Search

Additional file 7: Figure S6. Relative expression levels (log2 CPM) of 129 differentially expressed genes between female and male frogs. The dendrograms resulted from hierarchical clustering of expression levels after 100 replicates to estimate Approximately Unbiased p-values (numbers on nodes). Gene names are Uniprot identifiers and can be found in the reference transcriptome annotation file (see Availability of data and materials).

Additional file 6: Figure S5. Relative expression levels (log2 CPM) of 517 differentially expressed genes between sympatric and allopatric frogs. The dendrograms resulted from hierarchical clustering of expression levels after 100 replicates to estimate Approximately Unbiased p-values (numbers on nodes). Gene names are Uniprot identifiers and can be found in the reference transcriptome annotation file (see Availability of data and materials).

Additional file 9: Figure S8. Correlations of geography (left column; allopatry/sympatry) or sex (right column; male/female) with each of the module’s eigengenes (rows). The color of the cells indicates positive (orange) or negative (blue) correlations. The numbers in the cell are Pearson’s coefficients with associated FDR in parentheses, which were computed by correcting p-values for the 50 tests. Significantly correlated traits are shown in bold and italics.

Additional file 5: Figure S4. A comparison of expression evolution. Tip branch lengths on the two neighbor joining trees at the top represent the amount of expression evolution in each of the four groups compared: sympatric males (SM), allopatric males (AM), sympatric females (SF), and allopatric females (AF). The bar graph below indicates the ratios of branch lengths used to compare the relative expression evolution between two groups. Error bars show the 95% bootstrap confidence interval for each comparison. Additional file 1: Table S5 presents results of randomization tests used to determine if each ratio was significantly different from zero and if ratios for candidate loci were significantly greater than corresponding ratios from non-candidate loci. None of the tests were significant at the 0.05 level after correcting for multiple tests.

Additional file 4: Figure S3. Multidimensional scaling (MDS) plot of pairwise expression differences, based on normalized log2 counts per million for genes in the transcriptome-wide gene set. This plot was used to verify that no outliers existed. Numbers inside points correspond to the last two digits of the sample IDs in Additional file 1: Table S10.

Additional file 8: Figure S7. Relative expression levels (log2 CPM) across all samples of 24 differentially expressed genes between females and males in allopatry (A), and 34 differentially expressed genes between females and males in sympatry (B). The dendrograms resulted from hierarchical clustering of expression levels after 100 replicates to estimate Approximately Unbiased p-values (numbers on nodes). Gene names are Uniprot identifiers and can be found in the reference transcriptome annotation file (see Availability of data and materials).

Additional file 10: Figure S9. Flowchart describing computational steps to process, annotate, assemble RNA-Seq reads for the reference transcriptome (green boxes), and steps to process and count reads of brain RNA-Seq for analysis of differential gene expression analysis of candidate transcripts (orange boxes) and all transcripts (blue boxes).

Additional file 13: Figure S11. The effect of raising node correlations in the WGCNA analysis to a power β (soft threshold) on the fit (R2) to the assumption of a scale-free topology network. In a scale-free topology network, some nodes are highly connected (hub genes). The red line indicates a fit of R2 = 0.9 to a scale-free topology, indicating that gene-correlations should be elevated to a β = 6.

Additional file 2: Figure S1. The number of transcripts from the reference transcriptome mapping to each Gene Ontology category after gene annotation with Trinotate.