Data from: Genome-wide evidence for speciation with gene flow in Heliconius butterflies

Martin SH, Dasmahapatra KK, Nadeau NJ, Salazar C, Walters JR, Simpson F, Blaxter M, Manica A, Mallet J, Jiggins CD

Date Published: September 17, 2013

DOI: http://dx.doi.org/10.5061/dryad.dk712

 

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Title set31.Zupdated.autoANDchrZ.union.SNP.Fst.w100m2.5s20.csv
Downloaded 65 times
Description Pairwise Fst values for 100 kb sliding windows, sliding in increments of 20 kb. Fst for each pair of populations, for each window was calculated using the EGGLIB Python library.
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Title PANAMA.ALLSHARED.w100.rerooted
Downloaded 40 times
Description Maximum likelihood trees for all non-overlapping 100 kb windows for the cydno-melpomene data set. Genomic locations of trees, and the designated topologies are given by the file PANAMA.ALLSHARED.w100.topology.csv.
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Title PERU.ALLSHARED.w100.rerooted
Downloaded 29 times
Description Maximum likelihood trees for all non-overlapping 100 kb windows for the timareta-melpomene data set. Genomic locations of trees, and the designated topologies are given by the file PERU.ALLSHARED.w100.topology.csv.
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Title PANAMA.ALLSHARED.w100.topology
Downloaded 26 times
Description Genomic locations of non-overlapping 100 kb windows and topologies supported by the corresponding maximum likelihood tree in the cydno-melpomene dataset. The full newick trees are given in the file PANAMA.ALLSHARED.w100.nwk.
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Title PERU.ALLSHARED.w100.topology
Downloaded 20 times
Description Genomic locations of non-overlapping 100 kb windows and topologies supported by the corresponding maximum likelihood tree in the timareta-melpomene dataset. The full newick trees are given in the file PERU.ALLSHARED.w100.nwk.
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Title set31.Zupdated.autoANDchrZ.ALLSHARED.SNP.derFreqs.csv
Downloaded 60 times
Description Derived allele frequencies for each population sample at each variable site for which there was a high-quality genotype call for all 31 individuals, and the outgroup species were fixed for the ancestral state. Columns with the suffixes "_1" and "_2" give the allele frequencies for sample subsets of two individuals, used for calculating the denominator of the fraction introgression f statistic. Values were calculated using the script freq.py. Values for Z and autosomes were calculated separately due to ploidy differences between the sexes, and then the outputs were combined.
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Title Hmel1-1_Scaff-Chrom_Zcorrected_20120730
Downloaded 54 times
Description Chromosomal assignments of scaffolds and scaffold fragments. This file builds upon the chromosomal assignments provided by Dasmahapatra et al. 2012 doi:10.1038/nature11041, based on our read-depth analysis described in the supplementary information. Each scaffold is assigned to one or more scaffold "fragments", which are each assigned to a chromosome. Most scaffolds correspond to a single fragment that spans the length of the scaffold, but those that were found to be chimeric were split into 2 or 3 fragments, each of which then received a chromosomal assignment.
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Title Hmel1-1_hox_RAD_matepair_chromosomes_Zupdated
Downloaded 39 times
Description File providing the chromosomal assignment and scaffolds mapped to chromosomes in the Hmel1-1 assembly. This version has been modified to accommodate the new assignments of Z-linked scaffolds and those that that have been broken and re-named based on the read-depth analysis described in the supplementary information. See the file Hmel1-1_Scaff-Chrom_Zcorrected_20120730.txt submitted herewith for a summary of this information. Newly-assigned Z-linked scaffolds have been labled chrZ_unmapped, as their chromosomal position has not been mapped.
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Title ABBA_BABA_tests
Downloaded 121 times
Description This is a necessary input for the script auto_ABBA_BABA_jackknife.r. It defines the populations that will form p1 (non-recipient), p2 (recipient) and p3 (donor) in each test.
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Title freq.py
Downloaded 118 times
Description Script to calculate allele frequencies from a filtered VCF (.geno) file. Open in a text editor to see instructions on how to run it.
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Title auto_ABBA_BABA_jackknife.r
Downloaded 215 times
Description Code for running multiple ABBA BABA tests to calculate D an f statistics, using block-jackknifing to estimate variance.
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Title four_pop_test.r
Downloaded 72 times
Description Code to run the four-population test for admixture, with block-jackknifing to estimate variance.
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Title LD_with_snpStats.r
Downloaded 78 times
Description Code to estimate linkage disequilibrium between pairs of sites.
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Title filterTrees.py
Downloaded 58 times
Description Code used to filter newick-format trees based on their topology.
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Title set31.Zupdated.union.geno.part_1_of_2
Downloaded 2916 times
Description Filtered VCF or "calls" format file. Columns 1 and 2 are scaffold and position and columns 3 onwards give genotypes for each individual. Ambiguous bases are given for heterozygous sites. Only calls that passed the quality filtering described in the manuscript are given. Missing data or low-quality calls are given as Ns. This is the first half of a file that was split into two for uploading purposes.
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Title set31.Zupdated.union.geno.part_2_of_2
Downloaded 35 times
Description This is the second part of a two part file. Please see the description for set31.Zupdated.union.geno.part_1_of_2.
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Title set31.Zupdated.autoAndZ.ALLSHARED.PiDiv.w100m10s20.csv
Downloaded 64 times
Description Nucleotide diversity for each population and divergence (dxy) between each population pair for 100 kb sliding windows, sliding in increments of 20 kb.
Download set31.Zupdated.autoAndZ.ALLSHARED.PiDiv.w1...sv.gz (630.8 Kb)
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When using this data, please cite the original publication:

Martin SH, Dasmahapatra KK, Nadeau NJ, Salazar C, Walters JR, Simpson F, Blaxter M, Manica A, Mallet J, Jiggins CD (2013) Genome-wide evidence for speciation with gene flow in Heliconius butterflies. Genome Research 23: 1817-1828. http://dx.doi.org/10.1101/gr.159426.113

Additionally, please cite the Dryad data package:

Martin SH, Dasmahapatra KK, Nadeau NJ, Salazar C, Walters JR, Simpson F, Blaxter M, Manica A, Mallet J, Jiggins CD (2013) Data from: Genome-wide evidence for speciation with gene flow in Heliconius butterflies. Dryad Digital Repository. http://dx.doi.org/10.5061/dryad.dk712
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