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Short Citation:
Northwest Fisheries Science Center, 2022: Vertebrae classification models - Validating classification models that use morphometrics to identify ancient salmonid (Oncorhynchus spp.) vertebrae to species, https://www.fisheries.noaa.gov/inport/item/17790.

Item Identification

Title: Vertebrae classification models - Validating classification models that use morphometrics to identify ancient salmonid (Oncorhynchus spp.) vertebrae to species
Short Name: Vertebrae classification models (Validating classification models that use morphometrics to identify ancient salmonid (Oncorhynchus spp.) vertebrae to species)
Status: Completed
Creation Date: 2010-06-01
Publication Date: 2018-02-21
Abstract:

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).

Ancient vertebrae measurements.

Purpose:

Laboratory data

Notes:

Loaded by batch 4076, 01-22-2013 18:55

Supplemental Information:

Subject to Public Access to Research Results (PARR): Yes

Keywords

Theme Keywords

Thesaurus Keyword
UNCONTROLLED
None ancient DNA
None classification
None morphometrics
None vertebrae Identification
None Wenatchee River Basin

Spatial Keywords

Thesaurus Keyword
UNCONTROLLED
None NWFSC Montlake
None Wenatchee River basin

Instrument Keywords

Thesaurus Keyword
UNCONTROLLED
None Quantitative PCR Machine

Physical Location

Organization: Northwest Fisheries Science Center
City: Seattle
State/Province: WA
Country: USA

Data Set Information

Data Set Scope Code: Data Set
Data Set Type: Spreadsheet
Data Presentation Form: Table (digital)

Support Roles

Data Steward

CC ID: 847602
Date Effective From: 2015-10-01
Date Effective To:
Contact (Person): Jorgensen, Jeff
Address: 2725 Montlake Boulevard East
Seattle, WA 98112
Email Address: Jeff.Jorgensen@noaa.gov
Phone: 206-860-3286

Distributor

CC ID: 847603
Date Effective From: 2015-10-01
Date Effective To:
Contact (Organization): Northwest Fisheries Science Center (NWFSC)
Address: 2725 Montlake Boulevard East
Seattle, WA 98112
USA
Email Address: nmfs.nwfsc.metadata@noaa.gov
Phone: 206-860-3200
URL: NWFSC Home

Metadata Contact

CC ID: 847601
Date Effective From: 2015-10-01
Date Effective To:
Contact (Organization): Northwest Fisheries Science Center (NWFSC)
Address: 2725 Montlake Boulevard East
Seattle, WA 98112
USA
Email Address: nmfs.nwfsc.metadata@noaa.gov
Phone: 206-860-3200
URL: NWFSC Home

Originator

CC ID: 847605
Date Effective From: 2015-10-01
Date Effective To:
Contact (Person): Jorgensen, Jeff
Address: 2725 Montlake Boulevard East
Seattle, WA 98112
Email Address: Jeff.Jorgensen@noaa.gov
Phone: 206-860-3286

Point of Contact

CC ID: 847604
Date Effective From: 2015-10-01
Date Effective To:
Contact (Person): Jorgensen, Jeff
Address: 2725 Montlake Boulevard East
Seattle, WA 98112
Email Address: Jeff.Jorgensen@noaa.gov
Phone: 206-860-3286

Extents

Extent Group 1

Extent Group 1 / Geographic Area 1

CC ID: 847611
W° Bound: -122.3062
E° Bound: -122.3062
N° Bound: 47.6449
S° Bound: 47.6449
Description

NWFSC Montlake: Montlake

Extent Group 1 / Time Frame 1

CC ID: 847610
Time Frame Type: Continuing
Start: 2010-06-01

Extent Group 2

Extent Group 2 / Geographic Area 1

CC ID: 847614
W° Bound: -121.181
E° Bound: -120.3246
N° Bound: 48.1812
S° Bound: 47.2827
Description

Wenatchee River basin: Swiftwater Rockshelters midden

Extent Group 2 / Time Frame 1

CC ID: 847613
Time Frame Type: Continuing
Start: 2010-06-01

Access Information

Security Class: Unclassified
Data Access Procedure:

At this time, contact the Data Manager for information on obtaining access to this data set. In the near future, the NWFSC will strive to provide all data resources as a web service in order to meet the NOAA Data Access Policy Directive (https://nosc.noaa.gov/EDMC/PD.DA.php).

