As a scientist my research interests are in pure and applied biology particularly ornithology, ecotoxicology and forest ecology. The main focus of my research is to develop a deeper understanding of the impacts of environmental change and disturbance related to land-use change, climate change and environmental contaminants. I am also interested in the impacts of environmental change on industries such as food, forestry, environmental regulation, energy and on society. As an ornithologist I study all birds, and have focussed in particular on a few species of such as Dippers, Swans, Corncrakes, Choughs and Hen Harriers.

I have been studying the White-Throated Dipper, a small river bird, for more than 20 years. Over this time I have worked with a large team of researchers, ornithologists, volunteers and students. This is the first large-scale study of its kind in Ireland. Each year chicks are fitted with identification rings making it possible to identify birds in subsequent years, which provides data on survival, dispersal and population trends. Recently I have recorded a change in the timing of breeding as they now lay their eggs earlier than they had done previously. This is the first evidence of the impact of climate change on birds in Ireland and the long-term nature and wide scope of my research have made it possible to detect this type of environmental change. You can read more about my research in this area here.

Having undertaken research for my PhD on Lead toxicity in Mute Swans I have continued to work with swans and, for many years, now I have been tagging them and recording their behaviour, health and habits in both Ireland and Wales. I have published more than 20 research papers, and in one of these, published in the international journal Wildfowl, we described for the first time, the cause of pink coloration in swans which has been observed in many parts of Ireland, Britain and North America. This causes them to lose their waterproofing and consequently they cannot feed and may eventually die and impacts on populations of swans across their range.

It was very exciting for me to be part of the discovery of a new species of shrew in Ireland. Whilst undertaking their post-graduate research, John Lusby, University College Cork and BirdWatch Ireland and Dave Tosh, Queen’s University Belfast, spotted the unfamiliar remains of Greater White-toothed Shrew Crocidura russula in regurgitated food remains of Barn Owls and Kestrels in Ireland. These are the first Irish records of Greater White-toothed shrew, and provide compelling evidence of a recent introduction of this species to Ireland. The potential impact of this new mammal to Ireland, which is absent from Britain, on the ecology of habitats in Ireland may be considerable and is the focus of continued research.

My studies of forest ecology and forest birds has included extensive work on the Hen Harrier, one of Ireland’s rarest birds of prey. I have led a number of research projects in this area which have produced a large volume of work on this bird species and its interaction with changing landuse, particularly forest expansion and wind energy development. More details on this work can be found here.

Bird-Study Hen Harrier Circus cyaneus population trends in relation to wind farms. M.W. Wilson, D. Fernandez-Bellon, S. Irwin & J. O’Halloran. Bird Study, 2016, Volume 64, 20-29
MRev First record of greater white-toothed shrew Crocidura rassula in Ireland
D.G. Tosh, J. Lusby, W.I. Montgomery & J. O’Halloran
Mammal Review, 2008, Volume 38, 321-326
JZoo Blood lead levels in wintering and moulting Icelandic Whooper swans over two decades
M. O’Connell, R. Rees, O. Einarsson, C. Spray, S. Thorstensen & J. OHalloran
Journal of Zoology, 2008, Volume 276, 21-27
BE Lead Poisoning in Mute Swans (Cygnus olor) in Ireland: Recent changes
M. O’Connell, P. Smiddy & J.O’Halloran
Biology and Environment, 2009, Volume 109 53-60
Ibis Mismatches between breeding success and habitat preferences in Hen Harriers Circus cyaneus breeding in forested landscapes.
M.W. Wilson, B. O’Donoghue, B. O’Mahony, C. Cullen, T. O’Donoghue, G. Oliver, B. Ryan, P. Troake, S. Irwin, T.C. Kelly, J.J. Rotella & J. O’Halloran
Ibis, 2012, Volume 154, 578-589.
Wildfowl.jpg An investigation of a novel anomalous pink feather colouration in the Mute Swan Cygnus olor in Britain and Ireland
M. O’Connell, U. Keating, D. Mcelligott, P. O’Reilly, J. O’Callaghan & J. O’Halloran
Wildfowl, 2011, Volume 61, 152-165
Ibis The importance of pre-thicket conifer plantations for nesting Hen Harriers Circus cyaneus in Ireland
M.W. Wilson, S. Irwin, D.W. Norriss, S.F. Newton, K. Collins, T.C. Kelly & J. O’Halloran
Ibis, 2009, Volume 151, 332-343
PlosOne Invading and expanding: Range dynamics and ecological consequences of the Greater White-toothed Shrew (Crocidura russula) invasion in Ireland.
D. McDevitt, W. Montgomery, D.G. Tosh, J. Lusby, N. Reid, T.A. White, C.D. McDevitt, J. O’Halloran, J.B. Searle & J.M. Yearsley
PLoS ONE, 2014, 9:e100403.


I have studied a range of species, systems and scales of biological organisation in attempting to advance our knowledge and understanding of the impacts of environmental quality and change, on the fauna.  Each of these activities requires resources and collaboration.  Thus, while some of my research is low cost, much also requires substantial funding and has therefore been shaped, at least in part, by societal needs.  Studies of environmental impacts require interdisciplinary approaches and collaboration with other scientists and stakeholders is essential.

With members of the PLANFORBIO research team from UCC, TCD, WIT and Coillte

Over the last decade I have led the largest national forest ecology research project in Ireland which was undertaken in collaboration with Trinity College Dublin, Waterford Institute of Technology, Coillte, Forest Research UK, Swedish University of Agricultural Sciences and University of Alberta, Canada. This programme of research has been the single largest project on forest biodiversity in Ireland and has led to the generation of significant new knowledge on the ecology of range of forest species as well as the building significant critical research capacity through PhD and Masters training and the hosting of Marie Curie fellows.  A large number of research papers, together with policy and management recommendations have been developed and translated to industry as part of this work. You can read more about some of these projects on the UCC PLANFORBIO and Forest Ecology Research web pages.

FEM Can ground-based assessments of forest biodiversity reflect the biological condition of canopy assemblages?
S.M. Pedley, A. Oxbrough, R.D. Martin, S. Irwin, T.C. Kelly& J. O’Halloran

Forest Ecology and Management, 2016, Volume 359, 190-198
AppGeo Contemporary forest loss in Ireland: quantifying rare deforestation events in a fragmented forest landscape
J.L. Devaney, J.J. Redmond & J. O’Halloran 
Applied Geography, 2015, Volume 63, 346-356
BioCon The value of plantation forests for plant, invertebrate and bird diversity and the potential for cross-taxon surrogacy.
Irwin, S.M. Pedley, L. Coote, A.C. Dietzsch, M.W. Wilson, A. Oxbrough, O. Sweeney, K.M. Moore, R. Martin, D.L. Kelly, F.J.G. Mitchell, T.C. Kelly & J. O’Halloran
Biodiversity and Conservation, 2014, Volume 23, 697-714
birdstudycover Factors affecting the bird diversity of planted and semi-natural oak forests in Ireland
C.T. Graham, M.W. Wilson, T. Gittings, T.C. Kelly, S. Irwin, O. Sweeney & J. O’Halloran
Bird Study, 2014, Volume 61, 309-320
STE The impact of catchment conifer plantation forestry on the hydrochemistry of peatland lakes
T.J. Drinan, C.T. Graham, J. O’Halloran & S. Harrison
Science of The Total Environment, 2013, Volume 443, 608-620.
EcolInd Testing indicators of biodiversity for plantation forests
L. Coote, A.C. Dietzsch, M.W. Wilson, C.T. Graham, L. Fuller, A.T. Walsh, S. Irwin, D.L Kelly, F.J.G. Mitchell, T.C. Kelly & J. O’Halloran
Ecological Indicators, 2013, Volume 32, 107-115
CCES Surviving in a warmer world: environmental and genetic responses
A. Donnelly, A. Caffarra, C. Kelleher, B. O’Neill, E. Diskin, A. Pletsers, H. Proctor, R. Stirnemann, J. O’Halloran, J. Peñuelas, T. Hodkinso & T. Sparks
Climate Research, 2011, Volume 53, 245-262


During the  course of this research I was very proud to bring the Second International Conference on Biodiversity in Forest Ecosystems and Landscapes to UCC. This event showcased the excellent research that is being undertaken here in Ireland and brought more than 150 delegates from all corners of the globe to share their work. We hosted a range of networking events during the conference, allowing delegates both formal and informal opportunities for interaction. These included a very successful field excursion to native woodlands across Munster where researchers from our team shared their experiences of forest ecology research in Ireland with international delegates. The picture below shows the delegates during the field excursion.


