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.)

Abstract

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.

Genetic structure of Patagonian toothfish populations from otolith DNA

“…Indeed, otoliths represent a limited source of DNA since only two otoliths per fish can be collected; otolith collections are very valuable. According to Cuveliers et al (2009), a trade-off must be found between DNA quality and otolith preservation. Contrasting conclusions were given for several species concerning the effect of DNA extraction on ageing success (e.g.…”

“…Contrasting conclusions were given for several species concerning the effect of DNA extraction on ageing success (e.g. Cuveliers et al 2009). It underlines the importance of minimizing the damage to the otolith, depending on the method used and different factors such as incubating time or concentration of EDTA or SDS.…”

“…While otoliths are acellular and do not contain DNA, several studies have highlighted the possibility of extracting DNA from tissue remaining on the surface of archived otoliths, for example in Gadus morhua (Poulsen et al 2006). Even if the DNA from archived material is often highly degraded, otoliths appear to be effective for genetic studies and if non-destructive protocols for DNA extraction are used, the same otoliths can be used for ageing and/or microchemistry experiments (Cuveliers et al 2009). Use of the large collections of toothfish otoliths stored at a number of Southern Ocean fisheries research institutes provides the potential for more definitive analysis of spatial and temporal population genetics studies.…”

The use of archived tags in retrospective genetic analysis of fish

“…However, recent studies have shown that a number of different extraction methods can provide consistent yields of DNA with sufficient quality for amplification of various genetic markers (see Cuveliers et al . and Therkildsen et al . ).…”

“…Based on previous studies, it is known that the DNA on fish scales and otoliths is only available in low quantities and that it can be highly degraded (Hutchinson et al 1999;Nielsen et al 1999). However, recent studies have shown that a number of different extraction methods can provide consistent yields of DNA with sufficient quality for amplification of various genetic markers (see Cuveliers et al 2009 andTherkildsen et al 2010). Furthermore, it has been demonstrated that the DNA from historical otoliths can also be used for medium-and high-throughput SNP genotyping (Poulsen et al 2011;Therkildsen et al 2013).…”