Data from: Adaptive introgression from distant Caribbean islands contributed to the diversification of a microendemic adaptive radiation of trophic specialist pupfishes

Martin CH, Richards EH

Date Published: August 11, 2017

DOI: http://dx.doi.org/10.5061/dryad.33418

 

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Title Script to call function that calculates f4 statistic in sliding windows across genome
Downloaded 3 times
Description Python script used to call the function that calculates f4 statistic in sliding windows across genome that is described in genomics_f4_ejredit.py. Modified from Simon H. Martin's script for calculating D and fd statistics in sliding windows (https://github.com/simonhmartin/genomics_general/ABBABABBA.py).
Download ABBABABAwindows_f4_ejredit.py (12.58 Kb)
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Title Script to calculate f4 statistic in sliding window across genome
Downloaded 2 times
Description Script to calculate f4 statistic in sliding window across genome. Modified from Simon H. Martin's script to calculate D and fd statistics in sliding windows across genome (https://github.com/simonhmartin/genomics_general/genomics.py). See this website for details and options for running the function.
Download genomics_f4_ejredit.py (55.92 Kb)
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Title SAGUARO input file
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Description The feature file required for SAGUARO analysis consisting of information on SNPs from 43 pupfishes. This file was converted into this format from a vcf file.
Download filtered_snps_all.feature.tar.gz (362.3 Mb)
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Title Sliding window f4 statistic file
Downloaded 2 times
Description Input file of SNP genotypes across 43 pupfishes used for calculating f4 statistic in sliding windows across genome. This file was converted into this format from a vcf file.
Download filtered_snps_all_diplo.geno.tar.gz (743.0 Mb)
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Title Treemix input files for candidate adaptive introgression regions
Downloaded 2 times
Description The SNP matrix files used in the Treemix analysis of each candidate region. Files are labeled by scaffold and starting position of the region.
Download treemix_files.tar.gz (111.7 Kb)
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When using this data, please cite the original publication:

Richards EJ, Martin CH (2017) Adaptive introgression from distant Caribbean islands contributed to the diversification of a microendemic adaptive radiation of trophic specialist pupfishes. PLOS Genetics 13(8): e1006919. http://dx.doi.org/10.1371/journal.pgen.1006919

Additionally, please cite the Dryad data package:

Martin CH, Richards EH (2017) Data from: Adaptive introgression from distant Caribbean islands contributed to the diversification of a microendemic adaptive radiation of trophic specialist pupfishes. Dryad Digital Repository. http://dx.doi.org/10.5061/dryad.33418
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