Östergren, Johan and Palm, Stefan and Gilbey, John and Dannewitz, Johan
(2020).
Close relatives in population samples: Evaluation of the consequences for genetic stock identification.
Molecular Ecology Resources. 20
, 498-510
[Journal article]
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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.
Authors/Creators: | Östergren, Johan and Palm, Stefan and Gilbey, John and Dannewitz, Johan | ||||||
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Title: | Close relatives in population samples: Evaluation of the consequences for genetic stock identification | ||||||
Series Name/Journal: | Molecular Ecology Resources | ||||||
Year of publishing : | 2020 | ||||||
Volume: | 20 | ||||||
Page range: | 498-510 | ||||||
Number of Pages: | 13 | ||||||
Publisher: | Wiley | ||||||
ISSN: | 1755-098X | ||||||
Language: | English | ||||||
Publication Type: | Journal article | ||||||
Article category: | Scientific peer reviewed | ||||||
Version: | Published version | ||||||
Copyright: | Creative Commons: Attribution 4.0 | ||||||
Full Text Status: | Public | ||||||
Subjects: | (A) Swedish standard research categories 2011 > 1 Natural sciences > 106 Biological Sciences (Medical to be 3 and Agricultural to be 4) > Ecology (A) Swedish standard research categories 2011 > 4 Agricultural Sciences > 401 Agricultural, Forestry and Fisheries > Fish and Aquacultural Science (A) Swedish standard research categories 2011 > 1 Natural sciences > 106 Biological Sciences (Medical to be 3 and Agricultural to be 4) > Genetics (medical genetics to be 30107 and agricultural genetics to be 40402) | ||||||
Keywords: | Colony, family sampling, genetic differentiation, individual assignment, mixed stock analysis, Salmo salar | ||||||
URN:NBN: | urn:nbn:se:slu:epsilon-p-105091 | ||||||
Permanent URL: | http://urn.kb.se/resolve?urn=urn:nbn:se:slu:epsilon-p-105091 | ||||||
Additional ID: |
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ID Code: | 16839 | ||||||
Faculty: | NJ - Fakulteten för naturresurser och jordbruksvetenskap | ||||||
Department: | (NL, NJ) > Department of Aquatic Resources | ||||||
Deposited By: | SLUpub Connector | ||||||
Deposited On: | 04 May 2020 12:00 | ||||||
Metadata Last Modified: | 21 Aug 2020 00:08 |
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