Population genetics provides new insights into biomarker prevalence in dab (Limanda limanda L.): a key marine biomonitoring species

Bioindicators are species for which some quantifiable aspect of its biology, a biomarker, is assumed to be sensitive to ecosystem health. However, there is frequently a lack of information on the underlying genetic and environmental drivers shaping the spatiotemporal variance in prevalence of the biomarkers employed. Here, we explore the relative role of potential variables influencing the spatiotemporal prevalence of biomarkers in dab, Limanda limanda, a species used as a bioindicator of marine contaminants. Firstly, the spatiotemporal genetic structure of dab around UK waters (39 samples across 15 sites for four years: 2005–2008) is evaluated with 16 microsatellites. Two temporally stable groups are identified corresponding to the North and Irish Seas (average between basin = 0.007; = 0.022). Secondly, we examine the association between biomarker prevalence and several variables, including genetic structuring, age and contaminant exposure. Genetic structure had significant interactive effects, together with age and some contaminants, in the prevalence of some of the biomarkers considered, namely hyperpigmentation and liver lesions. The integration of these data sets enhanced our understanding of the relationship between biomarker prevalence, exposure to contaminants and population-specific response, thereby yielding more informative predictive models of response and prospects for environmental remediation.

SNP discovery using Next Generation Transcriptomic Sequencing in Atlantic herring (Clupea harengus)

The introduction of Next Generation Sequencing (NGS) has revolutionised population genetics, providing studies of non-model species with unprecedented genomic coverage, allowing evolutionary biologists to address questions previously far beyond the reach of available resources. Furthermore, the simple mutation model of Single Nucleotide Polymorphisms (SNPs) permits cost-effective high-throughput genotyping in thousands of individuals simultaneously. Genomic resources are scarce for the Atlantic herring (Clupea harengus), a small pelagic species that sustains high revenue fisheries. This paper details the development of 578 SNPs using a combined NGS and high-throughput genotyping approach. Eight individuals covering the species distribution in the eastern Atlantic were bar-coded and multiplexed into a single cDNA library and sequenced using the 454 GS FLX platform. SNP discovery was performed by de novo sequence clustering and contig assembly, followed by the mapping of reads against consensus contig sequences. Selection of candidate SNPs for genotyping was conducted using an in silico approach. SNP validation and genotyping were performed simultaneously using an Illumina 1,536 GoldenGate assay. Although the conversion rate of candidate SNPs in the genotyping assay cannot be predicted in advance, this approach has the potential to maximise cost and time efficiencies by avoiding expensive and time-consuming laboratory stages of SNP validation. Additionally, the in silico approach leads to lower ascertainment bias in the resulting SNP panel as marker selection is based only on the ability to design primers and the predicted presence of intron-exon boundaries. Consequently SNPs with a wider spectrum of minor allele frequencies (MAFs) will be genotyped in the final panel. The genomic resources presented here represent a valuable multi-purpose resource for developing informative marker panels for population discrimination, microarray development and for population genomic studies in the wild.

Inhibition of prostaglandin biosynthesis during postluteolysis and effects on CL regression, prolactin, and ovulation in heifers

The beginning of postluteolysis (progesterone, <1 ng mL(-1)) in heifers was targeted by using 8 h after ultrasonic detection of a 25% decrease in CL area (cm2) and was designated Hour 0. Flunixin meglumine (FM; n=10) to inhibit PGF2α secretion or vehicle (n=9) were given intramuscularly at Hours 0, 4, 8, 16, 24, 32, and 40. The dose of FM was 2.5 mg/kg at each treatment. Blood sampling and measurement of the CL and dominant follicle were done every 8 h beginning 14 days postovulation in each group. Blood samples for detection of pulses of PRL and pulses of a metabolite of PGF2α (PGFM) were obtained every hour for 24 h beginning at Hour 0. Pulse concentrations of both PGFM and PRL were lower in the FM group than in the vehicle group. Concentration of PRL was greatest at the peak of a PGFM pulse. Neither CL area (cm2) nor progesterone concentration differed between groups during Hours 0 to 48 (postluteolysis). Ovulation occurred in nine of nine heifers in the vehicle group and in three of 10 heifers in the FM group. The anovulatory follicles in the FM group grew to 36.2±2.9 mm, and the wall became thickened from apparent luteinization. The hypothesis that PGF2α was involved in the continued P4 decrease and structural CL regression during postluteolysis was not supported. However, the hypotheses that pulses of PGFM and PRL were temporally related and that systemic FM treatment induced an anovulatory follicle were supported.

