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UCD School of Biology and Environmental Science

Scoil na BitheolaĆ­ochta agus na hEolaĆ­ochta Comhshaoil UCD


Publications 2014-2015


S.X. Cadrin, L. Kerr, S. Mariani (2013). Stock Identification Methods. Amsterdam, London, New York, San Diego: Elsevier.

Kelly-Quinn, M. & Baars, J-R. (2012). The Remarkable Rye Water. Kileen: Hudson.

McAinsh MR, Ng CKY (2012). Measurement of Cytosolic-free Ca2+ in Plant Tissue In: D.G. Lambert(Eds.). Calcium Signaling Protocols, 3rd Edition. New York: Humana Press.

McDevitt, AD. and Zachos, FE. (2012). Genetic analyses of natural and anthropogenic movements in deer In: Sykes, N., Baker, K. and Carden, R.F(Eds.). Deer and People: Past, Present and Future. Oxford: Windgather Press.

McDevitt AD (2013) Invasions and Expansions: the greater white-toothed shrew in Ireland Genetics Society News, 68:51-52.

Tobin, B. and Nieuwenhuis, M. (2012). The importance of long-term monitoring of forest growth and climate in Ireland Forestry and Energy Review, 2 (2):34-35.

McDevitt AD, Carden RF (2012). Irelands ancient deer Deer, 16:23-26.

McDevitt, A.D., O’Toole, P., Edwards, C.J. and Carden, R.F. (2012). Landscape genetics of red deer (Cervus elaphus, Linnaeus 1758) in Killarney National Park, County Kerry Irish Naturalists Journal, :23-30.

McDevitt AD, Carden RF (2012). Squatters Rights - The Native Problem Irish Wildlife, Winter:22-25.

Kochmann, J; OBeirn, F; Yearsley, JM; Crowe, TP; (2013) Environmental factors associated with invasion: modelling occurrence data from a coordinated sampling programme for Pacific oysters. Biological Invasions, .

Yearsley, JM; Viard, F; Broquet,T (2013). The effect of collective dispersal on the genetic structure of a subdivided population. Evolution, .

Ryan, D; Yearsley, JM; Kelly-Quinn, M (2013). Quantifying the effect of Semi-Natural Riparian Cover on Stream Temperatures: Implications for Salmonid Habitat Management. Fisheries Management and Ecology, .

Carlsson J, Gauthier D, Carlsson JEL, Coughlan JP, Dillane E, FitzGerald RD, Keating FU, McGinnity P, Mirimin L & Cross TF (2013). Rapid, economical SNP and microsatellite discovery based on de novo assembly of a reduced representation genome in a non-model organism: a case study of Atlantic cod Gadus morhua. Journal of Fish Biology, 82:944-958.

Collins PC, Croot P, Carlsson J, Colaço A, Grehan A, Hyeong K, Kennedy R, Mohn C, Smith S, Yamamoto H, Rowden A. (2013) A primer for the Environmental Impact Assessment of mining at seafloor massive sulfide deposits. Marine Policy, 42:198-209.

M.I. Khalil, G. Kiely, P. O'Brien and C. Müller (2013). Estimation of organic carbon stocks in agricultural soils in Ireland using combined empirical and GIS approaches. Geoderma, 193-194:222-235.

Zachos, F.E., Apollonio, M., Barmann, E.V., Festa-Bianchet, M., Gohlich, U., Habel, J.C., Haring, E., Kruckenhauser, L., Lovari, S., McDevitt, A.D., Pertoldi, C., Rossner, G.E., Sanchez-Villagra, M.R., Scandura, M. and Suchentrunk, F. (2013) Species inflation and taxanomic artefacts - a critical comment on recent trends in mammalian classification. Mammalian Biology, 78:1-6.

Shinde, S., Shinde, R., Downey, F. and Ng, C.K.Y. (2013). Abiotic stress-induced oscillations in steady-state transcript levels of Group 3 LEA protein genes in the moss, Physcomitrella patens. Plant Signaling and Behaviour, 8 (1).

