Genetic assignment predicts depth of benthic settlement for 0-group Atlantic cod.

Atlantic cod is a keystone species that remains among the most economically important demersal fish in the North Atlantic. Throughout its distribution range, Atlantic cod is composed of populations with varying environmental preferences and migratory propensities. This life-history variation is likely to have contributed to the niche width and large population sizes of Atlantic cod, and its relative resilience to environmental change and exploitation. The Icelandic cod stock is currently managed as a single unit, but early research indicates population variation by depth and temperature and distinct offshore and inshore spawning components. Pelagic 0-group juveniles from different spawning grounds coexist in nursery areas around Iceland, but their genetic composition or habitat partitioning had not been examined post benthic settlement. In the current study we examine the genetic composition of Atlantic cod juvenile aggregations at nearshore nursery grounds in NW-Iceland and report distinct segregation by the depth of offshore and inshore juvenile cod. The physiological mechanism of this segregation is not known, but the pattern demonstrates the need to consider population structure at nursery grounds in the application of marine spatial planning and other area-based conservation tools.

Personality in juvenile Atlantic cod ecotypes and implications for fisheries management.

Animals show among-individual variation in behaviors, including migration behaviors, which are often repeatable across time periods and contexts, commonly termed "personality." These behaviors can be correlated, forming a behavioral syndrome. In this study, we assessed the repeatability and correlation of different behavioral traits, i.e., boldness, exploration, and sociality, and the link to feeding migration patterns in Atlantic cod juveniles. To do so, we collected repeated measurements within two short-term (3 days) and two long-term (2 months) intervals of these personality traits and genotypes of the Pan I locus, which is correlated with feeding migration patterns in this species. We found high repeatabilities for exploration behavior in the short- and long-term intervals, and a trend for the relationship between exploration and the Pan I locus. Boldness and sociality were only repeatable in the second short-term interval indicating a possible development of stability over time and did not show a relation with the Pan I locus. We found no indication of behavioral syndromes among the studied traits. We were unable to identify the existence of a migration syndrome for the frontal genotype, which is the reason that the link between personality and migration remains inconclusive, but we demonstrated a possible link between exploration and the Pan I genotype. This supports the need for further research that should focus on the effect of exploration tendency and other personality traits on cod movement, including the migratory (frontal) ecotype to develop management strategies based on behavioral units, rather than treating the population as a single homogeneous stock.

Activity vs exploration: Locomotion in a known and unknown environment differs in Atlantic cod juveniles (Gadus morhua).

Individuals within a population often behave differently and these differences can be consistent over time and/or context, also termed "animal personality". Animal personality has been commonly classified into five axes with studies aiming to validate these axes. One subject that has surprisingly not received full attention yet is the difference between the two personality axes "activity" and "exploration-avoidance", i.e. behaviour in a known vs an unknown environment. Despite this clear difference in definition, many studies measure activity in an unknown environment and term it activity, while underlying motivations between the two environments are different. This study aimed to detect the two personality traits "activity" and "exploration" in Atlantic cod juveniles, and to investigate whether they support the distinctive definitions proposed by previous authors. This study showed significant consistency in locomotion variation in both environments, i.e. personality. In addition, the two environments clearly elicited different behaviours; Atlantic cod juvenile behaviour was more repeatable and they moved more in the known vs the unknown environment, and no correlation of the proportional locomotion between the two was found. This demonstrates that locomotion in both environments, i.e. the personality axes "activity" and "exploration", should not be confused nor treated as if they reflect the same personality trait.

Fishing for DNA? Designing baits for population genetics in target enrichment experiments: Guidelines, considerations and the new tool supeRbaits.

