Audrey J. Geffen

Outlier SNP markers reveal fine-scale genetic structuring across European hake populations (Merluccius merluccius)

Shallow population structure is generally reported for most marine fish and explained as a consequence of high dispersal, connectivity and large population size. Targeted gene analyses and more recently genome‐wide studies have challenged such view, suggesting that adaptive divergence might occur even when neutral markers provide genetic homogeneity across populations. Here, 381 SNPs located in transcribed regions were used to assess large‐ and fine‐scale population structure in the European hake (Merluccius merluccius), a widely distributed demersal species of high priority for the European fishery. Analysis of 850 individuals from 19 locations across the entire distribution range showed evidence for several outlier loci, with significantly higher resolving power. While 299 putatively neutral SNPs confirmed the genetic break between basins (FCT = 0.016) and weak differentiation within basins, outlier loci revealed a dramatic divergence between Atlantic and Mediterranean populations (FCT range 0.275–0.705) and fine‐scale significant population structure. Outlier loci separated North Sea and Northern Portugal populations from all other Atlantic samples and revealed a strong differentiation among Western, Central and Eastern Mediterranean geographical samples. Significant correlation of allele frequencies at outlier loci with seawater surface temperature and salinity supported the hypothesis that populations might be adapted to local conditions. Such evidence highlights the importance of integrating information from neutral and adaptive evolutionary patterns towards a better assessment of genetic diversity. Accordingly, the generated outlier SNP data could be used for tackling illegal practices in hake fishing and commercialization as well as to develop explicit spatial models for defining management units and stock boundaries.

A genomic island linked to ecotype divergence in Atlantic cod

The genomic architecture underlying ecological divergence and ecological speciation with gene flow is still largely unknown for most organisms. One central question is whether divergence is genome‐wide or localized in ‘genomic mosaics’ during early stages when gene flow is still pronounced. Empirical work has so far been limited, and the relative impacts of gene flow and natural selection on genomic patterns have not been fully explored. Here, we use ecotypes of Atlantic cod to investigate genomic patterns of diversity and population differentiation in a natural system characterized by high gene flow and large effective population sizes, properties which theoretically could restrict divergence in local genomic regions. We identify a genomic region of strong population differentiation, extending over approximately 20 cM, between pairs of migratory and stationary ecotypes examined at two different localities. Furthermore, the region is characterized by markedly reduced levels of genetic diversity in migratory ecotype samples. The results highlight the genomic region, or ‘genomic island’, as potentially associated with ecological divergence and suggest the involvement of a selective sweep. Finally, we also confirm earlier findings of localized genomic differentiation in three other linkage groups associated with divergence among eastern Atlantic populations. Thus, although the underlying mechanisms are still unknown, the results suggest that ‘genomic mosaics’ of differentiation may even be found under high levels of gene flow and that marine fishes may provide insightful model systems for studying and identifying initial targets of selection during ecological divergence.

The influence of nursery ground processes in the determination of year-class strength in juvenile plaice Pleuronectes platessa L. in Port Erin Bay, Irish Sea

The interannual variability in settlement and mortality of juvenile plaice Pleuronectes platessa L. was investigated between 1992 and 1998 on Port Erin Bay, west side of the Isle of Man, Irish Sea. The dampening influence of factors operating on the nursery grounds was especially obvious in 1992 and 1996. In these years extremely high numbers of individuals settled, yet the population sizes in July were similar to other years. Thus the nursery ground processes were likely to be density dependent. Shrimp and crab densities were low in Port Erin Bay and probably had little predatory impact on young plaice. Crustacean densities were not significantly related to winter temperatures. In the Irish Sea, year-class strength is determined during the nursery ground phase, in contrast to the North Sea where determination of year-class strength occurs prior to the nursery ground phase.

Sperm traits and fertilization success of male and sex-reversed female rainbow trout (Oncorhynchus mykiss)

Abstract Sperm motility, density, adenosine triphosphate (ATP) concentration, and fertilization rates of sex-reversed female (XX-male) rainbow trout ( Oncorhynchus mykiss ) were compared to those of normal (XY-male) males. The relationships between sperm traits, fertilization rates, and characteristics of individual fish (weight, gonadosomatic index) were assessed. The fertilization rate of sperm stripped from normal males averaged 81% (s.d. 16%). The sperm of sex-reversed females had to be removed directly from the testes and achieved average fertilization rates of 60% (s.d. 13%). Testicular sperm from normal males was motile for shorter periods of time and produced lower fertilization rates than testicular sperm from sex-reversed fish. Fertilization rates were positively correlated with higher initial sperm motility, but not with sperm density or ATP concentrations.

