The University of Toledo

Population and Fishery Genetics of Yellow Perch

  Genetic studies Across North America:  mitochondrial control region - Species identification - lake comparisons - Lake Erie Structure

Yellow Perch: Research to date has analyzed 1229 specimens of yellow perch for 15 microsatellite loci among 33 population groups, including outlying samples from Atlantic coastal and southern groups. Continuing work focuses on temporal comparisons and monitoring.

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Lake Erie sampling locations and primary genetic barriers for Yellow Perch based on 15 microsatellite loci for 549 individuals.  This map is interactive - selecting a point will show the genetic information for those samples. 

Genetic diversity patterns across large connected systems and isolated relict populations: Biogeography from two genomes for the yellow perch

Osvaldo J. Sepulveda Villet and Carol A. Stepien

Abstract: Populations of the yellow perch Perca flavescens across North America have fluctuated  in contemporary times due to unstable recruitment patterns, exploitation, and stocking. The purpose of the present study is to analyze population genetic diversity and divergence patterns across its native North American range to interpret phylogeographic relationships and contemporary anthropogenic influences.  We employ a dual genome approach, analyzing complete sequences from the mitochondrial DNA control region (912 base pairs) and 15 nuclear microsatellite loci from 664 adult spawning yellow perch at 24 native location sites, including all five Great Lakes, the upper Mississippi River watershed, Lake Champlain, Atlantic coast (St. John’s River in Maine, Hudson River, Chesapeake Bay, Albermarle Sound, and Cape Fear), and Gulf coastal relict populations (Chattahoochee and Apalachicola Rivers). Analyses include pairwise divergences, hierarchical AMOVA partitioning, Mantel regression, genetic distance trees, Bayesian assignment tests, 3-dimensional factorial correspondence, and Monmonier geographic networks. Divergence patterns reflect influence of two distinct glacial refugia in the current genetic structure of Great Lakes sites, with some evidence of contribution from a third glacial refugium in a single Great Lakes. Southern Gulf coast relict populations are distinct and separate from all other sites, and represent unique pockets of genetic identity and isolation. Overall, highest  genetic diversity is found in sites of tentative glacial refugia, with highest values present in South Atlantic coastal sites. Implications of the influence of glacial refugia on current native populations are important in the context of fishery management and conservation efforts.

Figure 1. Map showing yellow perch sampling sites across North America (lettered according to Table 1). Lines indicate primary barriers to gene flow based on 15 microsatellite loci (ranked I-X, in order of decreasing magnitude) from the BARRIER analysis (Manni et al. 2004b).  Significance of barriers given as percent bootstrap and number of loci that support it.

Figure 2a.

Figure 2b.

Figure 2. Phylogenetic relationships among yellow perch showing A) neighbor joining tree of population samples, based on Nei’s (1972) distance (Ds) with 15 microsatellite loci constructed In PHYLIP (Felsenstein 2005), and B) maximum likelihood tree of Kimura (1980) 2-parameter genetic distances from mtDNA control region haplotypes, rooted to Eurasian perch Perca fluviatilis and constructed in MEGA 5 (Tamura et al. 2011). Percentages denote nodal support from 2000 bootstrap resampling events. Vertical bars denote primary geographical regions.

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Figure 3. Estimated yellow perch A) population structure using Bayesian STRUCTURE analyses (Pritchard et al. 2000, 2004) for K= 17 groups using 15 microsatellite loci.  Optimal K=17 (pp=0.999) was determined from ΔK likelihood evaluations (Evanno et al. 2005). Individuals are represented by thin vertical lines, partitioned into K colored segments that represent the estimated membership fractions. B) mtDNA control region haplotype frequencies across North American sampling sites. Colors denote 26 recovered haplotypes. Vertical black lines separate different spawning samples.

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Genetic studies Across North America:  mitochondrial control region - Species identification - lake comparisons- Lake Erie Structure