Supplemental Material for Kottler et al., 2019

Figure S1 presents the results of the RAD-sequencing analysis. Figure S2 shows the analysis of G. affinis and G. holbrooki pooled-sequencing reads aligned to the genome of X. maculatus using 10 kb windows. Figure S3 represents a molecular phylogeny of fish sox9. Figure S4 are alignments of male G. holbrooki and G. affinis gipc1and sox9b alleles and protein sequences. Figure S5 are multiple species alignments of Gipc1 and Sox9 protein sequences. Figure S6 contains PCR results demonstrating that sox9bY was generated by allelic diversification. Figure S7 contains pictures of melanic and non-melanic G. holbrooki. Table S1 gives information on the fish used for pool sequencing. Table S2 presents the results of the allele-specific PCRs. Table S3 contains the annotated loci within the 100 kb windows with the highest density of sex-specific SNPs. Table S4 contains the sex chromosome genotypes of F1 fish (pedigree WLC20074) from a cross between a G. affinis female (WLC1313) and a G. holbrooki male (WLC2514) determined by PCR. Table S5 gives information on the number of offspring of non-melanic females and non-melanic males derived from melanic strains.