Population dynamics of 0-group flounder (Platichthys flesus L.) in Galway Bay, West of Ireland and the value of flounder from shore angling tourism in Ireland

The economic value of flounder from shore angling around Ireland was assessed. Flounder catches from shore angling tournaments around Ireland were related to domestic and overseas shore angling expenditure in order to determine an economic value for the species. Temporal trends in flounder angling catches, and specimen (trophy) flounder reports were also investigated. Flounder was found to be the most caught shore angling species in competitions around Ireland constituting roughly one third of the shore angling competition catch although this did vary by area. The total value of flounder from shore angling tourism was estimated to be of the order of €8.4 million. No significant temporal trends in flounder angling catches and specimen reports were found. Thus there is no evidence from the current study for any decline in flounder stocks. The population dynamics of 0-group flounder during the early benthic stage was investigated at estuarine sites in Galway Bay, west of Ireland. Information was analysed from the March to June sampling period over five years (2002 to 2006). Spatial and temporal variations in settlement and population length structure were analysed between beach and river habitats and sites. Settlement of flounder began from late March to early May of each year, most commonly in April. Peak settlement was usually in April or early May. Settlement was recorded earlier than elsewhere, although most commonly was similar to the southern part of the UK and northern France. Settlement was generally later in tidal rivers than on sandy beaches. Abundance of 0-group flounder in Galway Bay did not exhibit significant inter -annual variability. 0-group flounder were observed in dense aggregations of up to 105 m'2, which were patchy in distribution. Highest densities of 0-group flounder were recorded in limnetic and oligohaline areas as compared with the lower densities in polyhaline and to a lesser extent mesohaline areas. Measurements to of salinity allowed the classification of beaches, and tidal river sections near the mouth, into a salinity based scheme for length comparisons. Beaches were classified as polyhaline,the lower section of rivers as mesohaline, and the middle and upper sections as oligohaline. Over the March to June sampling period 0-group flounder utilised different sections at different length ranges and were significantly larger in more upstream sections. During initial settlement in April, 0-group flounder of 8-10 mm (standard length, SL) were present in abundance on polyhaline sandy beaches. By about 10mm (SL), flounder were present in all polyhaline, mesohaline and (oligohaline) sections. 0-group flounder became absent or in insignificant numbers in polyhaline and mesohaline sections in a matter of weeks after first appearance. From April to June, 0-group flounder of 12-30mm (SL) were found in more upstream locations in the oligohaline sections. About one month (May or June) after initial settlement, 0-group flounder became absent from the oligohaline sections. Concurrently, flounder start to reappear in mesohaline and polyhaline areas at approximately 30mm (SL) in June. The results indicate 0-group flounder in the early benthic stage are associated with low salinity areas, but as they grow, this association diminishes. Results strongly suggest that migration of 0-group flounder between habitats takes place during the early benthic phase.

Population dynamics of O-group plaice, Pleuronectes platessa L., on sandy beach nursery grounds in Galway Bay, the West Coast of Ireland, 2002 to 2006.

The recruitment of 0-group plaice to sandy beach nursery grounds in Galway Bay was examined, using a Riley push-net, from February to June in 2005 and 2006. Sampling was carried out every two weeks on spring tides. Three beaches were sampled, Ballyloughan, Silverstrand and Glann na Ri. Archived 0-group plaice, for Ballyloughan and Silverstrand, from 2004, were processed. Results were compared to findings from a previous study carried out in 2002 and 2003 (Allen 2004). Otolith microstructure analysis was used to determine hatching dates, larval duration, settlement dates, post-larval age and daily growth rates of 0-group plaice in April and May 2005. Results were compared to a previous study (Allen 2004). Hatching dates in Galway Bay ranged from late January to early April in 2005. No significant difference in hatching dates was observed between years or between beaches sampled. Larval duration of 0-group plaice in Galway Bay ranged from 21 to 45 days for fish sampled in April and May 2005. No significant difference was observed in larval age between beaches sampled in Galway Bay or between years in April 2003 and 2005. A significant difference was observed between larval age and years in May 2003 and 2005, however no significant difference was observed between beaches. Settlement timing was calculated using push-net data and otolith microstructure analysis. Settlement of 0-group plaice in Galway Bay generally started in early March and finished in May. Settlement patterns, calculated using otolith microstructure analysis, in 2003 and 2005, were not significantly different to one another. There was also no difference in settlement patterns between the beaches sampled. Results from the present study showed no spatial difference in the pelagic life cycle stages of fish caught in April and May 2003 and 2005.

