In many marine fish species, genetic population structure is typically weak because populations are large, evolutionarily young and have a high potential for gene flow. We tested whether genetic markers influenced by natural selection are more efficient than the presumed neutral genetic markers to detect population structure in Atlantic herring (Clupea harengus), a migratory pelagic species with large effective population sizes. We compared the spatial and temporal patterns of divergence and statistical power of three traditional genetic marker types, microsatellites, allozymes and mitochondrial DNA, with one microsatellite locus, Cpa112, previously shown to be influenced by divergent selection associated with salinity, and one locus located in the major histocompatibility complex class IIA (MHC-IIA) gene, using the same individuals across analyses. Samples were collected in 2002 and 2003 at two locations in the North Sea, one location in the Skagerrak and one location in the low-saline Baltic Sea. Levels of divergence for putatively neutral markers were generally low, with the exception of single outlier locus/sample combinations; microsatellites were the most statistically powerful markers under neutral expectations. We found no evidence of selection acting on the MHC locus. Cpa112, however, was highly divergent in the Baltic samples. Simulations addressing the statistical power for detecting population divergence showed that when using Cpa112 alone, compared with using eight presumed neutral microsatellite loci, sample sizes could be reduced by up to a tenth while still retaining high statistical power. Our results show that the loci influenced by selection can serve as powerful markers for detecting population structure in high gene-flow marine fish species.

An experimental study was performed to disentangle parental and environmental effects on the growth of Atlantic cod Gadus morhua larvae and juveniles. Eggs were collected during the spawning season from spawning pairs (families) kept separately in specially designed spawning compartments. Newly hatched larvae were released simultaneously into two mesocosms of 2,500 and 4,400 m(3). Larval growth was monitored by sampling over a 10 week period, after which juveniles were transferred to on-growing tanks, where they were tagged and kept for up to 2 years. Maternal origin was determined by individual microsatellite genotyping of the larvae (n = 3949, 24 families) and juveniles (n = 600). The results showed significant positive correlations between egg size and larval size during the whole mesocosm period. Correlations, however, weakened with time and were no longer significant at the first tank-rearing sampling at an age of 9 months. Significant family-specific differences in growth were observed. The coefficient of variation (c.v.) was calculated in order to examine variation in standard length of larvae during the mesocosm period. Inter-family c.v. was on average 69% of intra-family c.v. Differences in zooplankton densities between the two mesocosms were reflected in larval growth, condition factor and c.v. Low food abundance appeared to reduce c.v. and favour growth of larvae that showed relatively slow growth at high food abundance. It is suggested that genetically determined variation in growth potential is maintained by environmental variability.

We analysed cytochrome oxidase I (COI) barcodes for 35 putative fish species collected in the Scotia Sea, and compared the resultant molecular data with field-based morphological identifications, and additional sequence data obtained from GenBank and the Barcode of Life Data System (BOLD). There was high congruence between morphological and molecular classification, and COI provided effective species-level discrimination for nearly all putative species. No effect of geographic sampling was observed for COI sequence variation. For two families, including the Liparidae and Zoarcidae, for which morphological field identification was unable to resolve taxonomy, DNA barcoding revealed significant species-level divergence. However, the dataset lacked sufficient sensitivity for resolving species within the Bathydraco and Artedidraco genera. Analysis of cytochrome b for these two genera also failed to resolve taxonomic identity. The data are discussed in relation to emergent priorities for additional taxonomic studies. We emphasize the utility of DNA barcoding in providing a valuable taxonomic framework for fundamental population studies through assigning life history stages or other morphologically ambiguous samples to parental species.

Studies of the pantophysin (Pan I*) locus in Atlantic cod Gadus morhua and other marine gadoids indicate that the locus is under positive selection; in Atlantic cod, genotypic variation at this locus has been linked to differences in growth. Here, we present preliminary data comparing the growth and condition of different Atlantic cod Pan I* genotypes within families held under seminatural mesocosm conditions. Larvae from three full-sibling families carrying Pan I*bb or Pan I*ab genotypes were reared for 10 weeks in two mesocosms. Multivariate analysis of variance indicated that larvae carrying the Pan I*ab genotype exhibited significantly higher standard length, dry weight, and RNA: DNA ratio (condition factor) than did larvae that carried the Pan I*bb genotype, potentially indicating selection. The influence of linked loci cannot be excluded; indeed, the absence of a significant correlation between genotype and growth in one family may substantiate this. The lack of differences in survival among genotypes indicates that moderate selective effects are acting primarily through size-specific mortality and fecundity. The proposed putative fitness effects, together with documented marked geographic differentiation in the wild, have implications for Atlantic cod population structure, effective migration rates, recruitment, and local adaptation, which are of particular relevance in a species threatened by continuing exploitation and rising sea temperatures.

