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Characterizing the nature of genetic differentiation among individuals and populations and its distribution across the genome is increasingly important to inform both conservation and management of exploited species. Atlantic Halibut (Hippoglossus hippoglossus) is an ecologically and commercially important fish species, yet knowledge of population structure and genomic diversity in this species remains lacking. Here, we use restriction-site associated DNA sequencing and a chromosome-level genome assembly to identify over 86 000 single nucleotide polymorphisms mapped to 24 chromosome-sized scaffolds, genotyped in 734 individuals across the Northwest Atlantic. We describe subtle but significant genome-wide regional structuring between the Gulf of St. Lawrence and adjacent Atlantic continental shelf. However, the majority of genetic divergence is associated with a large putative chromosomal rearrangement (5.74 megabases) displaying high differentiation and linkage disequilibrium, but no evidence of geographic variation. Demographic reconstructions suggest periods of expansion coinciding with glacial retreat, and more recent declines in Ne. This work highlights the utility of genomic data to identify multiple sources of genetic structure and genomic diversity in commercially exploited marine species.

Atlantic salmon (Salmo salar) populations throughout the North Atlantic have declined in recent decades largely due to reduced marine survival, yet our understanding of marine distribution patterns and migratory routes remains limited. Here, we assigned archived individual samples (n = 3891) collected over a half century (1968–2018) throughout the North Atlantic to region of origin using range-wide genetic assignment. In the Northwest Atlantic, the distribution of assignments reinforced the importance of the Labrador Sea as an aggregation area, with 73% of all reporting groups detected. Moreover, individuals from six European reporting groups were identified in the Northwest Atlantic, and detections decreased with decreasing latitude spanning an area from Greenland to southern Newfoundland. In the Northeast Atlantic, six North American reporting groups were detected in samples from around the Faroe Islands. Based on the distribution of samples, estimates of trans-Atlantic migration distance averaged 3861 and 2889 km for North American and European salmon respectively. Our analysis highlights the widespread importance of the Labrador Sea and Faroe Islands to the species marine distribution patterns, and the prevalence of long-distance trans-Atlantic migration. Ultimately, the results suggest that environmental conditions experienced by many Atlantic salmon populations span much of the North Atlantic Ocean.

To develop more reliable marine species distribution models (SDMs), we examine how genetic, climatic, and biotic interaction gradients give rise to prediction error in marine SDM. Genetic lineages with distinct ecological requirements spanning genetic gradients have yet to be treated separately in marine SDM, which are often constrained to modeling the potential distribution of one biological unit (e.g. lineage or species) at a time. By comparing SDM performance for the whole species or where observation and predictions were partitioned among geographically discontinuous genetic lineages, we first identified the appropriate biological unit for modeling sea scallop. Prediction errors, in particular contiguous omissions at the northern range margins were effectively halved in genetic lineage SDM (Total error=15%) verses whole species SDM. Remaining SDM prediction error was strongly associated with: i) Sharp climatic gradients (abrupt and persistent spatial shifts in limiting temperatures) found within continental shelf breaks and bottom channels. ii) A biotic gradient in the predation of sea scallop juveniles by the sand star within the Hudson Shelf USA. Our findings highlight how the accuracy of marine SDM is dependent on capturing the appropriate biological unit for modeling (e.g. lineages rather than species) and adequately resolving limiting abiotic and biotic interaction gradients.

The West Greenland Atlantic Salmon (Salmo salar) fishery represents the largest remaining mixed-stock fishery for Atlantic Salmon in the Northwest Atlantic and targets multi-sea-winter (MSW) salmon from throughout North America and Europe. We evaluated stock composition of salmon harvested in the waters off West Greenland (n = 5684 individuals) using genetic mixture analysis and individual assignment to inform conservation of North American populations, many of which are failing to meet management targets. Regional contributions to this fishery were estimated using 2169 individuals sampled throughout the fishery between 2011 and 2014. Of these, 22% were identified as European in origin. Major North American contributions were detected from Labrador (∼20%), the Southern Gulf/Cape Breton (29%), and the Gaspe Peninsula (29%). Minor contributions (∼5%) were detected from Newfoundland, Ungava, and Quebec regions. Region-specific catches were extrapolated using estimates of composition and fishery catch logs and harvests ranged from 300 to 600 and 2000 to 3000 individuals for minor and major constituents, respectively. To evaluate the temporal stability of the observed fishery composition, we extended the temporal coverage through the inclusion of previously published data (1995–2006, n = 3095) and data from archived scales (1968–1998, n = 420). Examination of the complete time-series (47 years) suggests relative stability in stock proportions since the late 1980s. Genetic estimates of stock composition were significantly associated with model-based estimates of returning MSW salmon (individual years r = 0.69, and overall mean r = 0.96). This work demonstrates that the analysis of both contemporary and archived samples in a mixed-stock context can disentangle levels of regional exploitation and directly inform assessment and conservation of Atlantic Salmon in the West Greenland interceptory Atlantic Salmon fishery.

