The increasing feasibility of assembling large genomic datasets for non-model species presents both opportunities and challenges for applied conservation and management. A popular theme in recent studies is the search for large-effect loci that explain substantial portions of phenotypic variance for a key trait(s). If such loci can be linked to adaptations, 2 important questions arise: 1) Should information from these loci be used to reconfigure conservation units (CUs), even if this conflicts with overall patterns of genetic differentiation? 2) How should this information be used in viability assessments of populations and larger CUs? In this review, we address these questions in the context of recent studies of Chinook salmon and steelhead (anadromous form of rainbow trout) that show strong associations between adult migration timing and specific alleles in one small genomic region. Based on the polygenic paradigm (most traits are controlled by many genes of small effect) and genetic data available at the time showing that early-migrating populations are most closely related to nearby late-migrating populations, adult migration differences in Pacific salmon and steelhead were considered to reflect diversity within CUs rather than separate CUs. Recent data, however, suggest that specific alleles are required for early migration, and that these alleles are lost in populations where conditions do not support early-migrating phenotypes. Contrasting determinations under the US Endangered Species Act and the State of California’s equivalent legislation illustrate the complexities of incorporating genomics data into CU configuration decisions. Regardless how CUs are defined, viability assessments should consider that 1) early-migrating phenotypes experience disproportionate risks across large geographic areas, so it becomes important to identify early-migrating populations that can serve as reliable sources for these valuable genetic resources; and 2) genetic architecture, especially the existence of large-effect loci, can affect evolutionary potential and adaptability.

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For more than 100 years, two dams blocked upstream migration of steelhead Oncorhynchus mykiss (anadromous Rainbow Trout) on the Elwha River, Washington. Prior to the removal of both dams (completed in 2015), 30 spatiotemporal collections of resident Rainbow Trout, steelhead, hatchery steelhead, and hatchery-derived Rainbow Trout (1,949 individuals) were made from 17 sites in the river, and the pattern of genetic diversity and connectivity were evaluated using 13 microsatellite loci. Wild-origin steelhead spawned below the downstream dam and were genetically distinguishable from upriver (above dam) resident Rainbow Trout (F ST = 0.034), and the resident Rainbow Trout segregated into two distinct groups (F ST = 0.056). Nonnative-origin hatchery steelhead varied from the indigenous steelhead (F ST = 0.029), and the hatchery trout differed from the resident trout (F ST = 0.163). Collections of resident Rainbow Trout from the upper portion of the basin were distinguished by lower estimates of genetic variability (H e , A R , and A/L) and effective population size compared with resident Rainbow Trout in the middle reaches of the Elwha River. The break between the two trout groups coincided with Rica Canyon, 8 river kilometers upstream from the Glines Canyon Dam (the upstream dam), suggesting that the upper and middle trout groups represent historic O. mykiss groups separated by flow conditions in the canyon prior to dam construction. Anticipating the potential for genetic exchange between steelhead and resident Rainbow Trout following dam removal, we evaluated the ability of the microsatellite baseline to distinguish F 1 crosses between the life history groups with computer simulations. These results demonstrate how a genetic baseline can be used as a conservation management tool to measure potential genetic introgression among resident populations and recolonizing anadromous populations.