• Eutrophication from agricultural sources : a comparison of SWAT, HSPF and SHETRAN/GOPC phosphorus models for three Irish catchments - Final Report

      Nasr, Ahmed Elssidig; Bruen, Michael (University College Dublin. Centre for Water Resources Research, 02/07/2012)
      Phosphorous has been implicated as the primary cause of the deterioration of surface water quality in Ireland. Extensive water quality surveys revealed that diffuse sources (runoff and subsurface flows) from agricultural land are the major contributors of phosphorus to surface waters. The mechanism of phosphorus movement from land to water can be described by a number of mathematical models that vary in modelling approaches and scales (plot, field and catchment). In this work three efficient mathematical models of diffuse source pollution in general and of phosphorus in particular have been applied, for the first time, to three Irish catchments (Clarianna (Co. Tipperary), Dripsey (Co. Cork) and Oona (Co. Tyrone)) in order to explore the suitability of these models in Irish conditions for future use in implementing the European Water Framework Directive (WFD). The models are: (i) Soil Water Assessment Tool (SWAT), (ii) Hydrological Simulation Programme FORTRAN (HSPF) and (iii) Système Hydrologique Européen TRAnsport (SHETRAN). The first two can model phosphorus production directly while the third can calculate fields of various hydrological variables relevant to phosphorous modelling. For the latter, a generic phosphorus modelling component called Grid Oriented Phosphorus Component (GOPC) has been developed here to model the phosphorus detachment and transport by taking as inputs the hydrological fields produced by any physically-based distributed catchment model such as SHETRAN. The three models have been successfully transferred to Irish conditions and this required the build up of a database consisting of topographic, land use and soil maps, water quality and weather data. The models application involved two stages. In the first stage, hydrological variables (evaporation, runoff, etc.) within the catchment domains were simulated by each of the three models. The second stage uses the outputs of the first in order to estimate the amount of phosphorus loss from the catchments. The SWAT, HSPF, and SHETRAN/GOPC models have been calibrated and then compared and assessed on the basis of their ability to fit and reproduce the flow discharges and phosphorus loads and concentrations for the three test catchments. The findings from the flow and phosphorus calibrations of SWAT and HSPF models were generally consistence with what have been found from previous studies outside Ireland. However, the simple structure of the first order kinetics method used for phosphorus modelling in HSPF has generally impeded the freedom of the phosphorus calibration which was noticeably difficult. Application of the SHETRAN model to the study catchments has illustrated the importance of carefully assigning the parameters related to the soil water modelling, particularly the parameters of the van Genuchten soil-hydraulic function, in order to obtain the best results. The GOPC performance has been found to depend significantly on the SHETRAN model which provided the required hydrological variables. The flow comparison has showed that in the three catchments, the HSPF model was the best in simulating the mean daily discharges. Moreover discharge simulation from an independent validation run of the three models in the Oona catchment have also demonstrated the superiority of the hydrological component of HSPF. However, the best calibration results for daily total phosphorus loads in the study catchments has been achieved by the SWAT model. However from the validation in the Oona catchment the HSPF has been found better than the other two models, SWAT and GOPC, in simulating the total phosphorus loads. Generally the results of total phosphorus loads from the GOPC in the three catchments were quite good and this model has reproduced some observed values better than the best model, SWAT. Simulation of the daily dissolved reactive phosphorus loads by the three models in the study catchments have showed big differences between the simulated and the observed data in most of the cases. Results for mean daily total and dissolved reactive phosphorus concentrations from the three models were not as good as the results for the loads in the three catchments.
    • Eutrophication from agricultural sources : a comparison of SWAT, HSPF and SHETRAN/GOPC phosphorus models for three Irish catchments : executive summary

      Nasr, Ahmed Elssidig; Bruen, Michael (University College Dublin. Centre for Water Resources Research, 02/07/2012)
    • Irish Famine Facts

      Keating, John (Teagasc, Ballsbridge, Dublin 4, 1996-06)
      The Irish Famine of 1845-1850 caused over one million deaths and forced a further one million people to flee the country. In this book, the author sets out to provide a synopsis of the documented facts and scientific background to the famine. The poverty, the hardship of subsistence living and the role of the potato in pre-famine Irleand are described. So also is the coming of blight and the response of the Government and voluntary bodies to the famine. The consequences of the disaster for the people are dealt with in detail. The book is fully illustrated and presents in a concise format the story of one of the greatest human tragedies of the nineteenth century.
    • Marriage exchanges, seed exchanges, and the dynamics of manioc diversity

