Data from: Diagnostic SNPs reveal widespread introgressive hybridization between introduced bighead and silver carp in the Mississippi River Basin

Hybridization among conspecifics in native and introduced habitats has important implications for biological invasions in new ecosystems. Bighead (Hypophthalmichthys nobilis) and silver carp (H. molitrix) are genetically isolated and occur in sympatry within their native range. Following their introduction to North America, however, introgressant hybrids have been reported throughout their expanded range within the Mississippi River Basin (MRB). The extent of introgression, both spatially and generationally, is largely unknown. Therefore, we examined mixed-species populations from across the MRB to characterize the extent of interspecific gene flow. We assayed 2798 individuals from nine locations with a suite of species-diagnostic SNPs (57 nuclear and one mitochondrial). Forty-four per cent (n = 1244) of individuals displayed hybrid genotypes. Moreover, the composition of hybrid genotypes varied among locations and represented complex hybrid swarms with multiple generations of gene flow. Introgressive hybrids were identified from all locations, were bidirectional and followed a bimodal distribution consisting primarily of parental or parental-like genotypes and phenotypes. All described hybrid categories were present among individuals from 1999 to 2008, with parents and later-generation backcrosses representing the largest proportion of individuals among years. Our mitochondrial SNP (COII), tested on a subset of 730 individuals, revealed a silver carp maternal bias in 13 of 21 (62%) F1 hybrids, in all silver carp backcrosses, and maintained throughout many of the bighead carp backcrosses. The application of this suite of diagnostic markers and the spatial coverage permits a deeper examination of the complexity in hybrid swarms between two invasive, introduced species.Asian carp nuclear and mitochodrial SNP genotypes MOEA unique code for each individual is given in the first column and each location sampled is represented by a four character acronym described in the manuscript. The top 2 rows are bighead carp and silver carp species-specific SNPs that correspond to each locus (row 3). Column two is the mitochondrial COII locus followed by 57 nuclear SNP loci.Bighead and Silver carp parents mtDNA (COII) sequencesEach entry is in fasta format and starts with a four character location code, a unique number identifier for each individual, and a four letter code representing bighead carp (BHCP) or silver carp (SVCP) as resolved at 57 nuclear SNP loci. These are trimmed sequences representing the parents used for SNP discovery.parentsfastacorrect.txtSNP genotypes plus field and lab data on each fishA unique code for each individual is given in the first column and each location sampled is represented by a four character acronym described in the manuscript. The top 2 rows are bighead carp and silver carp species-specific SNPs that correspond to each locus (row 3). Column ten is the mitochondrial COII locus followed by 57 nuclear SNP loci. Following each unique individual code, starting in column 2 and ending in column 9, is the river reach of capture, river of capture, 57 locus genetic identification based on manual and NewHybrids assignment, morphological field identification, total length (mm), total weight (g), age as determined by postcleithra annuli counts, and birth year determined by subtracting the age from the year of capture.Asian carp nuclear and mitochodrial SNP genotypes plus individual data for each fish.xls