Investigating the long term planning framework for the Galway Bay community from climate change.

This research looked at the scientific evidence available on climate change and in particular, projections on sea level rise which ranged from 0.5m to 2m by the end of the century. These projections were then considered in an Irish context. A review of current policy in Ireland revealed that there was no dedicated Government policy on climate change or coastal zone management. In terms of spatial planning policy, it became apparent that there was little or no guidance on climate change either at a national, regional or local level. Therefore, to determine the likely impacts of sea level rise in Ireland based on current spatial planning practice and policy, a scenario-building exercise was carried out for two case study areas in Galway Bay. The two case study areas were: Oranmore, a densely populated town located to the east of Inner Galway Bay; and Tawin Island, a rural dispersed community, located to the south east of Inner Galway Bay. A ‘best’ and ‘worse’ case scenario was envisaged for both areas in terms of sea level rise. In the absence of specific climate change policies it was projected that in the ‘best’ case scenario of 0.5m sea level rise, Tawin Island would suffer serious and adverse impacts while Oranmore was likely to experience slight to moderate impacts. However, in the ‘worse’ case scenario of a 2m sea level rise, it was likely that Tawin Island would be abandoned while many houses, businesses and infrastructure built within the floodplain of Oranmore Bay would be inundated and permanently flooded. In this regard, it was the author’s opinion that a strategic and integrated climate change policy and adaptation plan is vital for the island of Ireland that recognises the importance of integrated land use and spatial planning in terms of mitigation and adaptation to climate change.

Molecular epidemiology of sexually transmitted human papillomavirus in a self referred group of women in Ireland

Background: Human papillomavirus (HPV) causes cervical cancer and external genital warts. The purpose of this study is to document the genotype distribution of HPV in females aged between 18 and 34 who self-referred to an STI clinic with visible external genital warts (EGW). Scrapings were taken from visible external genital warts (EGW). These scrapings were analysed by PCR for the presence of HPV DNA. Positive samples were then genotyped by means of a commercially available assay (LiPA). A comparison of genotyping results determined by the LiPA assay and direct amplicon DNA sequencing was also performed. Results: Ninety-two patients out of 105 samples (88%) had detectable levels of HPV DNA. The majority of individuals with EGW (66%) showed the presence of two or more genotypes. The most common HPV genotypes present in the study population were HPV-6, HPV-11, HPV-16, HPV-18, HPV-33 and HPV-53. Potential effects of vaccination on HPV molecular epidemiology indicate that 40% of the patients could have been protected from the high risk genotypes HPV-16 and HPV-18.Conclusion: This is the first report of the molecular epidemiology of external genital warts in women aged between 18 and 34 from Ireland based on results from a LiPA assay. The study shows that most individuals are infected with multiple genotypes including those with high oncogenic potential and that the newly available HPV vaccines could have a significant impact on prevalence of the most common HPV genotypes in this study population.

Performance study of the Galway Bay wave energy test site floating power system

The Galway Bay wave energy test site promises to be a vital resource for wave energy researchers and developers. As part of the development of this site, a floating power system is being developed to provide power and data acquisition capabilities, including its function as a local grid connection, allowing for the connection of up to three wave energy converter devices. This work shows results from scaled physical model testing and numerical modelling of the floating power system and an oscillating water column connected with an umbilical. Results from this study will be used to influence further scaled testing as well as the full scale design and build of the floating power system in Galway Bay.

Report of the Working Group for the Bay of Biscay and the Iberian waters Ecoregion (WGBIE). 13-19 May 2016, ICES HQ, Copenhagen, Denmark

