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  • Validating classification models that use morphometrics to identify ancient salmonid (Oncorhynchus spp.) vertebrae to species


Northwest Fisheries Science Center (NWFSC) Conservation Biology CB - Mathematical Biology and Systems Monitoring


Salmonid vertebrae ID
Validating classification models that use morphometrics to identify ancient salmonid (Oncorhynchus spp.) vertebrae to species
Using morphometric characteristics of modern salmonid (Oncorhynchus spp.) vertebrae, we have developed classification models to identify salmonid vertebrae to the species level with relatively low error rates. This is a study to validate the performance of our classification models on ancient salmonid specimens using analysis of ancient DNA. We have putatively identified a sample of ancient (ca. 1000 to 2900 ybp) vertebrae (from the Wenatchee River basin) to species with our models. Using molecular markers to identify the ancient vertebrae to species, we will be able to evaluate the performance of our models that use vertebral morphology for species identification. If identification methods that are based on vertebral morphology perform successfully, we will have a rapid, low cost, nondestructive method to identify ancient salmonid vertebrae. If applied to midden sites throughout the Columbia River basin, and potentially to other river systems draining into the Pacific Ocean, we will improve our understanding of historical anadromous salmonid occupancy and have a more complete picture of historical population and ESU structure. Additionally, the results of this work have the potential to make a significant contribution to inland and coastal anthropological/archaeological investigations. Collaborators include: Virginia Butler (Portland State University, Dept. of Anthropology), Harriet Huber (AFSC), and Dongya Yang (Simon Fraser University, Ancient DNA Laboratory)

Research Themes

Recovery and rebuilding of marine and coastal species
The Pacific Northwest is home to several iconic endangered species, including Pacific salmon and killer whales, and several rockfish species. Mandates such as the Endangered Species Act, MagnusonStevens Act, and the Marine Mammal Protection Act, grant NOAA Fisheries the authority to manage the recovery of depleted species and stocks. The NWFSC contributes to species recovery through research, monitoring and analysis, providing NOAA managers and regional stakeholders the tools and information they need to craft effective regulations and develop sustainable plans for recovery.

Research Foci

Characterize the population biology of species, and develop and improve methods for predicting the status of populations
To evaluate species status and recovery, it is necessary to understand key aspects of the population biology of the species in question. This includes basic information on abundance, age structure, recruitment, spatial distribution, life history and how the species interacts with its ecosystem. For some recovering species, including most overfished groundfish stocks, many ESA-listed Pacific salmon stocks, and high profile species such as Southern Resident killer whales, this basic information is often reasonably well understood. For other recovering species, such as Pacific eulachon and some ESA-listed rockfish species, even basic information (e.g. stock abundance) is unknown. Even for well-studied species, key information on survival rates for critical life stages and how the environment affects these vital rates is lacking. Without basic information on species dynamics, achieving other goals such as quantifying relationships between human activities and species recovery or even knowing if species recovery goals are being met will not be successful. The NWFSC, in partnership with regional stakeholders, including states, tribes and industry, is conducting research to collect and monitor critical demographic information for recovering species.


Wenatchee River Basin
interior Columbia River Basin subwatershed
ancient DNA
ancient DNA
statistical technique
vertebrae Identification
salmon bone identification


None associated


Species Oncorhynchus clarkii
cutthroat trout
Species Oncorhynchus gorbuscha
humpback salmon, pink salmon
Species Oncorhynchus keta
chum salmon, dog salmon, Keta salmon
Species Oncorhynchus kisutch
Coho salmon, silver salmon
Species Oncorhynchus mykiss
rainbow trout, steelhead trout, syeelhead trout
Species Oncorhynchus nerka
kokanee, red salmon, sockeye salmon
Species Oncorhynchus tshawytscha
Chinook salmon, king salmon, spring salmon


Jeff Jorgensen
Principal Investigator