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Biodiversity and ecosystem functions

Work Package Biodiversity and Ecosystems

Research Deliverable 
Biodiversity and ecosystem function


Researchers at the James Hutton Institute, the Royal Botanic Garden Edinburgh and Biomathematics and Statistics Scotland are working together to provide scientific evidence to underpin the Scottish Biodiversity Strategy. At the core of our work is understanding how management actions interact with biodiversity to deliver the outcomes we want. This ranges from understanding how the genetic diversity in one crop can be exploited to make farming more resilient to restoring populations of rare mountain plants. In addition, we use this understanding to provide indicators of how healthy ecosystems are for use by policy makers.

Aim of Research

There remain large gaps in understanding how changes in management and the environment alter community composition and, hence, ecosystem functions. This Research Deliverable (RD) addresses how ecosystem functions are regulated by the traits of species present, and how potential limits for the maintenance of ecosystem function can be captured in ecosystem health metrics. It also has the aim of identifying indices of ecosystem function that can be applied to assess ecosystem health at a range of scales (from field to national) so that management actions can be targeted to improve ecosystem health and to conserve and restore biodiversity.


2021 / 2022
2021 / 2022

We have continued to deliver important findings from our research in Year 6 of the Programme. Our continued work on Bere barley has shown it is better able to compete with grass weeds than elite varieties and it harbours more plasticity. This work led to a paper in a high-profile journal detailing new methods to look at plasticity in plants. We have continued to develop the upland grazing work by using drone imagery to provide plot-wide measures of biomass to model pipit nesting densities. Our crop mixtures work developed a successful integration of open data approaches with farmer participation in crop mixture trials, an approach that will be developed into the next Programme.


  • Increased grazing drives homogenisation but reduced grazing increases turnover in upland habitat mosaics: A new paper in Biodiversity and Conservation by SEFARI scientists reports that increased grazing led to more homogenous vegetation across an upland mosaic of different vegetation types. The increased grazing led to an increase of grazing tolerant species in the vegetation types less preferred by the sheep. In contrast, removing the grazing resulted in a greater turnover of species, particularly in the less preferred vegetation where species capable of responding to the removal of grazing had persisted. Decisions about grazing management of the uplands involve many trade-offs; this study at Glen Finglas identified potential trade-offs between stability and homogenisation to add to existing ones on the biodiversity of different groups of species and on ecosystem services.
  • Collaborative research with farmers to improve agrobiodiversity. Intercropping is a practice that could improve sustainability and safeguard biodiversity in agricultural habitats but is not commonly practiced. We carried out collaborative trials of crop mixtures with farmers across Scotland who were looking for practices that reduce inputs, increase future sustainability and minimise the environmental footprint. Trial results were disseminated widely through webinars and on farm events, and through the Crop Mixtures Data Explorer tool, which is an open data platform that we co-developed with agricultural stakeholders to support decisions about using crop mixtures. The benefits of this collaborative approach to research, explained in a SEFARI case study, are that it has supported uptake of intercropping by a growing number of farmers and shown how research can be translated into practical use in the Scottish farming community.
  • Using genetically mixed plants to increase success rates of conservation translocations. We have translocated 900 Cicerbita alpina plants into 5 new sites in Scotland. Plants derived from a crossing experiment and are a mix of selfed, crossed within, crossed between different Scottish populations, as well as crosses between Scottish and Norwegian plants. We have planted the exact same mix of plants into each site so that any difference in performance between sites can be attributed to environmental and not genetic factors. Early preliminary monitoring results of the first growing season after planting indicate that crossed plants, which have a higher genetic diversity and lower inbreeding, have better growth rates and therefore survival prospects compared to selfed or crosses within populations at all 5 translocation sites.
  • Spatial Planning for Rainforest Restoration. Our analysis has shown how future woodland planting can actively target different landscape positions to create refugia that protect Scotland’s rainforest diversity under climate change. With the increased risk of future summer heat waves and droughting, riparian woodland is particularly important in this regard, by providing necessary moisture to vulnerable species; the amount of additional woodland required to maintain species populations decreases as reforestation becomes focussed along riparian systems. Tree species mixtures are also critical, with the decline of ash posing a particular threat to vulnerable rainforest diversity. The work has been shared with partners from the Alliance for Scotland’s Rainforest, and specific case studies are now being developed to support site management plans. To improve the quantitative measurement of microclimates, dataloggers have been placed into multiple microhabitats across three climatically contrasting woodland NNRs.
  • Realising sustainable and resilient food- and feed-systems demands diversification of crops and downstream value chains: A recent publication in Frontiers of Agricultural Science and Engineering from leaders of six EU projects, including SEFARI researchers, highlights that there are significant technological and institutional barriers to diversification in crops and downstream value chains. They point to an urgent need to establish multi-actor networks to facilitate diversification and help ensure the necessary cooperation among all agri-food system stakeholders.
  • Potential of Bere barley diversity for sustainability in marginal soils: We have shown that extant barley landraces selected over many generations on marginal soils have adapted to tolerate limited micronutrient availability. Our findings and the interest generated show that Bere barley constitutes a valuable resource of untapped adaptive genetic variation, with the opportunity to identify useful cultivars and genes controlling the key adaptive traits to underpin crop improvement in marginal soils. Moreover, the heritage and sustainability value of Bere barley has direct value to the Scottish rural economy through use in high-value products. The population of Bere barley genotypes safeguarded in this work are now being used by individual crofters in participatory breeding and assessment programmes and by new distillers and maltsters (Raasay and Crafty Maltsters) to select the best varieties for their commercial purposes.
2020 / 2021
2020 / 2021

