Publications archive

Refereed publications and major reports from the Agroecology group

Newton, A.C., Begg, G.S., Swanston, J.S. 2008. Deployment of diversity for enhanced crop function. Annals of Applied Biology (doi:10.1111/j.1744-7348.2008.00303.x).

Monocultures are used in high-input systems to maximise short term profitability, but over time yield and quality can become unstable. This paper considers how diversity can be reintroduced to cropping systems to confer stability without compromising quality. It combines expertise between three of SCRI's programmes: Pathology (ACN), Genetics (JSS) and Environment (GSB).

Squire, G.R., Hawes, C., Begg, G.S., Young, M.W. 2009. Cumulative impact of GM herbicide-tolerant cropping on arable plants assessed through species-based and functional taxonomies. Environmental Science and Pollution Research 16(1), 85-94. Published online 2 December 2008 (doi: 10.1007/s11356-008-0072-6).

In a gradualist approach to the introduction of crop biotechnology, the findings of experimentation at one scale are used to predict the outcome of moving to a higher scale of deployment. Species-accumulation curves are examined here as a method of indicating regional-scale impacts on botanical diversity from multiple field experiments (using as a case study the two weed-management treatments in the UK's GM crop trials). Species-accumulation provided simple parameters that captured the net result of numerous local effects of treatments on plant species. The method may be applied more generally to explore the effects changes in field management on species and functional types.

Johnson, S.N., Murray, P.J. (eds) 2008. Root feeders - an ecosystem perspective. CAB International, Wallingford, 272 pages.

Cover image of the Root Feeders book Interactions between plants and herbivores can affect a plant's growth and development, and ultimately its economic value. Research has traditionally concentrated on above ground herbivores, which are usually readily visible or accessible. Below ground herbivores, both vertebrates and invertebrates, have considerable influence on crops and ecosystems, but are a much greater challenge for scientific study, not least because they are difficult to observe. Some root feeders are agricultural pests, but others can be biological control agents or affect the community dynamics of plants, soil micro-organisms or above ground organisms. This book includes chapters on visualising root feeders in the soil, their roles in agriculture, grassland and forest ecosystems and case studies on management and control.

McMenemy, L.S., Mitchell, C., Johnson, S.N. 2008. Biology of the european large raspberry aphid (Amphorophora idaei): its role in virus transmission and resistance breakdown in red raspberry. Agricultural and Forest Entomology (early view section).

This Review Article synthesises existing knowledge of this important aphid, particularly its role in transmitting viruses that reduce the raspberry harvest.  The aphid has evolved rapidly to overcome both resistance genes in the crop plants and the insecticides used to control it. Options for sustained control in the future are considered. This is Lindsay's (PhD student) first paper and and is a combined effort between the multi-trophic interactions group in Agroecology and SCRI's soft fruit research.

Broadley, M.R., White, P.J., Hammond, J.P., Graham, N.S., Bowen, H.C., Emmerson, Z.F., Grey, R.G., Iannetta, P.P.M., McNicol, J.W., May, T.S. 2008. Evidence for neutral transcriptome evolution in plants. New Phytologist 180 (doi:10.1111/j.1469-8137.2008.02640.x).

Editor's Choice in the 3 October 2008 issue of the journal Science (322, 17) under the heading Evolution: neutral plantings, this collaboration between scientists at the University of Nottingham and SCRI examined evolutionary processes in gene expression using species of the Cruciferae (cabbage family).

Cullen, D.W., Squire, G.R., McNicol, J.W, Jacobs, H.H., Osborne, J.L., Ford, L., Ramsay, G., Scrimgeour, C., Young, M.W. 2008. Development and validation of gas chromatography and real-time quantitative PCR for the quantification of landscape-scale gene flow from varieties of high erucic (HEAR) oilseed rape. Journal of the Science of Food and Agriculture 88(13), 2253-2264. Published online: 8 September 2008 (doi:10.1002/jsfa.3340).

The methods are described for examining the movement of genes among crops in agricultural landscapes of the UK. Fields of low erucic acid oilseed rape (the commonest type) were used as the 'receptor' for pollen and high erucic types as the 'donor'. When cross pollination occurs from a high- to a low-erucic plant, the content of erucic acid in the resulting seed is raised well above the 'low' value. Using experimental receptor and donor fields of about two hectares each in area, the biochemical method of detecting the raised erucic acid was found to be at least as sensitive as the DNA-based method of detecting the transmission of genetic material. This is the first main paper from a Defra-funded project on gene flow in landscapes: the project group combined DNA and biochemical detection methods with statistics and field expertise in experiments at both SCRI and Rothamsted Research (Rothamsted). Future papers will report on the origin of impurities from different sources, including cross pollination, in actual landscapes where the low- and high-erucic types are grown near each other.  

