Additional file 5: of Genome-wide analysis of ionotropic receptors provides insight into their evolution in Heliconius butterflies

Heatmap of IR gene expression for each H. melpomene biological replicate utilized in this study. Exact FPKM numbers can be found in Table 4 and Additional file 4. (EPS 8200 kb

Additional file 3: Figure S2. of Divergence with gene flow across a speciation continuum of Heliconius butterflies

Phylogenetic relationships under a relaxed clock. The phylogenetic tree generated when substitution rates among lineages are allowed to vary. The tree shows H. himera nested within the H. erato radiation. Results for Bayesfactor comparison of strict and relaxed molecular clock topologies are shown in upper left corner. (PNG 109 kb

Additional file 4: Figure S3. of Divergence with gene flow across a speciation continuum of Heliconius butterflies

Absolute genomic divergence across the red color pattern (D) interval and unlinked loci. Sliding window (15-kb window size, 5-kb step size) absolute genomic divergence (dxy) across the red (D) interval and genomic regions unlinked to color pattern. See Additional file 1: Table S2 for the taxa pairs included in each comparison and samples sizes. (A) Parapatric hybrid zones. (B) Allopatric postman versus rayed comparisons. (C) Allopatric postman versus postman comparisons. (D) Allopatric rayed versus rayed comparisons. (PDF 29 kb

Data and tree for MrBayes analysis of Heliconius erato clade color unlinked loci

Input sequences and run parameters (.nex files) and resulting tree (.tre file) for MrBayes analysis. Analyzed the Heliconius erato clade across 350-kb unlinked to color pattern

Genotype calls for Heliconius erato clade (vcf format)

Vcf files were generated by aligning to a reference using BWA. Genotypes were called using GATK. File prefix is _. Files are standard vcf format

Data and trees for BEAST analysis of Heliconius erato clade

Input sequences with run parameters (xml files) and resulting trees (annot files) for BEAST analysis. Analyzed the Heliconius erato clade across 350-kb unlinked to color pattern. Compared relaxed clock to strict clock

Hinesetal_BMCGenomics_fulldatainfo

This file includes accessory information on each transcript contig used from the associated microarray study, including annotation results from various analyses, mean values across probes for that gene across the tested conditions, and significance across the variety of statistical analyses performed. By column this dataset includes: | Transcript ID – The identifications assigned to each transcript on the array. These IDs are referenced in the text and sequences for each contig are available at . | Blast2Go Annotation – Annotation term assigned during the Blast2Go analysis of these transcripts. | Flybase Gene ID and Flybase Annotation Abbr. – The gene ID the contig blasted to in Flybase and the name assigned to that gene. | Manual Anno Flybase Gene ID and Manual Anno Flybase Anno Abbr. – Flybase gene identifications and terms for genes that did not hit to Flybase with the contig sequence but were whose identity were determined manually using various parameters outlined in the manuscript. | Significant for Hindwing, Significant for Forewing – If an ID is listed, that gene was significant in either the hindwing or forewing analyses. | Lsmean columns – These provide the mean expression across probes across each array condition, including in the title Race, Stage, and (for forewings) Wing Section. | -log10(p-value) columns– These provide the p-values from ANOVAs for the two listed pairwise comparisons of those Lsmeans | Significant Index columns – Indicate whether p-values of various pairwise comparisons were significant (1) or not (0). | Columns FR – GT- IDs are listed where significant differences were found with various analyses, described in the manuscript. | Columns GU – HM – These refer to the genes that are differentially expressed in an ANOVA along the proximal-distal forewing axis and the significance columns refer to whether there was significance for each of the wing section comparisons. F1 is the basal section, F2 is the medial section, and F3 is the apical section

Heliconius erato hybrids (Peru) images

Heliconius erato hybrids (Peru) image

Heliconius melpomene amaryllis (Peru) images

Heliconius melpomene amaryllis (Peru) image

Nadeau_GR_2014_scripts

Zipped archive of script