A ranking system for reference libraries of DNA barcodes: application to marine fish species from Portugal

BACKGROUND

The increasing availability of reference libraries of DNA barcodes (RLDB) offers the opportunity to the screen the level of consistency in DNA barcode data among libraries, in order to detect possible disagreements generated from taxonomic uncertainty or operational shortcomings. We propose a ranking system to attribute a confidence level to species identifications associated with DNA barcode records from a RLDB. Here we apply the proposed ranking system to a newly generated RLDB for marine fish of Portugal.

METHODOLOGY/PRINCIPAL FINDINGS

Specimens (n = 659) representing 102 marine fish species were collected along the continental shelf of Portugal, morphologically identified and archived in a museum collection. Samples were sequenced at the barcode region of the cytochrome oxidase subunit I gene (COI-5P). Resultant DNA barcodes had average intra-specific and inter-specific Kimura-2-parameter distances (0.32% and 8.84%, respectively) within the range usually observed for marine fishes. All specimens were ranked in five different levels (A-E), according to the reliability of the match between their species identification and the respective diagnostic DNA barcodes. Grades A to E were attributed upon submission of individual specimen sequences to BOLD-IDS and inspection of the clustering pattern in the NJ tree generated. Overall, our study resulted in 73.5% of unambiguous species IDs (grade A), 7.8% taxonomically congruent barcode clusters within our dataset, but awaiting external confirmation (grade B), and 18.7% of species identifications with lower levels of reliability (grades C/E).

CONCLUSION/SIGNIFICANCE

We highlight the importance of implementing a system to rank barcode records in RLDB, in order to flag taxa in need of taxonomic revision, or reduce ambiguities of discordant data. With increasing DNA barcode records publicly available, this cross-validation system would provide a metric of relative accuracy of barcodes, while enabling the continuous revision and annotation required in taxonomic work.

Species, sex, size and male maturity composition of previously unreported elasmobranch landings in Kuwait, Qatar and Abu Dhabi Emirate

This paper presents data from the first major survey of the diversity, biology and fisheries of elasmobranchs in the Persian (Arabian) Gulf. Substantial landings of elasmobranchs, usually as gillnet by-catch, were recorded in Kuwait, Qatar and the Emirate of Abu Dhabi (part of the United Arab Emirates), although larger elasmobranchs from targeted line fisheries were landed in Abu Dhabi. The elasmobranch fauna recorded was distinctive and included species that are undescribed, rare and have a highly restricted known distribution. Numerical abundance was dominated by sharks (c. 80%), of which carcharhinids were by far the most important. The milk shark Rhizoprionodon acutus and whitecheek shark Carcharhinus dussumieri together comprised just under half of all recorded individuals. Around 90% of recorded sharks were small (50-90 cm total length, L(T) ) individuals, most of which were mature individuals of species with a small maximum size (<100 cm L(T) ), although immature individuals of larger species (e.g. Carcharhinus sorrah and other Carcharhinus spp.) were also important. The most frequently recorded batoid taxa were cownose rays Rhinoptera spp., an undescribed whipray, and the granulated guitarfish Rhinobatos granulatus. The first size, sex and maturity data for a wide range of Gulf elasmobranch species are presented (including L(T) at 50% maturity for males of four shark species) and include some notable differences from other locations in the Indo-West Pacific Ocean. A number of concerns regarding the sustainability of the fishery were highlighted by this study, notably that most of the batoid species recorded are classed by the IUCN Red List as vulnerable, endangered, data deficient or not evaluated. Despite their considerable elasmobranch landings, none of the three countries sampled have developed a 'Shark Plan' as encouraged to do so under the FAO International Plan of Action: Sharks. Furthermore, Kuwait and Qatar currently report zero or no elasmobranch landings to the FAO.