Population structure of the Dover sole, Solea solea L., in a background of high gene flow

Abstract To investigate the genetic population structure of the Dover sole, Solea solea L., allozyme electrophoresis was performed on 303 fish collected from seven locations ranging from Cumbria, Great Britain, to Greece. A total of 22 enzyme systems were analysed, coded by 33 loci. Of these, 27 loci were polymorphic using the P 99 criterion. A phenogram using Prevostis Distance generated by the Wagner method exhibited a geographic pattern in the clustering of populations. Estimates of N m (effective number of migrants per generation between populations) were sufficiently high to imply near-panmixia between the North Sea, Bay of Biscay and the Irish Coast populations, indicating a probable movement of migrants through the English Channel. However, despite this high level of gene flow, striking patterns of geographic differentiation were observed at a few loci. Allele frequencies at loci ACOH, EST-I-1, PEP-I-2 exhibited genetic patchiness on both local and range-wide (within the northern and southern European basins) scales. This pattern of genetic patchiness could be the result of localised selection, genetic drift or single-generation sampling effects. Estimates of mean heterozygosity ( H ) were inversely related to latitude. Evolutionary processes such as genetic drift and founder effect, and/or selection, may have produced the observed difference in the number of alleles between the basins. Moreover, the absence of isolation by distance provides support for a model of geographic isolation. Such a pattern of genetic patchiness, revealing a slight reduction of genetic variability in the northern European basin, may suggest a population bottleneck, or local reduction in population size. Various physical parameters, especially water temperature during the reproductive period, vary within the range of the species, and may produce or maintain this genetic differentiation. These results indicate the role of both ecological and evolutionary structuring mechanisms in determining the genetic population structure of S . solea .

Frequent skipped spawning in the world’s largest cod population

Life-history theory suggests that animals may skip reproductive events after initial maturation to maximize lifetime fitness. In iteroparous teleosts, verifying past spawning history is particularly difficult; the degree of skipped spawning at the population level therefore remains unknown. We unequivocally show frequent skipped spawning in Northeast Arctic cod (NEAC) in a massive field and laboratory effort from 2006 to 2008. This was verified by postovulatory follicles in temporarily arrested ovaries close to the putative spawning period. At the population level, “skippers” were estimated to be approximately equally abundant as spawning females in 2008, constituting ∼24% of the females 60–100 cm. These females never truly started vitellogenesis and principally remained on the feeding grounds when spawners migrated southward, avoiding any migration costs. The proximate cause of skipping seems to be insufficient energy to initiate oocyte development, indicating that skipped spawning may partly be a density-dependent response important in population regulation. Our data also indicate more skipping among smaller females and potential tradeoffs between current and future reproductive effort. We propose that skipped spawning is an integral life-history component for NEAC, likely varying annually, and it could therefore be an underlying factor causing some of the currently unexplained large NEAC recruitment variation. The same may hold for other teleosts.

Development of Atlantic cod (Gadus morhua) exposed to produced water during early life stages: Effects on embryos, larvae, and juvenile fish

Produced water (PW) contains numerous toxic compounds of natural origin, such as dispersed oil, metals, alkylphenols (APs), and polycyclic aromatic hydrocarbons (PAHs). In addition, PW also contains many different chemicals which have been added during the oil production process. In the study described here, cod were exposed to real PW collected from an oil production platform in the North Sea. This was done in order to best recreate the most realistic field-exposure regime in which fish will be affected by a wide range of chemicals. The biological effects found in this study therefore cannot be assigned to one group of chemicals alone, but are the result of exposure to the complex chemical mixture found in real PW. Since APs are well known to cause endocrine disruption in marine organisms, we focused our chemical analysis on APs in an attempt to better understand the long-term effects of APs from PW on the biology of fish. In this study, cod were exposed to several concentrations of real PW and 17β-oestradiol (E(2)), a natural oestrogen, at different developmental stages. Cod were exposed to PW either during the embryo and early larvae stage (up to 3 months of age) or during the early juvenile stage (from 3 to 6 months of age). Results showed that, in general, APs bioconcentrate in fish tissue in a dose and developmental stage dependent manner during PW exposure. However, juveniles appeared able to effectively metabolise the short chain APs. Importantly, PW exposure had no effect on embryo survival or hatching success. However, 1% PW clearly interfered with the development of normal larval pigmentation. After hatching most of the larvae exposed to 1% PW failed to begin feeding and died of starvation. This inability to feed may be linked to the increased incidence of jaw deformities seen in these larvae. In addition, cod exposed to 1% PW, had significantly higher levels of the biomarkers vitellogenin and CYP1A in plasma and liver, respectively. No similar effects were seen in cod exposed to either 0.1% or 0.01% PW.

