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Proc Natl Acad Sci U S A. 2019 Jan 2;116(1):177-186. doi: 10.1073/pnas.1811559115. Epub 2018 Dec 4.

Anthropogenic habitat alteration leads to rapid loss of adaptive variation and restoration potential in wild salmon populations.

Author information

Department of Animal Science, University of California, Davis, CA 95616;
Center for Watershed Sciences, University of California, Davis, CA 95616.
Hatfield Marine Science Center, Coastal Oregon Marine Experiment Station, Department of Fisheries and Wildlife, Oregon State University, Newport, OR 97365.
Department of Animal Science, University of California, Davis, CA 95616.
Historical Research Associates, Inc., Seattle, WA 98101.
Ancient DNA Laboratory, Department of Archaeology, Simon Fraser University, Burnaby, BC, Canada V5A 1S6.
Wild Salmon Center, Portland, OR 97209.
BioArCh, Department of Archaeology, University of York, Heslington, York YO1 7EP, United Kingdom.
Department of Anthropology, University of British Columbia, Vancouver, BC, Canada V6T 1Z1.
Department of Anthropology, Portland State University, Portland, OR 97207.


Phenotypic variation is critical for the long-term persistence of species and populations. Anthropogenic activities have caused substantial shifts and reductions in phenotypic variation across diverse taxa, but the underlying mechanism(s) (i.e., phenotypic plasticity and/or genetic evolution) and long-term consequences (e.g., ability to recover phenotypic variation) are unclear. Here we investigate the widespread and dramatic changes in adult migration characteristics of wild Chinook salmon caused by dam construction and other anthropogenic activities. Strikingly, we find an extremely robust association between migration phenotype (i.e., spring-run or fall-run) and a single locus, and that the rapid phenotypic shift observed after a recent dam construction is explained by dramatic allele frequency change at this locus. Furthermore, modeling demonstrates that continued selection against the spring-run phenotype could rapidly lead to complete loss of the spring-run allele, and an empirical analysis of populations that have already lost the spring-run phenotype reveals they are not acting as sustainable reservoirs of the allele. Finally, ancient DNA analysis suggests the spring-run allele was abundant in historical habitat that will soon become accessible through a large-scale restoration (i.e., dam removal) project, but our findings suggest that widespread declines and extirpation of the spring-run phenotype and allele will challenge reestablishment of the spring-run phenotype in this and future restoration projects. These results reveal the mechanisms and consequences of human-induced phenotypic change and highlight the need to conserve and restore critical adaptive variation before the potential for recovery is lost.


biodiversity; conservation; evolution; genetics; salmon

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