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Genetic structure of Wisconsin's naturally recruiting walleye populations


July 2006 - January 2009


Genetic diversity has been recognized as a vital component of fish management in Wisconsin. An explicit goal of the state‘s walleye management plan has been to preserve the genetic integrity of naturally recruiting walleye populations. A prerequisite to achieving this goal is understanding the distribution of genetic diversity within and among the State‘s walleye populations. My objectives were to 1) to determine whether there is significant genetic structure among Wisconsin‘s naturally recruiting walleye populations, and 2) if this resolved genetic structure was consistent with contemporary fisheries management zones employed for Wisconsin‘s walleye. Genetic diversity for these walleye populations was measured at 10 microsatellite loci and genetic structure was delineated through a process known as genetic stock identification (GSI). Genetic stock identification is a series of hierarchical tests consisting of genic differentiation, genetic distance, AMOVA, and pairwise FST comparisons to identify putative genetic units. Genetic diversity levels throughout the sampled populations were high (Ho = 0.7144, HE = 0.7677) and comparable to other walleye studies (Wirth et al. 1999; Borer et al. 1999; Eldridge et al. 2002; Cena et al. 2006; Franckowiak et al. 2009) using a similar
suite of microsatellite loci. Results however showed current fisheries management units
were not consistent with this genetic structure. Delineation of genetic units using GSI
identified 21 significant genetic units among the 26 sampled populations suggesting
populations are primarily maintaining localized gene pools. Iterative analyses examining
the ratio of among-group variance to within-group variance was performed to identify
higher level genetic units (i.e., putative stocks). Eight putative genetic units, mostly
consistent with geographic location of the populations and not with current watershed regions, were identified using the ratio comparing among-group variance to within-group variance. Significant inbreeding coefficients were observed in half the sampled walleye populations. No relation was observed between inbreeding and population size or effective population size. A trend was observed where inbreeding predominately occurred in walleye populations from large systems; 81.5% (9/13) of all systems with a surface area > 500 ha showed significant inbreeding whereas 31.3% (4/13) of populations with a surface area of < 500 ha showed significant inbreeding. Several factors could account for these data including the preferential sampling in large systems of a single walleye spawning area, coupled with known philopatry of walleye, resulting in biased
sampling of cohorts and/or related individuals. Current management strategies should be
re-evaluated in light of these findings to better define management zones that can effectively conserve the genetic integrity of naturally recruiting walleye populations. This re-evaluation should weigh the cost of increasing the number of genetic units managed with the short- and long-term impacts on the genetic integrity of Wisconsin‘s walleye populations. A primary conflict between genetic structure and geographical location were the populations located in the Upper Chippewa River basin were more genetically similar to populations found in the Upper Wisconsin River basin. Geographical (glacial recession and stream capture) and anthropogenic (stocking across basin boundaries) are both reasonable explanations for this disruptive pattern. This issue requires further research to determine the biological reality of the resolved structure with strong implications for future management.

Research Products and Activities


  • Hammen, J.L. 2009. Genetic structure of Wisconsin’s naturally recruiting walleye populations. M.S. Thesis. University of Wisconsin-Stevens Point. 102 p.
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  • Hammen, J.J., B.L. Sloss, and M.A. Bozek. August 2008. Walleye genetic diversity and stock structure in Wisconsin. North Central Division of the American Fisheries Society Walleye Technical Committee and Esocid Technical Committee Joint Meeting Lake Tomahawk, Wisconsin.

Current Staff

Federal Staff: 2

Masters Students: 10

Phd Students: 0

Post Docs: 0

University Staff: 6

5 Year Summary

Students graduated: 13

Scientific Publications: 33

Presentations: 114



  • Brian SlossPrincipal Investigator
  • Jeremy HammenStudent

Funding Agencies

  • Wisconsin Department of Natural Resources


Wisconsin Cooperative Fishery Research Unit Cooperators

  1. U.S. Geological Survey
  2. University of Wisconsin-Stevens Point
  3. Wisconsin Department of Natural Resources