10.25386/genetics.9767519.v1 Verena A. Kottler Verena A. Kottler Romain Feron Romain Feron Indrajit Nanda Indrajit Nanda Christophe Klopp Christophe Klopp Kang Du Kang Du Susanne Kneitz Susanne Kneitz Frederik Helmprobst Frederik Helmprobst Dunja K. Lamatsch Dunja K. Lamatsch Céline Lopez-Roques Céline Lopez-Roques Jerôme Lluch Jerôme Lluch Laurent Journot Laurent Journot Hugues Parrinello Hugues Parrinello Yann Guiguen Yann Guiguen Manfred Schartl Manfred Schartl Supplemental Material for Kottler et al., 2019 GSA Journals 2019 mosquitofish sex determination pool sequencing gipc1 sox9b Genetics 2019-11-08 15:04:29 Dataset https://gsajournals.figshare.com/articles/dataset/Supplemental_Material_for_Kottler_et_al_2019/9767519 Figure S1 presents the results of the RAD-sequencing analysis. Figure S2 shows the analysis of <i>G. affinis </i>and <i>G. holbrooki </i>pooled-sequencing reads aligned to the genome of <i>X. maculatus </i>using 10 kb windows. Figure S3 represents a molecular phylogeny of fish <i>sox9</i>. Figure S4 are alignments of male <i>G. holbrooki </i>and <i>G. affinis </i><i>gipc1</i>and <i>sox9b </i>alleles and protein sequences. Figure S5 are multiple species alignments of Gipc1 and Sox9 protein sequences. Figure S6 contains PCR results demonstrating that <i>sox9bY </i>was generated by allelic diversification. Figure S7 contains pictures of melanic and non-melanic <i>G. holbrooki</i>. 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 F<sub>1 </sub>fish (pedigree WLC20074) from a cross between a <i>G. affinis </i>female (WLC1313) and a <i>G. holbrooki </i>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.