Restriction site‐associated DNA sequencing generates high‐quality single nucleotide polymorphisms for assessing hybridization between bighead and silver carp in the U nited S tates and C hina

Bighead carp ( H ypophthalmichthys nobilis ) and silver carp ( H . molitrix ) are invasive species and listed as US federally injurious species under the Lacy Act. They have established populations in much of the M ississippi River Basin ( MRB ; M ississippi, I llinois, and M issouri rivers) and are capable of producing fertile hybrids and complex introgression. Characterizing the composition of this admixture requires a large set of high‐quality, evolutionarily conserved, diagnostic genetic markers to aid in the identification and management of these species in the midst of morphological ambiguity. Restriction site‐associated DNA ( RAD ) sequencing of 45 barcoded bighead and silver carp from the U nited S tates and C hina produced reads that were aligned to the silver carp transcriptome yielded 261 candidate single nucleotide polymorphisms ( SNP s) with fixed allelic differences between the two species. We selected the highest quality 112 SNP loci for validation using 194 putative pure‐species and F 1 hybrids from the MRB and putative bighead carp and silver carp pure species from C hina ( A mur, P earl and Y angtze rivers). Fifty SNP s were omitted due to design/amplification failure or lack of diagnostic utility. A total of 57 species‐diagnostic SNP s conserved between carp species in US and C hinese rivers were identified; 32 were annotated to functional gene loci. Twenty‐seven of the 181 (15%) putative pure species were identified as hybrid backcrosses after validation, including three backcrosses from the A mur River, where hybridization has not been documented previously. The 57 SNP s identified through RAD sequencing provide a diagnostic tool to detect population admixture and to identify hybrid and pure‐species A sian carps in the U nited S tates and C hina.