Simulating UK plant biodiversity under climate change to aid landscape decision making
Lead Research Organisation:
University of Glasgow
Department Name: College of Medical, Veterinary, Life Sci
Abstract
Landscapes are composed of multiple habitats as well as the biodiversity that resides within them, and are a product of interactions between species present, climate, geography and human use. They provide many ecosystem services, such as provision of food and water, regulation of climate and carbon cycling, which are vital for a stable future for our society, economy, health and wellbeing. Plants form the basis of all terrestrial ecosystems and are fundamental to providing these ecosystem services. Landscape decisions should therefore be underpinned by tools that enable prediction of plant responses to global change and landscape management. However, current approaches to modelling plant species distributions are deficient for this purpose as they focus on individual, or a small number of, species; ignore interactions between species; or only model a small number of plant functional types.
A systems approach will be used to address this significant gap in current real-world landscape decision support by developing tools to predict (including uncertainty quantification) current and future distribution of all ~1,800 UK plant species in a manner that accounts for competitive interactions between species. This will enable effective assessment of the impacts of landscape decisions and/or climate change, e.g. in specific locations or on important habitat types such as peatlands. Invasive non-natives are considered a growing threat to ecosystem services and through extension to ~200,000 plant species worldwide this tool also enables assessment of the impact of invasive non-native plant species on current and potential future UK landscapes. Pests and diseases also represent a significant challenge and tools developed by this project will be a valuable resource for managing landscapes for plant health, for example, by providing distributions of at-risk populations - i.e. the distribution of plant hosts for any disease or pest of interest. Future work could explore the potentially critical feedbacks between the dynamics of plant community distributions and the transmission of pests and diseases by coupling models of these processes.
This project builds on an existing coarse spatial scale model for all plant biodiversity on Earth and an ongoing NERC-funded project developing a higher resolution version for UK plant species. The latter project makes use of the more detailed climate, land use and plant coverage records available for the UK. However, further refinements are needed to properly quantify structural and process uncertainty within this framework. Without such work predictions of the effect of climate change and land use decisions that emerge from these models could be misleading.
Currently niche preferences are parameterised by observational data with no uncertainty assessment. In terms of structural uncertainty, it is critical to account for between-species heterogeneity better by establishing how each species grows and reproduces (its functional type). Building on existing digitisation expertise at the Natural History Museum we therefore propose to extract relevant functional type information from existing taxonomic descriptions to create a more extensive trait database for all UK native and non-native plant species. As well as being a valuable resource in its own right and extensible to all global plant records, this work will be used within the project to enhance the simulation model to capture the relative differences in growth, competition and dispersal between species. Comparison with the current model based on a limited number of functional types will highlight the role of structural complexity and the impact of non-linearities on model output. We will also develop tools to quantify uncertainty in these models using available plant species distribution data so that we can correctly capture the impact of planned and expected land use and climate change, and ultimately guide future landscape decision making.
A systems approach will be used to address this significant gap in current real-world landscape decision support by developing tools to predict (including uncertainty quantification) current and future distribution of all ~1,800 UK plant species in a manner that accounts for competitive interactions between species. This will enable effective assessment of the impacts of landscape decisions and/or climate change, e.g. in specific locations or on important habitat types such as peatlands. Invasive non-natives are considered a growing threat to ecosystem services and through extension to ~200,000 plant species worldwide this tool also enables assessment of the impact of invasive non-native plant species on current and potential future UK landscapes. Pests and diseases also represent a significant challenge and tools developed by this project will be a valuable resource for managing landscapes for plant health, for example, by providing distributions of at-risk populations - i.e. the distribution of plant hosts for any disease or pest of interest. Future work could explore the potentially critical feedbacks between the dynamics of plant community distributions and the transmission of pests and diseases by coupling models of these processes.
This project builds on an existing coarse spatial scale model for all plant biodiversity on Earth and an ongoing NERC-funded project developing a higher resolution version for UK plant species. The latter project makes use of the more detailed climate, land use and plant coverage records available for the UK. However, further refinements are needed to properly quantify structural and process uncertainty within this framework. Without such work predictions of the effect of climate change and land use decisions that emerge from these models could be misleading.
Currently niche preferences are parameterised by observational data with no uncertainty assessment. In terms of structural uncertainty, it is critical to account for between-species heterogeneity better by establishing how each species grows and reproduces (its functional type). Building on existing digitisation expertise at the Natural History Museum we therefore propose to extract relevant functional type information from existing taxonomic descriptions to create a more extensive trait database for all UK native and non-native plant species. As well as being a valuable resource in its own right and extensible to all global plant records, this work will be used within the project to enhance the simulation model to capture the relative differences in growth, competition and dispersal between species. Comparison with the current model based on a limited number of functional types will highlight the role of structural complexity and the impact of non-linearities on model output. We will also develop tools to quantify uncertainty in these models using available plant species distribution data so that we can correctly capture the impact of planned and expected land use and climate change, and ultimately guide future landscape decision making.
