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Implications of Large-Effect Loci for Conservation: A Review and Case Study with Pacific Salmon

May 4, 2022


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.

Other Key Words: Phenology


Robin Waples, Michael Ford, Krista Nichols, Marty Kardos, Jim Myers, Tasha Thompson, Eric Anderson, Ilana Koch, Garrett McKinney, Michael Miller, Kerry Naish, Shawn Narum, Kathleen O’Malley, Devon Pearse, George Pess, Thomas Quinn, Todd Seamons, Adrian Spidle, Kenneth Warheit, and Stuart Willis


Waples, R.S., M.J. Ford, K. Nichols, M. Kardos, J. Myers, T.Q. Thompson, E.C. Anderson, I.J. Koch, G. McKinney, M.R. Miller, K. Naish, S.R. Narum, K.G. O’Malley, D.E. Pearse, G.R. Pess, T.P. Quinn, T.R. Seamons, A. Spidle, K.I. Warheit, and S.C. Willis. 2022. Implications of large-effect loci for conservation: a review and case study with Pacific salmon. Journal of Heredity 113(3):121-144. Online at



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Media Type

Journal Article