We evaluated the influence of environmental exposure of juvenile Atlantic cod (Gadus morhua) to inform interpretations of natal origins and movement patterns using otolith geochemistry. Laboratory rearing experiments were conducted with a variety of temperature (∼5, 8.5, and 12°C) and salinity (∼25, 28.5, and 32 PSU) combinations. We measured magnesium (Mg), manganese (Mn), strontium (Sr), and barium (Ba), expressed as a ratio to calcium (Ca), using laser ablation inductively coupled plasma mass spectrometry (ICP-MS), and stable carbon (δ13C) and oxygen (δ18O) isotopes using isotope ratio monitoring mass spectrometry. Temperature and salinity significantly affected all elements and isotopes measured, except salinity on Mg:Ca. We detected significant interactions among temperature and salinity for Mn:Ca and Ba:Ca partition coefficients (ratio of otolith chemistry to water chemistry), with significant temperature effects only detected in the 32 and 28.5 PSU salinity treatments. Similarly, we detected a significant interaction between temperature and salinity in incorporation of δ13C, with a significant temperature effect except at intermediate salinity. These results support the contention that environmental mediation of otolith composition varies among species, thus limiting the ability of generalized models to infer life history patterns from chemistry. Our results provide essential baseline information detailing environmental influence on juvenile Atlantic cod otolith composition, punctuating the importance of laboratory validations to translate species-specific otolith composition when inferring in situ life histories and movements.

The roles of ecological speciation and reinforcement in the formation of contemporary diversity remain contentious. In the present study, we contrast phenotypic and molecular divergence within morphologically diverged bimodal sympatric and allopatric pairs of rainbow smelt, Osmerus mordax. We hypothesize that, in sympatry, evidence of selection associated with resource partitioning will be visible through strong divergence, reinforcement, and greater character displacement. Parallel morphological divergence was observed between the two trophic forms (macrophagous and microphagous), with several examples of greater trait divergence in sympatry than allopatry. Mitochondrial DNA sequence analysis indicated no association between historical clades and morphology; however, Bayesian clustering using microsatellites supported the isolation of these morphs under both allopatry and sympatry. Estimates of genetic isolation were one order of magnitude lower than measures of morphological divergence, consistent with a hypothesis of strong contemporary selection. Using experimental crosses, we obtained similar rates of fertilization success among the allopatric hybrid and pure crosses; whereas, in the sympatric hybrid crosses, fertilization rates dropped by 30-50%, suggesting a clear role for reinforcement through prezygotic incompatibilities. The present study supports the hypothesis that processes of post-glacial radiation and diversification differ between sympatry and allopatry, and indicates a role for reinforcement and ecological processes in recent sympatric diversification.

Aging is associated with alterations in the immune system, effects which may be exacerbated by inadequate zinc (Zn) status. We examined the relationship between Zn status and markers of immunity and the effect of supplementation with 15 mg or 30 mg Zn/d for 6 months on immune status in healthy individuals. Zn status was assessed by dietary intake and biochemical indices. Immune status was assessed by multiple flow cytometric methods. At baseline, Zn concentration was positively associated with lymphocyte subpopulation counts and T-lymphocyte activation. Zn supplementation of 30 mg/d significantly lowered B-lymphocyte count, albeit at month 3 only. Lower doses of Zn (15 mg Zn/d) significantly increased the ratio of CD4 to CD8 T lymphocytes at month 6. Overall, these findings suggest that total Zn intake (diet plus supplementation) of up to 40 mg Zn/d do not have significant long-term effects on immune status in apparently healthy persons aged 55-70 years.

Northern Ireland (NI) has one of the lowest rates of breast-feeding initiation and duration in both the UK and the industrialized world. This study therefore aimed to explore the relationship between infant-feeding attitudes and feeding intention and outcome in expectant mothers within NI. Expectant mothers (n = 200) were recruited from hospital antenatal booking clinics. Each completed a demographic questionnaire and the self-administered Iowa Infant Feeding Attitude Scale (IIFAS). Participants (n = 192) were followed up after birth through the Northern Ireland Maternity System. The IIFAS distinguished between those mothers who intended to breast-feed (higher IIFAS scores) and those who intended to artificially feed (lower IIFAS scores) as well as between those who breast-fed and those who artificially fed on discharge from hospital. The IIFAS was also able to distinguish between mothers in regard to feeding intention and outcome on the basis of education, socio-economic class, income and marital status. This suggests that the IIFAS could prove useful in the targeting and evaluation of intervention to promote breast-feeding.

Motivation: Genomic datasets generated by high-throughput technologies are typically characterized by a moderate number of samples and a large number of measurements per sample. As a consequence, classification models are commonly compared based on resampling techniques. This investigation discusses the conceptual difficulties involved in comparative classification studies. Conclusions derived from such studies are often optimistically biased, because the apparent differences in performance are usually not controlled in a statistically stringent framework taking into account the adopted sampling strategy. We investigate this problem by means of a comparison of various classifiers in the context of multiclass microarray data. Results: Commonly used accuracy-based performance values, with or without confidence intervals, are inadequate for comparing classifiers for small-sample data. We present a statistical methodology that avoids bias in cross-validated model selection in the context of small-sample scenarios. This methodology is valid for both k-fold cross-validation and repeated random sampling. Contact: dp.berrar@ulster.ac.uk