Environmental risk assessment of genetically modified organisms Volume 4: challenges and opportunities with Bt cotton in Vietnam. Edited by David A Andow, Angelika Hilbeck, Nguyen Van Tuat, 2008. CABI Publishing, Wallingford, UK. ISBN 978 1 845493 390 6. 384 pages.

Cover image of the Environmental risk assessment of genetically modified organisms Volume 4: challenges and opportunities with Bt cotton in Vietnam bookThis is the latest volume in a series of books reporting the results of workshops on the risk assessment of GM crops, targeted at specific crops and countries. Nick Birch from Agroecology and Ron Wheatley from Plant Soil Interactions participated in the workshops and were joint authors on several articles in the latest and previous volumes. These contributions extend EPI's experience on GM assessments to the tropics and sub-tropics. The CABI website gives the full list of volumes and topics.  

Karley, A.J., Hawes, C., Iannetta, P.P.M., Squire, G.R. 2008. Intraspecific variation in Capsella bursa-pastoris in plant quality traits for insect herbivores. Weed Research 48, 147-156.

A new line of work on our model arable plant, shepherd's purse - a species with many ecologically functional forms, here showing trade-offs in traits that link to herbivory.

Begg, G.S., Elliott, M.J., Cullen, D.W., Iannetta, P.P.M., Squire, G.R. 2008. Heterogeneity in the distribution of genetically modified and conventional oilseed rape within fields and seed lots. Transgenic Research (doi:10.1007/s11248-008-9166-7).

Detecting and managing impurities in crops is necessary to ensure quality in the food chain. It's easy enough if you can see the impurity, but what if it looks similar to the crop itself, as does weedy (volunteer) oilseed rape? Here, we brought together in-house statistics, mathematical modelling, qPCR(DNA)- and protein-based detection methods with field sampling to produce the first (yes!) quantitative description of spatial variation in GM and non-GM volunteers in a non-GM crop. The methods will be applied generally in future work on sampling impurities and weedy plants and on more basic population biology.  Our thanks go to the farmer who allowed us on the field!

Hawes, C., Haughton, A.J., Bohan, D.A., Squire, G.R. 2009 Functional approaches for assessing plant and invertebrate abundance patterns in arable systems. Basic and Applied Ecology 10, 34-47 (doi:10.1016/j.baae.2007.11.007).

The taxonomic unit of 'species' is used for recording and reference but allows no direct link from the plant or invertebrate to any ecological process. This work examines a functional as distinct from a species-based approach to arable food webs. 375 plant species and 182 invertebrate taxa were condensed into 20 plant and 36 invertebrate functional types, defined according to trophic (feeding) behaviour and traits that affect capture, availability and quality of resource. Two main resource-consumer interaction-groups were identified that were differently affected by grass and broafleaf weeds and responded to a range of agronomic factors. GM herbicide tolerant crops had systematic effects on these trophic groups but such effects were smaller than differences between the types of crop. The study, by a group from SCRI and Rothamsted Research, used the unique resource of data from the Farm Scale Evaluations to tackle some general questions in arable ecology.

Caron-Lormier, G., Humphry, R.W., Bohan, D.A., Hawes, C., Thorbek, P. 2008 Asynchronous and synchronous updating in individual-based models. Ecological Modelling (doi:10.1016/j.ecolmodel.2007.10.049).

If an elephant and a rat both go for the same banana and the elephant gets there first, the rat gets none and goes hungry. We may imagine that in real life but how does it work in modelled life. When modelled organisms are distributed in space, how are decisions made as to which first interacts with which. Two methods - called asynchronous and synchronous scheduling - are compared here in a simple individual based model (IBM) of biological interactions. The methods lead to different results, which we need to account for when modelling the fluxes of energy and matter in systems. 'The work appears to be the first evidence of the importance of scheduling methods on emergent properties for IBMs'. The authors are from Rothamsted Research, SCRI and Syngenta. 

Debeljak, M., Squire, G.R., Demsar, D., Young, M.W., Dzeroski, S. 2008 Relations between the oilseed rape volunteer seedbank, and soil factors, weed functional groups and geographical location in the UK. Ecological Modelling 212, 138-146 (doi:10.1016/j.ecolmodel.2007.10.019).