Sample richness and genetic diversity as drivers of chimera formation in nSSU metagenetic analyses

Eukaryotic diversity in environmental samples is often assessed via PCR-based amplification of nSSU genes. However, estimates of diversity derived from pyrosequencing environmental data sets are often inflated, mainly because of the formation of chimeric sequences during PCR amplification. Chimeras are hybrid products composed of distinct parental sequences that can lead to the misinterpretation of diversity estimates. We have analyzed the effect of sample richness, evenness and phylogenetic diversity on the formation of chimeras using a nSSU data set derived from 454 Roche pyrosequencing of replicated, large control pools of closely and distantly related nematode mock communities, of known intragenomic identity and richness. To further investigate how chimeric molecules are formed, the nSSU gene secondary structure was analyzed in several individuals. For the first time in eukaryotes, chimera formation proved to be higher in both richer and more genetically diverse samples, thus providing a novel perspective of chimera formation in pyrosequenced environmental data sets. Findings contribute to a better understanding of the nature and mechanisms involved in chimera formation during PCR amplification of environmentally derived DNA. Moreover, given the similarities between biodiversity analyses using amplicon sequencing and those used to assess genomic variation, our findings have potential broad application for identifying genetic variation in homologous loci or multigene families in general.

Multigene molecular systematics confirm species status of morphologically convergent Pagurus hermit crabs

INTRODUCTION

In spite of contemporary morphological taxonomy appraisals, apparent high morphological similarity raises uncertainty about the species status of certain Pagurus hermit crabs. This is exemplified between two European species, Pagurus excavatus (Herbst, 1791) and Pagurus alatus (Fabricius 1775), whose species status is still difficult to resolve using morphological criteria alone.

METHODOLOGY/PRINCIPAL FINDINGS

To address such ambiguities, we used combinations of Maximum Likelihood (ML) and Bayesian Inference (BI) methods to delineate species boundaries of P. alatus and P. excavatus and formulate an intermediate Pagurus phylogenetic hypothesis, based upon single and concatenated mitochondrial (cytochrome oxidase I [COI]) and nuclear (16S and 28s ribosomal RNA) gene partitions. The molecular data supported the species status of P. excavatus and P. alatus and also clearly resolved two divergent clades within hermit crabs from the Northeast Atlantic Ocean and the Mediterranean Sea.

CONCLUSIONS/SIGNIFICANCE

Despite the abundance and prominent ecological role of hermit crabs, Pagurus, in North East Atlantic Ocean and Mediterranean Sea ecosystems, many important aspects of their taxonomy, biology, systematics and evolution remain poorly explored. The topologies presented here should be regarded as hypotheses that can be incorporated into the robust and integrated understanding of the systematic relationships within and between species of the genus Pagurus inhabiting the Northeast Atlantic Ocean and the Mediterranean Sea.

[Advanced approaches to studying the population diversity of marine fishes: new opportunities for fisheries control and management]

Recent conceptual and technological advances now enable fisheries geneticists to detect and monitor the dynamics and distribution of marine fish populations more effectively than ever before. Information on the extent of genetically-based divergence among populations, so-called "population diversity", is crucial in the quest to manage exploited living resources sustainably since it endows evolutionary potential in the face of environmental change. The generally limited dialogue between scientists, fisheries managers and policy makers, however, continues to constrain integration of population genetic data into tangible policy applications. Largely drawing on the approach and outputs from a European research project, FishPopTrace, we provide an example how the uncovering of marine fish population diversity enables players from genetics, forensics, management and the policy realm to generate a framework tackling key policy-led questions relating to illegal fishing and traceability. We focus on the use of single-nucleotide polymorphisms (SNPs) in European populations of cod, herring, hake and common sole, and explore how forensics together with a range of analytical approaches, and combined with improved communication of research results to stakeholders, can be used to secure sufficiently robust, tractable and targeted data for effective engagement between science and policy. The essentially binary nature of SNPs, together with generally elevated signals of population discrimination by SNPs under selection, allowed assignment of fish to populations from more areas and with higher certainty than previously possible, reaching standards suitable for use in a court of law. We argue that the use of such tools in enforcement and deterrence, together with the greater integration of population genetic principles and methods into fisheries management, provide tractable elements in the arsenal of tools to achieve sustainable exploitation and conservation of depleted marine fish stocks.

