Additional file 1 of Neurogenomic divergence during speciation by reinforcement of mating behaviors in chorus frogs (Pseudacris)

Additional file 1: Table S1. Number of read pairs, average sequence length, and percentage of sequences with Phred Score. Table S2. Coverage of assembled trancripts against proteins in the Uniprot/Swissprot and Xenopus tropicalis databases. Table S3. Sample information and statisticts of brain RNA-Seq reads used in the differential expression analysis. Please see the main text Methods for detail on read processing and quality control. Table S4. Differential Expression of Candidate Synaptic Transmission Genes between reinforced (sympatric) and ancestral (allopatric) populations. The 554 candidate transcripts for which expression data were availble are shown. Signifcance of likelihood ratio tests conducted were corrected for multiple tests within each of the three sets of samples: 1) both sexes combined (left section), 2) females only (center section), and 3) males only (right section). Q-values resulting from the correction were compared to alpha = 0.05 for significance (highlighed). Note that log fold change (logFC) is expressed so that positive values mean that sympatric poplations are overexpressed relative to allopatry, whereas negative values mean that sympatric populations are underexpressed relative to allopatry. Table S5. Results of randomization tests comparing divergence evolution. The test statistic for the first eight tests is the difference between the branch lengths for the 2 compared groups, averaged across the genes in the set. Qvalues were obtained by correcting the p-values for twelve tests. Table S6. Differential Expression of all Transcripts between reinforced (sympatric) and ancestral (allopatric) populations (left three sections), as well as between males and females (right three sections). Signifcance of likelihood ratio tests conducted were corrected for multiple tests within each of the six sets of samples. FDR values resulting from the correction were compared to alpha = 0.05 for significance (FDR shown for significant tests only). Note that log fold change (logFC) is expressed so that positive values mean that sympatric populations are overexpressed relative to allopatry, whereas negative values mean that sympatric populations are underexpressed relative to allopatry. Note LogFC is the effect size, with positive values corresponding to overexpression in sympatry. Table S7. Identity, gene ontology (GO) pathways, and co-expression network module membership of differentially expressed genes. Table S8. Module properties and hub genes. The hub genes were selected via the chooseTopHubInEachModule function in WGCNA. The secondary annotated hub gene was defined as the gene, other than the hub gene, with the highest degree (number of connections) that included annotation. Neighborhood connectivity of a node refers to the average connectivity of all its neighbors. The clustering coefficient of a node is the ratio of connections of its neighbors and the maximum number of possible connections between neighbors. The number of differentially expressed genes bewteen any comparison is shown for each module, as well as the number of possible social/mate preference, synatic plasticity (SPG), and immediate early genes (IEG). Table S9. Trait-Module correlation analysis and enriched pathways (based on the Xenopus tropicalis and Homo sapiens Gene Ontology databases) at FDR < 0.1 via g:Profiler2. Signicance of correlation with Geography and Sex were corrected simultaneously (50 tests) to produce q-values. Pathway terms containing keywords (“synap-” in red and “neuro-” and “neura-” in green in Enriched pathways column) were analyzed to determine whether they were concentrated in each module (see Methods). Significance values, based on randomization tests (see Methods), for these 25 tests were corrected for multiple tests to procude q-values that were compared to 0.05 to determine significance. Table S10. Information of the samples used in the differential gene expression analyses. The RIN (RNA Integrity Number) are provided as measured in a Agilent Bioanalyzer. Ratios are showed as measured from Qubit (Thermo Fisher).