Comparing RADseq and microsatellites for estimating genetic diversity and relatedness - Implications for brown trout conservation

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http://hdl.handle.net/10138/300622

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Lemopoulos , A , Prokkola , J M , Uusi-Heikkilä , S , Vasemägi , A , Huusko , A , Hyvarinen , P , Koljonen , M-L , Koskiniemi , J & Vainikka , A 2019 , ' Comparing RADseq and microsatellites for estimating genetic diversity and relatedness - Implications for brown trout conservation ' , Ecology and Evolution , vol. 9 , no. 4 , pp. 2106-2120 . https://doi.org/10.1002/ece3.4905

Title: Comparing RADseq and microsatellites for estimating genetic diversity and relatedness - Implications for brown trout conservation
Author: Lemopoulos, Alexandre; Prokkola, Jenni M.; Uusi-Heikkilä, Silva; Vasemägi, Anti; Huusko, Ari; Hyvarinen, Pekka; Koljonen, Marja-Liisa; Koskiniemi, Jarmo; Vainikka, Anssi
Contributor: University of Helsinki, Department of Agricultural Sciences
Date: 2019-02
Language: eng
Number of pages: 15
Belongs to series: Ecology and Evolution
ISSN: 2045-7758
URI: http://hdl.handle.net/10138/300622
Abstract: The conservation and management of endangered species requires information on their genetic diversity, relatedness and population structure. The main genetic markers applied for these questions are microsatellites and single nucleotide polymorphisms (SNPs), the latter of which remain the more resource demanding approach in most cases. Here, we compare the performance of two approaches, SNPs obtained by restriction-site-associated DNA sequencing (RADseq) and 16 DNA microsatellite loci, for estimating genetic diversity, relatedness and genetic differentiation of three, small, geographically close wild brown trout (Salmo trutta) populations and a regionally used hatchery strain. The genetic differentiation, quantified as F-ST, was similar when measured using 16 microsatellites and 4,876 SNPs. Based on both marker types, each brown trout population represented a distinct gene pool with a low level of interbreeding. Analysis of SNPs identified half- and full-siblings with a higher probability than the analysis based on microsatellites, and SNPs outperformed microsatellites in estimating individual-level multilocus heterozygosity. Overall, the results indicated that moderately polymorphic microsatellites and SNPs from RADseq agreed on estimates of population genetic structure in moderately diverged, small populations, but RADseq outperformed microsatellites for applications that required individual-level genotype information, such as quantifying relatedness and individual-level heterozygosity. The results can be applied to other small populations with low or moderate levels of genetic diversity.
Subject: ddRADseq
fisheries
population genetics
relatedness
salmonids
EFFECTIVE POPULATION-SIZE
SALMON SALMO-SALAR
HETEROZYGOSITY-FITNESS CORRELATIONS
SINGLE NUCLEOTIDE POLYMORPHISM
CROSS-SPECIES AMPLIFICATION
ATLANTIC SALMON
LINKAGE DISEQUILIBRIUM
R-PACKAGE
HABITAT FRAGMENTATION
INBREEDING DEPRESSION
1181 Ecology, evolutionary biology
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