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Fish stocking has been utilized for over a century to offset extirpations or declines in abundance of many native species. These historical declines and hatchery contributions have led to uncertainty surrounding whether many contemporary populations are native, introgressed with hatchery sources, or entirely of hatchery origin. Such uncertainty is problematic for the conservation of native biodiversity as it hampers management agencies' ability to prioritize the conservation of indigenous locally adapted populations. Fortunately, genetic and genomic tools have allowed researchers to investigate these questions, often through the use of clustering or assignment approaches that are predicated on identifiable and consistent divergence between native populations and hatchery sources. Here, we apply these methods to restriction-site associated DNA (RAD) data from 643 brook trout (Salvelinus fontinalis) originating from 13 wild populations and an exogenous hatchery strain to investigate the extent of historical extirpations, hatchery contributions, and processes affecting population structure in a small area of the previously unglaciated Driftless Area of Wisconsin, USA. The results from these analyses suggest that wild populations in this region are genetically distinct even at small spatial scales, lack strong hydrologically associated population structure, rarely exchange gene flow, and have small effective population sizes. Furthermore, wild populations are substantially diverged from known hatchery strains and show minimal evidence of introgression in clustering analyses. However, we demonstrate through empirically informed simulations that distinct wild populations may potentially be hatchery-founded and have since diverged through rapid genetic drift. Collectively, the apparent lack of hydrological population structure and potential for rapid drift in the Driftless Area suggest that many native populations may have been historically extirpated and refounded by stocking events. If this is the case, then commonly used genomic clustering methods and their associated model selection criteria may result in underestimation of hatchery introgression in the face of rapid drift. 

Synopsis Metabolism is a fundamental attribute of all organisms that influences how species affect and are affected by their natural environment. Differences between sexes in ectothermic species may substantially alter metabolic scaling patterns, particularly in viviparous or live-bearing species where females must support their basal metabolic costs and that of their embryos. Indeed, if pregnancy is associated with marked increases in metabolic demand and alters scaling patterns between sexes, this could in turn interact with natural sex ratio variation in nature to affect population-level energy demand. Here, we aimed to understand how sex and pregnancy influence metabolic scaling and how differences between sexes affect energy demand in Gambusia affinis (Western mosquitofish). Using the same method, we measured routine metabolic rate in the field on reproductively active fish and in the laboratory on virgin fish. Our data suggest that changes in energy expenditure related to pregnancy may lead to steeper scaling coefficients in females (b = 0.750) compared to males (b = 0.595). In contrast, virgin females and males had similar scaling coefficients, suggesting negligible sex differences in metabolic costs in reproductively inactive fish. Further, our data suggest that incorporating sex differences in allometric scaling may alter population-level energy demand by as much as 20–28%, with the most pronounced changes apparent in male-biased populations due to the lower scaling coefficient of males. Overall, our data suggest that differences in energy investment in reproduction between sexes driven by pregnancy may alter allometric scaling and population-level energy demand.