 -t 60 -c Alternate_t123-0.4_t23-0.2.yml:0.1,Background_t123-0.6_t21-0.4.yml:0.9. This will generate 10000 windows, 10% of which will be generated using the model described in the file Alternate_t123-0.4_t23-0.2.yml and 90% of which will be generated using Background_t123-0.6_t21-0.4.yml, using 60 threads. See the model files folders for the YAML files generated for this paper. The CSV files for the models will be made available in a Data Dryad repository on publication and can be made available on request. A single model, as used for the null models reported in the paper, can be run like this: ./shared_ancestry_simulator.R -w 10000 -t 60 -c Background_t123-0.6_t21-0.4.yml:1. The YAML files are generated using run_model_combinations.py.
Download shared_ancestry_simulator.R (18.58 Kb)
Details View File Details
Title generate_summary_statistics.R
Downloaded 27 times
Description Summary statistics for the models found in the partition.summary and dxy.summary files were generated as follows: ./generate_summary_statistics.R -m model_files_win10000_s0.01_l5000_r5 -l Model_parameter_list.csv -t 10 ./generate_summary_statistics.R -m model_files_win10000_s0.01_l5000_r50 -l Model_parameter_list.csv -t 10 Summary files are produced for alternate and null models and for ms and Seq-Gen output. The Seq-Gen files used for the paper analyses are included in the repository.
Download generate_summary_statistics.R (11.89 Kb)
Details View File Details
Title model_files_win10000_s0.01_l5000_r5.alternate_models.dxy.summary.sg.tsv
Downloaded 10 times
Download model_files_win10000_s0.01_l5000_r5.alter...sg.tsv (3.581 Mb)
Details View File Details
Title model_files_win10000_s0.01_l5000_r5.alternate_models.partition.summary.sg.tsv
Downloaded 7 times
Download model_files_win10000_s0.01_l5000_r5.alter...sg.tsv (262.8 Kb)
Details View File Details
Title model_files_win10000_s0.01_l5000_r5.null_models.dxy.summary.sg.tsv
Downloaded 6 times
Download model_files_win10000_s0.01_l5000_r5.null_...sg.tsv (341.6 Kb)
Details View File Details
Title model_files_win10000_s0.01_l5000_r5.null_models.partition.summary.sg.tsv
Downloaded 7 times
Download model_files_win10000_s0.01_l5000_r5.null_...sg.tsv (22.55 Kb)
Details View File Details
Title model_files_win10000_s0.01_l5000_r50.alternate_models.dxy.summary.sg.tsv
Downloaded 11 times
Download model_files_win10000_s0.01_l5000_r50.alte...sg.tsv (3.481 Mb)
Details View File Details
Title model_files_win10000_s0.01_l5000_r50.alternate_models.partition.summary.sg.tsv
Downloaded 5 times
Download model_files_win10000_s0.01_l5000_r50.alte...sg.tsv (264.2 Kb)
Details View File Details
Title model_files_win10000_s0.01_l5000_r50.null_models.partition.summary.sg.tsv
Downloaded 5 times
Download model_files_win10000_s0.01_l5000_r50.null...sg.tsv (22.64 Kb)
Details View File Details
Title model_files_win10000_s0.01_l5000_r50.null_models.dxy.summary.sg.tsv
Downloaded 7 times
Download model_files_win10000_s0.01_l5000_r50.null...sg.tsv (345.2 Kb)
Details View File Details
Title model_results_table.R
Downloaded 8 times
Description Summarize all tests for differences in mean dXY in a single table.
Download model_results_table.R (4.812 Kb)
Details View File Details
Title model_results_table
Downloaded 7 times
Description Summary of all tests for differences in mean dXY.
Download model_results_table.txt (360.3 Kb)
Details View File Details
Title Heliconius_autosome_windows_5kb
Downloaded 22 times
Description Results of analysis of Heliconius autosomes, with 5kb windows.
Download Heliconius_autosome_windows_5kb.csv (17.05 Mb)
Details View File Details
Title Heliconius_autosome_windows_10kb
Downloaded 8 times
Description Results of analysis of Heliconius autosomes, with 10 kb windows.
Download Heliconius_autosome_windows_10kb.csv (7.290 Mb)
Details View File Details
Title Heliconius_autosome_windows_20kb
Downloaded 16 times
Description Results of analysis of Heliconius autosomes, with 20 kb windows.
Download Heliconius_autosome_windows_20kb.csv (3.774 Mb)
Details View File Details
Title Heliconius_Zchromosome_windows_50kb
Downloaded 11 times
Description Results of analysis of Heliconius autosomes, with 50 kb windows.
Download Heliconius_autosome_windows_50kb.csv (1.927 Mb)
Details View File Details
Title Heliconius_Zchromosome_windows_5kb
Downloaded 12 times
Description Results of analysis of Heliconius Z chromosome, with 5 kb windows.
Download Heliconius_Zchromosome_windows_5kb.csv (567.2 Kb)
Details View File Details
Title Heliconius_Zchromosome_windows_10kb
Downloaded 7 times
Description Results of analysis of Heliconius Z chromosome, with 20 kb windows.
Download Heliconius_Zchromosome_windows_10kb.csv (251.5 Kb)
Details View File Details
Title Heliconius_Zchromosome_windows_20kb
Downloaded 10 times
Description Results of analysis of Heliconius Z chromosome, with 20 kb windows.
Download Heliconius_Zchromosome_windows_20kb.csv (131.1 Kb)
Details View File Details
Title Heliconius_Zchromosome_windows_50kb
Downloaded 9 times
Description Results of analysis of Heliconius Z chromosome, with 50 kb windows.
Download Heliconius_Zchromosome_windows_50kb.csv (61.63 Kb)
Details View File Details
Title Figure_S2.R
Downloaded 11 times
Description Script to generate Figure S2.
Download Figure_S2.R (9.334 Kb)
Details View File Details
Title Figure_S4.R
Downloaded 12 times
Description Script to generate Figure S5.
Download Figure_S4.R (7 Kb)
Details View File Details

When using this data, please cite the original publication:

Martin SH, Davey JW, Jiggins CD (2015) Evaluating the use of ABBA-BABA statistics to locate introgressed loci. Molecular Biology and Evolution 32(1): 244-257. http://dx.doi.org/10.1093/molbev/msu269

Additionally, please cite the Dryad data package:

Martin SH, Davey JW, Jiggins CD (2014) Data from: Evaluating the use of ABBA-BABA statistics to locate introgressed loci. Dryad Digital Repository. http://dx.doi.org/10.5061/dryad.j1rm6
Cite | Share
Download the data package citation in the following formats:
   RIS (compatible with EndNote, Reference Manager, ProCite, RefWorks)
   BibTex (compatible with BibDesk, LaTeX)

Search for data

Be part of Dryad

We encourage organizations to: