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Allan Lilly

Staff picture: Allan Lilly
Environmental and Biochemical Sciences
Environmental and Biochemical Sciences
Soil Hydrologist
+44 (0)344 928 5428 (*)

The James Hutton Institute
Aberdeen AB15 8QH
Scotland UK


Allan Lilly is a soil scientist with particular interest in hydropedology. He has a background in soil survey, biophysical resource analysis and land evaluation and has been responsible for both systematic soil survey and land evaluation at a national level and contract soil surveys at detailed scales.

Current research interests

I have over 40 years experience in soil hydrology, soil survey and soil mapping, hydropedology and bio-physical resource analysis and have been responsible for systematic soil survey and data collection for input into the Scottish Soils Database. I have authored or contributed to over 120 technical reports and have published over 60 papers in peer reviewed science journals. A key aspect of my work is to make soils data more robust and readily accessible to other researchers for use in models. I was a key researcher in the development of the HYPRES database of soil hydrological properties for Europe and the development of the hydrological classification for UK soils (HOST). I currently lead a project to enhance and improve the national soils datasets improving these key national datasets through the provision of new data, updating and revising existing data including making new interpretations and development of web access to soil data. I have developed methods for estimating the hydrological characteristics of soils from existing data and integrating these data into spatially-scaled hydrological and hydro-geochemical models. I also oversaw the development of field protocols and sampling procedures for the resampling of the National Soil Inventory. Based on previous work with both collecting and interpreting soil data, he has also been working to assess the impact of climate and land use change on soil. In particular, he has been developing methods for generating robust input data for land use and climate change modelling as well as assessing the potential of Scottish soils to sequester carbon.

I am the current Chair of the European Soil Bureau Network and a member of European Soil Partnership Pillar 4 Working Group on soil data and information. I have been a visiting scientist at the Victoria Department of Primary Industries and at CSIRO, Australia as well as the USDA_ARS station in Beltsville, Maryland. I spent a year in the Netherlands working on an EU funded project to develop a soil hydrological database. I was elected a Fellow of the Institute of Soil Science (F.I.Soil Sci) in 2015.


  • Hollis, J. M.; Lilly, A. (2022) The Fragile Skin Soil Landscapes of the UK, Published by British Society of Soil Science. ISBN 978-1-3999-2275-3
  • Lilly, A. (2020) Soil survey: a field based science., In: Burt, T. & Thompson, D. (eds.). Curious About Nature: A Passion for Fieldwork. Cambridge University Press. Chapter 29, pp246-262.
  • Baggaley, N.J.; Poggio, L.; Gimona, A.; Lilly, A. (2016) Comparison of traditional and geostatistical methods to estimate and map the carbon content of Scottish soils., In: Zhang, G.L., Brus, D., Liu, F., Song, X.D. and Lagacherie, P. (eds.). Digital Soil Mapping Across Paradigms, Scales and Boundaries. Springer Environmental Science and Engineering. Springer, Singapore, pp103-111.
  • Lilly, A.; Aitkenhead, M.J.; Black, H.I.J. (2014) Assessing carbon in Scottish soils using traditional and novel analytical approaches., In: Arrouays, D., McKenzie, N., Hempel, J., Richer de Forges, A.C. & McBratney, A. (eds.). GlobalSoilMap: Basis of the global spatial soil information system. Proceedings of the 1st GlobalSoilMap Conference, Orleans, France, 7-9 October 2013. CRC Press/Balkema, Leiden, pp287-290.
  • Lilly, A.; Nemes, A.: Wosten, J.H.M.; Hiederer, R. (2014) Experiences and challenges in developing European soil hydrological databases., In: Teixeira, W.G., Ceddia, M.B., Ottoni, M.V. & Donnagema, G.K. (eds.). Application of Soil Physics in Environmental Analyses: Measuring, Modelling and Data Integration, Progress in Soil Science, Springer International Publishing, Switzerland, Chapter 19, pp453-465
  • Lilly, A.; Dunn, S.M.; Baggaley, N.J. (2012) Hydrological classifications of soils and their use in hydrological modeling., In: Lin, H. (ed.). Hydropedology: Synergistic Integration of Soil Science and Hydrology. Academic Press, Elsevier B.V., Chapter 17, pp537-557.
  • Smith, P.; Ashmore, M.; Black, H.I.J.; Burgess, P.; Evans, C.; Hails, R.; Potts, S.; Quine, T.; Thomson, A.; Biesmeijer, K.; Breeze, T.; Broadmeadow, M.; Ferrier, R.C.; Freer, J.; Hansom, J.; Haygarth, P.; Hesketh, H.; Hicks, K.; Johnson, A.; Kay, D.; Kunin, W.; Lilly, A.; May, L.; Memmott, J.; Orr, H.; Pickup, R.; Purse, B.; Squire, G. (2011) Regulating services., In: UK National Ecosystem Assessment. Understanding Nature's Value to Society. Technical Report. Cambridge, UNEP-WCMC, Chapter 14, pp535-596.
  • Lilly, A.; Hudson, G.; Hough, R.L.; NSIS Resampling Team (2011) Scotland's soil resource., In: Marrs, S.J., Foster, S., Hendrie, C., Mackey, E.C. & Thompson, D.B.A. (eds.). The Changing Nature of Scotland. TSO Scotland, Edinburgh, Chapter 4, 45-52.
  • Helliwell, R.C.; Lilly, A.; Bell, J. (2007) Soils of Lochnagar: their development, distribution, properties and influence on surface water chemistry., In: Lochnagar: The Natural History of a Mountain Lake Developments in Paleoenvironmental Research (DPER) (ed. Neil L. Rose). Volume 12, Springer, pp93-120.
  • Lilly, A.; Lin, H. (2004) Using soil morphological attributes and soil structure in pedotransfer functions., In: Development of Pedotransfer Functions in Soil Hydrology, (eds. Y. Pachepsky and W.J. Rawls). Developments in Soil Science 30, Elsevier. Chapter 7, pp115-141. ISBN: 978-0-444-51705-0
  • Nemes, A., Wosten, J.H.M., Lilly, A. and Oude Voshaar, J.H. (1999) Evaluation of different techniques for interpolation of the particle-size distribution., In: Characterization and Measurement of the Hydraulic Properties of Unsaturated Porous Media. Proceedings of International Workshop, Riverside, California, October 22-24, 1997. Eds. M.Th. Van Genuchten, F.J. Leij and L. Wu. pp1307-1316.
  • Lilly, A., Wosten, J.H.M., Nemes, A. and Le Bas, C. (1999) The development and use of the HYPRES database in Europe., In: Characterisation and Measurement of the Hydraulic Properties of Unsaturated Porous Media. Proceedings of International Workshop, Riverside, California, October 22-24, 1997. Eds. M.Th. Van Genuchten, F.J. Leij and L. Wu. pp1283-1294.
  • Lilly, A.; Bell, J.S. (1995) 1:625000 scale groundwater vulnerability map of Scotland., Macaulay Land Use Research Institute, Aberdeen.
  • Langan, S.J.; Lilly, A.; Smith, B.F.L. (1995) The distribution and sensitivity of soils to acidification under heath and moorland vegetation in Scotland., In: Heaths and Moorlands: Cultural Landscapes (eds. D.B.A. Thompson, A.J. Hester and M.B. Usher). HMSO, Edinburgh.

  • Stutter, M.; Gagkas, Z.; Lilly, A. (2022) Landscape typing based on hillslope and floodplain soil water models to functionally target sixteen riparian management options, Webpage and Zenodo doi
  • Hare, M.; McBride, A.; Addy, S.; Pakeman, R.; Donaldson-Selby, G.; Rivington, M.; Gagkas, Z.; Jabloun, M.; Lilly, A.; Wilkinson, M.; Akoumianaki, I. (2022) Moderating extremes in water availability in Scotland a review of the role of functioning wetlands, Moderating extremes - Main Report vFINAL 20220302.pdf
  • Cloy, J.M.; Lilly, A.; Hargreaves, P.R.; Gagkas, Z.; Dolan, S.; Baggaley, N.J.; Stutter, M.I.; Crooks, B.; Elrick, G.; McKenzie B.M. (2022) A state of knowledge overview of identified pathways of diffuse pollutants to the water environment., CREW Report.
