DOI: 10.5061/dryad.3c8s8
title: Data from: Genomic characterization of sex-identification markers in Sebastes carnatus and Sebastes chrysomelas rockfishes

description: Fish have evolved a variety of sex-determining (SD) systems including male
 heterogamy (XY), female heterogamy (ZW) and environmental SD. Little is
 known about SD mechanisms of Sebastes rockfishes, a highly speciose genus
 of importance to evolutionary and conservation biology. Here, we
 characterize the sex determination system in the sympatrically distributed
 sister species Sebastes chrysomelas and Sebastes carnatus. To identify
 sex-specific genotypic markers, double digest restriction site –
 associated DNA sequencing (ddRAD-seq) of genomic DNA from 40 sexed
 individuals of both species was performed. Loci were filtered for presence
 in all of the individuals of one sex, absence in the other sex and no
 heterozygosity. Of the 74 965 loci present in all males, 33 male-specific
 loci met the criteria in at least one species and 17 in both. Conversely,
 no female-specific loci were detected, together providing evidence of an
 XY sex determination system in both species. When aligned to a draft
 reference genome from Sebastes aleutianus, 26 sex-specific loci were
 interspersed among 1168 loci that were identical between sexes. The
 nascent Y chromosome averaged 5% divergence from the X chromosome and
 mapped to reference Sebastes genome scaffolds totalling 6.9Mbp in length.
 These scaffolds aligned to a single chromosome in three model fish
 genomes. Read coverage differences were also detected between sex-specific
 and autosomal loci. A PCR-RFLP assay validated the bioinformatic results
 and correctly identified sex of five additional individuals of known sex.
 A sex-determining gene in other teleosts gonadal soma-derived factor
 (gsdf) was present in the model fish chromosomes that spanned our
 sex-specific markers.
description: batch_7.2.sumstats.tsvStacks1.04 populations output provides summary statistics for each locus containing SNPs. To identify sex markers, we split each species into male and female samples: S. chrysomelas males were assigned to Pop 1, S. chrysomelas females were assigned to Pop 2, S. carnatus males were assigned to Pop 3, and S. carnatus females were assigned to Pop 4. See the Stacks manual for headers.batch_7.catalog.tags.tsvStacks1.04 denovo_map.pl pipeline was used to construct a catalog of loci from ddRAD-seq reads of S. carnatus and S. chrysomelas samples. . We specified a minimum depth of coverage (m) of two, a maximum number of mismatches between stacks (alleles) within an individual (M) of two, and a maximum number of mismatches between individuals (n) of one to build the catalog. M and n allow for assembly of polymorphic loci within individuals and fixed differences among individuals at a locus, respectively. See the Stacks manual for headers.matches.tsvSamples' stacks are matched to the catalog to create a matches.tsv file for each sample. We counted the matches to the catalog to find the depth of each locus in each individual sample. This file must be unzipped. See the Stacks manual for headers.Fixed differencesThis R script was used to identify loci with SNPs that are differently fixed between males and females (ie all males are heterozygous, all females are homozygous). The loci identified are on the sex chromosomes, but given our parameters they have not diverged enough for Stacks to split them into separate loci. We tested the scrip on loci that mapped to select scaffolds where sex-specific markers were found, and then we applied the script to filter the entire sumstats.tsv file.scaffCheck.RFiltering for sex-specific lociThe R script counts each samples' matches (matches.tsv) to the catalog (Batch_7.catalog.tags.tsv) and tabulates the depth of each locus in each individual. We then filtered for presence in all of one sex and none of the other sex. We identified loci present in all males and no females.B7combined.R