The ICES Working Group for the Bay of Biscay and the Iberic waters Ecoregion (WGBIE) met in Copenhagen, Denmark during 13–14 May 2016. There were 22 stocks in its remit distributed from ICES Divisions 3.a–4.a though mostly distributed in Sub Areas 7, 8 and 9. There were 21 participants, some of whom joined the meeting re-motely. The group was tasked with conducting assessments of stock status for 22 stocks using analytical, forecast methods or trends indicators to provide catch forecasts for eight stocks and provide a first draft of the ICES advice for 2016 for fourteen stocks. For the remaining stocks, the group had to update catch information and indices of abundance where needed. Depending on the result of this update, namely if it would change the perception of the stock, the working group drafted new advice. Analytical assessments using age-structured models were conducted for the northern and southern stocks of megrim and the Bay of Biscay sole. The two hake stocks and one southern stock of anglerfish were assessed using models that allow the use of only length-structured data (no age data). A surplus-production model, without age or length structure, was used to assess the second southern stocks of anglerfish. No ana-lytical assessments have been provided for the northern stocks of anglerfish after 2006. This is mostly due to ageing problems and to an increase in discards in recent years, for which there is no reliable data at the stock level. The state of stocks for which no analytical assessment could be performed was inferred from examination of commer-cial LPUE or CPUE data and from survey information. Three nephrops stocks from the Bay of Biscay and the Iberian waters are scheduled for benchmark assessments in October 2016. The WGBIE meeting spent some time review-ing the progress towards the benchmark (see Annex 6) together with longer term benchmarks (2017 and after, see section 1.) for sea bass in the Bay of Biscay, all an-glerfish and hake stocks assessed by the WG. For the northern megrim stock, the sched-ule an inter-benchmark meeting was completed successfully and the group reviewed the outcome and accepted the category 1 update assessment. A recurrent issue significantly constrained the group’s ability to address the terms of reference this year. Despite an ICES data call with a deadline of six weeks before the meeting, data for several stocks were resubmitted during the meeting which lead to increased workloads during the working group, as in that case, the assessments could not be carried out in National Laboratories prior to the meeting as mentioned in the ToRs. This is an important matter of concerns for the group members. Section 1 of the report presents a summary by stock and discusses general issues. Sec-tion 2 provides descriptions of the relevant fishing fleets and surveys used in the as-sessment of the stocks. Sections 3–18 contains the single stock assessments.

Modelling and control of a floating oscillating water column

A novel numerical model of a Bent Backwards Duct Buoy (BBDB) Oscillating Water Column (OWC) Wave Energy Converter was created based on existing isolated numerical models of the different energy conversion systems utilised by an OWC. The novel aspect of this numerical model is that it incorporates the interdependencies of the different power conversion systems rather than modelling each system individually. This was achieved by accounting for the dynamic aerodynamic damping caused by the changing turbine rotational velocity by recalculating the turbine damping for each simulation sample and applying it via a feedback loop. The accuracy of the model was validated using experimental data collected during the Components for Ocean Renewable Energy Systems (CORES) EU FP-7 project that was tested in Galway Bay, Ireland. During the verification process, it was discovered that the model could also be applied as a valuable tool when troubleshooting device performance. A new turbine was developed and added to a full scale model after being investigated using Computational Fluid Dynamics. The energy storage capacity of the impulse turbine was investigated by modelling the turbine with both high and low inertia and applying three turbine control theories to the turbine using the full scale model. A single Maximum Power Point Tracking algorithm was applied to the low-inertia turbine, while both a fixed and dynamic control algorithm was applied to the high-inertia turbine. These results suggest that the highinertia turbine could be used as a flywheel energy storage device that could help minimize output power variation despite the low operating speed of the impulse turbine. This research identified the importance of applying dynamic turbine damping to a BBDB OWC numerical model, revealed additional value of the model as a device troubleshooting tool, and found that an impulse turbine could be applied as an energy storage system.

Population genetic structure of brown crab (Cancer pagurus) in Irish waters

The brown crab (Cancer pagurus) fishery in Ireland is one of the most important financially and socio-economically, with the species worth approximately €15m per year in the first half of the decade. Only mackerel (Scomber scombrus) and Dublin Bay prawn (Nephrops norvegicus) are of greater value. Despite this, very little research has been conducted to describe the stock structure of brown crab on a national scale. In this study a country-wide assessment of genetic population structure was carried out. Sampling was conducted from commercial fishing boats from 11/06 to 04/08 at seven sample sites representing the central Irish brown crab fisheries, with one sample site from the UK also included in the study. Six microsatellite markers, specifically developed for brown crab, were used to assess genetic diversity and estimate population differentiation parameters. Significant genetic structuring was found using F-statistics (Fst = 0.007) and exact tests, but not with Bayesian methods. Samples from the UK and Wexford were found to be genetically distinct from all other populations. Three northern populations from Malm Head and Stanton Bank were genetically similar with Fst estimates suggesting connectivity between them. Also, Stanton Bank, again on the basis of Fst estimates, appeared to be connected to populations down the west coast of Ireland, as far south as Kerry. Two Galway samples, one inside and one outside of Galway Bay, were genetically differentiated despite their close geographic proximity. It is hypothesised that a persistent northerly summer current could transport pelagic larvae from populations along the southwest and west coasts of Ireland towards Stanton Bank in the North, resulting in the apparent connectivity observed in this study.

