Historical and ethnographic records and ongoing cultural traditions highlight the importance of fishing to native peoples of the Upper Klamath Basin. Previous researchers have discussed the importance of fish to past people in the basin, but a systematic review of taxa and their abundance through time had not been closely considered until our study. We analyzed over 15,000 fish remains from six sites located above Upper Klamath Lake and obtained 11 new radiocarbon dates, which—in conjunction with previous records—suggest the fishery extends to ~5,300 cal B.P. Three fish families are represented in most time periods—suckers (Catostomidae), minnows (Cyprinidae), and salmon/trout (Salmonidae)—but suckers dominate. Their prominence, particularly large-bodied forms, is consistent with foraging models that rank this fish highly. Distinctive patterns in body-part representation are argued to reflect butchery linked to storage, rather than postdepositional destruction. The Holocene fish records suggest long-term stability in fishing practices.

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.