We looked for patterns in a large ecological data set, applying data-mining techniques at the Josef Stefan Institute in Ljubljana to the baseline survey in the Farm Scale Evaluations - an approach new to both collaborating groups that revealed some unexpected and non-trivial factors in the abundance and distribution of weedy (volunteer) oilseed rape. Questions - why is there more in the north and west of the UK, and why does it coincide with the determinate broadleaf group of weeds that includes Capsella?


ECOGEN - Soil ecological and economic evaluation of genetically modified crops. Pedobiologia 51. 2007. Edited by Bryan Griffiths. Special Issue of the journal containing a range articles jointly authored by staff in the Agroecology and Plant Soil Interactions groups in the EPI Programme at SCRI with their collaborators in Europe.

Cover image of the Pedobiologia Special IssueThis issue of the journal Pedobiologia presents results of the ECOGEN project, completed 2007, on the ecological and economic evaluation of a GM crop - Bt maize. The multi-disciplinary team comprised groups from Denmark, The Netherlands, France, Slovenia and SCRI. Effects of Bt maize on soil organisms and processes were small, not all in the same direction, mostly transient and less than effects between agronomic processes (for example, tillage) and crop varieties. ECOGEN is one of the few projects that has attempted to develop a framework for examining both the biophysical and the economic effects of a new type of crop. By doing so, it opened appoaches to environmental risk assessment that will be further developed by SCRI and its European collaborators.

Birch, A.N.E., Griffiths, B.S., Caul, S., Thompson, J., Heckmann, L.H., Krogh, P.H., Cortet, J. 2007. The role of laboratory, glasshouse and field scale experiments in understanding the interactions between genetically modified crops and soil ecosystems: A review of the ECOGEN project. Pedobiologia 51, 251-60 (doi:10.1016/j.pedobi.2007.04.008).

One of the papers co-authored by SCRI in the ECOGEN special issue above. It compared effects of Bt maize in the laboratory, in small more or less enclosed chambers (mesocosms) and in field crops in Denmark and France. Effects at the small scale were found not to be good predictors of the effects of Bt maize on organisms and processes in the field.

Bown, J.L., Pachepsky, E., Eberst, E., Bausenwein, U., Millard, P., Squire, G.R., Crawford, J.W. 2007. Consequences of intraspecific variation for the structure and function of ecological communities Part 1: Model development and predicted patterns of diversity. Ecological Modelling 207, 264-276

Pachepsky, E., Bown, J.L., Eberst, E., Bausenwein, U., Millard, P., Squire, G.R., Crawford, J.W. 2007. Consequences of intraspecific variation for the structure and function of ecological communities Part 2: Linking diversity and function. Ecological Modelling 207, 277-285

Bohan, D.A., Hawes, C., Haughton, A.J., Denholm, I., Champion, G.T., Perry, J.N., Clark, S.J. 2007.  Statistical models to evaluate invertebrate–plant trophic interactions in arable systems. Bulletin of Entomological Research 97, 265-280.

Johnson, S.N., Zhang, X., Crawford, J.W., Gregory, P.J., Young, I.M. 2007. Egg hatching and survival time of soil-dwelling insect larvae: a partial differential equation model and experimental validation. Ecological Modelling 202, 493-502.

Zhang, X., Johnson, S.N., Crawford, J.W., Gregory, P.J., Young, I.M. 2007. A general random walk model for the leptokurtic distribution of organism movement: theory and application. Ecological Modelling 200, 79-88

Johnson, S.N., Crawford, J.W., Gregory, P.J., Grinev, D.V., Mankin, R.W., Masters, G.J., Murray, P.J., Wall, D.H., Zhang, X. 2007. Non-invasive techniques for investigating and modeling root-feeding insects in managed and natural systems. Agricultural and Forest Entomology 9, 39-46.

Begg, G.S., Cullen, D.W., Iannetta, P.P.M., Squire, G.R. 2007. Sources of uncertainty in the quantification of genetically modified oilseed rape contamination in seed lots. Transgenic Research 16, 51-63.

Cover image of the journal showing leaf-shape variation in CapsellaIannetta, P.P.M., Begg, G., Hawes, C., Young, M., Russell, J., Squire, G.R. 2007. Variation in Capsella (shepherd's purse): an example of intra-specific functional diversity. Physiologia Plantarum 129, 542-554.

Previous published output

A full account research papers, reports and conference proceedings before 2007 can be found under the main research topics accessible on the Agroecology main page.