Critical bed shear stress and threshold of motion of maërl biogenic gravel

Critical bed shear stress for incipient motion has been determined for biogenic free-living coralline algae known as maërl. Maërl from three different sedimentary environments (beach, intertidal, and open marine) in Galway Bay, west of Ireland have been analysed in a rotating annular flume and linear flume. Velocity profile measurements of the benthic boundary layer, using an Acoustic Doppler Velocimeter, have been obtained in four different velocity experiments. The bed shear stress has been determined using three methods: Law of the Wall, Turbulent Kinetic Energy and Reynolds Stress. The critical Shields parameter has been estimated as a non-dimensional mobility number and the results have been compared with the Shields curve for natural sand. Maërl particles fall below this curve because its greater angularity allows grains to be mobilised easier than hydraulically equivalent particles. From previous work, the relationship between grain shape and the settling velocity of maërl suggests that the roughness is greatest for intertidal maërl particles. During critical shear stress determinations, beds of such rough particles exhibited the greatest critical shear stress probably because the particle thalli interlocked and resisted entrainment. The Turbulent Kinetic Energy methodology gives the most consistent results, agreeing with previous comparative studies. Rarely-documented maërl megaripples were observed in the rotating annular flume and are hypothesised to form at velocities ~10 cm s-1 higher than the critical threshold velocity, where tidal currents, oscillatory flow or combined-wave current interaction results in the preferential transport of maërl. A determination of the critical bed shear stress of maërl allows its mobility and rate of erosion and deposition to be evaluated spatially in subsequent applications to biological conservation management.

Contents of water, sulphur, total organic and inorganic carbon, XRF counts of Ti, S and Ca and radiocarbon ages of sediment core Co1008 from Skua Lake, Rauer Group, East Antarctica

Limited information on the East Antarctic Ice Sheet (EAIS) geometry during Marine Isotope Stage 3 (MIS 3; 60-25 ka) restricts our understanding of its behaviour during periods of climate and sea level change. Ice sheet models forced by global parameters suggest an expanded EAIS compared to the Holocene during MIS 3, but field evidence from East Antarctic coastal areas contradicts such modelling, and suggests that the ice sheet margins were no more advanced than at present. Here we present a new lake sediment record, and cosmogenic exposure results from bedrock, which confirm that Rauer Group (eastern Prydz Bay) was ice-free for much of MIS 3. We also refine the likely duration of the Last Glacial Maximum (LGM) glaciation in the region. Lacustrine and marine sediments from Rauer Group indicate the penultimate period of ice retreat predates 50 ka. The lacustrine record indicates a change from warmer/wetter conditions to cooler/drier conditions after ca. 35 ka. Substantive ice sheet re-advance, however, may not have occurred until much closer to 20 ka. Contemporary coastal areas were still connected to the sea during MIS 3, restricting the possible extent of grounded ice in Prydz Bay on the continental shelf. In contrast, relative sea levels (RSL) deduced from field evidence indicate an extra ice load averaging several hundred metres thicker ice across the Bay between 45 and 32 ka. Thus, ice must either have been thicker immediately inland (with a steeper ice profile), or there were additional ice domes on the shallow banks of the outer continental shelf. Further work is required to reconcile the differences between empirical evidence of past ice sheet histories, and the history predicted by ice sheet models from far-field temperature and sea level records.