Khalil, M.I, Kiely, G., O'Brien, P. and Mueller, C. (2013). Organic carbon stocks in agricultural soils in Ireland using combined empirical and GIS approaches. Geoderma, 193-194:222-235.

Piotrowska, K., Connolly, J, Finn, J., Black, A. and Bolger, T. (2013). Evenness and plant species identity affect earthworm diversity and community structure in grassland soils. Soil Biology and Biochemistry, 57:713-719.

Dix, L., Ward, D.T. and Stewart, G.S. (2013). Urea transporter protein UT-B in bovine parotid gland. Journal of Dairy Science, 96 (3):1685-1690.

McDevitt, A.D., Oliver, M.K., Piertney, S.B., Szafraska, P.A., Konarzewski, M. and Zub, K. (2013). Individual variation in dispersal associated with phenotype influences fine-scale genetic structure in weasels. Conservation Genetics, 14:499-509.

Sommer S, McDevitt AD, Balkenhol N (2013). Landscape genetic approaches in conservation biology and management. Conservation Genetics, 14:249-251.

McDevitt AD, Carden RF, Coscia I, Frantz AC (2013). Are wild boar roaming Ireland once more?. European Journal of Wildlife Research, Online .

Dalton E, Griffin D, Gallagher TF, Vetten N, Milbourne D (2013.) The effect of pyramiding two potato cyst nematode resistance loci to Globodera pallida Pa2/3 in potato. Molecular Breeding, 31 (4):921-930.

deMenezes, A., Clipson, N and Doyle, E (2012). Comparative transcriptomics reveals wides[read community responses during phenanthrene degradation in soil. Environmental Microbiology, 14 (9):2577-2588.

Miller, D., Jessel, A. and Mariani, S. (2012). Seafood mislabelling: comparisons of two western European case studies assist in defining influencing factors, mechanisms and motives. Fish and Fisheries, 13 (3):345-358.

Olajuyigbe, S., Tobin, B. and Nieuwenhuis, M. (2012). Temperature and moisture effects on respiration rate of decomposing logs in a Sitka spruce plantation in Ireland. Forestry, 85 (4):485-496.

Steinthorsdottir, M., Woodward, F. I., Surlyk, F., McElwain, J. C. (2012). Deep-time evidence of a link between elevated CO2 concentrations and perturbations in the hydrological cycle via drop in plant transpiration. Geology, 40 (9):815-818.

Augustenborg, C., McBennett, L., Connolly, L., Priegnitz, U., Finnan, J. and Mueller, C. (2012). Farmers perspectives for the development of a bioenergy industry in Ireland. Global Change Biology (Bioenergy), 4 (5):597-610.

Kochmann, Judith, Carlsson, Jens, Crowe, Tasman P., Mariani, Stefano (2012). Genetic Evidence for the Uncoupling of Local Aquaculture Activities and a Population of an Invasive Species - A Case Study of Pacific Oysters (Crassostrea gigas). Journal of Heredity, 103 (5):661-671.

Kochmann, J., Carlsson, J., Crowe, T.P. and Mariani, S. (2012). Genetic evidence for the uncoupling of local aquaculture activities and a population of an invasive species - a case study of Pacific oysters (Crassostrea gigas). Journal of Heredity, 103 (5):661-671.

Kochmann, J., Carlsson, J., Crowe, T. P. & Mariani, S. (2012). Genetic evidence for the uncoupling of local aquaculture activities and a population of an invasive species: a case study of Pacific oysters (Crassostrea gigas). Journal of Heredity, 103:661-671.

Varela JA, Bexiga MG, Aberg C, Simpson JC, Dawson KA. (2012). Quantifying size-dependent interactions between fluorescently labeled polystyrene nanoparticles and mammalian cells. Journal Of Nanobiotechnology, 10 (1).

Meade, G., Pierce, K., O'Doherty, J.V., Mueller, C., Hepp, S., Lanigan, G. and Mc Cabe, T. (2012). Gaseous emissions of methane and carbon dioxide following land application of high and low nitrogen pig manures to winter wheat at three key crop growth stages. Journal of Agricultural Science, .

