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Close relatives in population samples: Evaluation of the consequences for genetic stock identification

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
Title:Close relatives in population samples: Evaluation of the consequences for genetic stock identification
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:
Type of IDID
DOI10.1111/1755-0998.13131
Web of Science (WoS)000516819700013
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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