Comparing RADseq and microsatellites for estimating genetic diversity and relatedness - Implications for brown trout conservation
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 resour...
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ftunivhelsihelda:oai:helda.helsinki.fi:10138/300622 2024-01-07T09:42:16+01:00 Comparing RADseq and microsatellites for estimating genetic diversity and relatedness - Implications for brown trout conservation Lemopoulos, Alexandre Prokkola, Jenni M. Uusi-Heikkilä, Silva Vasemägi, Anti Huusko, Ari Hyvarinen, Pekka Koljonen, Marja-Liisa Koskiniemi, Jarmo Vainikka, Anssi Department of Agricultural Sciences 2019-04-02T09:34:01Z 15 application/pdf http://hdl.handle.net/10138/300622 eng eng Wiley 10.1002/ece3.4905 Suomen Akatemia, Grant/Award Number: 266321 and 286261; Natural Resources Institute Finland (Luke); Finnish Cultural Foundation 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 85062097657 60da1e68-4602-4f35-82f7-11886709ba77 http://hdl.handle.net/10138/300622 000461114900044 cc_by openAccess info:eu-repo/semantics/openAccess 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 Article publishedVersion 2019 ftunivhelsihelda 2023-12-14T00:15:18Z 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. Peer reviewed Article in Journal/Newspaper Atlantic salmon Salmo salar HELDA – University of Helsinki Open Repository Ecology and Evolution 9 4 2106 2120 |
institution |
Open Polar |
collection |
HELDA – University of Helsinki Open Repository |
op_collection_id |
ftunivhelsihelda |
language |
English |
topic |
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 |
spellingShingle |
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 Lemopoulos, Alexandre Prokkola, Jenni M. Uusi-Heikkilä, Silva Vasemägi, Anti Huusko, Ari Hyvarinen, Pekka Koljonen, Marja-Liisa Koskiniemi, Jarmo Vainikka, Anssi Comparing RADseq and microsatellites for estimating genetic diversity and relatedness - Implications for brown trout conservation |
topic_facet |
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 |
description |
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. Peer reviewed |
author2 |
Department of Agricultural Sciences |
format |
Article in Journal/Newspaper |
author |
Lemopoulos, Alexandre Prokkola, Jenni M. Uusi-Heikkilä, Silva Vasemägi, Anti Huusko, Ari Hyvarinen, Pekka Koljonen, Marja-Liisa Koskiniemi, Jarmo Vainikka, Anssi |
author_facet |
Lemopoulos, Alexandre Prokkola, Jenni M. Uusi-Heikkilä, Silva Vasemägi, Anti Huusko, Ari Hyvarinen, Pekka Koljonen, Marja-Liisa Koskiniemi, Jarmo Vainikka, Anssi |
author_sort |
Lemopoulos, Alexandre |
title |
Comparing RADseq and microsatellites for estimating genetic diversity and relatedness - Implications for brown trout conservation |
title_short |
Comparing RADseq and microsatellites for estimating genetic diversity and relatedness - Implications for brown trout conservation |
title_full |
Comparing RADseq and microsatellites for estimating genetic diversity and relatedness - Implications for brown trout conservation |
title_fullStr |
Comparing RADseq and microsatellites for estimating genetic diversity and relatedness - Implications for brown trout conservation |
title_full_unstemmed |
Comparing RADseq and microsatellites for estimating genetic diversity and relatedness - Implications for brown trout conservation |
title_sort |
comparing radseq and microsatellites for estimating genetic diversity and relatedness - implications for brown trout conservation |
publisher |
Wiley |
publishDate |
2019 |
url |
http://hdl.handle.net/10138/300622 |
genre |
Atlantic salmon Salmo salar |
genre_facet |
Atlantic salmon Salmo salar |
op_relation |
10.1002/ece3.4905 Suomen Akatemia, Grant/Award Number: 266321 and 286261; Natural Resources Institute Finland (Luke); Finnish Cultural Foundation 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 85062097657 60da1e68-4602-4f35-82f7-11886709ba77 http://hdl.handle.net/10138/300622 000461114900044 |
op_rights |
cc_by openAccess info:eu-repo/semantics/openAccess |
container_title |
Ecology and Evolution |
container_volume |
9 |
container_issue |
4 |
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2106 |
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2120 |
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1787423212374589440 |