Planned Impact
The first important output from this project will be a larger and more comprehensive database of plant functional traits, including species from beyond UK shores, without some of the issues of taxonomic bias and incomplete coverage currently affecting some of the largest of these initiatives to date, such as TRY. Plant functional ecology has developed in recent years into a discipline whose insights are incorporated into a range of studies of effective conservation prioritisation. Beyond this project there is a great deal of scope to apply these data for further studies of plant functional ecology and questions around the measurement of and interaction between different aspects of diversity: for example, the relationship between species richness and functional diversity, the role of plant traits in determining range size and conservation status, and the importance of functional diversity in promoting ecological stability.
The development of the first species-level plant biodiversity simulator for the UK will provide an urgently needed tool for predicting the biodiversity impact of landscape decisions. As such, it will be of particular importance to conservationists and policy makers, such as the Scottish Government and its bodies (e.g. Scottish Natural Heritage) and Defra. Critically, the simulator will allow the user to compare and contrast different land-use change decisions and use them to evaluate their respective impacts on regional biodiversity. We will also be able to assess the ability of plant species to adapt to different climate change scenarios in the presence and absence of mitigating land use policy. In this way, the simulator draws together the two major strands of human-influenced environmental change, climate change and land-use decisions, and seeks to improve our understanding of the impact of these factors on the natural environment.
An important factor of this project is the ease with which it can be scaled up to larger continental and even global scales beyond the UK. This is particularly relevant to many developing countries that currently lack the capacity to undertake large-scale analyses of their own flora and may struggle to produce national-scale biodiversity indicators measuring their own performance towards meeting the international targets of the Convention on Biological Diversity, for instance. Working together with overseas counterparts with whom the Natural History Museum (NHM) has already established an effective working relationship, the NHM is in an outstanding position to help translate the outcomes from this project into on-the-ground decision making projects in a range of developing countries, particularly within tropical Africa. The NHM also serves as an important focus for debate on issues of biodiversity conservation within the UK, with its unique combination of historical collections, contemporary scientists and experienced team of science communicators. The broad implications of this research in terms of our understanding of the effect of policy decisions means that the results of this work will also be of significant interest to the general public. Outreach activities through NHM, for example the annual European Researchers' Night (approx. 2-5000 researchers), will promote engagement with people of all ages and backgrounds, and seek to inspire them to engage further with the impact of government decisions.
The development of the first species-level plant biodiversity simulator for the UK will provide an urgently needed tool for predicting the biodiversity impact of landscape decisions. As such, it will be of particular importance to conservationists and policy makers, such as the Scottish Government and its bodies (e.g. Scottish Natural Heritage) and Defra. Critically, the simulator will allow the user to compare and contrast different land-use change decisions and use them to evaluate their respective impacts on regional biodiversity. We will also be able to assess the ability of plant species to adapt to different climate change scenarios in the presence and absence of mitigating land use policy. In this way, the simulator draws together the two major strands of human-influenced environmental change, climate change and land-use decisions, and seeks to improve our understanding of the impact of these factors on the natural environment.
An important factor of this project is the ease with which it can be scaled up to larger continental and even global scales beyond the UK. This is particularly relevant to many developing countries that currently lack the capacity to undertake large-scale analyses of their own flora and may struggle to produce national-scale biodiversity indicators measuring their own performance towards meeting the international targets of the Convention on Biological Diversity, for instance. Working together with overseas counterparts with whom the Natural History Museum (NHM) has already established an effective working relationship, the NHM is in an outstanding position to help translate the outcomes from this project into on-the-ground decision making projects in a range of developing countries, particularly within tropical Africa. The NHM also serves as an important focus for debate on issues of biodiversity conservation within the UK, with its unique combination of historical collections, contemporary scientists and experienced team of science communicators. The broad implications of this research in terms of our understanding of the effect of policy decisions means that the results of this work will also be of significant interest to the general public. Outreach activities through NHM, for example the annual European Researchers' Night (approx. 2-5000 researchers), will promote engagement with people of all ages and backgrounds, and seek to inspire them to engage further with the impact of government decisions.