Induction of PGFM pulses and luteolysis by sequential estradiol-17β treatments in heifers

The effects of sequential induction of PGFM pulses by estradiol-17β (E2) on prominence of PGFM pulses and progesterone (P4) concentration were studied in heifers. Three treatments of vehicle (n = 12) or E2 (n = 12) at doses of 0.05 or 0.1 mg were given at 12-h intervals beginning on Day 15 postovulation. Blood samples were collected every 12 h from Days 13-24 and hourly for 12 h after the first and third treatments. On Day 15, all heifers were in preluteolysis and on Day 16 were in preluteolysis in the vehicle-treated heifers (n = 11) and either preluteolysis (n = 4) or luteolysis (n = 8) in the E2-treated heifers. Peak concentration of induced PGFM pulses during preluteolysis on Day 15 was greater (P < 0.04) than for pulses during preluteolysis on Day 16. The interval from ovulation to the beginning of luteolysis was shorter (P < 0.04) in the E2-treated heifers than in the vehicle-treated heifers. An E2-induced PGFM pulse was less prominent (P < 0.008) in heifers in temporal association with a transient resurgence in P4 than in heifers with a progressive P4 decrease. The hypothesis that repeated E2 exposure stimulates increasing prominence of PGFM pulses was not supported. Instead, repeated exposure reduced the prominence of PGFM pulses, in contrast to the stimulation from the first E2 treatment. Reduced prominence of a PGF(2α) pulse during luteolysis can lead to a transient resurgence in P4 concentration.

Effect of dose of estradiol-17β on prominence of an induced 13,14-dihydro-15-keto-PGF(2α) (PGFM) pulse and relationship of prominence to progesterone, LH, and luteal blood flow in heifers

Various doses of estradiol-17β (E(2)) were used in heifers to induce a pulse of 13,14-dihydro-15-keto-prostaglandin F(2α) (PGFM). The effect of E(2) concentration on the prominence of PGFM pulses and the relationship between prominence and intrapulse concentration of progesterone (P(4)), LH, and luteal blood flow were studied. A single dose of 0 (vehicle), 0.01, 0.05, or 0.1 mg of E(2) was given (n = six/group) 14 d after ovulation. Blood samples were collected, and luteal blood flow was evaluated hourly for 10 h after the treatment. The 0.05-mg dose increased and the 0.1-mg dose further increased the prominence of the induced PGFM pulse, compared with the 0.0-mg dose and the 0.01-mg dose. The PGFM pulses were subdivided into three different prominence categories (<50, 50 to 150, and >150 pg/mL at the peak). In the 50 to 150 category, P(4) concentration increased (P < 0.05) between -2 h and 0 h (0 h = peak of PGFM pulse). In the >150 category, P(4) decreased (P < 0.05) between -1 h and 0 h, LH increased (P < 0.05) at 1 h, and luteal blood flow apparently decreased (P < 0.05) at 2 h of the PGFM pulse. The novel results supported the following hypotheses: (1) an increase in E(2) concentration increases the prominence of a PGFM pulse, and (2) greater prominence of a PGFM pulse is associated with a greater transient intrapulse depression of P(4) at the peak of the PGFM pulse. In addition, the extent of the effect of prostaglandin F(2α) on the increase in LH and changes in blood flow within the hours of a PGFM pulse was related positively to the prominence of the PGFM pulse.

Faunal histories from Holocene ancient DNA

Recent studies using ancient DNA have been instrumental in advancing understanding of the impact of Holocene climate change on biodiversity. Ancient DNA has been used to track demography, migration and diversity, and is providing new insights into the long-term dynamics of species and population distributions. The Holocene is key to understanding how the past has impacted on the present, as it bridges the gap between contemporary phylogeographic studies and those with inference on Pleistocene patterns, based on ancient DNA studies. Here, we examine the major patterns of Holocene faunal population dynamics and connectivity; highlighting the dynamic nature of species and population responses to Holocene climatic change, thereby providing an 'analogue' for understanding potential impacts of future change.

Seminal parameters and field fertility of cryopreserved donkey jack semen after insemination of horse mares

REASONS FOR PERFORMING STUDY

As mule production is often concentrated in remote areas of the world, a simplified semen cryopreservation protocol is required.

AIM

To compare the seminal parameters of cryopreserved donkey semen in lactose-EDTA and lactose-yolk extenders and the fertility rates on horse mares.