O'Farrell, B., Dennis, C., Benzie, J., McGinnity, P., Carlsson, J., de Eyto, E., Coughlan, J., Igoe, F., Meehan, R. and Cross, T. (2012). Balancing selection on MHC class I in wild brown trout (Salmo trutta). Journal of Fish Biology, 81 (4):1357-1374.

D. J. Buckley, M. G. Lundy, E. S. M. Boston, D. D. Scott, Y. Gager, P. Prodohl, F. Marnell, W. I. Montgomery, E. C. Teeling (2012). The spatial ecology of the whiskered bat (Myotis mystacinus) at the western extreme of its range provides evidence of regional adaptation. Mammalian Biology, .

Lenhart, K., Bunge, M., Ratering, S., Neu, T.R., Schüttmann, I., Greule, M., Kammann, C., Schnell, S., Mueller, C., Zorn, H. and Keppler, F. (2012). Evidence for methane production by saprotrophic fungi. Nature Communications, 3, Article No. 1046.

Roth SD, Schüttrumpf J, Milanov P, Abriss D, Ungerer C, Quade-Lyssy P, Simpson JC, Pepperkok R, Seifried E, Tonn T. (2012). Chemical Chaperones Improve Protein Secretion and Rescue Mutant Factor VIII in Mice with Hemophilia A. PLoS ONE, 7 (9).

Feeley, H.B., Bruen, M., Blacklocke, S., Baars, J-R, & Kelly-Quinn, M. (2012). Significant changes in the hydrochemistry and drivers of episodic acidity in headwater streams draining plantation forest in Ireland: increasing role of organic acidity with the reduction of anthropogenic deposition. Science of the Total Environment, 443:173-183.

Goodman, S.M., Puechmaille, S., Friedli-Weyeneth, N., Gerlach, J., Ruedi, M., Schoeman, C., Stanley, W.T. and Teeling, E.C. (2012). Phylogeny of the Emballonurini bats (Family Emballonuridae): new genus of Emballonura and species of Coleura. Journal Of Mammalogy, .

Walters, C., Maltby, A., Dietz, C., Fenton, B., Jones, G., Obrist, M., Puechmaille, S.J., Sattler, T., Siemers, B., Jones, K., Parsons, S. (2012). A continental-scale tool for acoustic identification of European bats. Journal of Applied Ecology, 49 (5):1064-1074.

Corrigan, A., Horgan, K., Clipson, N. and Murphy, R.A. (2012). Effect of Dietary Prebiotic (Mannan Oligosaccharide) Supplementation on the Caecal Bacterial Community Structure of Turkeys. Microbial Ecology, 64:826-836.

Green D. S., Boots B. & Crowe T. P. (2012). Effects of non-indigenous oysters on microbial diversity and ecosystem functioning. PLoS ONE, 7 (10).

Lundy, M.G.,Harrison, A., Buckley, D.J., Boston, E.S., Scott, D.D., Teeling, E.C., Montgomery, W.I., Houghton, J.D.R. (2012). Prey field switching based on preferential behaviour can induce Levy flights. Proceedings of the Royal Society B - Biological Sciences.

Inselsbacher, E., Wanek, W., Strauss, J., Zechmeister-Boltenstern, S. and Mueller, C. (2012). A novel 15N tracer model reveals: Plant nitrate uptake governs nitrogen transformation rates in agricultural soils. Soil Biology and Biochemistry,

Thong, V.D., Dietz, C., Denzinger, A., Bates, P.J.J., Puechmaille, S.J., Callou, C. and Schnitzler, H-U. (2012). Resolving a mammal mystery: the identity of Paracoelops megalotis (Chiroptera: Hipposideridae). Zootaxa, 3505:75-85.

Martin, G.D., Coetzee, J., Baars, J-R. (2012). Hydrellia lagarosiphon Deeming (Diptera: Ephydridae), a potential biological control agent for the submerged aquatic weed, Lagarosiphon major (Ridley) Moss (Hydrocharitaceae). African Entomology, .

