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Population and Fishery Genetics of Yellow Perch

  Genetic studies Across North America:  mitochondrial control regionSpecies 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. 

Waterscape genetics of the yellow perch (Perca flavescens): Patterns across large connected ecosystems and isolated relict populations

Osvaldo J. Sepulveda-Villet and Carol A. Stepien

Molecular Ecology (2012) volume 21, pages 5795-5826

Abstract: Comparisons of a species’ genetic diversity and divergence patterns across large connected populations vs. isolated relict areas provide important data for understanding potential response to global warming, habitat alterations and other perturbations. Aquatic taxa offer ideal case studies for interpreting these patterns, because their dispersal and gene flow often are constrained through narrow connectivity channels that have changed over geological time and/or from contemporary anthropogenic perturbations. Our research objective is to better understand the interplay between historic influences and modern-day factors (fishery exploitation, stocking supplementation and habitat loss) in shaping population genetic patterns of the yellow perch Perca flavescens (Percidae: Teleostei) across its native North American range. We employ a modified landscape genetics approach, analysing sequences from the entire mitochondrial DNA control region and 15 nuclear DNA microsatellite loci of 664 spawning adults from 24 populations. Results support that perch from primary glacial refugium areas (Missourian, Mississippian and Atlantic) founded contemporary northern populations. Genetic diversity today is highest in southern (never glaciated) populations and also is appreciable in northern areas that were founded from multiple refugia. Divergence is greater among isolated populations, both north and south; the southern Gulf Coast relict populations are the most divergent, reflecting their long history of isolation. Understanding the influence of past and current waterway connections on the genetic structure of yellow perch populations may help us to assess the roles of ongoing climate change and habitat disruptions towards conserving aquatic biodiversity.

YP Map

Figure 1. Map of yellow perch sampling sites across North America (lettered according to Table 1). Dashed line indicates maximum extent of the Wisconsinan glaciations, dotted line delineates the boundaries of the Laurentian Great Lakes watershed. Arrows denote likely routes of postglacial population colonizations, adapted from Mandrak & Crossman (1992) to our findings. Solid lines indicate major barriers to gene flow based on 15 lsat loci (ranked I–X, in the order of decreasing magnitude) from the BARRIER analysis (Manni et al. 2004b). Thickness of barriers depict locus support. Loci support/mean FST are as follows: Barrier I, 13 loci/0.364; II, 11 loci/0.247; III, 11 loci/0.342; IV, 9 loci/0.282; V, 10 loci/0.239; VI, 9 loci/0.207; VII, 7 loci/0.177; VIII, 6 loci/0.173; IX, 5 loci/0.141; X, 6 loci/0.098.

YP Trees

Figure 2. Trees showing yellow perch relationships: (a) neighbor-joining tree of populations from lsat data, based on Nei’s (1972) distance in PHYLIP (Felsenstein 2008) and (b) Bayesian 50% majority rule consensus trees of 26 yellow perch mtDNA control region haplotypes, rooted to the Eurasian perch Perca fluviatilis and constructed in MrBayes 3.1.2 (Huelsenbeck & Ronquist 2001; Ronquist & Huelsenbeck 2003). Tree is congruent with our maximum likelihood (ML) analyses (Appendix VII). Values above nodes = Bayesian posterior probability/percentage support from 1000 bootstrap pseudoreplications in ML. Values below nodes = estimated divergence times (given as millions of years) as determined in r8s 1.71 (Sanderson 2003) and 95% confidence intervals (in parentheses) as determined in BEAST 1.7.2 (Drummond et al. 2012) and TRACER 1.4 (Rambaut & Drummond 2007). Letters in parentheses denote sampling sites in which haplotypes were recovered. Vertical bars denote geographical regions.

YP haplotype network

Figure 3. Statistical parsimony network among yellow perch mtDNA control region haplotypes (numbered) constructed in TCS 1.21 (Clement et al. 2000). Circles are sized according to total observed frequency of the haplotype. Letters in circles denote sample sites where that haplotype was recovered. Asterisks in circles denote haplotypes recovered and identified in Sepulveda-Villet et al. (2009) but not recovered in this study. Lines indicate a single mutational step between the haplotypes. Small, unlabelled circles represent hypothesized unsampled haplotypes. Dashed lines enclosing haplotype groups denote major regional delineations used in this study. Circle colours also reflect haplotype identities as portrayed in Fig 4b.

YP Structure

Figure 4. Estimated yellow perch population structure from (a) Bayesian STRUCTURE analyses (Pritchard et al. 2000; Pritchard & Wen 2004) for K = 17 groups using 15 lsat loci. Optimal K = 17 (pp = 0.999) was determined from DK likelihood evaluations (Evanno et al. 2005). Individuals are represented by thin vertical lines, partitioned into K coloured segments that represent estimated membership fractions. (b) mtDNA control region frequencies of 26 haplotypes. Vertical black lines separate different spawning groups. Bar colours reflect haplotype identities as portrayed in Fig. 3.

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

Last Updated: 8/18/17