Complex pattern of genetic structuring in the Atlantic salmon (Salmo salar L.) of the River Foyle system in northwest Ireland: disentangling the evolutionary signal from population stochasticity

Little is known about the microevolutionary processes shaping within river population genetic structure of aquatic organisms characterized by high levels of homing and spawning site fidelity. Using a microsatellite panel, we observed complex and highly significant levels of intrariver population genetic substructure and Isolation-by-Distance, in the Atlantic salmon stock of a large river system. Two evolutionary models have been considered explaining mechanisms promoting genetic substructuring in Atlantic salmon, the member-vagrant and metapopulation models. We show that both models can be simultaneously used to explain patterns and levels of population structuring within the Foyle system. We show that anthropogenic factors have had a large influence on contemporary population structure observed. In an analytical development, we found that the frequently used estimator of genetic differentiation, F-ST, routinely underestimated genetic differentiation by a factor three to four compared to the equivalent statistic Jost's D-est (Jost 2008). These statistics also showed a near-perfect correlation. Despite ongoing discussions regarding the usefulness of "adjusted" F-ST statistics, we argue that these could be useful to identify and quantify qualitative differences between populations, which are important from management and conservation perspectives as an indicator of existence of biologically significant variation among tributary populations or a warning of critical environmental damage.

Exploring the Transcriptome of Atlantic Salmon (Salmo salar) Skin, a Major Defense Organ

The skin of fish is the first line of defense against pathogens and parasites. The skin transcriptome of the Atlantic salmon is poorly characterized, and currently only 2,089 expressed sequence tags (ESTs) out of a total of half a million sequences are generated from skin-derived cDNA libraries. The primary aim of this study was to enhance the transcriptomic knowledge of salmon skin by using next-generation sequencing (NGS) technology, namely the Roche-454 platform. An equimolar mixture of high-quality RNA from skin and epidermal samples of salmon reared in either freshwater or seawater was used for 454-sequencing. This technique yielded over 600,000 reads, which were assembled into 34,696 isotigs using Newbler. Of these isotigs, 12 % had not been sequenced in Atlantic salmon, hence representing previously unreported salmon mRNAs that can potentially be skin-specific. Many full-length genes have been acquired, representing numerous biological processes. Mucin proteins are the main structural component of mucus and we examined in greater detail the sequences we obtained for these genes. Several isotigs exhibited homology to mammalian mucins (MUC2, MUC5AC and MUC5B). Mucin mRNAs are generally > 10 kbp and contain large repetitive units, which pose a challenge towards full-length sequence discovery. To date, we have not unearthed any full-length salmon mucin genes with this dataset, but have both N- and C-terminal regions of a mucin type 5. This highlights the fact that, while NGS is indeed a formidable tool for sequence data mining of non-model species, it must be complemented with additional experimental and bioinformatic work to characterize some mRNA sequences with complex features.

Source as a controlling factor on the quality and interpretation of sediment magnetic records from the northern North Atlantic

Magnetic properties of eight particle size ranges from nine locations in Iceland and 26 locations in southern Greenland reveal the importance of source variation for our understanding of paleomagnetic and environmental magnetic records in the marine environment. These terrestrial samples show varying degrees of particle size dependence with all samples showing that the silt fraction possesses greater concentrations of ferrimagnetic minerals than either clay or sand. Fine pseudo-single domain (PSD) size magnetic grains dominate the magnetic assemblage of all Icelandic fractions. In contrast, Greenlandic samples possess greater variation in magnetic grain size; only fine silt and clay are as magnetically fine as the Icelandic PSD grains, while Greenlandic silts and sands are dominated by coarser PSD and multi-domain grains. These observations from potential marine sediment sources suggest that the silt size fraction is a likely driver for much of the concentration-dependent parameters derived from bulk magnetic records and that the magnetic grain size of the silt fraction can be used to discriminate between Icelandic and Greenlandic sources. Using these results to examine magnetic grain size records from marine sediment cores collected across the northern North Atlantic suggests that source, not just transport-controlled physical grain-size, has a significant impact on determining the magnetic grain size at a particular location. Homogeneity of magnetic grain size in Icelandic sediments at least partially explains the consistent quality of paleomagnetic records derived from cores surrounding Iceland and their ability to buffer large environmental changes. © 2013 Elsevier B.V.