      Deletrea, Marc; McKey, Doyle B.; Hodkinson, Trevor R (National Academy of Sciences, 2012-07-02)
      The conservation of crop genetic resources requires understanding the different variables-cultural, social, and economic-that impinge on crop diversity. In small-scale farming systems, seed exchanges represent a key mechanism in the dynamics of crop genetic diversity, and analyzing the rules that structure social networks of seed exchange between farmer communities can help decipher patterns of crop genetic diversity. Using a combination of ethnobotanical and molecular genetic approaches, we investigated the relationships between regional patterns of manioc genetic diversity in Gabon and local networks of seed exchange. Spatially explicit Bayesian clustering methods showed that geographical discontinuities of manioc genetic diversity mirror major ethnolinguistic boundaries, with a southern matrilineal domain characterized by high levels of varietal diversity and a northern patrilineal domain characterized by low varietal diversity. Borrowing concepts from anthropology-kinship, bridewealth, and filiation-we analyzed the relationships between marriage exchanges and seed exchange networks in patrilineal and matrilineal societies. We demonstrate that, by defining marriage prohibitions, kinship systems structure social networks of exchange between farmer communities and influence the movement of seeds in metapopulations, shaping crop diversity at local and regional levels.
    • Modelling phosphorus loss from agricultural catchments : a comparison of the performance of SWAT, HSPF and SHETRAN for the Clarianna catchment

      Nasr, Ahmed Elssidig; Bruen, Michael; Parkin, Geoff; Birkinshaw, Steve; Moles, Richard; Byrne, Paul; Environmental Protection Agency (IWA Publishing, 02/07/2012)
      Much research in Europe at present has been directed at generating and assessing modelling tools for use in catchment management, driven by the requirements and schedule of the Water Framework Directive. A logical first step is to assess the suitability of existing models for this task so that any resources used in generating new models can be targeted at actual modelling needs. Crucial questions, relating to the model structure and complexity and spatial and temporal scales required must also be addressed. This paper reports a comparison of the performance and suitability of three "off-the-shelf" distributed catchment models, each with a different level of complexity, applied to modelling phosphorous losses from the Clarianna catchment in Ireland. In this paper, the performance of three such models (SWAT, HSPF and SHETRAN/GOPC) is compared, both in estimating discharges and phosphorous loads in the Clarianna catchment. The flow comparison has showed that the HSPF model was the best in simulating the mean daily discharges. However, the best calibration results for daily total phosphorus loads in the study catchment has been achieved by the SWAT model.
    • Molecular genetic typing reveals further insights into the diversity of animal-associated Staphylococcus aureus

      Smyth, Cyril James; Hartigan, James Patrick (Society for General Microbiology, 2012-07-02)
      Staphylococcus aureus is an important pathogen of man, but is also able to colonize and cause disease in a wide variety of mammals and birds. An extended multilocus sequencing approach, involving multilocus sequence typing (MLST), sas typing, spa typing and agr typing, was used to examine the molecular diversity of 118 S. aureus isolates recovered from a range of host species and to compare these data with the known diversity of human-derived isolates. MLST revealed that the commonest animal-associated MLST types were ST133, ST5, ST71, ST97, ST126 and ST151. ST133 appears to be an ungulate-animal-specific genotype, as no evidence of ST133 associating with humans has yet been found in the literature. Novel and unique sas alleles were identified in the animal-associated strains that may represent animal-associated sas alleles. However, sas typing exhibited a lower typeability than MLST for the animal strains (91.3 %). Phylogenetic analyses using neighbour-joining and maximum-parsimony trees localized ruminant-associated MLST lineages to both previously identified S. aureus subspecies aureus subgroups, thus explaining the finding of all four agr types within the ruminant-associated strains. S. aureus isolates recovered from chickens and rabbits were genotypically more similar to known human genotypes than the ruminant-associated lineages.
    • Multi-criteria and Decision Support Systems in support of the Water Framework Directive in Ireland

      Bruen, Michael; Nasr, Ahmed Elssidig (2012-07-02)
      The current challenge in the implementation of the Water Framework Directive in Ireland is to introduce programmes of measures that will address the targeted environmental objectives in each River Basin District (RBD). Introduction of such programmes requires that proposed measures be thoroughly evaluated and that decisions will involve multiple criteria and must include stakeholders preferences and opinions. Decision Support Systems (DSS) facilitate this process. Many such systems have been developed and used in relation to water quality. In addition to their technical, modeling, benefits, DSS can also form the basis of systems to communicate options, benefits and damages to stakeholders and to receive feedback on their attitudes and preferences. Such systems could also be involved in facilitating the subsequent negotiations and resulting compromises. In Ireland, a new research project, Wincoms, has commenced which will address these aspects and will provide recommendations for suitable systems to be used in Ireland.
    • Organic dairy farming: impacts on insect flower interaction networks and pollination

