Defining the Need for Genetic Stock Assignment when Describing Stock Demographics and Dynamics: an Example using Lake Whitefish in Lake Michigan

Abstract

Genetic stock assignment is not routinely used when describing the dynamics and demographics of individual stocks supporting mixed‐stock fisheries, and capture location and timing are often used as alternative assignment methods. However, variation in stock demographics and dynamics may not be accounted for if stock assignments based on capture location or timing do not accurately reflect genetic assignments. We used Lake Whitefish Coregonus clupeaformis in Lake Michigan as a model fishery to determine whether stock mixing could undermine efforts to describe stock status when using October capture location as a proxy for genetic stock assignment. Accuracy of stock assignments based on October capture location ranged from 54% to 100% among management zones. Metrics describing length and age distributions, weight at length, fecundity, and growth varied among genetic stocks. Stock‐specific metrics were typically similar between stock assignment methods (capture location versus genetics) because only one or two genetic stocks were collected in most locations and the majority of those fish were from spatially proximal stocks with similar metrics. However, more extensive mixing of Lake Whitefish stocks has been documented; thus, using capture location for stock assignment could result in incorrect conclusions regarding stock status and harvest management depending on stock composition. Ambiguity in genetic stock assignments was a problem in two management zones, where between 23% and 42% of Lake Whitefish did not assign to a specific stock with a probability of at least 0.70. In the future, using genomic techniques rather than microsatellites may provide different conclusions regarding genetic stock structure; these differences could affect the accuracy of using capture location for stock assignment. Use of capture location as a proxy for genetic stock assignment may not be warranted for all mixed‐stock fisheries but may be appropriate when stock mixing is limited or is restricted to stocks with consistently similar characteristics.

Mixed‐stock analysis using Rapture genotyping to evaluate stock‐specific exploitation of a walleye population despite weak genetic structure

“…Application of mixed‐stock assessments that use similar techniques as large marine fisheries has been beneficial in large lacustrine fisheries (Andvik et al, 2016; Bott et al, 2009; Potvin & Bernatchez, 2001; Tibihika et al, 2020), especially for species with similar life‐history attributes as marine populations (Ludsin et al, 2014). Such assessments in freshwater ecosystems have been hampered by limited genetic differentiation among spawning stocks (e.g., the North American Great Lakes; Chen, Euclide, et al, 2020; Isermann et al, 2020), highlighting to need for approaches that can detect weak genetic structure.…”

High‐density genomic data reveal fine‐scale population structure and pronounced islands of adaptive divergence in lake whitefish (Coregonus clupeaformis) from Lake Michigan

“…Lake whitefish ( Coregonus clupeaformis ) in the Laurentian Great Lakes of North America are an excellent model for investigating adaptive differentiation as they spawn in heterogenous habitats, ranging from eutrophic tributaries to oligotrophic rocky reefs, and at least some lake whitefish exhibit spawning site fidelity (Ebener et al, 2010 ). Differences in spawning site‐specific selection pressures may contribute to variations in metrics such as length, age distribution, weight at length, fecundity and growth among spawning populations (Isermann et al, 2020 ). Lake whitefish also represent an economically and culturally important resource throughout the region (Ebener et al, 2008 ).…”

“…Past genetic research using 11 microsatellite loci identified six genetic stocks of lake whitefish within Lake Michigan (VanDeHey et al, 2009 ), with two stocks on the northwestern side and four stocks on the eastern side. However, low pairwise F ST values (VanDeHey et al, 2009 ) and ambiguity in genetic stock assignments (Isermann et al, 2020 ) suggest a limited number of neutral microsatellite markers do not provide adequate power for delineating Lake Michigan lake whitefish stocks, prompting calls for genomics approaches to investigate stock structure. Moreover, genomic approaches may be useful for identifying locally adaptive variants that are key to long‐term species persistence but that could be overlooked when establishing management units based on neutral or genome‐wide variation (Funk et al, 2012 ; Nielsen et al, 2012 ).…”