  • Baggaley, N.; Britton, A.; Barnes, A.; Buckingham, S.; Holland, J.; Lilly, A.; Pakeman, R.; Rees, B.; Taylor, A.; Yeluripati, J. (2021) Understanding carbon sequestration in upland habitats, Climate x Change Research Report
  • Lilly, A.; Baggaley, N.J.; Donnelly, M.D. (2021) What is the cost of soil erosion in Scotland?, SEFARI Gateway.
  • Glendell, M.; Troldborg, M.; Vintent, A.; Gagkas, Z.; Lilly, A. (2020) Field level modelling of pesticide pollution risk in Jersey., James Hutton Limited Contract Report to Jersey Water, 45pp.
  • Neilson, R.; Lilly, A.; Aitkenhead, M.; Artz, R.R.E.; Baggaley, N.; Giles, M.E.; Holland, J.; Loades, K.; Ovando Pol, P.; Rivington, M.; Roberts, M.; Yeluripati, J. (2020) Measuring the vulnerability of Scottish soils to a changing climate., ClimateXChange Report, 42pp.
  • Lilly, A.; Baggaley, N.J.; Yeluripati, J. (2020) A review of the effects of land use and land management changes on soil organic carbon stocks in hill farms., Climate-Positive Farming Reviews, hosted on the Glensaugh Climate-Positive Farm Website, 30pp.
  • Rickson, R.J.; Baggaley, N.; Deeks, L.K.; Graves, A.; Hannam, J.; Keay, C.; Lilly, A. (2020) Developing a method to estimate the costs of soil erosion in high-risk Scottish catchments., Draft Final Commissioned Report to Scottish Government, October 2019. Project UCR/004/18 CRF CR/2015/15.
  • Donnelly, D.; Towers, W.; Lilly, A.; Matthews, K.B. (2020) Method for applying biophysical constraints to delineate Areas of Natural Constraint in Scotland (2019)., Report to Scottish Government, 54pp.
  • Matthews, K.B.; Wardell-Johnson, D.; Miller, D.G.; Baggaley, N.; Lilly, A.; Matthews, R.B.; Fitton, N.; Jones, E.; Smith, J.; Smith, P.; Perks, M.; Bathgate, S.; Taylor, P.; Randle, T.; Ray, D. (2018) Analysis of the potential change in carbon stocks from new forestry planting in Scotland., CxC website
  • Lilly, A.; Baggaley, N.J.; Loades, K.W.; McKenzie, B.M.; Troldborg, M. (2018) Soil erosion and compaction in Scottish soils: adapting to a changing climate., ClimateXChange Report, 21pp.
  • Lilly, A.; Baggaley, N.J. (2018) Report on testing of the Syngenta Interra runoff app for Scotland., Report to Syngenta Crop Protection AG, Basel, 8pp.
  • Poggio, L.; Gimona, A.; Gagkas, Z.; Lilly, A. (2018) 3D digital soil mapping for Scottish soils using remote sensing., Internal Report for RESAS.
  • Troldborg, M.; Baggaley, N.; Lilly, A. (2018) Development of Bayesian Belief Network to assess soil erosion risk., Summary Report from Workshop, SEPA, Silvan House, Edinburgh, 15 March 2018, 3pp.
  • Rees, R.M.; Buckingham, S.; Chapman, S.J.; Jones, S.; Lilly, A.; Mathews, R.B.; Morison, J.I.L.; Perks, M.; Vanguelova, E.I.; Yamulki, S.; Yeluripati, J. (2018) Soil carbon and land use in Scotland., Final Report to ClimateXChange, Rapid Evidence Assessment.
  • Lilly, A. (2017) Towards identifying and addressing hydrological constraints in Australian soils., Internal Report for CSIRO.
  • Baggaley, N.J.; Lilly, A.; Riach, D. (2017) Rapid survey of soil erosion in the north east of Scotland after unprecedented winter rainfall., Macaulay Development Trust Report, 30 March 2017.
  • Baggaley, N.; Lilly, A.; Riach, D. (2017) Rapid survey of soil erosion in the north east of Scotland after unprecedented winter rainfall., Macaulay Development Trust Report.
  • Matthews, K.B.; Wardell-Johnson, D.; Miller, D.G.; Baggaley, N.; Lilly, A.; Matthews, R.B.; Fitton, N.; Jones, E.; Smith, J.; Smith, P.; Perks, M.; Bathgate, S.; Taylor, P.; Ray, D. (2017) Analysis of the net change in carbon stocks from future forestry planting in Scotland., Meeting with Forestry Commission Scotland and Climate Exchange Directorate Staff, ECCI, Edinburgh, 23 January 2017.