      Stout, Jane Catherine; Power, Eileen (Wiley, 2012-07-02)
      1. Pollination interactions comprise a network of connections between flowers and insect visitors. They are crucial for reproductive success in many angiosperms but are threatened by intensive agricultural practices. Although less intensive approaches, including organic farming, could improve farmland biodiversity, it is not clear whether or not these approaches enhance wild plant pollination and the stability of insect–flower interaction networks. 2. We investigated the effects of organic vs. conventional farming on insect–flower interaction network size and structure, bee and hoverfly diversity, and pollination in 10 pairs of organic and conventional dairy farms in the Republic of Ireland. 3. We found that insect–flower interaction networks on organic farms were larger and more asymmetrically structured than networks on conventional farms. Overall, however, networks contained fewer taxa and niche overlap and plant ⁄ animal ratios were relatively low compared with previously documented insect–flower interaction networks. Organic farms did attract higher numbers of bees partly because of higher floral abundances (mainly Trifolium sp.). Hoverfly evenness was greater in organic farms but neither abundance, richness nor evenness was related to floral abundance, suggesting organic farms provide additional resources for hoverflies. Pollination of Crataegus monogyna hawthorn was higher on organic farms, although pollen deposition was limited. 4. Synthesis and applications. Organic dairy farming can increase the size and alter the structure of insect–flower interaction networks. However, network stability was not improved and all networks (organic and conventional) were vulnerable because of their small size, low niche overlap and low plant ⁄ animal ratios. Nonetheless, organic farming provided more flowers that attracted more flower visitors and improved pollination of C. monogyna. We suggest that strategic management of important flowers for pollinators in hedgerows and pastures should be endorsed in agri-environmental schemes. Sowing Trifolium spp., and allowing these plants to flower, could benefit bees, but more research into hoverfly ecology is necessary before realistic conservation recommendations can be made for this group. We conclude that organic farming, although not the solution in its present form, can benefit insect biodiversity, insect–flower interaction networks and insect-mediated pollination.
    • Pathogenomic analysis of the common bovine Staphylococcus aureus clone (ET3): emergence of a virulent subtype with potential risk to public health

      Smyth, Cyril James; Hartigan, James Patrick (University of Chicago Press, 2012-07-02)
      A common clone (ET3) of Staphylococcus aureus is responsible for a large proportion of cases of bovine mastitis and occasionally causes zoonotic infections of humans. In the present study, we report the identification of a virulent clonal subtype (ST151) of ET3, which resulted in increased tissue damage and mortality in a mouse model of mastitis. ST151 has undergone extensive diversification in virulence and regulatory‐gene content, including the acquisition of genetic elements encoding toxins not made by other ET3 strains. Furthermore, ST151 had elevated levels of RNAIII and cytolytic toxin–gene expression, consistent with the enhanced virulence observed during experimental infection. Previously, the ST151 clone was shown to be hypersusceptible to the acquisition of vancomycin‐resistance genes from Enterococcus spp. Taken together, these data indicate the emergence of a virulent subtype of the common ET3 clone, which could present an enhanced risk to public health.
    • Physically-based, distributed, catchment modelling for estimating sediment and phosphorus loads to rivers and lakes : issues of model complexity, spatial and temporal scales and data requirements

      Nasr, Ahmed Elssidig; Bruen, Michael; Jordan, Philip; Moles, Richard; Kiely, Gerard; Byrne, Paul (Office of Public Works, 02/07/2012)
    • Semi-supervised linear discriminant analysis

      Toher, Deirdre; Downey, Gerard; Murphy, Thomas Brendan; Science Foundation Ireland; Teagasc (Wiley, 02/07/2012)
      Fisher's linear discriminant analysis is one of the most commonly used and studied classification methods in chemometrics. The method finds a projection of multivariate data into a lower dimensional space so that the groups in the data are well separated. The resulting projected values are subsequently used to classify unlabeled observations into the groups. A semi-supervised version of Fisher's linear discriminant analysis is developed, so that the unlabeled observations are also used in the model fitting procedure. This approach is advantageous when few labeled and many unlabeled observations are available. The semi-supervised linear discriminant analysis method is demonstrated on a number of data sets where it is shown to yield better separation of the groups and improved classification over Fisher's linear discriminant analysis.
    • The significance of the differences in soil phosphorus representation and transport procedures in the SWAT and HSPF models and a comparison of their performance in estimating phosphorus loss from an agriculture catchment in Ireland

      Nasr, Ahmed Elssidig; Bruen, Michael; Moles, Richard; Byrne, Paul; O'Regan, Bernadette (TWRI, 02/07/2012)
      Phosphorus transported from agriculture land has been identified as a major source of water pollution in a large number of Irish catchments. Models of this process are required in order to design and assess management measures. This paper reports on the comparison and assessment of two of the most promising physically-based distributed models, SWAT and HSPF, with particular emphasis on their suitability for Irish conditions. The representation of the overall soil phosphorus cycle is similar in both models but there is a significant difference in the level of detail in describing the chemical and biochemical processes in each model. Also there are differences in modeling the mechanisms by which phosphorus is removed from the soil column and either transported in dissolved form with the runoff water or in particulate form attached to eroded or detached sediment. These differences could have a significant influence on performance when using either of the models to simulate phosphorus loss from any catchment. Both models are applied to estimating the phosphorus concentration at the outlet of the Clarianna catchment in north Tiperrary (Ireland). This catchment is small (23km2) and the landuse is mainly pasture on grey brown podozilic soils. The results of model calibration are presented along with an assessment of the usefulness of the model outputs as a water quality management tool.