Targeted sequencing is an increasingly popular next-generation sequencing (NGS) approach for studying populations that involves focusing sequencing efforts on specific parts of the genome of a species of interest. Methodologies and tools for designing targeted baits are scarce but in high demand. Here, we present specific guidelines and considerations for designing capture sequencing experiments for population genetics for both neutral genomic regions and regions subject to selection. We describe the bait design process for three diverse fish species: Atlantic salmon, Atlantic cod and tiger shark, which was carried out in our research group, and provide an evaluation of the performance of our approach across both historical and modern samples. The workflow used for designing these three bait sets has been implemented in the R-package supeRbaits, which encompasses our considerations and guidelines for bait design for the benefit of researchers and practitioners. The supeRbaits R-package is user-friendly and versatile. It is written in C++ and implemented in R. supeRbaits and its manual are available from Github: https://github.com/BelenJM/supeRbaits.

A millennium of trophic stability in Atlantic cod (Gadus morhua): transition to a lower and converging trophic niche in modern times.

Stable isotope analyses of zooarchaeological material can be used to examine ecological variability in exploited species at centennial to millennial scales. Climate change is a notable driver of marine ecosystem change, although historical fishing is also likely to have impacted past marine systems. Fishing removes the oldest and largest individuals and may thereby result in shorter trophic pathways and reduced niche width of predatory fish species. In the current study we examine the trophic niche of Atlantic cod, haddock and Atlantic wolffish, in the last millennium using δ13C and δ15N values of bone collagen. We report a lower trophic level of Atlantic cod and haddock but higher level of wolffish in present times, following centuries at consistent and higher trophic levels of Atlantic cod. This results in a concurrent converging trophic niche of the demersal fish. We suggest that the current data set provides a valuable historical baseline facilitating interpretation of current variability in the trophic ecology of northern demersal fish.

Evidence of unidirectional hybridization and second-generation adult hybrid between the two largest animals on Earth, the fin and blue whales.

Biodiversity in the oceans has dramatically declined since the beginning of the industrial era, with accelerated loss of marine biodiversity impairing the ocean's capacity to maintain vital ecosystem services. A few organisms epitomize the damaging and long-lasting effects of anthropogenic exploitation: Some whale species, for instance, were brought to the brink of extinction, with their population sizes reduced to such low levels that may have caused a significant disruption to their reproductive dynamics and facilitated hybridization events. The incidence of hybridization is nevertheless believed to be rare, and very little information exists on its directionality. Here, using genetic markers, we show that all but one whale hybrid sample collected in Icelandic waters originated from the successful mating of male fin whale and female blue whale, thus suggesting unidirectional hybridization. We also demonstrate for the first time the existence of a second-generation adult (male) hybrid resulting from a backcross between a female hybrid and a pure male fin whale. The incidence of hybridization events between fin and blue whales is likely underestimated and the observed unidirectional hybridization (for F1 and F2 hybrids) is likely to induce a reproductive loss in blue whale, which may represent an additional challenge to its recovery in the Atlantic Ocean compared to other rorquals.

A millennium of north-east Atlantic cod juvenile growth trajectories inferred from archaeological otoliths.

Archaeological excavations of historical fishing sites across the North Atlantic have recovered high quantities of Atlantic cod (Gadus morhua) bones. In the current study we use Atlantic cod otoliths from archaeological excavations of a historical fishing sites in north-west Iceland, dated to AD 970 -AD 1910 to examine historical growth trajectories of cod. No large scale growth variations or shifts in growth patterns were observed in the current chronologies, supporting the stability of historical Atlantic cod growth trajectories. The most significant variation in growth patterns was consistent with those that have been observed in recent times, for example, reduced early juvenile growth during periods of colder ocean temperature. The current results represent a high resolution chronological record of north-east Atlantic cod growth, greatly increasing the prior temporal range of such data, thereby providing a valuable baseline for a broad range of studies on Atlantic cod growth.

Interactions between boldness, foraging performance and behavioural plasticity across social contexts.