Our work on crop mixtures has resulted in a paper in a special feature in Journal of Ecology on facilitative mechanisms underlying the effects of biodiversity on ecosystem functioning where we synthesise the links between ecological theory and agronomic performance of species and cultivar mixtures. In addition to improving outputs by increasing crop diversity at the field scale, a range of publications have identified the food security, health and environmental benefits of increasing crop diversity at the farm and landscape scale, particularly through the increased use of legume crops in Scottish farming. We have continued to build genetic stock and expertise in propagation and replanting of Cicerbita alpina (alpine sow thistle) and have used this material to build up populations in the Cairngorms. Similarly, we are starting to build up stock of Woodsia ilvensis (oblong woodsia). We have continued to explore the potential for Bere barley to supply genetic material for breeding to improve phosphorus and manganese acquisition and heavy metal tolerance and published a number of papers on this. The Glen Finglas research has produced two papers, one shows that the slow pace of change in vegetation composition is having little functional impact where grazing has been increased or abandoned, whilst the other has shown that bird species composition is starting to change towards more woodland and scrub species where succession to woodland is starting. We have provided a number of SEFARI case studies including one on the issues of grazing in the uplands based on the Glen Finglas work and another on the impact of liming on biodiversity which shows that hill grasslands are relatively resilient to increased liming and there is little impact on plants worms or soil properties in the short-term. We have also continued to develop WaderMap as a tool to collate information on different wader conservation activities and to display trends in wader population data.


