Bighead carp (Hypophthalmichthys nobilis) and silver carp (H. molitrix) were imported from China to the United States in the early 1970s, escaped, and now hybridize widely in the Mississippi River Basin. Native-range fish from China serve as references, with fish from three invaded sites sampled in 2009-2011, typed at 57 species-diagnostic SNPs.
Format
A list with:
- genotypes
Integer matrix, 1,354 fish x 57 SNPs, counting silver carp (species 2) alleles (0, 1, 2;
NAmissing). The SNPs are on separate assays and are not mapped.- groups
"ref1"(bighead carp from the Pearl and Yangtze rivers, 16),"ref2"(silver carp from the same rivers, 20),"IMAR"(Illinois River, Marseilles Reach, the invasion front, 545),"PL26"(upper Mississippi River, Pool 26, 365) and"MKY"(lower Mississippi River, Kentucky, 408).- truth
Data frame, one row per group:
group,n,site,sampledandmax_hybrid_age(an upper bound).- animals
Data frame, one row per fish:
id,group,published_class(the class published by Lamer et al. 2015 from NewHybrids and manual checks:"BH","SV","F1","F2", backcrosses"BxBH"to"Bx4SV", and later"FxBH","FxSV") andbirth_year(capture year minus the age read from the postcleithrum bone).- description
A short description.
Source
Data package of Lamer et al. (2015) on Dryad, doi:10.5061/dryad.kp6j2 (invaded sites). CC0 1.0.
Data package of Lamer et al. (2013) on Dryad, doi:10.5061/dryad.5j2v6 (native-range reference fish). CC0 1.0.
Truth
Both species were imported in 1973 and were in open waters by the early 1980s. With a generation time of at least 3 years, hybrids sampled in 2009-2011 are at most about 12 generations old (37 years / 3), and probably 6-12; each site was colonized later than the basin as a whole, so its own hybrids are likely younger. Hybridization is ongoing: F1s were born as late as 2006. The published classes are inferred, not known pedigrees. The references are partly circular, because some Yangtze fish were used to choose the SNPs, so they look perfectly fixed. Nets targeted fish over 400 mm, so recent cohorts are under-represented.
Licence
The genotypes are from two Dryad packages, released under CC0 1.0 (public domain dedication). Three of the nine invaded sites were kept, and genotypes were recoded to count silver carp alleles.
References
Lamer JT, Ruebush BC, Arbieva ZH, McClelland MA, Epifanio JM, Sass GG (2015) Diagnostic SNPs reveal widespread introgressive hybridization between introduced bighead and silver carp in the Mississippi River Basin. Molecular Ecology 24:3931. doi:10.1111/mec.13285
Lamer JT, Sass GG, Boone JQ, Arbieva ZH, Green SJ, Epifanio JM (2013) Restriction site-associated DNA sequencing generates high-quality single nucleotide polymorphisms for assessing hybridization between bighead and silver carp in the United States and China. Molecular Ecology Resources. doi:10.1111/1755-0998.12152
Examples
mk <- diagnostic_markers(carp$genotypes, carp$groups, "ref1", "ref2")
sc <- hybrid_scores(carp$genotypes, mk)
aggregate(cbind(S, H) ~ group, data.frame(sc, group = carp$groups), mean)
#> group S H
#> 1 IMAR 0.6115810 0.10918435
#> 2 MKY 0.9752853 0.01700759
#> 3 PL26 0.4701654 0.05260538
#> 4 ref1 0.0000000 0.00000000
#> 5 ref2 1.0000000 0.00000000
table(carp$groups, classify_hybrids(sc)$class)
#>
#> BC1_species1 BC1_species2 BC2_species1 BC2_species2 F1 F2 later pure1
#> IMAR 14 8 23 86 14 1 60 150
#> MKY 0 0 1 11 0 0 25 6
#> PL26 2 0 6 23 4 3 37 172
#> ref1 0 0 0 0 0 0 0 16
#> ref2 0 0 0 0 0 0 0 0
#>
#> pure2
#> IMAR 189
#> MKY 365
#> PL26 118
#> ref1 0
#> ref2 20