title: TaqMan DNA technology confirms likely overestimation 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.
abstract: Recent substantial declines in northeastern Atlantic cod stocks necessitate improved biological knowledge and the development of techniques to complement standard stock assessment methods (which largely depend on accurate commercial catch data). In 2003, an ichthyoplankton survey was undertaken in the Irish Sea and subsamples of 'cod-like' eggs were analysed using a TaqMan multiplex, PCR (polymerase chain reaction) assay (with specific probes for cod, haddock and whiting). The TaqMan method was readily applied to the large number of samples (n = 2770) generated during the survey and when combined with a manual DNA extraction protocol had a low failure rate of 6%. Of the early stage 'cod-like' eggs (1.2-1.75 mm diameter) positively identified: 34% were cod, 8% haddock and 58% whiting. As previous stock estimates based on egg surveys for Irish Sea cod assumed that the majority of 'cod-like' eggs were from cod, the TaqMan results confirm that there was probably substantial contamination by eggs of whiting and haddock that would have inflated estimates of the stock biomass.
authors.affiliation: The Centre for Environment, Fisheries and Aquaculture Science, Pakefield Road, Lowestoft, Suffolk, United Kingdom, NR33 OHT. c.j.fox@cefas.co.uk
authors.forename: C J
authors.initials: CJ
authors.lastname: Fox
authors.forename: M I
authors.initials: MI
authors.lastname: Taylor
authors.forename: R
authors.initials: R
authors.lastname: Pereyra
authors.forename: M I
authors.initials: MI
authors.lastname: Villasana
authors.forename: C
authors.initials: C
authors.lastname: Rico
mesh_terms: D000818:Animals; D001267:Atlantic Ocean; D017931:DNA Primers; D005398:Fisheries / Q000379:methods*; D005399:Fishes / Q000235:genetics*; D005456:Fluorescent Dyes / Q000378:metabolism; D010063:Ovum / Q000378:metabolism*; D016133:Polymerase Chain Reaction / Q000379:methods*; D011156:Population Density; D012107:Research Design; D013045:Species Specificity; D019914:Taq Polymerase / Q000378:metabolism
chemical_list: D017931:DNA Primers; D005456:Fluorescent Dyes; D019914:Taq Polymerase