  • Biodiversity trends and changes across northern Europe are being driving by rising temperatures. A Europe-wide collaboration including SEFARI researchers analysed 161 biodiversity time series (over 15 to 91 years duration) covering 6,200 marine, terrestrial, and freshwater species from 21 European countries. The paper published in Nature Communications showed that local trends in biodiversity often deviate significantly from global patterns. In particular, the composition of species communities has undergone extensive changes at the local level. For northern Europe, the trend is towards an increase in diversity and species numbers which could be attributed to a combination of climate change (e.g., new species adapted to warmer conditions, spread of alien species and recovery from past disturbances and pollution (e.g., acidification). The study also showed declines in insect species abundances in the Atlantic bio-geo-region (UK, France, Belgium, Spain, Denmark and Germany), corroborating recent reports of worldwide declines of local terrestrial insect communities. The study emphasised the need to standardise biodiversity monitoring schemes and to integrate long-term biodiversity and environmental monitoring data, which will allow conservation measures to be better tailored at the local level.
  • Enabling more sustainable food- and feed-systems: As part of an EU-wide team, a SEFARI researcher has discerned twenty-one enabling approaches to increase the production and consumption of home-grown legumes. These practical approaches present integrated strategies to benefit the environment, society, and the economy (Balázs et al., 2021). One such approach is processing beans for brewing and distilling, which demonstrates the environmental, nutritional, and commercial potential of the new, more sustainable agri-feed and -food systems (Black et al. 2021).
  • Bere barley diversity contributes to sustainability and value chain diversification: SEFARI scientists have made further discoveries related to the importance of maintaining Bere barley diversity for its value to sustainability. Scotland’s traditional barley variety, Bere, has been shown to be particularly able to cope with micronutrient deficiency and traditional growth with seaweed as a fertiliser has driven the evolution of this ability (Brown et al. 2020). Genes associated with the ability of Bere to cope with manganese deficiency specifically have been identified (Cope et al. 2020). The importance of Bere as a heritage variety with value chain diversification credentials has been recognised in its inclusion in a successful bid for EU Horizon 2020 funding (RADIANT), which secured additional funding of €6M for the consortium. 
  • Biodiversity-function relationships in sustainable crop production: SEFARI scientists have produced a review article that links fundamental ecological understanding of the role of biodiversity in delivering ecosystem functions to the pressing need for developing sustainable crop production systems. The article reviews the potential benefits to multiple ecosystem functions and services from enhancing diversity in crop systems, for example through intercropping, and is relevant to research, as well as those interested in the development of sustainable farming policy.
2019 / 2020
2019 / 2020

Research has been performed to understand the mechanisms underpinning diversity benefits in arable plant communities including an experiment testing mixtures (up to six species) of cereals (barley, wheat), oil seeds (oil seed rape, linseed) and legumes (pea, faba bean) to understand how trait diversity contributes to improved productivity. A paper was published from the 2016 field trial that showed that increasing the number of barley genotypes in a mixture reduced the available niche space for weeds. The fate of newly reintroduced populations of Cicerbita alpina (alpine sow-thistle) has been followed and it appears that identity of the source population is an important determinant of survival. Material to re-establish the native fern Woodsia ilvensis (oblong woodsia) is ready for testing for drought-resistance. Fieldwork observations have been carried out at Glen Finglas to establish how long-term differences in grazing influence food quality for invertebrates and birds and the accompanying lab work is underway. Research on bere barley work has identified genetic markers that influence micronutrient uptake, revealing genetic diversity in traditional landraces that could benefit commercial barley by improving growth in nutrient-deficient soils. Modelling research has shown that maintenance of within-species diversity of insect herbivores (aphid pests) depends on the efficiency of their natural enemies. WaderMap, an application to bring together data on wader conservation projects and other environmental data, was successfully received and sampling in the large-scale liming experiment carried out. The two new bryophyte-based Ecosystem Health Indicators were launched on SEWeb accompanied by a SEFARI case study and the publication of the associated paper. Work on western oakwoods showed that long-term declines in lichen diversity have occurred over the last 50 years, whilst new work is focussed on identifying new sites for woodland regeneration to maximise potential colonisation by woodland specialists.


