Data from: Genomic architecture of adaptive color pattern divergence and convergence in Heliconius butterflies

 

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Title Neighbor-joining trees of H. erato and H. melpomene combined using aligned fragments from the region of highest association
Downloaded 8 times
Description Trees output from a neighbor-joining distance analysis run in PAUP*4b10 of the aligned fragments in melperato_alignedfrags_D454to742KB_DATA.nex. NJ trees were constructed to test monophyly of fragments across the peak region of association (from 454 -742KB in H. erato) in the red color pattern interval. The format is a nexus tree file format with extra notes from PAUP* output.
Download melperato_alignedfrags_454to742KB_NJTREES.nex (64.92 Kb)
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Title Aligned sequence fragments of H. erato and H. melpomene combined from the region of highest association
Downloaded 17 times
Description Fragments within the peak of association within the red pattern interval (454KB to 742KB in H. erato) that were aligned across Heliconius erato and Heliconius melpomene individuals. Alignments involved automated alignment followed by manual filtering to remove regions of poor alignment. This file was used for getting NJ trees across each fragment to test monophyly (melperato_alignedfrags_454to742KB_NJTREES.nex).
Download melperato_alignedfrags_D454to742KB_DATA.nex (3.828 Mb)
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Title Data and resulting phylogenetic tree of H. erato and H. melpomene involving Bayesian analysis of SNPs from the 515 - 580 KB peak of highest association
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Description This datafile involved extracting the most reliable SNPS from the highest peak of association from 515-580KB. Automated alignments of fragments from these region (see melperato_alignedfragsD454to742KB_DATA.nex) were manually adjusted to improve alignments, fragments were concatenated, and SNPS with invariant sites and >20% missing data were removed. This was used for a Bayesian analysis of sequences from the highest peak involving both H. erato and H. melpomene. This nexus formatted file includes Bayes block and the resulting consensus Bayesian tree.
Download melperato_manalignSNPsD515to580Bayes_DATATREE.nex (76.61 Kb)
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Title Manual alignments of fragments within the 65KB window for H. erato and H. melpomene
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Description This file is provided for visualization of the manual alignments used to extract the SNPs that went into the Bayesian analysis of H. erato and H. melpomene across the 65KB peak of association (515-580KB in H. erato; melperato_manalignSNPsD515to580Bayes_DATATREE.nex). It involves H. melpomene and H. erato aligned fragments from this region (see melperato_alignedfrags_D454to742KB_DATA.nex) that have been concatenated and manually aligned. The file is in nexus format.
Download melperato65KB_manalignfragsDATA.nex (738.4 Kb)
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Title Sequence alignments from across the red pattern interval of Heliconius erato
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Description This nexus file includes all SNP data for each individual of Heliconius erato sequenced across the four hybrid zones aligned against the full red color pattern interval (D interval). Ns represent missing or excluded data from low quality sequence calls.
Download wgserato_Dregion_aligned.nex (42.66 Mb)
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Title Aligned sequences of Heliconius erato from across the color pattern unlinked BAC including cinnabar
Downloaded 15 times
Description This nexus file includes all SNP data for each individual of Heliconius erato sequenced across the four hybrid zones aligned against the color pattern-unlinked BAC region that includes the gene cinnabar. Ns represent missing or excluded data from low quality sequence calls.
Download Unlinked_Cinn_Final_29March2009.nex (7.082 Mb)
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Title Aligned sequences of Heliconius erato across the color pattern-unlinked BAC 46F09
Downloaded 13 times
Description This nexus file includes all SNP data for each individual of Heliconius erato sequenced across the four hybrid zones aligned against the color pattern-unlinked BAC region 46F09. Ns represent missing or excluded data from low quality sequence calls.
Download Unlinked_Hera_46F09.nex (3.442 Mb)
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Title Aligned sequences of Heliconius erato across the color pattern-unlinked BAC 48A16
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Description This nexus file includes all SNP data for each individual of Heliconius erato sequenced across the four hybrid zones aligned against the color pattern-unlinked BAC 48A16. Ns represent missing or excluded data from low quality sequence calls.
Download Unlinked_Hera_48A16.nex (6.568 Mb)
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Title Sequence data used for performing 15KB sliding window phylogenetic analysis of the H. erato red pattern interval
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Description Sequence data of Heliconius erato used to perform 15KB sliding window distance-based (neighbor-joining) phylogenetic analysis across the red pattern interval. The file includes the script that generated the trees using PAUP*4b10.
Download Hera_D_15KBslidingnjtreesDATA.nex (42.68 Mb)
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Title Likelihood scores for geographic and color-based trees for Heliconius erato across the red pattern interval
Downloaded 12 times
Description Sequence data of Heliconius erato across the red color pattern interval and scripts used to obtain scores of the likelihood of two alternative phylogenetic tree topologies (geographic - GEO; color-pattern based - D) explaining the data across 15KB sliding windows. The file includes sequences, trees used to compute likelihood scores, and the script run in PAUP* to calculate the likelihood scores for each tree.
