²WI Cooperative Fishery Research Unit, College of Natural Resources, University of Wisconsin-Stevens Point, 800 Reserve Street, Stevens Point, WI54481

³South Dakota State University Department of Natural Resource Management Northern Plains Biostress Laboratory P O Box 214B, Brookings, SD 57007

⁴Michigan Department of Natural Resources, Charlevoix Fisheries Research Station, 96 Grant St., Charlevoix, MI 49720

⁵Wisconsin Department of Natural Resources, 110 South Neenah Ave., Sturgeon Bay, WI 54235

⁶School of Fisheries and Ocean Science, University of Alaska-Fairbanks, 905 Koyokuk Dr., Fairbanks, AK 99775

December 2011

Abstract

Six genetic stocks of lake whitefish exist in Lake Michigan representing regional spawning aggregates with genetically-distinct characteristics. Concerns exist about the potential mixed-stock characteristics of Lake Michigan’s lake whitefish commercial fishery, the temporal stability of these six stocks, and the impacts these two issues have on stock-specific management of this resource. The genetic stock-structure model and microsatellite reference database for lake whitefish spawning aggregates in Lake Michigan provides a framework for addressing some of these key information gaps. The objectives of this research were (1) to use multi-locus microsatellite data and mixed stock analysis to identify the stock of origin for lake whitefish sampled from the 2009-2010 Lake Michigan commercial harvest, and (2) to determine if contemporary genetic stock boundaries are consistent with historical genetic structure in Lake Michigan lake whitefish using archived scale samples from the historic commercial harvest. Mixed-stock analysis was conducted on 18 commercial harvest samples collected from Spring 2009-Fall 2010. Results showed considerable variability in stock composition over the lake with, on average, 2-4 genetic stocks contributing large proportions to all harvest samples. The predominant stocks were the North and Moonlight Bay stock (NMB), Big Bay de Noc stock (BBN), the Northern stock (NOR; Epoufette and Naubinway), and the Northeastern stock (NOE; Grand Traverse Bay and Hog Island). For most samples, the dominant stock harvested was <60% showing significant admixture in most samples. Samples from WFM-08 were the most homogeneous of all samples with 80.3% of the sample estimated to be from the Southern stock (SOU; Saugatuk, Ludington, Muskegon, MI). Multiple samples surveyed from NMB and BBN across spring, summer, and fall of both sample years showed changes between seasons in some years, and between years. Interestingly, samples from zone WI-02 consistently were estimated to be comprised of a majority of BBN fish as opposed to the geographically proximate NMB stock. The findings have implications for stock-specific management and the allocation of fish to various quotas as these data show in many cases, not even a majority (≥50%) of sampled fish were from the geographically proximate stock. The temporal stability of contemporary stocks was confirmed with a majority consensus of chi-square tests of allele counts, genic differentiation, FST, Dest, and a neighbor-joining tree of genetic distance. Divergence between temporal samples and contemporary samples suggest changes have occurred from 1973 to present however in all cases, contemporary stocks were most similar to temporal samples from the geographically proximate stock. Therefore, this observed temporal stability supports the previously developed genetic stock-model.