  • Long-term consequences of upland grazing: SEFARI scientists have demonstrated that likely changes in grazing levels in the uplands (e.g. in response to changes in agricultural support payments, profitability of upland farming and conservation priorities) can take many years to affect upland plant communities. Specifically, it took 15 years for the tripling of sheep numbers or the complete removal of sheep to impact on most species. Some communities were very resistant to change, particularly those most attractive to grazers, which had lost plant species capable of responding to reduced grazing levels.
  • Natural enemy regulation of diversity in insect herbivores. SEFARI scientists have shown evidence for a novel mechanism that could be responsible for maintaining genetic diversity within aphid populations.  Aphids frequently shown resistance to parasitism by parasitoid wasps but the reason why susceptible and resistant aphids coexist has never been explained. Modelling work has shown that this could come about if parasitoid wasps suffer a fitness cost when switching between different aphid types. These findings are important for targeted biological control of aphid pests. 
  • Monitoring biodiversity through citizen science: SEFARI scientists have analysed citizen science data to document a five-decade decline in species that are associated with Scotland’s ancient woodlands. This was used as evidence to the State of Nature Report 2019 Solutions to reverse the trend were identified and have been used to inform the new strategy of the Atlantic Woodland Alliance consortium. This includes targeting efforts to the expansion of existing woodlands with old-growth structure, and which include populations of dispersal-limited species.
  • Towards truly sustainable agri-food value-chains: RESAS-supported research on legumes (e.g. peas and beans) was recently reported in partnership with the EU TRUE project in the outcome of an EU-wide ‘consensus opinion of stakeholders’ exercise. Three recommended action areas were identified to help realise more-sustainable legume-supported agri-food systems around: investment in agri-food and -feed research and knowledge transfer; reducing reliance on the use of inorganic nitrogen fertiliser; plus greater foci on nutrition, health policies and public campaigns that promote the inclusion of home-grown legumes in the human diet.
  • A toast to reduce Scotland’s protein import dependency: RESAS-supported work to help realise more cropping of pulses (e.g. peas and beans) in Scotland, carried out in partnership with Scottish-based SMEs, revealed that the use of home-grown peas to make gin also provided a high-protein ‘co-product’ for animal feed. The pea co-product can offset animal feed imports, and the two high-value products were achieved with a reduced carbon footprint (compared to conventional wheat gin). A commercial product (World’s first climate-positive gin) will be launched in February shortly after World Pulses Day (FAO-UN, Feb 10th). 
2018 / 2019
2018 / 2019

Year 3 progress included a successful analysis of the barley:weed drought study and a new experiment on barley:weed interactions. The Cicerbita alpina (Alpine blue sow-thistle) reintroduction work made great strides in understanding the role of genetic diversity and restoration success, whilst the bere barley work has initiated the transfer of genes into elite varieties to cope with alkaline soils. A new fieldwork approach looking at management cascades through different trophic levels has started successfully at Glen Finglas and The work on Ecosystem Health Indicators has progressed well and is nearly ready for launching on SEWeb. Due to the cold spring, sowing of the grassland diversification experiment was delayed until May when conditions were more suitable. However, the dry summer meant that germinations was slow and consequently no monitoring was carried out in summer 2018. Research into effects of lime addition on trophic interactions continued to progress well, including  the ongoing monitoring of three experimental study sites to contribute data on the effects of lime addition on soil characteristics, earth worm abundance, sward productivity, and vegetation diversity. Combined with the baseline data and ongoing monitoring this will provide data for later analyses to better understand the effects of lime addition on the availability of key soil invertebrates for breeding waders.


