Additional file 2 of Transcriptomic analysis of cave, surface, and hybrid samples of the isopod Asellus aquaticus and identification of chromosomal location of candidate genes for cave phenotype evolution

Additional file 2: Supplementary File 1: Late-stage differential expression, CAVE_rr vs SURF_rs reads, mapped both to CAVE_rr and SURF_rs assemblies. Supplementary File 2: Mid-stage differential expression, CAVE_rr vs SURF_rs reads, mapped both to CAVE_rr and SURF_rs assemblies. Supplementary File 3: Allele-specific expression, surface-biased, within F1 hybrids between CAVE_rr and SURF_rs populations. Supplementary File 4: Allele-specific expression, cave-biased, within F1 hybrids between CAVE_rr and SURF_rs populations. Supplementary File 5: Allele-specific expression using allele counting for three F1 hybrid samples. Supplementary File 6: Genes linked to regions responsible for orange pigment, no pigment, and eye loss.