Download Hera_D_15KBslidingLIKLscoresDATA.nex (42.70 Mb)
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Title Phylogenetic trees from the 15KB sliding window analysis of H. erato along the red pattern interval
Downloaded 14 times
Description Distance based neighbor-joining trees across the sliding window derived from Hera_D_15KBsliding njtreesDATA.nex. Trees are ordered by position along the d-interval, staggered every 5KB. The file is in nexus format.
Download D15kbsliding_NJTREES.nex (109.0 Kb)
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Title Data and phylogenetic tree for the Bayesian analysis of H. erato in region 1 of the red pattern interval
Downloaded 158 times
Description Includes region 1 of 5 separate partitions of the red pattern interval based on optimal tree partitioning from the MDL method. Includes the SNPs from 1 to 324665, the Bayes block that went into the analysis, and the resulting Bayesian consensus tree.
Download D1to324K_BayesTREEDATA.nex (1.173 Mb)
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Title Data and phylogenetic tree for the Bayesian analysis of H. erato in region 2 of the red pattern interval
Downloaded 78 times
Description Includes region 2 of 5 separate partitions of the red pattern interval based on optimal tree partitioning from the MDL method. Includes the SNPs from Bases 324,666 to 474,310, the Bayes block that went into the analysis, and the resulting Bayesian consensus tree.
Download D324to474K_BayesDATATREE.nex (639.8 Kb)
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Title Data and phylogenetic tree for the Bayesian analysis of H. erato in region 3 of the red pattern interval
Downloaded 56 times
Description Includes region 3 of 5 separate partitions of the red pattern interval based on optimal tree partitioning from the MDL method. Includes the SNPs from Bases 474,311 to 773,020, the Bayes block that went into the analysis, and the resulting Bayesian consensus tree.
Download D474to773K_BayesDATATREE.nex (1.173 Mb)
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Title Data and phylogenetic tree for the Bayesian analysis of H. erato in region 4 of the red pattern interval
Downloaded 35 times
Description Includes region 4 of 5 separate partitions of the red pattern interval based on optimal tree partitioning from the MDL method. Includes the SNPs from Bases 773,021 to 846,050, the Bayes block that went into the analysis, and the resulting Bayesian consensus tree.
Download D773to846K_DATATREE.nex (272.2 Kb)
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Title Data and phylogenetic tree for the Bayesian analysis of H. erato in region 5 of the red pattern interval
Downloaded 32 times
Description Includes region 5 of 5 separate partitions of the red pattern interval based on optimal tree partitioning from the MDL method. Includes the SNPs from Bases 846,050 to 945,009, the Bayes block that went into the analysis, and the resulting Bayesian consensus tree.
Download D846K+_BayesDATATREE.nex (414.8 Kb)
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Title Bayesian phylogeny of sequence unlinked to color pattern in H. erato
Downloaded 29 times
Description "Color pattern unlinked" Bayesian phylogenetic tree of H. erato derived from SNPs from the 3 color pattern unlinked regions combined (cinnabar BAC, BAC 46F09, BAC 48A16) and excluding sites with >20% missing data. Also includes Bayes block and the resulting Bayesian consensus tree. The file is in nexus format.
Download bestunlinked_BayesDATATREE.nex (240.8 Kb)
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Title Sequence data and Bayesian phylogenetic tree of Heliconius erato from the 65 KB peak of association in the red pattern interval
Downloaded 13 times
Description The sequence data and Bayesian consensus tree generated of H. erato from the 65KB region (515 to 580 KB) of highest association in the red pattern interval. The data excludes sites with >20% missing data or that were invariant. This is the same data file as for Splitstree except sites variable only in heterozygotes are removed as these are considered as missing data in the analysis and are effectively constant. The file also includes the Bayes block for running in MrBayes.
Download bestsnpsD515to580KB_Bayes_DATATREE.nex (69.71 Kb)
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Title Sequence data for Splitstree analysis of Heliconius erato from the 65 KB peak of association in the red pattern interval
Downloaded 14 times
Description The sequence data used for Splitstree analysis of H. erato from the 65KB region (515 to 580 KB) of highest association in the red pattern interval. The data excludes sites with >20% missing data or that were invariant. The file includes sites that had variation only in heterozygotes as Splitstree analysis can take into account heterozygote information.
Download best_D_515to580KSplitstreeDATA.nex (229.2 Kb)
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Title Genotype calls for Heliconius, 4 erato and 2 melpomene populations (vcf format)
Downloaded 42 times
Description Vcf files were generated by aligning to a reference using BWA. Genotypes were called using GATK. File prefix is <location>_<race>. Files are standard vcf format.
Download vcfs4dryad.zip (759.2 Mb)
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When using this data, please cite the original publication:

Supple MA, Hines HM, Dasmahapatra KK, Lewis JJ, Nielsen DM, Lavoie C, Ray DA, Salazar C, McMillan WO, Counterman BA (2013) Genomic architecture of adaptive color pattern divergence and convergence in Heliconius butterflies. Genome Research 23(8): 1248-1257. http://dx.doi.org/10.1101/gr.150615.112

Additionally, please cite the Dryad data package:

Supple MA, Hines HM, Dasmahapatra KK, Lewis JJ, Nielsen DM, Lavoie C, Ray DA, Salazar C, McMillan WO, Counterman BA (2013) Data from: Genomic architecture of adaptive color pattern divergence and convergence in Heliconius butterflies. Dryad Digital Repository. http://dx.doi.org/10.5061/dryad.rr65n
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