Novel polymorphic microsatellite loci for distinguishing rock bass (Ambloplites rupestris), Roanoke bass (Ambloplites cavifrons), and their hybrids

Mol Biol Rep. 2016 Oct;43(10):1035-9. doi: 10.1007/s11033-016-4049-0. Epub 2016 Aug 2.


The rock bass (Ambloplites rupestris) is a popular sport-fish native to the Mississippi and Great Lakes basins of North America. The species has been widely introduced outside its native range, including into Atlantic-slope streams of Virginia where it may hybridize with an imperiled, similar-looking congener, the Roanoke bass (Ambloplites cavifrons). In this study, we identified and evaluated novel molecular markers to facilitate identification of these species and study the extent of hybridization. Using molecular libraries developed from A. rupestris, we identified a suite of candidate nuclear microsatellite loci, synthesized primer sets, and tested these markers for amplification and polymorphism in populations of both species. We then calculated standard diversity statistics within and differentiation statistics between species, the latter providing an indication of marker power for distinguishing the species and their hybrids. Additionally, we evaluated our efficiency for identifying hybrids by classifying simulated genotypes of known ancestry. Eleven loci were polymorphic (2-22 alleles per locus) and reliably amplified in both species. Multilocus genetic differentiation between A. cavifrons and A. rupestris was quite high (F ST = 0.66; D LR = 19.3), indicating the high statistical power of this marker set for species and hybrid identification. Analyses of simulated data suggested these markers reliably distinguish between hybrids and non-hybrids, as well as between F1 hybrids and backcrossed individuals. This panel of 11 loci should prove useful for understanding patterns of hybridization between A. rupestris and A. cavifrons. As the first microsatellite markers developed for Ambloplites, these markers also should prove broadly useful for population genetic studies of this genus.

Keywords: Ambloplites; Bass; Genetic diversity; Hybridization; Microsatellite.

MeSH terms

  • Animals
  • Bass / classification*
  • Bass / genetics*
  • Genetic Markers / genetics*
  • Genotype
  • Hybridization, Genetic
  • Introduced Species
  • Microsatellite Repeats*
  • Phylogeny
  • Species Specificity


  • Genetic Markers