Nonamplified (null) alleles are a common feature of microsatellite genotyping and can bias estimates of allele and genotype frequencies, thereby hindering population genetic analyses. The frequency of microsatellite null alleles in diploid populations can be estimated for populations that are in Hardy-Weinberg equilibrium. However, many microsatellite data sets are from nonequilibrium populations, often with known inbreeding coefficients (F) or fixation indices (F-IS or F-ST). Here, we propose a novel null allele estimator that can be used to estimate the null allele frequency and adjust visible allele frequencies in populations for which independent estimates of F, F-IS or F-ST are available. The algorithm is currently available as an Excel macro that can be downloaded at no cost from http://www.microchecker.hull.ac.uk/ and will be incorporated into the software MICRO-CHECKER.

Using samples of Atlantic cod Cadus morhua L. from the North Sea, and previously published genetic data from the Irish and Celtic Seas, Iceland, and Norwegian fjord and offshore populations, we describe striking macro- and micro-geographic patterns in pantophysin (PanI) allele frequencies. The relatively abrupt discontinuity in PanI allele frequency distribution at 2 different locations is not congruent with standard patterns of isolation by distance and could arise from population admixtures, historical or contemporary natural selection, behavioural segregation or a combination of these factors. Here, we examined the relationships between the distributions of PanI alleles and temperature, salinity and depth. In the northeast Atlantic, temperature was highly correlated with PanI allele frequency, even when the effect of geographic distance was removed. In the Norwegian fjords, partial Mantel tests indicated that temperature, salinity and depth all had a significant effect on PanI allele frequency in juvenile fish. However, a sample from the brackish waters of the eastern Baltic Sea suggested that salinity may be linked to Pan I allele frequency distribution and that the relationship with temperature was weaker in areas of low salinity. Strong correlations between Pan I allele frequencies and key environmental variables, together with evidence from the available literature, suggested that environmental conditions play an important role in determining the distribution of different PanI genotypes. The combined use of environmental data, PanI genotyping and neutral markers may provide a valuable approach to examine local adaptation, levels of gene flow and stock structuring.

The Atlantic herring Clupea harengus has played a pivotal role in the formulation of ideas relating to population structuring in marine fishes, yet considerable uncertainty remains as to the extent to which phenotypic and genetic differentiation coincide in such a highly mobile species. In this study, we examined genetic population structure across the major herring spawning aggrega- tions in the North Sea and adjacent waters over 2 years, 2002 and 2003. We analysed 1660 spawning individuals across 9 microsatellite loci. Data were analysed using several approaches, taking into account the effect of location, year-class and sex, as well as pooling all individuals together, making no assumption as to the number of populations present in the data set. The results suggest the pres- ence of a genetically homogeneous unit off Northern Scotland, and a temporally stable pattern of iso- lation by distance determined predominantly by the divergence of the English Channel samples and, in 2003, by the Norwegian spring spawners. Our data suggest that the current view of North Sea herring as a unit-stock might be adequate, but confirm the considerable degree of demographic independence of the herring populations in the English Channel. Despite major recent population collapses, genetic data indicated no evidence of bottlenecks affecting the genetic diversity of extant North Sea herring populations. Finally, despite evidence of weak population structuring, we discuss the risks of underestimating population differentiation in marine fish of large population sizes, and with reference to herring population history and dynamics, we attempt to reconcile the existing theories on herring population structure.

DNA degradation, low DNA concentrations and primer-site mutations may result in the incorrect assignment of microsatellite genotypes, potentially biasing population genetic analyses. MICRO-CHECKER is WINDOWS(R)-based software that tests the genotyping of microsatellites from diploid populations. The program aids identification of genotyping errors due to nonamplified alleles (null alleles), short allele dominance (large allele dropout) and the scoring of stutter peaks, and also detects typographic errors. MICRO-CHECKER estimates the frequency of null alleles and, importantly, can adjust the allele and genotype frequencies of the amplified alleles, permitting their use in further population genetic analysis.