  • Public engagement for biosecurity: Research on plant and animal biosecurity from the RBGE, James Hutton Institute, Moredun Research Institute, and SRUC was distilled into an interactive, permanent public exhibit at the John Hope Gateway. SEFARI work is presented in a series of interactive panels demonstrating how plant and animal diseases move around the world, and actions the public can take to protect Scotland’s natural and economic assets. This exhibit is prominently placed in the entrance to the RBGE (694,000 international and local visitors in 2016), with portable panels in construction to further spread the message at public events across Scotland.
  • Major new database on multi-scale plant diversity published:  The James Hutton Institute was the main UK contributor to a new international database of vegetation data - GrassPlot. The difference between this database and others is that all the plot data were collected at multiple scales. The main aim of collecting and publishing these data is to facilitate studies on the scale- and taxon-dependency of biodiversity patterns and drivers along macroecological gradients. For instance, it will allow researchers to analyse how scale dependent relationships such as the species-area curve vary with climate.
  • Importance of crop mixtures research brought to the fore through Parliamentary Reception and new publication: Research on potential benefits of crop mixtures for sustainable food production was highlighted during a SEFARI Showcase event at the Scottish Parliament. The event’s keynote address was given by the Cabinet Secretary for Rural Economy and Connectivity, Fergus Ewing MSP. In addition, concepts developed through WP1.3 work on crop mixtures contributed to delivery of a new research paper in Nature Ecology and Evolution. This shows that some of the effects which might help to deliver benefits from crop mixtures evolve best in species rich plant communities, indicating benefits for sustainability from conserving species.
  • Evolving for mixture benefits: Concepts developed through our crop mixtures work (RD1.3.1 and RD2.3.8) concerning the beneficial interactions between neighbouring species have contributed to delivery of a new research paper by Schöb et al. This study shows for the first time that some of the effects which help to deliver benefits from crop mixtures evolve best in a species rich plant community. Importantly this work demonstrates how higher diversity helps promote ecosystem functions, and that breeding for crop mixtures (a potential sustainable production approach) may need novel trait combinations which only emerge in species-rich systems.
  • Establishing landraces as living heritage: SEFARI scientists in collaboration with Archaeologists from University of Sheffield have identified and confirmed the origins of barley landraces in the archaeological record using morphometrics and genetics, helping to establish its status as living heritage and helping secure its commercial future through providing the grain with heritage credentials that can be used in marketing of products.
  • Ancient barley landraces adapted to marginal soils demonstrate exceptional tolerance to micronutrient limitation: SEFARI scientists in collaboration with University of Copenhagen and University of Highlands and Islands, Orkney have identified a unique Mn efficient phenotype in Bere landraces that can be potentially used to cope with micronutrient deficiencies seen in crops grown in marginal calcareous soils in the western and northern isles of Scotland and in many of the cereal producing lands on a global scale.


2017 / 2018
2017 / 2018

Year 2 progress included an experiment to investigate how increasing the genetic diversity of barley improved the tolerance of the crop to drought; this was not the case but increasing diversity suppressed weeds and reduced disease incidence. Alpine blue sow-thistle Cicerbita alpina was re-introduced into three new sites in the Cairngorms. The translocated populations include an experimental approach to test the resilience of different genotypes with the aim of increasing in situ seed-set (see Highlights below). Baseline data of the effects of lime addition to trophic interactions, in particular its impacts on potential invertebrate prey of wading birds, have been collected.  Information on grass productivity and quality is also being collected. We have developed additional Ecosystem Health Indicators relating to nitrogen pollution and climate change based on moss and liverwort records in the National Biodiversity Network and their habitat preferences and provided initial results that will feed into the Scottish Biodiversity Strategy. Based on information on epiphyte species distributions, a report identifying priority areas for restoration has been used to inform the development of the Atlantic Woodland Alliance.