Data Access Constraints:

NA

Distribution Information

Distribution 1

CC ID: 847607
Start Date: 2018-02-21
End Date: Present
Download URL: https://www.webapps.nwfsc.noaa.gov/apex/parr/salmonid_vertebrae_height_and_length_measurements/data/page/
Distributor: Northwest Fisheries Science Center (NWFSC) (2015-10-01 - Present)
File Name: Salmonid vertebrae height and length measurements
Description:

Measurements of salmonid vertebrae.

Distribution 2

CC ID: 847606
Start Date: 2018-02-21
End Date: Present
Download URL: https://www.webapps.nwfsc.noaa.gov/apex/parrdata/inventory/tables/table/salmonid_vertebrae_height_and_length_measurements
Distributor: Northwest Fisheries Science Center (NWFSC) (2015-10-01 - Present)
File Name: Salmonid vertebrae height and length measurements
Description:

Measurements of salmonid vertebrae.

URLs

URL 1

CC ID: 847608
URL: https://www.webapps.nwfsc.noaa.gov/apex/parrdata/inventory/datasets/dataset/10923
Name: Vertebrae classification models
URL Type:
Online Resource
File Resource Format: Web site
Description:

NWFSC Dataset Information page. ancient vertebrae measurements

Technical Environment

Description:

Spreadsheet - electronic files

Data Quality

Accuracy:

Low

Quality Control Procedures Employed:

Genetics lab qc, These data were collected and processed in accordance with established protocols and best practices under the direction of the project’s Principal Investigator. Contact the dataset Data Manager for full QA/QC methodology.

Data Management

Have Resources for Management of these Data Been Identified?: Yes
Approximate Percentage of Budget for these Data Devoted to Data Management: 0
Do these Data Comply with the Data Access Directive?: No
Is Access to the Data Limited Based on an Approved Waiver?: No
If Distributor (Data Hosting Service) is Needed, Please Indicate: No
Approximate Delay Between Data Collection and Dissemination: 0 days
If Delay is Longer than Latency of Automated Processing, Indicate Under What Authority Data Access is Delayed:

No Delay

Actual or Planned Long-Term Data Archive Location: NCEI-MD
Approximate Delay Between Data Collection and Archiving: 365
How Will the Data Be Protected from Accidental or Malicious Modification or Deletion Prior to Receipt by the Archive?:

The Northwest Fisheries Science Center facilitates backup and recovery of all data and IT components which are managed by IT Operations through the capture of static (point-in-time) backup data to physical media. Once data is captured to physical media (every 1-3 days), a duplicate is made and routinely (weekly) transported to an offsite archive facility where it is maintained throughout the data's applicable life-cycle.

Lineage

Lineage Statement:

DNA sequencing, modeling.

Child Items

Rubric scores updated every 15m

Rubric Score Type Title
Entity Salmonid vertebrae height and length measurements

Catalog Details

Catalog Item ID: 17790
GUID: gov.noaa.nmfs.inport:17790
Metadata Record Created By: Jeffrey W Cowen
Metadata Record Created: 2013-01-22 18:55+0000
Metadata Record Last Modified By: SysAdmin InPortAdmin
Metadata Record Last Modified: 2019-06-04 13:14+0000
Metadata Record Published: 2019-06-04
Owner Org: NWFSC
Metadata Publication Status: Published Externally
Do Not Publish?: N
Metadata Next Review Date: 2020-06-04