Influence of DNA isolation from historical otoliths on nuclear-mitochondrial marker amplification and age determination in an overexploited fish, the common sole (Solea solea L.)
Historical otolith collections are crucial in assessing the evolutionary consequences of natural and anthropogenic changes on the demography and connectivity of commercially important fish species. Hence, it is important to define optimal protocols for purifying DNA from such valuable information so...
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ftunivwagenin:oai:library.wur.nl:wurpubs/379158 2024-02-04T10:00:31+01:00 Influence of DNA isolation from historical otoliths on nuclear-mitochondrial marker amplification and age determination in an overexploited fish, the common sole (Solea solea L.) Cuveliers, E.L. Bolle, L.J. Volckaert, F.A.M. Maes, G.E. 2009 application/pdf https://research.wur.nl/en/publications/influence-of-dna-isolation-from-historical-otoliths-on-nuclear-mi https://doi.org/10.1111/j.1755-0998.2009.02516.x en eng https://edepot.wur.nl/5760 https://research.wur.nl/en/publications/influence-of-dna-isolation-from-historical-otoliths-on-nuclear-mi doi:10.1111/j.1755-0998.2009.02516.x info:eu-repo/semantics/restrictedAccess Wageningen University & Research Molecular Ecology Resources 9 (2009) 3 ISSN: 1755-098X cod gadus-morhua effective population-size fisheries-induced evolution genetic changes maturation reaction norms microsatellite dna new-zealand snapper north-sea old scale samples salmon salmo-salar info:eu-repo/semantics/article Article/Letter to editor info:eu-repo/semantics/publishedVersion 2009 ftunivwagenin https://doi.org/10.1111/j.1755-0998.2009.02516.x 2024-01-10T23:23:33Z Historical otolith collections are crucial in assessing the evolutionary consequences of natural and anthropogenic changes on the demography and connectivity of commercially important fish species. Hence, it is important to define optimal protocols for purifying DNA from such valuable information sources while avoiding any damage to the physical structure of the otolith. Before being able to conclude on the harmlessness of a method, it is important to validate protocols on different kinds of otoliths by testing purification methodologies under standardized conditions. Here we compare the effect of two DNA extraction methods on the success in identifying the age in an overexploited marine fish, the common sole (Solea solea L.). To ensure optimal future population genetic and demographic analyses, we assessed DNA quantity and tested the DNA quality by investigating the amplification success of a mitochondrial and nuclear marker. Our results show that the choice of the DNA extraction method had a significant effect on the success of using these otoliths in age and growth analyses. Standard commercial and published protocols resulted in a severe damaging of the otolith structure, hampering accurate preparation and analyses of the morphological structures of the otoliths. Shortening the lysis time and lowering the EDTA (ethylene diamine tetraacetic acid) and SDS (sodium dodecylsulphate) concentration turned out to be beneficial for the stability of otolith structure, while maintaining an overall high DNA quality measured through polymerase chain reaction amplification success. We therefore recommend that care should be taken when choosing the extraction method for a molecular study on archived samples, in order to enable the maximal use of information embedded in historical material Article in Journal/Newspaper Gadus morhua Salmo salar Wageningen UR (University & Research Centre): Digital Library New Zealand Molecular Ecology Resources 9 3 725 732 |
institution |
Open Polar |
collection |
Wageningen UR (University & Research Centre): Digital Library |
op_collection_id |
ftunivwagenin |
language |
English |
topic |
cod gadus-morhua effective population-size fisheries-induced evolution genetic changes maturation reaction norms microsatellite dna new-zealand snapper north-sea old scale samples salmon salmo-salar |
spellingShingle |
cod gadus-morhua effective population-size fisheries-induced evolution genetic changes maturation reaction norms microsatellite dna new-zealand snapper north-sea old scale samples salmon salmo-salar Cuveliers, E.L. Bolle, L.J. Volckaert, F.A.M. Maes, G.E. Influence of DNA isolation from historical otoliths on nuclear-mitochondrial marker amplification and age determination in an overexploited fish, the common sole (Solea solea L.) |