  • Avery, L.; Hough, R.L.; Potts, J.; Newman, G.; Lilly, A.; Lumsdon, D.; Abel, C.; Dodd, N.; Cook, Y.; McIntyre, S. (2016) Effect of maintenance and different raw water quality parameters on ultraviolet (UV) disinfection in private water supplies in Scotland., Report CR/2012/01, to Scottish Government, 31 January 2016.
  • Hallett, P.; Hall, R.; Lilly, A.; Baggaley, N.; Crooks, B.; Ball, B.; Raffan, A.; Braun, H.; Russell, T.; Aitkenhead, M.J.; Riach, D.; Rowan, J.; Long, A. (2016) Effect of soil structure and field drainage on water quality and flood risk., CREW Report, CRW 2014_03, 34pp.
  • Aitkenhead, M.J.; Black, H.I.J.; Squire, G.; McLeod, K.; Hastings, E.; Troldborg, M.; Aalders, I.H.; Towers, W.; Lilly, A.; Brown, I.; Coull, M.C.; Castellazzi, M.; Matthews, K.B.; Baggaley, N.J. (2016) A review of ecosystem service mapping within Scottish Government RESAS-funded research., Report for Scottish Government.
  • Nolan, A.J.; Henderson, D.J.; Hewison, R.L.; Riach, D.J.; Beesley, L.; Donnelly, D. (2016) Soil Survey Map Data and Reports, Scale 1:10,000, Volume 43 - Kindrogan Forest Blocks, Tay Forest District. (2015)., Digital data submitted to Forestry Commission, Scotland.
  • Lilly, A.; Chapman, S.J.; Perez-Fernandez, E.; Potts, J. (2016) Changes to C stocks in Scottish soils due to afforestation., Contract Report to Forestry Commission, 33pp.
  • Rossiter, D.G.; Vargas, R.; Omuto, C.; Carating, R.; Aparecida Da Silva, M.; Lilly, A.; Savin, I.; Moussadek, R.; Reinsch, T.; Grundy, M.; Viloria, J.; Nascimento, C.; Montanarella, L.; McKenzie, N. (2015) Global Soil Partnership Pillar 4 Implementation Plan: Towards a GSP sponsored Global Soil Information System., GSP Pillar 4 Implementation Plan Internal draft.
  • Lilly, A.; Bell, J.S.; Hudson, G.; Nolan, A.J.; Towers, W. (2015) Lilly, A., Bell, J.S., Hudson, G., Nolan, A.J. & Towers. W. 2011. National soil inventory of Scotland 2007-2009: profile description and soil sampling protocols. (NSIS_2). Technical Bulletin, James Hutton Institute., Scotland's Soils Website.
  • Lilly, A.; Bell, J.S.; Hudson, G.; Nolan, A.J.; Towers, W. (Compilers) (2015) Lilly, A., Bell, J.S., Hudson, G., Nolan, A.J. & Towers. W. (Compilers) 2010. National soil inventory of Scotland (NSIS_1); site location, sampling and profile description protocols. (1978-1988)., Scotland's Soils Website.
  • Lilly, A.; Baggaley, N.J. (2015) Developing simple indicators to assess the role of soils in determining risks to water quality., CREW Project Report to SEPA, CD2012_42, 18pp.
  • Mitchell, R.J.; Lilly, A.; Bell, J.S.; Cameron, C.; Donald, C.; Fielding, D.; Green, G.; Hewison, R.H.; McIntyre, S.; Newman, G.: Nolan, A.; Owen, J.; Smith, D.; Sturgeon, F.; Thompson, C.; Towers, W.; Williams E. (2014) Ecosystem effects of long-term herbivore exclusion., SNH Contract Report.

  • Bruneau, P.; Dobbie, K.; Lilly, A.; Loades, K.; Marks, S. (2022) Lessons learned from the development and use of Scotland’s soils website , Oral presentation World Congress of Soil Science
  • Robertson, A.H.J.; Pérez-Fernández, E.; Baggaley, N.J.; McKenzie, B.M.; Owen, I.J.; Lilly, A. (2019) Extending predictions of soil parameters for a national dataset., In: Engelsen, S.B., Sørensen, K.M. and van den Berg, D. (eds.). Proceedings of the 18th International Conference on Near Infrared Spectroscopy (ICNIRS2017), NIR Spectroscopy at Work in Industry, Copenhagen, Denmark, 11-15 June 2017. IM Publications, Chichester, pp123-127.