Fanning, P., Baars, J-R. (2012). Biology of the eucalyptus leaf beetle, Paropsisterna selmani (Chrysomelidae: Paropsini) a new pest of Eucalyptus species (Myrtaceae) in Ireland. Agricultural and Forest Entomology, .

Mangan, R., Baars, J-R. (2012). Use of life table statistics and degree day values to predict the colonisation success of Hydrellia lagarosiphon Deeming (Diptera: Ephydridae), a leaf mining fly of Lagarosiphon major (Ridley) Moss (Hydrocharitaceae), in Ireland and the rest of Europe. Biological Control, .

Broquet, T; Viard, F; Yearsley, JM (2012). Genetic drift and collective dispersal can result in chaotic genetic patchiness. Evolution, .

Benvenuto, C., Cheyppe-Buchmann, S., Bermond, G., Ris, N. and Fauvergue, X. (2012). Intraspecific hybridization, life history strategies and potential invasion success in a parasitoid wasp. Evolutionary Ecology, 26 (6):1311-1329.

Cocchiglia, L., Purcell, P. and Kelly-Quinn, M. (2012). A critical review of the effects of motorway river crossing construction on the aquatic environment. Freshwater Reviews, .

Coscia, I., Vogiatzi, E., Kotoulas, G., Tsigenopoulos, C. S., Mariani, S. (2012). Exploring neutral and adaptive processes in expanding populations of gilthead sea bream, Sparus aurata L., in the North-East Atlantic. Heredity, 108 (5):537-546.

O’Connor, N.E., Donohue, I.,Crowe, T.P & Emmerson, M. (2012). Distinguishing between direct and indirect effects of predators in complex ecosystems. Journal of Animal Ecology, Advance online publication.

M.M.R. Jahangir, P. Johnston, M.I. Khalil, J. Grant, C. Somers and K.G. Richards (2012). Evaluation of headspace equilibration methods for quantifying greenhouse gases in groundwater. Journal of Environmental Management, 111:208-212.

Carlsson, J., Gauthier, D., Carlsson, J.E.L., Coughlan, J.P., Dillane, E., FitzGerald, R.D., Keating, F.U., McGinnity, P., Mirimin, L. and Cross, T.F. (2012). Rapid, economical SNP and microsatellite discovery based on de novo assembly of a reduced representation genome in a non-model organism: a case study of Atlantic cod. Journal of Fish Biology,

Yi P, Higa A, Taouji S, Bexiga MG, Marza E, Arma D, Castain C, Le Bail B, Simpson JC, Rosenbaum J, Balabaud C, Bioulac-Sage P, Blanc JF, Chevet E (2012). Sorafenib-Mediated Targeting of the AAA+ ATPase p97/VCP Leads to Disruption of the Secretory Pathway, Endoplasmic Reticulum Stress, and Hepatocellular Cancer Cell Death. MOL CANCER,

Bulleri, F., L. Benedetti-Cecchi, M. Cusson, E. Maggi, F. Arenas, R. Aspden, I. Bertocci, T. P. Crowe, D. Davoult, B. K. Eriksson, S. Fraschetti, C. Golléty, J. Griffin, S. R. Jenkins, J. Kotta, P. Kraufvelin, M. Molis, I. Sousa Pinto, A. Terlizzi, N. Valdivia, D. M. Paterson. (2012). The temporal stability of European rocky shore assemblages: variation across a latitudinal gradient and the role of habitat-formers. Oikos, 121:1801-1809.

Chambers, J.P., Behpouri, A., Bird, A. and Ng, C.K.Y. (2012). Evaluation of the use of the polyubiquitin genes, Ubi4 and Ubi10 as reference genes for gene expression studies in Brachypodium distachyon. PLoS ONE, 7 (11).