Threats and knowledge gaps for ecosystem services provided by kelp forests: a northeast Atlantic perspective.

Kelp forests along temperate and polar coastlines represent some of most diverse and productive habitats on the Earth. Here, we synthesize information from >60 years of research on the structure and functioning of kelp forest habitats in European waters, with particular emphasis on the coasts of UK and Ireland, which represents an important biogeographic transition zone that is subjected to multiple threats and stressors. We collated existing data on kelp distribution and abundance and reanalyzed these data to describe the structure of kelp forests along a spatial gradient spanning more than 10° of latitude. We then examined ecological goods and services provided by kelp forests, including elevated secondary production, nutrient cycling, energy capture and flow, coastal defense, direct applications, and biodiversity repositories, before discussing current and future threats posed to kelp forests and identifying key knowledge gaps. Recent evidence unequivocally demonstrates that the structure of kelp forests in the NE Atlantic is changing in response to climate- and non-climate-related stressors, which will have major implications for the structure and functioning of coastal ecosystems. However, kelp-dominated habitats along much of the NE Atlantic coastline have been chronically understudied over recent decades in comparison with other regions such as Australasia and North America. The paucity of field-based research currently impedes our ability to conserve and manage these important ecosystems. Targeted observational and experimental research conducted over large spatial and temporal scales is urgently needed to address these knowledge gaps.

New records for the shallow-water chiton fauna (Mollusca, Polyplacophora) of the Azores (NE Atlantic)

Published records, original data from recent field work on all of the islands of the Azores (NE Atlantic), and a revision of the entire mollusc collection deposited in the Department of Biology of the University of the Azores (DBUA) were used to compile a checklist of the shallow-water Polyplacophora of the Azores. Lepidochitona cf. canariensis and Tonicella rubra are reported for the first time for this archipelago, increasing the recorded Azorean fauna to seven species.

North Atlantic marine radiocarbon reservoir ages through Heinrich event H4: A new method for marine age model construction

Cooling and sinking of dense saline water in the Norwegian–Greenland Sea is essential for the formation of North Atlantic Deep Water. The convection in the Norwegian–Greenland Sea allows for a northward flow of warm surface water and southward transport of cold saline water. This circulation system is highly sensitive to climate change and has been shown to operate in different modes. In ice cores the last glacial period is characterized by millennial-scale Dansgaard–Oeschger (D–O) events of warm interstadials and cold stadials. Similar millennial-scale variability (linked to D–O events) is evident from oceanic cores, suggesting a strong coupling of the atmospheric and oceanic circulations system. Particularly long-lasting cold stadials correlate with North Atlantic Heinrich events, where icebergs released from the continents caused a spread of meltwater over the northern North Atlantic and Nordic seas. The meltwater layer is believed to have caused a stop or near-stop in the deep convection, leading to cold climate. The spreading of meltwater and changes in oceanic circulation have a large influence on the carbon exchange between atmosphere and the deep ocean and lead to profound changes in the 14C activity of the surface ocean. Here we demonstrate marine 14C reservoir ages (R) of up to c. 2000 years for Heinrich event H4. Our R estimates are based on a new method for age model construction using identified tephra layers and tie-points based on abrupt interstadial warmings.

On sea level change in the North Sea influenced by the North Atlantic Oscillation: local and remote steric effects

In this study, contributions of both local steric and remote baroclinic effects (i.e., steric variations external to the region of interest) to the inter-annual variability of winter sea level in the North Sea, with respect to the North Atlantic Oscillation (NAO), for the period of 1953–2010 are investigated. On inter-annual time scales in this period, the NAO is significantly correlated to sea level variations in the North Sea only in the winter months (December–March), while its correlation to sea temperature over much of the North Sea is only significant in January and February. The discrepancy in sea level between observations and barotropic tide and surge models forced by tides and local atmospheric forcing, i.e., local atmospheric pressure effects and winds, in the present study are found to be consistent with previous studies. In the North Sea, local thermosteric effects caused by thermal expansion play a minor role on winter-mean NAO related sea level variability compared with atmospheric forcing. This is particularly true in the southeastern North Sea where water depths are mostly less than 25 m. Our calculations demonstrate that the discrepancy can be mostly explained by remote baroclinic effects, which appear as water mass exchanges on the continental shelf and are therefore only apparent in ocean bottom pressure. In the North Sea, NAO related sea level variations seem to be a hybrid of barotropic and baroclinic processes. Hence, they can only be adequately modelled with three-dimensional baroclinic ocean models that include contributions of baroclinic effects and large-scale atmospheric forcing external to the region of interest.