Despite increasing evidence that current exploitation rates can contribute to shifts in life-history traits and the collapse of marine fish stocks, few empirical studies have investigated the likely evolutionary impacts. Here, we used DNA recovered from a temporal series of archived North Sea cod (Gadus morhua) otoliths, to investigate genetic diversity within the Flamborough Head population between 1954 and 1998, during which time the population underwent two successive declines. Microsatellite data indicated a significant reduction in genetic diversity between 1954 and 1970 (total number of alleles: 1954, 46; 1960, 42; 1970, 37), and a subsequent recovery between 1970 and 1998 (total number of alleles: 1970, 37; 1981, 42; 1998, 45). Furthermore, estimates of genetic differentiation (F(ST) and R(ST)) showed a significant divergence between 1998 and earlier samples. Data are consistent with a period of prolonged genetic drift, accompanied by a replacement of the Flamborough Head population through an increased effective migration rate that occurred during a period of high exploitation and appreciable demographic and phenotypic change. Other studies indicate that diversity at neutral microsatellite loci may be correlated with variability at selected genes, thus compromising a population's subsequent recovery and adaptive potential. Such effects are especially pertinent to North Sea cod, which are threatened by continuing exploitation and rising sea temperatures.

Standard length, dry mass and RNA : DNA ratio measurements of 3876 Atlantic cod Gadus morhua larvae and juveniles from 26 families of recruit (fish during their first year of spawning) and repeat spawners (fish which were in their subsequent spawning season) reared in two mesocosms (2500 and 4400 m3) under semi‐natural conditions were analysed over a period of 10 weeks using microsatellites. Larvae from recruit spawners were significantly longer and heavier at hatch and throughout the 10 weeks. RNA : DNA ratios from recruit spawner offspring were only significantly higher at week 1. The smaller (2500 m3) mesocosm was characterized by low plankton density during the transition from endogenous to exogenous feeding followed by a higher density during the metamorphosis period (weeks 4 and 5), with the reverse pattern evident in the 4400 m3 mesocosm. Patterns of larval growth followed patterns of zooplankton density. Significant differences in RNA : DNA ratios between the mesocosms at all comparable sampling dates were found and within each mesocosm individual fish exhibited a wide range of growth and condition responses under the same environmental conditions. RNA : DNA ratios as a function of size differed in the amount of variability between mesocosms, indicating that the higher food density led to a higher proportion of well‐conditioned larvae in the first 3 weeks. Food availability probably has a major role in determining offspring growth and condition, with limited effects due to maternal effects in cases where the broodstock females are approximately of similar size and condition.

Previous studies of cod Gadus morhua population structure in European continental waters using molecular genetic markers have indicated high dispersal and limited structuring, in contrast to many tagging studies. More sensitive genetic techniques, in the form of microsatellite analysis, were used to reanalyse the population structure through the specific targeting of mature fish on spawning grounds. Significantly greater levels of differentiation were found than in previous studies, supporting the presence of 4 genetically distinct populations within the North Sea: Bergen Bank, Moray Firth, Flamborough Head and Southern Bight. Gene flow between the southern North Sea and eastern English Channel is largely restricted to populations within the Southern Bight (southern North Sea) and Beachy Head (eastern English Channel). The spawning stock in the central English Channel (Start Point) remains distinct from those in the Celtic Sea, Outer Hebrides, and central and northern North Sea. No evidence of sub-structuring within the Irish and Celtic Seas was found, in contrast to previous genetic studies, although the populations remained divergent from that of the Outer Hebrides. All European populations were significantly divergent from Canadian Scotian Shelf and Barents Sea (Bear Island) populations. The study indicates that the current fishery monitoring systems may need to be reassessed, particularly with respect to the North Sea, and highlights the value of using microsatellites combined with the targeting of spawning stocks to investigate subtle population structuring.

One of the effects of fishing is a reduction in average age and size in exploited fish stocks, leading to an increasing proportion of recruit spawners in the stock. Current management practice assumes equal viability of offspring from first time spawners and from repeat spawners, despite the fact that that first time spawners often produce smaller eggs than older spawners. The aim of this EU-project is to follow offspring from families of first time spawning and older cod, reared under identical and semi-natural conditions in marine enclosures (mesocosms). The parental origin of the larvae is identified using microsatellite DNA methodology. The advantage of this approach, compared to traditional laboratory rearing, is that rearing conditions are close to natural conditions, and all larvae are reared in the same environment. This eliminates the tank-to-tank variability often observed in traditional rearing experiments. The fish are reared from hatching, through the larval and juvenile stages, until sexual maturity. Growth rates, survival and nutritional condition will be measured using methods such as RNA/DNA ratio and otolith micro increment analysis. The results will be related to parental origin and quality measures of the eggs. It is intended to incorporate the results into management models for improvement of fishery management strategies. In this paper we will focus on a description of the project