The occurrence of PAHs and faecal sterols in Dublin Bay and their influence on sedimentary microbial communities

The source, concentration, and potential impact of sewage discharge and incomplete organic matter (OM) combustion on sedimentary microbial populations were assessed in Dublin Bay, Ireland. Polycyclic aromatic hydrocarbons (PAHs) and faecal steroids were investigated in 30 surface sediment stations in the bay. Phospholipid fatty acid (PLFA) content at each station was used to identify and quantify the broad microbial groups present and the impact of particle size, total organic carbon (%TOC), total hydrogen (%H) and total nitrogen (%N) was also considered. Faecal sterols were found to be highest in areas with historical point sources of sewage discharge. PAH distribution was more strongly associated with areas of deposition containing high %silt and %clay content, suggesting that PAHs are from diffuse sources such as rainwater run-off and atmospheric deposition. The PAHs ranged from 12 to 3072 ng/g, with 10 stations exceeding the suggested effect range low (ERL) for PAHs in marine sediments. PAH isomer pair ratios and sterol ratios were used to determine the source and extent of pollution. PLFAs were not impacted by sediment type or water depth but were strongly correlated to, and influenced by PAH and sewage levels. Certain biomarkers such as 10Me16:0, i17:0 and a17:0 were closely associated with PAH polluted sediments, while 16:1ω9, 16:1ω7c, Cy17:0, 18:1ω6, i16:0 and 15:0 all have strong positive correlations with faecal sterols. Overall, the results show that sedimentary microbial communities are impacted by anthropogenic pollution.

Synchronous reproduction may facilitate introgression in a hybrid mussel (Mytilus) population

Mussel populations on the Irish Atlantic coast comprise an interbreeding mixture of the blue mussel, Mytilus edulis (L.) and the Mediterranean mussel, Mytilus galloprovincialis (Lmk.). The occurrence of hybrid genotypes varies between sites but can be as high 80%. This study compares the reproductive cycle of M. edulis, M. galloprovincialis and their hybrids to determine if the extensive hybridisation observed at Irish Atlantic coast sites is linked to spawning synchrony between the two taxa. Mussels (40-45 mm size class) were collected monthly from a sheltered shore in Galway Bay from January to December 2005. Two major spawning events (March- June and September-October) were observed and gametogenesis took place throughout the year. The spawning cycles of the three taxa were largely overlapping. Small differences were observed in the timing of peak spawning which occurred in March and October in M. galloprovincialis and in May-June and September in M.edulis. Spawning of hybrid individuals was intermediate between the parental genotypes. Fecundity was slightly higher in M. galloprovincialis females compared to the other taxa (up to 30% difference, p<0.05). This apparent advantage is not shared by the sexes and is likely being offset by high numbers of hybrid genotypes releasing gametes during peak spawning of M. galloprovincialis. There was no evidence for increased mortality in hybrid males; sex ratios did not deviate from the 1:1 ratio. The results show that in this region of the hybrid zone the timing of reproduction does not present a barrier to gene flow between M. edulis and M. galloprovincialis. Nonetheless, small differences in the timing of peak spawning may increase the likelihood of conspecific fertilisation at certain times of the year. Hybrids outnumber the parental genotypes, undergo complete gametogenesis and show no evidence of depressed fitness (i.e. hybrids are reproductively competent suggesting a high degree of introgression.

Arm regeneration in two populations of Ophionereis reticulata (Echinodermata, Ophiuroidea)

This study compared the arm regeneration frequencies in two different populations of Ophionereis reticulata (Say, 1825) in Sao Sebastiao, Southeast Brazil and observed arm regeneration between age classes (juvenile and adults) and sexes (male and female). From the 1,170 individuals sampled, 1,089 (92.2%) showed signs of arm regeneration. The relative frequencies of regenerating arms in the two areas were not different (Baleeiro Isthmus: 91.3% and Grande Beach: 99.5%). Both areas also presented similar values for the number of arms regenerating/individual and in the frequency of regenerating individuals. The major part of the regenerating scars was concentrated in the distal portion of the arm. Sub-lethal predation is most likely the cause to the high rates of arm regeneration in O. reticulata. There was no significant differences in the regeneration rates between females (3.57 +/- 1.36 arms regenerating/individual) and males (3.47 +/- 1.42).

knOWLearn: a reuse-based approach for building ontologies in a semi-automatic way

In this poster paper we present an overview of knOWLearn, a novel approach for building domain ontologies in a semi-automatic fashion.

Verifying ontology requirements with SWIP

Verifying whether an ontology meets the set of established requirements is a crucial activity in ontology engineering. In this sense, methods and tools are needed (a) to transform (semi-)automatically functional ontology requirements into SPARQL queries, which can serve as unit tests to verify the ontology, and (b) to check whether the ontology fulfils the requirements. Thus, our purpose in this poster paper is to apply the SWIP approach to verify whether an ontology satisfies the set of established requirements.