DOI: 10.5061/dryad.92h1f12
title: Data from: Invasion genetics of the silver carp Hypophthalmichthys molitrix across North America: differentiation of fronts, introgression, and eDNA metabarcode detection

description: 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.
description: 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 &lt; 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 &lt; 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.txt