topic_facet |
cod gadus-morhua effective population-size fisheries-induced evolution genetic changes maturation reaction norms microsatellite dna new-zealand snapper north-sea old scale samples salmon salmo-salar |
description |
Historical otolith collections are crucial in assessing the evolutionary consequences of natural and anthropogenic changes on the demography and connectivity of commercially important fish species. Hence, it is important to define optimal protocols for purifying DNA from such valuable information sources while avoiding any damage to the physical structure of the otolith. Before being able to conclude on the harmlessness of a method, it is important to validate protocols on different kinds of otoliths by testing purification methodologies under standardized conditions. Here we compare the effect of two DNA extraction methods on the success in identifying the age in an overexploited marine fish, the common sole (Solea solea L.). To ensure optimal future population genetic and demographic analyses, we assessed DNA quantity and tested the DNA quality by investigating the amplification success of a mitochondrial and nuclear marker. Our results show that the choice of the DNA extraction method had a significant effect on the success of using these otoliths in age and growth analyses. Standard commercial and published protocols resulted in a severe damaging of the otolith structure, hampering accurate preparation and analyses of the morphological structures of the otoliths. Shortening the lysis time and lowering the EDTA (ethylene diamine tetraacetic acid) and SDS (sodium dodecylsulphate) concentration turned out to be beneficial for the stability of otolith structure, while maintaining an overall high DNA quality measured through polymerase chain reaction amplification success. We therefore recommend that care should be taken when choosing the extraction method for a molecular study on archived samples, in order to enable the maximal use of information embedded in historical material |
format |
Article in Journal/Newspaper |
author |
Cuveliers, E.L. Bolle, L.J. Volckaert, F.A.M. Maes, G.E. |
author_facet |
Cuveliers, E.L. Bolle, L.J. Volckaert, F.A.M. Maes, G.E. |
author_sort |
Cuveliers, E.L. |
title |
Influence of DNA isolation from historical otoliths on nuclear-mitochondrial marker amplification and age determination in an overexploited fish, the common sole (Solea solea L.) |
title_short |
Influence of DNA isolation from historical otoliths on nuclear-mitochondrial marker amplification and age determination in an overexploited fish, the common sole (Solea solea L.) |
title_full |
Influence of DNA isolation from historical otoliths on nuclear-mitochondrial marker amplification and age determination in an overexploited fish, the common sole (Solea solea L.) |
title_fullStr |
Influence of DNA isolation from historical otoliths on nuclear-mitochondrial marker amplification and age determination in an overexploited fish, the common sole (Solea solea L.) |
title_full_unstemmed |
Influence of DNA isolation from historical otoliths on nuclear-mitochondrial marker amplification and age determination in an overexploited fish, the common sole (Solea solea L.) |
title_sort |
influence of dna isolation from historical otoliths on nuclear-mitochondrial marker amplification and age determination in an overexploited fish, the common sole (solea solea l.) |
publishDate |
2009 |
url |
https://research.wur.nl/en/publications/influence-of-dna-isolation-from-historical-otoliths-on-nuclear-mi https://doi.org/10.1111/j.1755-0998.2009.02516.x |
geographic |
New Zealand |
geographic_facet |
New Zealand |
genre |
Gadus morhua Salmo salar |
genre_facet |
Gadus morhua Salmo salar |
op_source |
Molecular Ecology Resources 9 (2009) 3 ISSN: 1755-098X |
op_relation |
https://edepot.wur.nl/5760 https://research.wur.nl/en/publications/influence-of-dna-isolation-from-historical-otoliths-on-nuclear-mi doi:10.1111/j.1755-0998.2009.02516.x |
op_rights |
info:eu-repo/semantics/restrictedAccess Wageningen University & Research |
op_doi |
https://doi.org/10.1111/j.1755-0998.2009.02516.x |
container_title |
Molecular Ecology Resources |
container_volume |
9 |
container_issue |
3 |
container_start_page |
725 |
op_container_end_page |
732 |
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1789965852036038656 |