Jochum, M., Schneider, F. D., Crowe, T. P., Brose, U. & O'Gorman, E. J. (2012). Climate-induced changes in bottom-up and top-down processes independently alter a marine ecosystem. Philosophical Transactions of the Royal Society B, 367:2962-2970.

Twomey, M., Brodte, E., Jacob, U., Crowe, T. P. & Emmerson, M. C.  (2012). Idiosyncratic species effects confound size-based predictions of responses to climate change. Philosophical Transactions of the Royal Society B, 367:2971-2978.

Ciuti, S., Muhly, T.B., Patton, D.G., McDevitt, A.D., Musiani, M. and Boyce, M.S. (2012). Human selection of elk behavioural traits in a landscape of fear. Proceedings of the Royal Society B - Biological Sciences, 279 (1746):4407-4416.

Singan VR, Handzic K, Simpson JC (2012). Quantitative image analysis approaches for probing Rab GTPase localization and function in mammalian cells. Biochemical Society Transactions, 40 (6):1389-1393.

Arroyo, J., Kenny, J. and Bolger, T. (2012). A survey of the Oribatida and Mesostigmata (Acarina) of Irish forests. Bulletin of the Irish Biogeographical Society, 36:33-59.

Lynch, J.P., O'Kiely, P., Doyle, E.M. (2012). Yield, quality and ensilage characteristics of whole-crop maize, and of the cob and stover components - Harvest date and hybrid effects. Grass and Forage Science, .

Hunt, D.,Chambers, J.P., Behpouri, A., Kelly, S.P., Whelan, L., Pietrykowska, M., Downey, F., McCabe, P.F., Ng, C.K.Y. (2013). Brachypodium distachyon cell suspension cultures: establishment and utilisation. Cereal Research Communications,

Connolly, J., Bell, T. Bolger T., Brophy C., Carnus, T., Finn J. A., Kirwan, L, Isbell, F., Levine, J., Lüscher, A., Picasso, V., Roscher, C., Sebastia M. T., Suter, M., Weigelt, A. (2013). A Generalised Diversity-Interactions model improves predictions of the effects of changing biodiversity on ecosystem function. Journal of Ecology, 101:344-355.

Wilson, D., C. Farrell, C. Mueller and F. Renou-Wilson (2013). Rewetted industrial cutaway peatlands in western Ireland: a prime location for climate change mitigation. Mires and Peatlands, 11 (Article 01):1-22.

Publications for academic year 2013-14

Publications for academic year 2012-13

December 2010

Peer Reviewed Journal Articles

Baars, J-R. and Caffrey, J.M.  (2010) The Frond-feeding Weevil (Stenopelmus rufinasus Gyllenhal)(Coleoptera: Erirhinidae) a natural enemy of Azolla filiculoides in Ireland.  Irish Naturalists Journal , 30 (2):142-143.

Miller, D.M. & Mariani, S. (2010) Smoke, mirrors and mislabelled cod: poor transparency in the European seafood industry.  Frontiers in Ecology and the Environment, 8 (10):517-521. doi:10.1890/090212.

Belcher, C.M., Yearlsey, J.M., Hadden, R., McElwain, J.C. & Rein, G. (2010) Baseline intrinsic flammability of Earths ecosystems estimated from paleoatmospheric oxygen over the past 350 million year.  Proceedings of the National Academy of Sciences, 107 (52) 22448-22453. doi:10.1073/pnas.1011974107.

Fennell, M., Gallagher, T., and Osborne, B. (2010) Patterns of genetic variation in invasive populations of Gunnera tinctoria: an analysis at three spatial scales.  Biological Invasions, 12 (12) :1-151. doi: 10.1007/s10530-010-9813-9.

Longmore C., Fogarty K., Neat F., Brophy D., Trueman C., Milton A. & Mariani S. (2010) A comparison of otolith microchemistry and otolith shape analysis for the study of spatial variation in a deep-sea teleost, Coryphaenoides rupestris.  Environmental Biology of Fishes, 89 (3-4):591-605. doi: 10.1007/s10641-010-9674-1.

Publications for Academic Year 2012-13