  • Lilly, A. (2016) Land use change and greenhouse gas - improving the evidence base., Presentation at Theme 3 Meeting, The James Hutton Institute, Aberdeen, 11 March 2016.
  • Lilly, A.; Hallet, P.; Hall, R.; Russell, T.; Raffan, A.; Long, A.; Aitkenhead, M.; Baggaley, N.; Troldborg, M.; Crooks, B.; Ball, B. (2016) Are Scotland's soils physically degrading?, SRUC SEPA Conference, What Future for our Farming Systems? Environmental Challenges and Integrated Solutions, Radisson Blu Hotel, The Royal Mile, Edinburgh, 1-2 March 2016.
  • Towers, W.; Xiao, X.; Sneddon, S.; Woodfield, M.; Donnelly, D.; Lilly, A.; Miller, D.R.; Dobbie, K.; Bruneau, P.M.C. (2014) Delivery of soils information over the web., Proceedings of SRUC/SEPA Conference Agriculture and Environment, Delivering Multiple Benefits from our Land; Sustainable Development in Practice, Edinburgh, 15-16 April 2014, pp304-305.
  • Lilly, A.; Chapman, S.J. (2014) Assessing changes in carbon stocks of Scottish soils: lessons learnt., Soil Change Matter Workshop, Bendigo, Victoria, Australia, 24-27 March 2014.
  • Donnelly, D.; Miller, D.R.; Towers, W. (2013) Scottish Soil Database and Website., AGI Scotland Conference, University of Glasgow, 27 February 2013.
  • Troldborg, M.; Hough, R.L.; Aalders, I.H.; Towers, W.; Lilly, A.; Hallet, P.; Bengough, A.G.; McKenzie, B.M.; Ball, B. (2012) Assessing soil compaction risk using a Bayesian Belief Network., EUROSOIL 2012, Soil Science for the Benefit of Mankind and Environment, 4th International Congress of the European Confederation of Soil Science Societies (ECSSS), Bari, Italy, 2-6 July 2012. Oral presentation
  • Lilly, A. (2010) A hydrological classification of UK soils based on soil morphological data., World Congress of Soil Science: Soil Solutions for a Changing World, 19th, Brisbane Australia, 1-6 August 2010.
  • Baggaley, N.J.; Lilly, A.; Walker, R.; Castellazzi, M. (2010) An assessment of the data resolution required to run the PESERA soil erosion model at a catchment scale in a high latitude agricultural catchment., World Congress of Soil Science: Soil Solutions for a Changing World, 19th, Brisbane Australia, 1-6 August 2010.
  • McKenzie, B.M.; Krol, M.; Binnie, K.; Bengough, A.G.; Hallett, P.D.; Valentine, T.A.; Lilly, A. (2008) Putting together measures of soil physical quality., Eurosoil 2008, Vienna, Austria, 25-29 August 2008.
  • Pachepsky, Y.; Gimenez, D.; Lilly, A.; Nemes, A. (2008) Soil structure and soil hydrologic functioning: a hydropedological framework., Water and Soil: Key to Sustaining the Earth's Critical Zone. First International Hydropedology Conference, Penn State University, University Park, Pennsylvania, 28-31 July 2008.
  • Pachepsky, Y.A.; Lilly, A.; Gish, T.J. (2008) Structure and function in soil hydrology., European Geosciences Union, General Assembly 2008 Symposium: Soil Structure Forming Processes and Soil Functions, Vienna, Austria, 13-18 April 2008.
  • Reid, D.C.; Lilly, A.; Kay, D.; Drury, D.; O'Neill, D. (2004) Regulation of private water supplies (Small Community Supplies) in the UK., 11th Canadian National Conference and 2nd Policy Forum on Drinking Water: Promoting Public Health Through Safe Drinking Water, Canada, April 2004.