Sea-level changes in Iceland and the influence of the North Atlantic Oscillation during the last half millennium

We present a new, diatom-based sea-level reconstruction for Iceland spanning the last -500 years, and investigate the possible mechanisms driving the sea-level changes. A sea-level reconstruction from near the Icelandic low pressure system is important as it can improve understanding of ocean-atmosphere forcing on North Atlantic sea-level variability over multi-decadal to centennial timescales. Our reconstruction is from Viarhólmi salt marsh in Snæfellsnes in western Iceland, a site from where we previously obtained a 2000-yr record based upon less precise sea-level indicators (salt-marsh foraminifera). The 20th century part of our record is corroborated by tide-gauge data from Reykjavik. Overall, the new reconstruction shows ca0.6m rise of relative sea level during the last four centuries, of which ca0.2m occurred during the 20th century. Low-amplitude and high-frequency sea-level variability is super-imposed on the pre-industrial long-term rising trend of 0.65m per 1000 years. Most of the relative sea-level rise occurred in three distinct periods: AD 1620-1650, AD 1780-1850 and AD 1950-2000, with maximum rates of ~3±2mm/yr during the latter two of these periods. Maximum rates were achieved at the end of large shifts (from negative to positive) of the winter North Atlantic Oscillation (NAO) Index as reconstructed from proxy data. Instrumental data demonstrate that a strong and sustained positive NAO (a deep Icelandic Low) generates setup on the west coast of Iceland resulting in rising sea levels. There is no strong evidence that the periods of rapid sea-level rise were caused by ocean mass changes, glacial isostatic adjustment or regional steric change. We suggest that wind forcing plays an important role in causing regional-scale coastal sea-level variability in the North Atlantic, not only on (multi-)annual timescales, but also on multi-decadal to centennial timescales.

Molecular pedigree reconstruction and estimation of evolutionary parameters in a wild Atlantic salmon river system with incomplete sampling: a power analysis

Background: Pedigree reconstruction using genetic analysis provides a useful means to estimate fundamental population biology parameters relating to population demography, trait heritability and individual fitness when combined with other sources of data. However, there remain limitations to pedigree reconstruction in wild populations, particularly in systems where parent-offspring relationships cannot be directly observed, there is incomplete sampling of individuals, or molecular parentage inference relies on low quality DNA from archived material. While much can still be inferred from incomplete or sparse pedigrees, it is crucial to evaluate the quality and power of available genetic information a priori to testing specific biological hypotheses. Here, we used microsatellite markers to reconstruct a multi-generation pedigree of wild Atlantic salmon (Salmo salar L.) using archived scale samples collected with a total trapping system within a river over a 10 year period. Using a simulation-based approach, we determined the optimal microsatellite marker number for accurate parentage assignment, and evaluated the power of the resulting partial pedigree to investigate important evolutionary and quantitative genetic characteristics of salmon in the system.

Results: We show that at least 20 microsatellites (ave. 12 alleles/locus) are required to maximise parentage assignment and to improve the power to estimate reproductive success and heritability in this study system. We also show that 1.5 fold differences can be detected between groups simulated to have differing reproductive success, and that it is possible to detect moderate heritability values for continuous traits (h(2) similar to 0.40) with more than 80% power when using 28 moderately to highly polymorphic markers.

Conclusion: The methodologies and work flow described provide a robust approach for evaluating archived samples for pedigree-based research, even where only a proportion of the total population is sampled. The results demonstrate the feasibility of pedigree-based studies to address challenging ecological and evolutionary questions in free-living populations, where genealogies can be traced only using molecular tools, and that significant increases in pedigree assignment power can be achieved by using higher numbers of markers.