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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.

Whales have long been an important part of Pacific Northwest Coast human subsistence and lifeways. Native peoples on the Oregon Coast were not known to hunt whales, but a humpback whale phalange with an embedded bone harpoon at the Par-Tee site (35CLT20) and ethnographic accounts raised the possibility of opportunistic whale hunting. We analyzed a suite of whale remains from Par-Tee and performed ancient DNA-based species identifications on 30 specimens. The assemblage includes gray whales (Eschrichtius robustus, 60.7% of the assemblage), humpbacks (Megaptera novaeangliae, 32.1%), minkes (Balaenoptera acutorostrata, 3.6%), and orcas (Orcinus orca, 3.6%). While the species composition is similar to those found in archaeological deposits from systematic whaling areas in Washington and Vancouver Island, bone modification patterns and element representation reveal important differences. Our analysis demonstrates that whales were likely a supplementary part of human subsistence at Par-Tee and, while opportunistic whale hunting likely occurred, it may have been secondary to scavenging and utilization of beached and/or drift whales. [ABSTRACT FROM AUTHOR]