Individual growth of juvenile plaice (Pleuronectes platessa L.) on a small irish sea nursery ground (Port Erin Bay, Isle of Man, UK)

Abstract The individual growth rate of juvenile plaice ( Pleuronectes platessa L. was studied in Port Erin Bay, Isle of Man, between 1989 and 1993. All plaice larger than 85 mm were measured and tagged with individually numbered anchor tags and released. All recaptured fish were remeasured and re-released back into the bay. The tagging data were used to estimate the population size between May and April each year and the growth rate of individual fish. The growth of juvenile plaice in Port Erin Bay was compared to theoretical growth rates which were modulated by temperature alone or a combination of temperature and initial length. These data were also compared to population level growth rates calculated from changes in mean length per month from regular beam trawl series. A total of 2547 plaice larger than 85 mm were tagged with 435 recaptures. Over the sampling period there were minor differences in temperature between years. The population growth rate varied between 0.1 and 0.27 mm·d −1 whereas the individual growth rate varied between 0 and 1.67 mm·d −1 . There were significant differences in growth rate both between seasons and between years. During the summer the individual growth rate was significantly higher than the models predicted. Low temperatures often coincided with high densities so that it was difficult to separate the effects of density and temperature on growth rate. At the individual level growth rate tended to be highest when the conditions on the nursery ground were optimal whereas at the population level there did not appear to be a simple relationship.

Organ damage in Atlantic herring larvae as a result of ocean acidification

The dissolution of anthropogenically emitted excess carbon dioxide lowers the pH of the worlds ocean water. The larvae of mass spawning marine fishes may be particularly vulnerable to such ocean acidification (OA), yet the generality of earlier results is unclear. Here we show the detrimental effects of OA on the development of a commercially important fish species, the Atlantic herring (Clupea harengus). Larvae were reared at three levels of CO2: today (0.0385 kPa), end of next century (0.183 kPa), and a coastal upwelling scenario (0.426 kPa), under near-natural conditions in large outdoor tanks. Exposure to elevated CO2 levels resulted in stunted growth and development, decreased condition, and severe tissue damage in many organs, with the degree of damage increasing with CO2 concentration. This complements earlier studies of OA on Atlantic cod larvae that revealed similar organ damage but at increased growth rates and no effect on condition.

Age-related trends in otolith chemistry of Merluccius merluccius from the north-eastern Atlantic Ocean and the western Mediterranean Sea

Sagittal otoliths of European hake obtained from five geographic locations in the north-eastern Atlantic and western Mediterranean were examined using laser ablation and inductively coupled plasma mass spectrometry. Otolith sections were analysed for the isotopes 24 Mg, 55 Mn, 66 Zn, 85 Rb, 86 Sr, 138 Ba and 208 Pb, measured relative to 43 Ca counts. These analyses considered only age 0 (core area) and ages 1 to 3. Age-related trends in otolith elemental composition were observed in hake from all areas, but were masked by variability between locations. Elemental concentrations generally decreased outside the core, with some increase at age 3. The composition of the otolith core was very distinct from that of the other growth increments. In the Mediterranean, part of this differentiation was a result of Mn, which was present in the core at high concentrations compared with the rest of the otolith. Mediterranean otoliths also had higher concentrations of Sr, Zn and Ba in the core. For most samples a similar trend was observed, although samples from one of the Mediterranean areas showed some differences, mainly in the concentrations of Mg and Sr. These results provide new empirical evidence of the variation in elemental concentrations across hake otoliths with age, at least throughout the first 3 years of life.