Data from: Genome-wide patterns of divergence and gene flow across a butterfly radiation

Nadeau NJ, Martin SH, Kozak KM, Salazar C, Dasmahapatra KK, Davey JW, Baxter SW, Blaxter ML, Mallet J, Jiggins CD

Date Published: September 20, 2012

DOI: http://dx.doi.org/10.5061/dryad.j7q8p

 

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Title RAD_cydmelhec_data.geno
Downloaded 93 times
Description Space delimited tabular file giving the genotype calls used this paper. They were filtered from the .vcf files (generated by GATK unified genotyper) and represent all bases that were called with a genotype quality >=30 in multiple individuals. Individuals are in columns and genome positions in rows. Missing data are given as "N". This file was filtered for the relevant individuals and all sites with missing data removed prior to running analyses with any of the given scripts.
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Title clumpy
Downloaded 64 times
Description Python script used to split the single calls file(s) into individual RAD loci. The output consists of multiple files - one for each locus found - all in the same format as the original calls input file, and a comma separated values file with the start and end positions in the genome and length of each RAD locus.
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Title population_matrix_taxon
Downloaded 47 times
Description A file giving taxonomic groupings for each population for the AMOVA analysis
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Title population_matrix_CP
Downloaded 53 times
Description A file giving colour pattern groupings for each population for the AMOVA analysis
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Title Hmel_chromosomes_dec_2011_OLD_HOX_no_header_filtered
Downloaded 34 times
Description A file relating the scaffolds to chromosomes (inferred from RAD mapping from The Heliconius Genome Consortium 2012). This was used to generate genome-wide plots.
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Title Fst2
Downloaded 121 times
Description R script used to calculate Fst between all pairs of populations. Inputs are as Fst.r.
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Title population_matrix_geo
Downloaded 36 times
Description A file giving geographic groupings for each population for the AMOVA analysis
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Title geno_to_haplo_54
Downloaded 49 times
Description Perl script used to go from genotype calls to haplotype calls (not phased). This was done before running the Fst scripts but not AMOVAs.
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Title Fst
Downloaded 88 times
Description R script used to calculate the Fst values for the major race and species comparisons discussed in the paper. Inputs are the indidividual RAD locus haplotpe files and the summary statistics file generated by clump.py
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Title amova1
Downloaded 61 times
Description R script used to perform AMOVA analyses. Generates a distance matrix based to genotype calls and used the ade4 package to run Amovas. Inputs are the indidividual RAD locus genotype files and the summary statistics file generated by clump.py and character matrix files (see below).
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Title Fst_spcorr
Downloaded 53 times
Description R script used to calculate correlations between Fst values at increasing genomic distances. Input is the output from Fst.r.
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Title genotype_matrix
Downloaded 57 times
Description A starting genotype matrix assuming sepatare genotypes for each individual that is modified by the AMOVA script.
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When using this data, please cite the original publication:

Nadeau NJ, Martin SH, Kozak KM, Salazar C, Dasmahapatra KK, Davey JW, Baxter SW, Blaxter ML, Mallet J, Jiggins CD (2012) Genome-wide patterns of divergence and gene flow across a butterfly radiation. Molecular Ecology 22(3): 814–826. http://dx.doi.org/10.1111/j.1365-294X.2012.05730.x

Additionally, please cite the Dryad data package:

Nadeau NJ, Martin SH, Kozak KM, Salazar C, Dasmahapatra KK, Davey JW, Baxter SW, Blaxter ML, Mallet J, Jiggins CD (2012) Data from: Genome-wide patterns of divergence and gene flow across a butterfly radiation. Dryad Digital Repository. http://dx.doi.org/10.5061/dryad.j7q8p
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