Limited evidence for extensive genetic differentiation between X and Y chromosomes in Hybognathus amarus (Cypriniformes:Leuciscidae)

We used Nextera-tagmented reductively amplified DNA (nextRAD) sequencing data to discover SNPs in Rio Grande silvery minnow samples of known and unknown sex; and we produced two contig level genomes from Nanopore long-read sequencing. Raw NextRAD was aligned to each of the genomes. Subsequent SNP calling and filtering were repeated independently to obtain two datasets, one using the female genome as reference (female-referenced dataset) and another using the male genome (male-referenced dataset). The SNP calling identified 4.46 M raw variants in female-referenced dataset and of these 16,714 biallelic SNPs were retained after all filtering steps. For this set of SNPs, the average depth of coverage for the retained 64 females was 35.81 (ranging from 8.94 to 86.88) and 33.14 for the retained 53 males (ranging from 18.93 to 65.56). When using the male genome as reference we obtained 3.77 M raw variants and 17,920 biallelic SNPs. In this case the average depth of coverage for the same 64 fem..., We obtained Rio Grande silvery minnow fin clip samples from 190 individuals. 65 individuals identified as females and 63 identified as males were sampled from a captive population held at the Los Lunas Silvery Minnow Refugium (LLSMR; New Mexico). Sexes were identified by hatchery personnel based on external phenotypic traits during the spring, when females became ripe and produced eggs. Additionally, we obtained tissue samples from two full-sibling families, each composed of a female, a male and 30 larvae of unknown sex from another captive population held at the Albuquerque Biological Park (New Mexico). NextRAD libraries were generated from these 190 individuals at SNPsaurus, LLC (University of Oregon, Oregon). Two nextRAD libraries were prepared, each one containeng half of the samples, as described in Russello et al. (2015). Libraries were pooled and sequenced for 150 bp reads on two lanes of an HiSeq 4000 (University of Oregon). Additionally, two other individuals (collected by U.S....,