Vertebrae classification models - Validating classification models that use morphometrics to identify ancient salmonid (Oncorhynchus spp.) vertebrae to species
Data Set (DS) | Northwest Fisheries Science Center (NWFSC)GUID: gov.noaa.nmfs.inport:17790 | Updated: August 9, 2022 | Published / External
Summary
Short Citation
Northwest Fisheries Science Center, 2024: 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.
Full Citation Examples
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.
Distribution Information
-
Measurements of salmonid vertebrae.
-
Measurements of salmonid vertebrae.
NA
Child Items
Type | Title |
---|---|
Entity | Salmonid vertebrae height and length measurements |
Contact Information
Point of Contact
Jeff Jorgensen
Jeff.Jorgensen@noaa.gov
206-860-3286
Metadata Contact
Northwest Fisheries Science Center (NWFSC)
nmfs.nwfsc.metadata@noaa.gov
206-860-3200
NWFSC Home
Extents
-122.3062° W,
-122.3062° E,
47.6449° N,
47.6449° S
NWFSC Montlake: Montlake
2010-06-01 - Present
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 |
Instrument Keywords
Thesaurus | Keyword |
---|---|
UNCONTROLLED | |
None | Quantitative PCR Machine |
Physical Location
Organization: | Northwest Fisheries Science Center |
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City: | Seattle |
State/Province: | WA |
Country: | USA |
Data Set Information
Data Set Scope Code: | Data Set |
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Data Set Type: | Spreadsheet |
Data Presentation Form: | Table (digital) |
Support Roles
Data Steward
Date Effective From: | 2015-10-01 |
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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
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
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
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
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
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
Time Frame Type: | Continuing |
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Start: | 2010-06-01 |
Extent Group 2
Extent Group 2 / Geographic Area 1
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
Time Frame Type: | Continuing |
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Start: | 2010-06-01 |
Access Information
Security Class: | Unclassified |
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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
Start Date: | 2018-02-21 |
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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
Start Date: | 2018-02-21 |
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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
URL: | https://www.webapps.nwfsc.noaa.gov/apex/parrdata/inventory/datasets/dataset/10923 |
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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 |
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Data Quality
Accuracy: |
Low |
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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 |
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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. |
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Child Items
Rubric scores updated every 15m
Type | Title | |
---|---|---|
Entity | Salmonid vertebrae height and length measurements |
Catalog Details
Catalog Item ID: | 17790 |
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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: | 2022-08-09 17:11+0000 |
Metadata Record Published: | 2019-06-04 |
Owner Org: | NWFSC |
Metadata Publication Status: | Published Externally |
Do Not Publish?: | N |
Metadata Last Review Date: | 2019-06-04 |
Metadata Review Frequency: | 1 Year |
Metadata Next Review Date: | 2020-06-04 |