Publication Abstract

TaqMan DNA technology confirms likely previous over-estimation of cod (Gadus morhua L.) egg abundance in the Irish Sea: implications for the assessment of the cod stock and mapping of spawning areas using egg based methods

TaqMan DNA technology confirms likely previous over-estimation of cod (Gadus morhua L.) egg abundance in the Irish Sea: implications for the assessment of the cod stock and mapping of spawning areas using egg based methods

C.J. Fox, M.I. Taylor, R. Pereya, I. Rico and C. Rico

The recent substantial declines in North-eastern Atlantic cod stocks necessitate the development of new techniques to complement fisheries based stock assessment methods. Surveys of the distribution of fish eggs (ichthyoplankton) are one such fisheries independent method. Firstly, results from such surveys can be used to delimit spawning areas. Such information is vital for the design of effective closed fishing zones. Secondly, the results can be used to produce fisheries independent estimates of stock biomass by annual and daily egg production methods. Thirdly, the results can be used to initialise coupled-physical-biological models that aim to increase our understanding of recruitment dynamics. All these applications rely on our ability to identify early stage fish eggs to the species level. The classical identification technique relies on egg size and appearance (presence/absence of oil globules and other distinguishing features) but this method cannot discriminate between early stage eggs of species such as cod and haddock. In 2003, an ichthyoplankton survey was undertaken in the Irish Sea and sub-samples of 'cod-like' eggs were analysed using a TaqMan multiplex, PCR assay (with specific probes for cod, haddock and whiting) following robotic or manual extraction of DNA. The TaqMan was able to positively identify 85% of the 2,770 eggs collected for genetic analysis. Of the remaining eggs, 5% were identified as being from species other than cod, haddock or whiting for which we do not currently have specific probes. The majority of failed reactions were caused by problems with the robotic DNA extraction method initially employed as opposed to the TaqMan-PCR itself (27% failure rate). Once the robotic extraction was replaced by a manual protocol, the failure rate fell to 6%. The TaqMan method was readily applied to the large numbers of samples generated during the ichthyoplankton survey and the accuracy and reliability of this molecular identification method substantially increases the confidence that can be placed in spawning distribution maps and stock assessments of cod and haddock based on ichthyoplankton surveys. Of the eggs positively identified 32% were cod, 6% haddock and 62% whiting. Previous stock estimates based on the Annual Egg Production Method for Irish Sea cod were undertaken assuming that the majority of eggs between 1.2 and 1.75 mm diameter and lacking oil globules were indeed from cod. The TaqMan results confirm that there was likely substantial contamination of this size fraction of eggs by those of whiting and haddock. The application of the TaqMan method therefore partly explains the high biomass estimates for cod previously obtained for this region using the Annual Egg Production Method for stock assessment.

Reference:

C.J. Fox, M.I. Taylor, R. Pereya, I. Rico and C. Rico (2005). TaqMan DNA technology confirms likely previous over-estimation of cod (Gadus morhua L.) egg abundance in the Irish Sea: implications for the assessment of the cod stock and mapping of spawning areas using egg based methods. Molecular Ecology, 14: 879-884

C.J. Fox*, M.I. Taylor, R. Pereya, I. Rico and C. Rico

Molecular Ecology, 14: 879-884