Global ocean temperatures, increased occurrence of extreme weather events (such as El Niño), as well as growing coastal eutrophication, have all been linked to an increase in the incidence of HABs worldwide. Our studies at Lough Hyne Marine Reserve were chosen to examine the possible effects of climate change on emerging naturally occurring toxins. Our studies are the first to detect Pinnatoxin G in Irish waters, highlighting the ongoing spread of this algal toxin, most likely due to climate change.  Another natural toxin to animals is salt: as many animals carefully control the ions in their body fluids and tissues (some animals don’t control their fluids, these are called osmo-conformers).  In doing these studies we hope to understand what the possible impacts of human induced contaminants might be for biodiversity and ecosystem function.  One such contaminant might be increased levels of zinc which can pose a threat to animal and plant communities.  In our studies we have used module plant species, Lemna to help us understand some of the impacts of this metal on different ages of plants, by measuring photosynthetic rate.

Toxicon Assessment of emerging biotoxins (pinnatoxin G and spirolides) at Europe’s first marine reserve: Lough Hyne
McCarthy, V. Bane, M. Garcia Altares, F.N.A.M. van Pelt, A. Furey A & J. O’Halloran
Toxicon, 2015, Volume 108, 202-209
MER Does the marine biotoxin okadaic acid cause DNA fragmentation in the blue mussel and the pacific oyster?
M. McCarthy, J. O’Halloran, N.M. O’Brien, F.N.A.M. van Pelt. 
Marine Environmental Research, 2014, Volume 101, 153-160
AqBot Frond development gradients are a determinant of the impact of zinc on photosynthesis in three species of Lemnaceae
E. Lahive, J. O’Halloran & M.A.K. Jansen
Aquatic Botany, 2012, Volume 101, 55-63
MPoll The effects of salinity on the Manila clam (Ruditapes philippinarum) using the neutral red retention assay with adapted physiological saline solutions
B.M. Coughlan, G.A. Moroney, F.N.A.M van Pelt, N.M. O’Brien, J. Davenport & J. O’Halloran
Marine Pollution Bulletin, 2009, Volume 58, 1680-1684

A priority for me during my research career has been the dissemination and translation of findings not only to a scientific audience and policy makers, but also to the wider public and the community. I have been a regular contributor to Mooney Goes Wild RTE Radio 1 show for many years. In January 2016 I had the opportunity to revisit a documentary which I presented and which was first broadcast in 2004 and to share updates on our recent work on swans. I have also contributed to Eco Eye, an Irish television series about environmental issues presented by Duncan Stewart, where I was invited as an expert on biodiversity in Irish forests in 2008, and again in 2010 as an expert on Hen Harrier ecology in Ireland. You can see some examples of this work by clicking on the links below.

Mooney2004 Mooney2016 Ecoeye

In 2014 I was delighted to partner with the Lewis Glucksman Gallery at UCC to create an exhibition of animals in contemporary art entitled ‘Fieldworks‘. Featuring works by Irish and international artists, Fieldworks demonstrated how animals forage, nest and play within a variety of locations and offered a remarkable insight into life in often hidden corners of the animal kingdom. This exhibition featured a display of animal specimens, research materials and study materials used by scientists and an extensive programme of lectures, workshops, tours, courses and events.

Bird-habitats-frontIn 2012 I co-edited a book on the bird communities of all of the habitats in Ireland, which included contributions from 25 leading ornithologists and research scientists. This book was launched by Minister for Arts, Heritage and the Gaeltacht Mr. Jimmy Deenihan TD at a symposium at the RDS in Dublin In association with Dublin City of Science 2012. Each chapter was peer-reviewed by an international expert scientist and details case studies that show what can be done when scientific research is combined with practical land management. Since 1985 I have hosted the Cork Ornithology Research Conference at UCC every 5 years. This attracts researchers and members of the public from Ireland and the UK to review the latest research findings and to build collaborations for further research. The proceedings of these events is then published in the research journal Irish Birds. I have also made large contributions to international conferences and in 2009 was invited to chair the Scientific Committee of the European Ornithologists Union Conference in Zurich.

Research students have always been an important part of my academic work and I have supervised or co-supervised 41 PhD students and 31 Masters Students to date (click here for details) as well as a large number of undergraduate and Masters dissertation research projects.

Further information on my research activities can be found in my IRIS profile which you can view here.