  • Potential for crop improvement in marginal soils: New research has shown that extant barley landraces selected over many generations on marginal soils have adapted to tolerate soils with limited Manganese (Mn) availability. By contrast, modern elite varieties on similar soils fail to complete their lifecycle, due to their poor Mn efficiency. Landraces derived from regions with reduced soil fertility constitute a valuable resource of untapped adaptive genetic variation, with an opportunity to identify the key adaptive traits to underpin crop improvement in marginal soils.    
  • Rare plants may be helped by crops: A study investigating the interactions between a rare vascular plant - Valerianella rimosa - (broad fruited corn salad) and a barley crop has shown that the conditions found within the crop might help promote the establishment of the rare plant at the start of the growing season. When combined with the negative impact of the crop on common weeds, these findings indicate that crops may play a role in the conservation of some rare vascular plants by creating space in the farmland weed community.
  • Reintroduction of a rare plant to the Cairngorms: Studies of genetic diversity in populations of the rare Alpine blue sow-thistle have enabled the reintroduction of the species at three new locations in the Cairngorms. Contributing to both the Cairngorms Nature Action Plan and Priority Project 9 of the 2020 Route Map for Scotland’s Biodiversity, the translocated populations included an experimental approach to test the resilience of different genotypes with the aim of increasing the viable seed-set.
  • The destructive effects of Rhododendrons: Rhododendron ponticum shades out native understorey flora and has been the focus of removal by conservation groups. A paper on its effects in Celtic rainforests showed that even after removal of Rhododendron, woodlands did not automatically revert to their pre-invaded state; reseeding with native flowers and grasses is required to fully restore them. Media publicity included interviews for Radio Wales, Radio Scotland and Radio 4 (World at One) and reports in the Daily Mail, The Times, Horticulture Week, Sunday Post, Press and Journal, the Scotsman and others.
2016 / 2017
2016 / 2017

Progress in the Research Deliverable includes successful experiments on diversity-driven trophic interactions; these showed a postive relationship between weed species richness and barley productivity and that increasing barley diversity reduced weed performance through increased competition for light. Trials in Orkney and Dundee have been used to identify differnces in bere barley performance and potential useful traits to breed into modern barley cultivars. A long-term experiment assessing ecosystem effects of liming has been set up, with a particular focus on assessing the impact of liming on the provision of prey to wading birds, the improvement of quality and productivity of the grasslands and the impact of lime on soil carbon. Plant material to re-introduce Cicerbita alpina has been bred from extant Scottish and Norwegian populations; with propogation carried out to ensure no potential for disease spread. Analysis of a long-term experiment on trophic interactions in the uplands has revealed the importance of management on both insectivourous bird:invertebrate prey and predator:vole interactions. Collaboration with the Scottish Biodiversity Strategy indicators group has led to further refinement of the Natural Capital Asset Index. Connectivity work has produced indices of connectivity for woodlands in Scotland, used to start analyses of priority restoration sites for Atlantic Oak woodlands.


  • A new paper in Plant Ecology & Diversity demonstrates how arable weed diversity has negative impacts on new plant species establishing (especially rare plant species).
  • Workshop was held to improve collaboration between SRP research and major Scottish environmental indicators initiatives, including Ecosystem Health Indicators, Natural Capital Asset Index and the Soil Monitoring Action Plan; the outcome is an improved alignment of SRP research to end-user needs and which will support the future development of these initiatives.
  • WP1.3 researchers helped deliver the Scottish Biodiversity Strategy Science Conference at RBGE in November. Over 100 delegates attended, including government, agencies, eNGOs and the public (further information here).
  • The Ecosystems and Land Use Stakeholder Engagement Group (WP1.3 & 1.4) had its first meeting at Victoria Quay in November. Fifty-five stakeholders from government, agencies, Non-Governmental Organisations, membership organisations and universities attended and were engaged with ongoing work and identifying cooperation opportunities.

Future Activities

This was the final year of the 2016-2022 Strategic Research Programme which saw effort to catch up with Covid-19 effected work and an extension of current work into new areas.

Work on upland management will be extended through new work in the 2022-2027 Strategic Research Programme within the Topic on Biodiversity (D4), specifically the project “Identifying the causes of biodiversity change with specific references to the IPBES drivers”. The work on indicators will be developed in the project “Scotland’s biodiversity: People, Data and Monitoring” and research on woodland restoration in “Habitat management and restoration”. The work on crop species mixtures will be extended through a project working with farmers (SEAMS - Sustainability in Education and Agriculture using Mixtures). Population rescue work for Cicerbita alpina and Woodsia ilvensis will continue.

Selected Outputs




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