Fig. 2

Genes with allele-specific expression. Genes that showed allele-specific expression in F₁ samples using ASE-Tigar and also showed differential expression in cave versus samples (Additional file 1: Table S3; Additional file 2: Files 3 and 4) were subjected to allele counting through FreeBayes variant detector. The three F₁ hybrid samples were mapped to both the surface sequence of the gene and the cave sequence of the gene. A The numbers of cave alleles, C, and surface alleles, S, were counted for three to five distinct SNPs along the transcript (shown as the multiple rows next to each gene name in B, C). B Genes biased toward the cave allele are shown in red. C Genes biased toward the surface allele are shown in green. A binomial distribution function was performed in Excel to detect significant deviation from the null distribution 1:1 surface to cave allele. P-values are shown for the binomial distribution function for each comparison of cave to surface allele. p > .05 is white, 0.05 > p > .005 is light green or light red, 0.005 > p > 0.0005 is green or red, p < 0.0005 is dark green or dark red. Genes shown below are those for which at least two SNPs per gene showed significant allele-specific expression through the binomial distribution function across all samples, regardless of whether the surface sequence or cave sequence was used as a reference. Note In C, there are two paralogues of dopamine N-acetyltransferase