ABSTRACT: Boldness, the tendency to be explorative, risk prone and proactive, often varies consistently between individuals. An individual's position on the boldness-shyness continuum has many implications. Bold individuals may outperform shyer conspecifics during foraging as they cover more ground, accumulate information more rapidly and make more frequent food discoveries. Individual variation in boldness may also affect behavioural plasticity across environmental contexts, as the time to process new information, the ability to locate and memorise resources and the time and ability to apply prior information in a novel context all differ between individuals. The primary aim of the current study was to examine plasticity in, and covariation between, boldness, foraging speed and foraging accuracy across social foraging contexts. We showed that the stickleback that were shyest when foraging alone became relatively boldest when foraging in a social context and also delayed their entry to a known food patch the most in the presence of conspecifics. These results support the assertion that shyer foragers are more reactive to social cues and add to current knowledge of how an individual's position on the boldness-shyness continuum may correlate to foraging task performance and behavioural plasticity. We conclude that the correlation between boldness and behavioural plasticity may have broad relevance as the ability to adjust or retain behaviours in changing social environments could often have consequences for fitness. SIGNIFICANCE STATEMENT: Animal personality may affect how much individuals change their behaviour to suit different environments. We studied the link between threespine stickleback personality (boldness or shyness), foraging performance and change in foraging performance when either alone or in the presence of other stickleback. We found that shyer threespine stickleback were more reactive to the presence of other fish when foraging. When observed or joined by other fish, shy stickleback started exploring earlier, but entered a known food patch later, than when alone. Bolder stickleback changed their foraging behaviour much less in the presence of other fish. Our results suggest that how bold or shy individuals are may have important consequences on how well they adjust their foraging behaviour to environmental change.

Historical DNA reveals the demographic history of Atlantic cod (Gadus morhua) in medieval and early modern Iceland.

Atlantic cod (Gadus morhua) vertebrae from archaeological sites were used to study the history of the Icelandic Atlantic cod population in the time period of 1500-1990. Specifically, we used coalescence modelling to estimate population size and fluctuations from the sequence diversity at the cytochrome b (cytb) and Pantophysin I (PanI) loci. The models are consistent with an expanding population during the warm medieval period, large historical effective population size (NE), a marked bottleneck event at 1400-1500 and a decrease in NE in early modern times. The model results are corroborated by the reduction of haplotype and nucleotide variation over time and pairwise population distance as a significant portion of nucleotide variation partitioned across the 1550 time mark. The mean age of the historical fished stock is high in medieval times with a truncation in age in early modern times. The population size crash coincides with a period of known cooling in the North Atlantic, and we conclude that the collapse may be related to climate or climate-induced ecosystem change.

Detection and mapping of mtDNA SNPs in Atlantic salmon using high throughput DNA sequencing.

BACKGROUND: Approximately half of the mitochondrial genome inherent within 546 individual Atlantic salmon (Salmo salar) derived from across the species' North Atlantic range, was selectively amplified with a novel combination of standard PCR and pyro-sequencing in a single run using 454 Titanium FLX technology (Roche, 454 Life Sciences). A unique combination of barcoded primers and a partitioned sequencing plate was employed to designate each sequence read to its original sample. The sequence reads were aligned according to the S. salar mitochondrial reference sequence (NC_001960.1), with the objective of identifying single nucleotide polymorphisms (SNPs). They were validated if they met with the following three stringent criteria: (i) sequence reads were produced from both DNA strands; (ii) SNPs were confirmed in a minimum of 90% of replicate sequence reads; and (iii) SNPs occurred in more than one individual. RESULTS: Pyrosequencing generated a total of 179,826,884 bp of data, and 10,765 of the total 10,920 S. salar sequences (98.6%) were assigned back to their original samples. The approach taken resulted in a total of 216 SNPs and 2 indels, which were validated and mapped onto the S. salar mitochondrial genome, including 107 SNPs and one indel not previously reported. An average of 27.3 sequence reads with a standard deviation of 11.7 supported each SNP per individual. CONCLUSION: The study generated a mitochondrial SNP panel from a large sample group across a broad geographical area, reducing the potential for ascertainment bias, which has hampered previous studies. The SNPs identified here validate those identified in previous studies, and also contribute additional potentially informative loci for the future study of phylogeography and evolution in the Atlantic salmon. The overall success experienced with this novel application of HT sequencing of targeted regions suggests that the same approach could be successfully applied for SNP mining in other species.

Immune response against equine gammaherpesvirus in Icelandic horses.

