Advantages and Challenges of Genetic Stock Identification in Fish Stocks with Low Genetic Resolution
Abstract Genetic stock identification (GSI) is widely applied to mixed‐stock fisheries for many commercially exploited species. However, the accuracy of GSI depends on the level of differentiation among stocks. To evaluate our ability to estimate contributions in mixed‐stock fisheries of Pink Salmon...
Published in: | Transactions of the American Fisheries Society |
---|---|
Main Authors: | , , , , |
Format: | Article in Journal/Newspaper |
Language: | English |
Published: |
Wiley
2014
|
Subjects: | |
Online Access: | http://dx.doi.org/10.1080/00028487.2013.855258 https://afspubs.onlinelibrary.wiley.com/doi/pdf/10.1080/00028487.2013.855258 |
id |
crwiley:10.1080/00028487.2013.855258 |
---|---|
record_format |
openpolar |
spelling |
crwiley:10.1080/00028487.2013.855258 2024-06-23T07:55:56+00:00 Advantages and Challenges of Genetic Stock Identification in Fish Stocks with Low Genetic Resolution Araujo, H. Andres Candy, John R. Beacham, Terry D. White, Bruce Wallace, Colin 2014 http://dx.doi.org/10.1080/00028487.2013.855258 https://afspubs.onlinelibrary.wiley.com/doi/pdf/10.1080/00028487.2013.855258 en eng Wiley http://onlinelibrary.wiley.com/termsAndConditions#vor Transactions of the American Fisheries Society volume 143, issue 2, page 479-488 ISSN 0002-8487 1548-8659 journal-article 2014 crwiley https://doi.org/10.1080/00028487.2013.855258 2024-05-31T08:10:50Z Abstract Genetic stock identification (GSI) is widely applied to mixed‐stock fisheries for many commercially exploited species. However, the accuracy of GSI depends on the level of differentiation among stocks. To evaluate our ability to estimate contributions in mixed‐stock fisheries of Pink Salmon Oncorhynchus gorbuscha , a species with limited population genetic differentiation, we analyzed 46 odd‐year Pink Salmon stocks belonging to a baseline of genotypes from southern British Columbia, the Fraser River, and Puget Sound. Samples were obtained without replacement from the baseline (known mixtures), and 16 microsatellite loci were used for analysis with two software packages (cBayes and ONCOR) to evaluate the accuracy of using this marker set to identify the correct region, subregion, and spawning site. The correct subregion was identified for Pink Salmon from southern British Columbia and Puget Sound. However, incorrect assignments were observed for the Fraser River subregions and the stock‐specific estimates. In addition, we used simulated baselines with the average genetic differentiation index F ST ranging from 0.0007 to 0.04 (the range of F ST values observed in Pink Salmon stocks) to identify biases in the GSI software programs. The results suggested that stock‐level genetic identification is subject to significant biases (>15%) when the average F ST among baseline stocks is less than 0.01. ONCOR was more accurate than cBayes in identifying the correct stock at small mean F ST values (<0.01), but there was no significant difference between the software packages at larger F ST values. Our results can help to improve GSI methods and to identify their limitations, especially for stocks with low genetic separation. Article in Journal/Newspaper Oncorhynchus gorbuscha Pink salmon Wiley Online Library Fraser River ENVELOPE(-62.243,-62.243,56.619,56.619) Transactions of the American Fisheries Society 143 2 479 488 |
institution |
Open Polar |
collection |
Wiley Online Library |
op_collection_id |
crwiley |
language |
English |
description |
Abstract Genetic stock identification (GSI) is widely applied to mixed‐stock fisheries for many commercially exploited species. However, the accuracy of GSI depends on the level of differentiation among stocks. To evaluate our ability to estimate contributions in mixed‐stock fisheries of Pink Salmon Oncorhynchus gorbuscha , a species with limited population genetic differentiation, we analyzed 46 odd‐year Pink Salmon stocks belonging to a baseline of genotypes from southern British Columbia, the Fraser River, and Puget Sound. Samples were obtained without replacement from the baseline (known mixtures), and 16 microsatellite loci were used for analysis with two software packages (cBayes and ONCOR) to evaluate the accuracy of using this marker set to identify the correct region, subregion, and spawning site. The correct subregion was identified for Pink Salmon from southern British Columbia and Puget Sound. However, incorrect assignments were observed for the Fraser River subregions and the stock‐specific estimates. In addition, we used simulated baselines with the average genetic differentiation index F ST ranging from 0.0007 to 0.04 (the range of F ST values observed in Pink Salmon stocks) to identify biases in the GSI software programs. The results suggested that stock‐level genetic identification is subject to significant biases (>15%) when the average F ST among baseline stocks is less than 0.01. ONCOR was more accurate than cBayes in identifying the correct stock at small mean F ST values (<0.01), but there was no significant difference between the software packages at larger F ST values. Our results can help to improve GSI methods and to identify their limitations, especially for stocks with low genetic separation. |
format |
Article in Journal/Newspaper |
author |
Araujo, H. Andres Candy, John R. Beacham, Terry D. White, Bruce Wallace, Colin |
spellingShingle |
Araujo, H. Andres Candy, John R. Beacham, Terry D. White, Bruce Wallace, Colin Advantages and Challenges of Genetic Stock Identification in Fish Stocks with Low Genetic Resolution |
author_facet |
Araujo, H. Andres Candy, John R. Beacham, Terry D. White, Bruce Wallace, Colin |
author_sort |
Araujo, H. Andres |
title |
Advantages and Challenges of Genetic Stock Identification in Fish Stocks with Low Genetic Resolution |
title_short |
Advantages and Challenges of Genetic Stock Identification in Fish Stocks with Low Genetic Resolution |
title_full |
Advantages and Challenges of Genetic Stock Identification in Fish Stocks with Low Genetic Resolution |
title_fullStr |
Advantages and Challenges of Genetic Stock Identification in Fish Stocks with Low Genetic Resolution |
title_full_unstemmed |
Advantages and Challenges of Genetic Stock Identification in Fish Stocks with Low Genetic Resolution |
title_sort |
advantages and challenges of genetic stock identification in fish stocks with low genetic resolution |
publisher |
Wiley |
publishDate |
2014 |
url |
http://dx.doi.org/10.1080/00028487.2013.855258 https://afspubs.onlinelibrary.wiley.com/doi/pdf/10.1080/00028487.2013.855258 |
long_lat |
ENVELOPE(-62.243,-62.243,56.619,56.619) |
geographic |
Fraser River |
geographic_facet |
Fraser River |
genre |
Oncorhynchus gorbuscha Pink salmon |
genre_facet |
Oncorhynchus gorbuscha Pink salmon |
op_source |
Transactions of the American Fisheries Society volume 143, issue 2, page 479-488 ISSN 0002-8487 1548-8659 |
op_rights |
http://onlinelibrary.wiley.com/termsAndConditions#vor |
op_doi |
https://doi.org/10.1080/00028487.2013.855258 |
container_title |
Transactions of the American Fisheries Society |
container_volume |
143 |
container_issue |
2 |
container_start_page |
479 |
op_container_end_page |
488 |
_version_ |
1802648749520977920 |