  • Fitzsimons, V., Ball, D.F., O'Dochartaigh, B., MacDonald, A.M., Del Rio Maria, M., Auton, C. and Lilly, A. (2004) Mapping groundwater vulnerability in Scotland: a new approach for the Water Framework Directive., SAC/SEPA Biennial Conference on Agriculture and the Environment V: Water Framework Directive and Agriculture.
  • Betson, M.; Anthony, S.; Lord, E.; Dunn, S.M.; Lilly, A.; DeGroote, J.; Towers, W.; Struve, J.; Tagg, A.; Abbott, C.; Lewis, D.; MacDonald, J.; Badger, R.; Ferris, N.; Ward, B. (2004) A GIS decision support screening tool for diffuse pollution in Scotland and Northern Ireland., SAC/SEPA Biennial Conference on Agriculture and the Environment V: Water Framework Directive and Agriculture.
  • Dunn, S.M., Lilly, A., Vinten, A.J.A. and DeGroote, J. (2004) Nitrogen risk assessment model for Scotland: sensitivity analysis and implications for water quality prediction., Proceedings of SEPA / SAC Conference on Agriculture and the Environment, ( ed. D Lewis and L. Gairn), Edinburgh, 24-26 March 2004, pp94-100.
  • Lilly, A. (2004) Factors affecting the microbial quality of private water supplies in North-east Scotland., Environmental Health Scotland.
  • Dunn, S.M., Vinten, A.J.A., Lilly, A., DeGroote, J. and McGechan, M. (2003) Modelling nitrate losses from agricultural activities on a national scale., In: Diffuse Pollution and Basin Management (Ed. M.Bruen). Proceedings of the 7th International Specialised IWA Conference, Dublin, Ireland. ISBN 1902277767. (See website as at 04/10/2004)
  • Dunn, S.M.; Chalmers, N.; Stalham, M.; Lilly, A.; Crabtree, R.; Johnston, L. (2002) Modelling the influence of irrigation abstractions on Scotland's water resources., Proceedings of the IWA International Conference on River Basin Management, 9th, Edinburgh, September 2002. On cd-rom.
  • Domburg, P.; Lilly, A.; Dunn, S.M.; Edwards, A.C. (2002) Selecting effective areas for development of buffer strips at farm and river basin scale., Agricultural Effects on Ground and Surface Waters: Research at the Edge of Science and Society. Proceedings of an International Symposium, Wageningen, Netherlands, October 2000. IAHS Press,Wallingford, pp151-156.
  • Lilly, A.; Birnie, R.V.B.; Hudson, G.; Horne, P.L.; Gordon, J.E.; Puri, G. (2001) Inherent geomorphological risk of soil erosion by overland flow in Scotland., Earth Science and the Natural Heritage, Scottish Natural Heritage Conference Proceedings.
  • Lilly, A. (1999) Global soil hydrological databases : an example from Europe., Abstract for Modelling root water uptake in climate and hydrological models workshop. Restricted circulation.
  • Lamb, A.J., Gauld, J.H., Reid, D.C., Lilly, A., McGaw, B.A. and Curnow, J. (1998) Microbiological risk assessment of private water supplies., Royal Environmental Health Institute of Scotland Magazine, 10, 21-26.
  • Lilly, A. (1998) The influence of soils and land use on groundwater quality., The Royal Environmental Health Institute of Scotland Magazine, 10(5), pp4-6.
  • Miller, D.R.; Morrice, J.G.; Ferrier, R.C.; Wright, G.G.; Lilly, A. (1995) The integration of environmental variables and models for water catchment management., Proceedings of JEC '95, The Hague, 385-391.
  • Lilly, A. and Paterson, E. (1994) The availability and uses of soil physical data: a Scottish perspective., Conference on the Development of a European Soil Physics database, Wageningen, 1994.
  • Boorman, D.B., Hollis, J.M. and Lilly, A. (1991) The production of the Hydrology of Soil Types (HOST) data set., In: Proceedings of the 3rd National Hydrology Symposium, University of Southampton. British Hydrological Society.
  • Wilson, M.J.; Cresser, M.S.; Lilly, A.; Nolan, A.J. (1989) Vulnerable soils and their distribution., Proceedings of a Symposium on Acidification in Scotland, 1988. Organised by SDD, pp. 60-70.

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The James Hutton Research Institute is the result of the merger in April 2011 of MLURI and SCRI. This merger formed a new powerhouse for research into food, land use, and climate change.