Close relatives in population samples: Evaluation of the consequences for genetic stock identification
Abstract Determining the origin of individuals in mixed population samples is key in many ecological, conservation and management contexts. Genetic data can be analyzed using genetic stock identification (GSI), where the origin of single individuals is determined using Individual Assignment (IA) and...
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crwiley:10.1111/1755-0998.13131 2024-06-02T08:03:41+00:00 Close relatives in population samples: Evaluation of the consequences for genetic stock identification Östergren, Johan Palm, Stefan Gilbey, John Dannewitz, Johan Svenska Forskningsrådet Formas Havs- och Vattenmyndigheten 2020 http://dx.doi.org/10.1111/1755-0998.13131 https://api.wiley.com/onlinelibrary/tdm/v1/articles/10.1111%2F1755-0998.13131 https://onlinelibrary.wiley.com/doi/pdf/10.1111/1755-0998.13131 https://onlinelibrary.wiley.com/doi/full-xml/10.1111/1755-0998.13131 en eng Wiley http://creativecommons.org/licenses/by/4.0/ Molecular Ecology Resources volume 20, issue 2, page 498-510 ISSN 1755-098X 1755-0998 journal-article 2020 crwiley https://doi.org/10.1111/1755-0998.13131 2024-05-03T10:55:46Z Abstract Determining the origin of individuals in mixed population samples is key in many ecological, conservation and management contexts. Genetic data can be analyzed using genetic stock identification (GSI), where the origin of single individuals is determined using Individual Assignment (IA) and population proportions are estimated with Mixed Stock Analysis (MSA). In such analyses, allele frequencies in a reference baseline are required. Unknown individuals or mixture proportions are assigned to source populations based on the likelihood that their multilocus genotypes occur in a particular baseline sample. Representative sampling of populations included in a baseline is important when designing and performing GSI. Here, we investigate the effects of family sampling on GSI, using both simulated and empirical genotypes for Atlantic salmon ( Salmo salar ). We show that nonrepresentative sampling leading to inclusion of close relatives in a reference baseline may introduce bias in estimated proportions of contributing populations in a mixed sample, and increases the amount of incorrectly assigned individual fish. Simulated data further show that the induced bias increases with increasing family structure, but that it can be partly mitigated by increased baseline population sample sizes. Results from standard accuracy tests of GSI (using only a reference baseline and/or self‐assignment) gave a false and elevated indication of the baseline power and accuracy to identify stock proportions and individuals. These findings suggest that family structure in baseline population samples should be quantified and its consequences evaluated, before carrying out GSI. Article in Journal/Newspaper Atlantic salmon Salmo salar Wiley Online Library Molecular Ecology Resources 20 2 498 510 |
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English |
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Abstract Determining the origin of individuals in mixed population samples is key in many ecological, conservation and management contexts. Genetic data can be analyzed using genetic stock identification (GSI), where the origin of single individuals is determined using Individual Assignment (IA) and population proportions are estimated with Mixed Stock Analysis (MSA). In such analyses, allele frequencies in a reference baseline are required. Unknown individuals or mixture proportions are assigned to source populations based on the likelihood that their multilocus genotypes occur in a particular baseline sample. Representative sampling of populations included in a baseline is important when designing and performing GSI. Here, we investigate the effects of family sampling on GSI, using both simulated and empirical genotypes for Atlantic salmon ( Salmo salar ). We show that nonrepresentative sampling leading to inclusion of close relatives in a reference baseline may introduce bias in estimated proportions of contributing populations in a mixed sample, and increases the amount of incorrectly assigned individual fish. Simulated data further show that the induced bias increases with increasing family structure, but that it can be partly mitigated by increased baseline population sample sizes. Results from standard accuracy tests of GSI (using only a reference baseline and/or self‐assignment) gave a false and elevated indication of the baseline power and accuracy to identify stock proportions and individuals. These findings suggest that family structure in baseline population samples should be quantified and its consequences evaluated, before carrying out GSI. |
author2 |
Svenska Forskningsrådet Formas Havs- och Vattenmyndigheten |
format |
Article in Journal/Newspaper |
author |
Östergren, Johan Palm, Stefan Gilbey, John Dannewitz, Johan |
spellingShingle |
Östergren, Johan Palm, Stefan Gilbey, John Dannewitz, Johan Close relatives in population samples: Evaluation of the consequences for genetic stock identification |
author_facet |
Östergren, Johan Palm, Stefan Gilbey, John Dannewitz, Johan |
author_sort |
Östergren, Johan |
title |
Close relatives in population samples: Evaluation of the consequences for genetic stock identification |
title_short |
Close relatives in population samples: Evaluation of the consequences for genetic stock identification |
title_full |
Close relatives in population samples: Evaluation of the consequences for genetic stock identification |
title_fullStr |
Close relatives in population samples: Evaluation of the consequences for genetic stock identification |
title_full_unstemmed |
Close relatives in population samples: Evaluation of the consequences for genetic stock identification |
title_sort |
close relatives in population samples: evaluation of the consequences for genetic stock identification |
publisher |
Wiley |
publishDate |
2020 |
url |
http://dx.doi.org/10.1111/1755-0998.13131 https://api.wiley.com/onlinelibrary/tdm/v1/articles/10.1111%2F1755-0998.13131 https://onlinelibrary.wiley.com/doi/pdf/10.1111/1755-0998.13131 https://onlinelibrary.wiley.com/doi/full-xml/10.1111/1755-0998.13131 |
genre |
Atlantic salmon Salmo salar |
genre_facet |
Atlantic salmon Salmo salar |
op_source |
Molecular Ecology Resources volume 20, issue 2, page 498-510 ISSN 1755-098X 1755-0998 |
op_rights |
http://creativecommons.org/licenses/by/4.0/ |
op_doi |
https://doi.org/10.1111/1755-0998.13131 |
container_title |
Molecular Ecology Resources |
container_volume |
20 |
container_issue |
2 |
container_start_page |
498 |
op_container_end_page |
510 |
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1800748291352166400 |