Horses are hosts to two types of gammaherpesviruses, equine herpes virus (EHV) 2 and 5. While EHV-2 is ubiquitous in adult horses, EHV-5 has been less frequently described. Due to strong serological cross-reactivity, EHV-2 and -5 cannot be discriminated in broad spectrum antibody tests and are thus commonly referred to as gamma-EHV. Total IgG and IgG subclass response against gamma-EHV were determined in serum from 41 healthy Icelandic horses, thereof 20 adults, 10 foals aged 10 months, and 11 foals aged 1-4 months. Additionally, in 10 of the adult horses, interferon (IFN)-gamma and interleukin (IL)-4 expression were measured by real-time PCR in white blood cells upon in vitro stimulation with EHV-2. With the exception of one orphan foal, all tested individuals were seropositive for gamma-EHV. All but one adult had high titer of EHV-specific IgG4/7 (IgGb) in combination with much lower titer of IgG1 (IgGa) and IgG3/5 (IgG(T)), indicating a stabilized response. IgG titer and subclasses in the foals showed considerably more variation, possibly dependant on maternal antibodies and/or recent infection. In all the 10 horses tested for cytokine expression, IFN-gamma production exceeds production of IL-4. These results indicate that equine gammaherpesvirus infection is characterized by an induction of IgG1, IgG4/7 and IgG3/5 with prevailing IgG4/7 and cytokine profile dominated by IFN-gamma. To our knowledge, this is the first report on the cytokine and IgG subclass response against gamma-EHV in horses.

In vitro analysis of expression vectors for DNA vaccination of horses: the effect of a Kozak sequence.

One of the prerequisite for developing DNA vaccines for horses are vectors that are efficiently expressed in horse cells. We have analysed the ectopic expression of the human serum albumin gene in primary horse cells from different tissues. The vectors used are of pcDNA and pUC origin and include the cytomegalovirus (CMV) promoter. The pUC vectors contain CMV intron A whereas the pcDNA vectors do not. Insertion of intron A diminished the expression from the pcDNA vectors whereas insertion of a Kozak sequence upstream of the gene in two types of pUC vectors increased significantly the in vitro expression in primary horse cells derived from skin, lung, duodenum and kidney. We report for the first time the significance of full consensus Kozak sequences for protein expression in horse cells in vitro.

Positive assortative mating between recently described sympatric morphs of Icelandic sticklebacks.

Recently, models of sympatric speciation have suggested that assortative mating can develop between sympatric morphs due to divergence in an ecologically important character. For example, in sympatric pairs of threespine stickleback (Gasterosteus aculeatus L.) size-assortative mating seems to be instrumental in reproductive isolation. Here, we examine courtship behaviour and assortative mating of newly described sympatric stickleback morphs in Lake Thingvallavatn, Iceland. We find that the two morphs show strong positive assortative mating. However, the mechanism involved in mate choice does not seem to be as straightforward as in other similar systems of sympatric stickleback morphs and may involve variation in nest type.

Genomewide scan for hand osteoarthritis: a novel mutation in matrilin-3.

Osteoarthritis (OA) is the most common human joint disease, characterized by loss and/or remodeling of joint synovium, cartilage, and bone. Here, we describe a genomewide linkage analysis of patients with idiopathic hand OA who were carefully phenotyped for involvement of either or both the distal interphalangeal (DIP) joints and the first carpometacarpal (CMC1) joints. The best linkage peaks were on chromosomes 4q and 3p and on the short arm of chromosome 2. Genomewide significance was reached for a locus on chromosome 2 for patients with affected CMC1 joints (LOD = 4.97); this locus was also significant for patients with OA in both CMC1 and DIP joints (LOD = 4.44). The peak LOD score at this locus coincides with a gene, MATN3, encoding the noncollagenous cartilage extracellular matrix protein, matrilin-3. Subsequent screening of the genomic sequence revealed a missense mutation, of a conserved amino acid codon, changing threonine to methionine in the epidermal growth factor-like domain in matrilin-3. The missense mutation cosegregates with hand OA in several families. The mutation frequency is slightly more than 2% in patients with hand OA in the Icelandic population and has a relative risk of 2.1.