METHODS

TRIAL 1: Sperm total and progressive motility, vigour (scale 0-5), morphology (major and minor defects) and plasma membrane integrity (HOST) were evaluated in 25 ejaculates from 5 donkey jacks immediately after collection (raw), after chilling to 5°C (chilled) and after freezing/thawing. The semen was mixed with skimmed-milk extender, centrifuged, and then re-suspended in lactose-EDTA or lactose-yolk extender. Semen was loaded into 0.5 ml straws and chilled to 5°C for 1 h, after which samples were either evaluated (chilled semen) or placed above liquid nitrogen for 20 min prior to immersion. Seminal parameters were evaluated by ANOVA and Tukey's test. TRIAL 2: Cryopreserved semen from 3 males was used to inseminate 53 mares at 60 oestrous cycles randomly assigned to lactose-yolk (n = 30 cycles) or lactose-EDTA (n = 30 cycles) extenders. Pregnancy diagnosis was performed 15 and 25 days post ovulation. The pregnancy rates were compared using Chi-squared tests.

RESULTS

TRIAL 1: No significant differences were evident in any seminal parameters between extenders after either chilling or cryopreservation. Total and progressive motility were significantly (P<0.05) lower in cryopreserved semen than raw and chilled semen for both extenders. TRIAL 2: Pregnancy rates did not significantly differ between extenders (lactose-EDTA extender 53.33 and 43.33%; lactose-yolk 50.0 and 46.66% for Days 15 and 25 post ovulation, respectively).

CONCLUSIONS

Cryopreservation of donkey semen using the simplified lactose-yolk extender resulted in similar seminal parameters and fertility rates when compared to lactose-EDTA extender.

POTENTIAL RELEVANCE

Lactose-yolk extender may be advocated as a simple, easy to prepare extender, for use in geographically isolated enterprises producing mules throughout the world.

Successful extraction of DNA from archived alcohol-fixed white-eye fish specimens using an ancient DNA protocol

A protocol used routinely for rapid ancient DNA extraction was applied to fish tissue archived over 80 years ago. The method proved successful, whereas other extraction protocols failed. Researchers working on DNA from older archived fish samples are encouraged to continue to concentrate their efforts on 'white-eye' specimens, which indicate an alcohol-based fixative and are thus likely to yield viable DNA.

Systematic and evolutionary insights derived from mtDNA COI barcode diversity in the Decapoda (Crustacea: Malacostraca)

BACKGROUND

Decapods are the most recognizable of all crustaceans and comprise a dominant group of benthic invertebrates of the continental shelf and slope, including many species of economic importance. Of the 17635 morphologically described Decapoda species, only 5.4% are represented by COI barcode region sequences. It therefore remains a challenge to compile regional databases that identify and analyse the extent and patterns of decapod diversity throughout the world.

METHODOLOGY/PRINCIPAL FINDINGS

We contributed 101 decapod species from the North East Atlantic, the Gulf of Cadiz and the Mediterranean Sea, of which 81 species represent novel COI records. Within the newly-generated dataset, 3.6% of the species barcodes conflicted with the assigned morphological taxonomic identification, highlighting both the apparent taxonomic ambiguity among certain groups, and the need for an accelerated and independent taxonomic approach. Using the combined COI barcode projects from the Barcode of Life Database, we provide the most comprehensive COI data set so far examined for the Order (1572 sequences of 528 species, 213 genera, and 67 families). Patterns within families show a general predicted molecular hierarchy, but the scale of divergence at each taxonomic level appears to vary extensively between families. The range values of mean K2P distance observed were: within species 0.285% to 1.375%, within genus 6.376% to 20.924% and within family 11.392% to 25.617%. Nucleotide composition varied greatly across decapods, ranging from 30.8 % to 49.4 % GC content.

CONCLUSIONS/SIGNIFICANCE

Decapod biological diversity was quantified by identifying putative cryptic species allowing a rapid assessment of taxon diversity in groups that have until now received limited morphological and systematic examination. We highlight taxonomic groups or species with unusual nucleotide composition or evolutionary rates. Such data are relevant to strategies for conservation of existing decapod biodiversity, as well as elucidating the mechanisms and constraints shaping the patterns observed.

