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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.

Ancient DNA was extracted from 12 500 to 10 500 year old ground squirrel bones from Tse'K'wa, an archaeological site in the Peace River region of northeastern British Columbia, Canada. Analysis of mitochondrial DNA from seven individuals demonstrates that all are Urocitellus richardsonii (Richardson's ground squirrel), a species not found in the region today. Phylogenetic and sequence analyses indicate these individuals share a previously undocumented mitochondrial control region haplo-type that is most closely related to haplotypes observed in modern specimens from Saskatchewan and Montana. At the end of the Pleistocene these ground squirrels extended their range north and west into open vegetation communities that developed when ice sheets melted and glacial lakes drained. They were subsequently extirpated from the Peace River region when forests replaced earlier pioneering vegetation communities. Key words: Peace River, Late Pleistocene, paleoenvironment, Tse'K'wa, Charlie Lake Cave. De l'ADN ancien a ete extrait d'os de spermophiles de 12 500 a 10 500 ans d'age provenant de Tse'K'wa, un site archeologique de la region de la riviere de la Paix, dans le nord-est de la Colombie-Britannique (Canada). L'analyse d'ADN mitochondrial issu de sept individus demontre qu'il s'agit dans tous les cas d'Urocitellus richardsonii (spermophiles de Richardson), une espece aujourd'hui absente de la region. Des analyses phylogenetiques et de sequences indiquent que ces specimens ont tous en commun un haplotype de la region de controle mitochondriale qui n'avait pas encore ete documente et qui est le plus etroitement relie a des haplotypes observes dans des specimens modernes provenant de la Saskatchewan et du Montana. A la fin du Pleistocene, ces spermophiles ont elargi leur aire de repartition vers le nord et l'ouest pour former des communautes dans des regions de vegetation ouverte creees dans la foulee de la fonte de glaciers et la vidange de lacs glaciaires. Ils ont par la suite disparu de la region de la riviere de la Paix quand des forets ont remplace les communautes de plantes pionnieres. [Traduit par la Redaction] Mots-cles: riviere de la Paix, Pleistocene tardif, paleoenvironnement, Tse'K'wa, grotte du lac Charlie., Introduction Numerous species of ground squirrels live in a wide range of habitats in North America and the Old World (Yensen and Sherman 2003) and are potentially useful indicators of [...]

We describe a simple method for extracting polymerase chain reaction-amplifiable DNA from ancient bones without the use of organic solvents. Bone powders are digested with proteinase K, and the DNA is purified directly using silica-based spin columns (QIAquick[TM], QIAGEN). The efficiency of this protocol is demonstrated using human bone samples ranging in age from 15 to 5,000 years old. KEY WORDS DNA extraction; Ancient bone; PCR inhibitors; Silica-based spin columns

Marine mammals often exhibit significant sexual segregation in their diet and habitat use but these differences have not been studied systematically in historic or ancient populations due to the difficulties associated with determining the sex of skeletal elements based on gross morphology. Using a combined ancient DNA and stable isotope approach, we document a sexual difference in the foraging ecology of late 19th century beluga whales (Delphinapterus leucas) from the Canadian High Arctic. Using two PCR assays that coamplify fragments of the Y‐linked SRY and X‐linked ZFX genes, we assigned reproducible sex identities to 35 beluga specimens. This provided a basis for investigating sex‐specific differences in foraging ecology using stable carbon and nitrogen isotope analyses of bone collagen. These isotopic data demonstrate that although both males and females primarily consumed Arctic cod, males utilized a wider range of prey than females, feeding on high trophic level benthic prey (sculpins) to a greater extent. Because bone collagen integrates prey isotopic compositions over the course of several years these sex‐based differences in beluga bone collagen isotopic compositions reflect long‐term and sustained sexual differences in foraging. [ABSTRACT FROM AUTHOR]

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]