Acipenseriformes (sturgeons and paddlefishes) are of substantial conservation concern, and development of genomic resources for these species is difficult due to past whole genome duplication. Development of disomic markers for polyploid organisms can be challenging due to difficulty in resolving alleles at a single locus from those among duplicated loci. In this study, we detail the development of disomic markers for the endangered pallid sturgeon (Scaphirhynchus albus) found in North America. One of the strategies for pallid sturgeon conservation is to stock U.S. rivers with offspring of pure pallid sturgeon, but introgression with the sympatric shovelnose sturgeon (S. platorynchus) threatens pallid sturgeon genetic integrity. Currently, 19 microsatellite loci are used to differentiate between both species and their hybrids, but the markers are insufficient to robustly identify backcrosses. We performed double digest restriction site‐associated DNA sequencing (ddRADseq) on shovelnose sturgeon haploid gynogens to produce a reduced‐representation genomic reference. Contiguous sequences that were heterozygous within a haploid individual were flagged as potentially encompassing multiple loci. Approximately 60 individuals of each species from two management units were sequenced, and reads were mapped to the haploid reference to identify single nucleotide polymorphisms (SNPs) at individual loci. The final data set contained 11,082 microhaplotyped loci which offer at least an order of magnitude greater resolution for species discrimination than the current panel of 19 microsatellites. These markers will be used to examine a larger sample of Scaphirhynchus individuals throughout their ranges to determine the extent and trajectory of hybridization.
True sunfishes (genus Lepomis) of North America are renowned for hybridization, although hybrids often comprise of only a fraction of the sunfish population in natural systems. Species boundaries may be maintained through premating mechanisms (e.g., ethological and habitat isolation), which may be facilitated by the promiscuous sunfish mating system; primarily, singular males guard nests which multiple females visit. Natural hybridization occurs between redbreast (L. auritus (Linnaeus, 1758)) and pumpkinseed (L. gibbosus (Linnaeus, 1758)) sunfishes, but there is no published research into its extent and causes. In this study, we assessed the relationship of ecological variables to the prevalence of hybridization in a sunfish population in a freshwater lake. Nests of both species were evaluated for differences in substrate, date, water depth, temperature, and dissolved oxygen. Sequencing of one fragment of nuclear DNA (calmodulin intron 4) and one fragment of mitochondrial DNA (12S) was employed on adult males and eight offspring from each nest to determine genetic identity and hybridization direction. Nonparametric tests found a significant difference in substrate between species’ nests (p < 0.01), warranting further investigation into nest substrate as a mechanism for species maintenance. Furthermore, we observed asymmetrical hybridization with the less abundant species (redbreast sunfish) disproportionately affected.
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