![]() The role of genetic drift increases as population sizes decline, such that natural selection may be ineffective at removing deleterious mutations (Whitlock & Bürger, 2004 Wright, 1931), leading to “mutational meltdown” and eventually extirpation of small populations (Lynch et al., 1995). Most mutations are mildly deleterious (Fay et al., 2001 Keightley & Lynch, 2003 Ohta, 1995), and in a large, randomly outcrossing population, recombination and segregation are expected to keep the mutational load from significantly affecting absolute mean fitness (Agrawal & Whitlock, 2012 Haag & Roze, 2007). In small populations, the mutation‐selection balance can often be upset, making the frequency of deleterious mutations a conservation concern. ![]() The mutations that underlie allelic diversity occur on a spectrum that can be broadly reduced to three categories (advantageous, neutral, or deleterious), with the frequency of these categories varying under mutation‐selection balance. Since heritable genetic variation provides the foundation for adaptive capacity under selection, the maintenance of diversity is fundamental to the preservation of healthy populations (Hoban et al., 2013 Sgrò et al., 2011). Sources of selective pressure are numerous, and studies using genotype–environment association analyses that detect locally adapted populations can provide valuable insight on the environmental forces that influence population viability (Berg et al., 2015 Eizaguirre et al., 2012 Yeaman et al., 2016). Understanding the nature of resilience and the capacity for evolution in the face of rapidly changing environments is a cornerstone of conservation genomics. Our results shed light on the complex dynamics influencing these isolated populations and provide valuable information for their conservation. Notably, differences among lakes in the availability of estimated oxythermal habitat left no clear population genomic signature. ![]() Although the prevalence of deleterious mutations and inbreeding coefficients was significantly correlated with latitude, neutral and non‐neutral genetic diversity were most strongly correlated with lake surface area. High levels of genetic differentiation among populations were punctuated by a phylogeographic break and residual patterns of isolation‐by‐distance. We correlated these metrics to spatial and environmental factors including latitude, lake size, and measures of oxythermal habitat and found significant relationships between genetic metrics and broad and local factors. We also examined haplotype diversity in a region of the major histocompatibility complex involved in stress and immune system response. We used restriction site‐associated DNA capture (Rapture) sequencing to survey genomic diversity and differentiation in southern inland lake cisco populations and compared the frequency of deleterious mutations that potentially influence fitness across lakes. Here, we used genomic tools to investigate the nature of this pattern of resilience. Yet, cisco extirpations do not show a clear latitudinal pattern, suggesting that local environmental factors and potentially local adaptation may influence resilience. ![]() Populations of cisco, Coregonus artedi, in inland lakes have experienced numerous extirpations along the southern edge of their range in recent decades, which are thought to result from environmental degradation and loss of cold, well‐oxygenated habitat as lakes warm. This is particularly true at the edge of a species range, where populations often persist at the limits of their environmental tolerances. The dueling effects of selection and drift in a limited pool of genetic diversity make the responses of small populations to environmental perturbations erratic and difficult to predict. Small, isolated populations present a challenge for conservation. ![]()
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