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.