Temporal genetic homogeneity among shore crab (Carcinus maenas) larval events supplied to an estuarine system on the Portuguese northwest coast

Despite the importance of larval biology in the life histories of many marine animals, relatively little information exists on the dynamics and genetic composition of larval cohorts. The supply of megalopae larvae of the shore crab, Carcinus maenas, was measured on a daily basis during 8 months spread along two larval periods (2006 and 2007) at the Ria de Aveiro estuary, on the Portuguese northwest coast. A total of 10 microsatellite DNA loci were employed to explore the genetic structure, variability and relatedness of temporally distinct megalopal events, selected from the major pulses of supply. Larval variation was also compared genetically with that of a previously studied adult crabs sample, at the same loci, collected in 2006 and 2007 along the Iberian Peninsula. Results revealed a lack of genetic differentiation and identical diversity levels among larval events over time. No evidence of reduced genetic diversity between megalopae relative to the diversity assessed from the pooled sample of adults was found. Moreover, there was no evidence of any family relatedness among larvae from temporal events. The results obtained for C. maenas contradict predictions made by the sweepstakes reproduction hypothesis, in which large variance in reproductive success is expected, which is presumably detectable as sharp genetic discontinuities among separate larval events. Data here indicate conversely a high degree of temporal genetic stability among larval supply to a given estuary under variable oceanographic conditions, consistent with the hypothesis that sampled larvae were drawn from a large number of adults that do not differ in reproductive success.

Detecting population structure in a high gene-flow species, Atlantic herring (Clupea harengus): direct, simultaneous evaluation of neutral vs putatively selected loci

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.

Second-generation environmental sequencing unmasks marine metazoan biodiversity

Biodiversity is of crucial importance for ecosystem functioning, sustainability and resilience, but the magnitude and organization of marine diversity at a range of spatial and taxonomic scales are undefined. In this paper, we use second-generation sequencing to unmask putatively diverse marine metazoan biodiversity in a Scottish temperate benthic ecosystem. We show that remarkable differences in diversity occurred at microgeographical scales and refute currently accepted ecological and taxonomic paradigms of meiofaunal identity, rank abundance and concomitant understanding of trophic dynamics. Richness estimates from the current benchmarked Operational Clustering of Taxonomic Units from Parallel UltraSequencing analyses are broadly aligned with those derived from morphological assessments. However, the slope of taxon rarefaction curves for many phyla remains incomplete, suggesting that the true alpha diversity is likely to exceed current perceptions. The approaches provide a rapid, objective and cost-effective taxonomic framework for exploring links between ecosystem structure and function of all hitherto intractable, but ecologically important, communities.

Recent developments in sequencing technologies have provided the opportunity to investigate the biodiversity of ecosystems. Such a metagenomic approach, combined with taxon clustering, is used here to demonstrate that the species richness of a marine community in Scotland is much greater than anticipated.

Genomic signatures of local directional selection in a high gene flow marine organism; the Atlantic cod (Gadus morhua)

BACKGROUND

Marine fishes have been shown to display low levels of genetic structuring and associated high levels of gene flow, suggesting shallow evolutionary trajectories and, possibly, limited or lacking adaptive divergence among local populations. We investigated variation in 98 gene-associated single nucleotide polymorphisms (SNPs) for evidence of selection in local populations of Atlantic cod (Gadus morhua L.) across the species distribution.

RESULTS

Our global genome scan analysis identified eight outlier gene loci with very high statistical support, likely to be subject to directional selection in local demes, or closely linked to loci under selection. Likewise, on a regional south/north transect of central and eastern Atlantic populations, seven loci displayed strongly elevated levels of genetic differentiation. Selection patterns among populations appeared to be relatively widespread and complex, i.e. outlier loci were generally not only associated with one of a few divergent local populations. Even on a limited geographical scale between the proximate North Sea and Baltic Sea populations four loci displayed evidence of adaptive evolution. Temporal genome scan analysis applied to DNA from archived otoliths from a Faeroese population demonstrated stability of the intra-population variation over 24 years. An exploratory landscape genetic analysis was used to elucidate potential effects of the most likely environmental factors responsible for the signatures of local adaptation. We found that genetic variation at several of the outlier loci was better correlated with temperature and/or salinity conditions at spawning grounds at spawning time than with geographic distance per se.

CONCLUSION

These findings illustrate that adaptive population divergence may indeed be prevalent despite seemingly high levels of gene flow, as found in most marine fishes. Thus, results have important implications for our understanding of the interplay of evolutionary forces in general, and for the conservation of marine biodiversity under rapidly increasing evolutionary pressure from climate and fisheries induced changes in local environments.