Data from: Invasion genetics of the silver carp Hypophthalmichthys molitrix across North America: differentiation of fronts, introgression, and eDNA metabarcode detection

The invasive silver carp Hypophthalmichthys molitrix escaped from southern U.S. aquaculture during the 1970s to spread throughout the Mississippi River basin and steadily moved northward, now reaching the threshold of the Laurentian Great Lakes. The silver carp is native to eastern Asia and is a large, prolific filter-feeder that decreases food availability for fisheries. The present study evaluates its population genetic variability and differentiation across the introduced range using 10 nuclear DNA microsatellite loci, sequences of two mitochondrial genes (cytochrome b and cytochrome c oxidase subunit 1), and a nuclear gene (ribosomal protein S7 gene intron 1). Populations are analyzed from two invasion fronts threatening the Great Lakes (the Illinois River outside Lake Michigan and the Wabash River, leading into the Maumee River and western Lake Erie), established areas in the southern and central Mississippi River, and a later Missouri River colonization. Results discern considerable genetic diversity and some significant population differentiation, with greater mtDNA haplotype diversity and unique microsatellite alleles characterizing the southern populations. Invasion fronts significantly differ, diverging from the southern Mississippi River population. About 3% of individuals contain a unique and very divergent mtDNA haplotype (primarily the southerly populations and the Wabash River), which may stem from historic introgression in Asia with female largescale silver carp H. harmandi. Nuclear microsatellites and S7 sequences of the introgressed individuals do not significantly differ from silver carp. MtDNA variation is used in a high-throughput sequence assay that identifies and distinguishes invasive carp species and their population haplotypes (including H. molitrix and H. harmandi) at all life stages, in application to environmental (e)DNA water and plankton samples. We discerned silver and bighead carp eDNA from 10 bait shops in the Great Lakes watershed, indicating that release from retailers comprises another likely vector. Our findings provide key baseline population genetic data for understanding and tracing the invasion's progression, facilitating detection, and evaluating future trajectory and adaptive success.Silver carp microsatellite genotype data in Arlequin input formatSVCPAllPops-ARLEQUIN.arpSilver carp mtDNA seqeunce data in Arlequin input formatSVC8.arpPrimer trimming scriptPerl script trims primers and removes sequences with spacer primers that are incorrect (likely index hops). Script cycles through results folders, and puts results in a separate folder for DADA2 merging.CarpTrimForDadaCycleSpacer-2.plBlastCycle500Perl script returns top 500 BLAST results for each results file in a directory.SummarizeBlasteDNAEnvironmentSepASVsPerl script summarizes blast results. For each sequence it makes a string containing all the species hits that had the lowest e value for that query. Script removes hits with % identity of query cover < 90. Script also prints if an ASV had no BLAST results or if all e values were equal to the minimum. Returns a table with columns: Sample, Species (String of lowest e value hits), N ASVs, N reads, Proportion of reads, Sequence name (from sample results file).MorphVeDNASummarizeErrMoreConsScript compares morphological results to eDNA results. Removes ASVs < than the max error calculated from positive controls. Requires eDNA results input, SppStatus.txt, and INMorph.txt.SppStatusList of species and their bait status per state sampled. B=legal bait, NA=Native non-bait, I=Invasive, W=GLANSIS watch list species not yet established in North America.INmorphList of extractions and morphological sampling results. Columns: Extraction, Shop name (anonymized to protect proprietor), Region, State, Advertised species, Extraction, Unadvertised species.INMorph.tx