Organisations
- University of Glasgow (Lead Research Organisation)
- Natural History Museum (Collaboration)
- Natural Resources Wales (Collaboration)
- University of Copenhagen (Collaboration)
- UK Centre for Ecology & Hydrology (Collaboration)
- UNIVERSITY OF EDINBURGH (Collaboration)
- SWANSEA UNIVERSITY (Collaboration)
- NatureScot (Collaboration)
- UNIVERSITY OF EXETER (Collaboration)
- NatureScot (Scottish Natural Heritage) (Project Partner)
Publications
Harris C
(2022)
Strong phylogenetic signals in global plant bioclimatic envelopes
in Global Ecology and Biogeography
McMonagle C
(2022)
Trends in the diversity of mortality causes and age-standardised mortality rates among subpopulations within Scotland, 2001-2019.
in SSM - population health
Mitchell SN
(2022)
FAIR data pipeline: provenance-driven data management for traceable scientific workflows.
in Philosophical transactions. Series A, Mathematical, physical, and engineering sciences
Sarker S
(2021)
Solving the fourth-corner problem: forecasting ecosystem primary production from spatial multispecies trait-based models
in Ecological Monographs
Shadbolt N
(2022)
The challenges of data in future pandemics.
in Epidemics
Description | A plant biodiversity simulator for the UK developed under a previous NERC grant has been enhanced, allowing more realistic mechanisms to be incorporated and aiding our understanding of how UK plant biodiversity will be impacted by climate change and landscape decisions. |
Exploitation Route | The simulation environment is publicly available for use by other researchers, and the first manuscript is under revision and the second is under review describing the work. We can now see realistic effects being played out in the simulator as land use changes impact biodiversity in realistic ways. Further work is needed to tune this model in detail to data from specific interventions, and we are working with Natural Resources Wales to investigate ways of achieving this. We are also working to improve the detailed modelling of individual species so that their unique characteristics can be properly incorporated into the model. We also believe that this model could incorporate features of the JULES Joint UK Land Environment Simulator to begin to better capture more complex and detailed aspects of resource use and competition into the model. Ultimately we believe it would be useful to investigate using EcoSISTEM as a new base layer for an earth systems model such as UKESM1. |
Sectors | Environment |
URL | https://github.com/EcoJulia/EcoSISTEM.jl |
Description | We have begun a collaboration with Natural Resources Wales to understand the impact of climate change and remediation work on welsh peatland. |
First Year Of Impact | 2021 |
Sector | Environment |
Impact Types | Policy & public services |
Description | Integrating a biodiversity digital twin with a FAIR data pipeline for reproducible science |
Amount | £39,970 (GBP) |
Organisation | Natural Environment Research Council |
Sector | Public |
Country | United Kingdom |
Start | 03/2023 |
End | 07/2023 |
Description | Diversity |
Organisation | Natural History Museum |
Department | Lepidoptera Collection |
Country | United Kingdom |
Sector | Charity/Non Profit |
PI Contribution | We have provided an understanding of the links between the fundamental mathematics studied by the mathematicians with whom we collaborate and the applied biodiversity problems that the ecologists we work with wish to understand. |
Collaborator Contribution | Tom Leinster at the University of Edinburgh has been providing mathematical expertise to understand the fundamental properties of diversity measures. Jill Thompson at CEH and Neil Brummitt at NHM have been providing practical assistance in understanding the underlying biodiversity that we are studying. Michael Krabbe Borregaard at NHMD has been working on development of Julia code to help with analyses. |
Impact | How to partition diversity (arXiv paper) multidisciplinary - maths, ecology, biodiversity BB/P004202/1 Mathematical Theory and Biological Applications of Diversity (further funding) multidisciplinary - maths, ecology, biodiversity, evolutionary biology |
Start Year | 2012 |
Description | Diversity |
Organisation | UK Centre for Ecology & Hydrology |
Country | United Kingdom |
Sector | Public |
PI Contribution | We have provided an understanding of the links between the fundamental mathematics studied by the mathematicians with whom we collaborate and the applied biodiversity problems that the ecologists we work with wish to understand. |
Collaborator Contribution | Tom Leinster at the University of Edinburgh has been providing mathematical expertise to understand the fundamental properties of diversity measures. Jill Thompson at CEH and Neil Brummitt at NHM have been providing practical assistance in understanding the underlying biodiversity that we are studying. Michael Krabbe Borregaard at NHMD has been working on development of Julia code to help with analyses. |
Impact | How to partition diversity (arXiv paper) multidisciplinary - maths, ecology, biodiversity BB/P004202/1 Mathematical Theory and Biological Applications of Diversity (further funding) multidisciplinary - maths, ecology, biodiversity, evolutionary biology |
Start Year | 2012 |
Description | Diversity |
Organisation | University of Copenhagen |
Department | Natural History Museum of Denmark |
Country | Denmark |
Sector | Public |
PI Contribution | We have provided an understanding of the links between the fundamental mathematics studied by the mathematicians with whom we collaborate and the applied biodiversity problems that the ecologists we work with wish to understand. |
Collaborator Contribution | Tom Leinster at the University of Edinburgh has been providing mathematical expertise to understand the fundamental properties of diversity measures. Jill Thompson at CEH and Neil Brummitt at NHM have been providing practical assistance in understanding the underlying biodiversity that we are studying. Michael Krabbe Borregaard at NHMD has been working on development of Julia code to help with analyses. |
Impact | How to partition diversity (arXiv paper) multidisciplinary - maths, ecology, biodiversity BB/P004202/1 Mathematical Theory and Biological Applications of Diversity (further funding) multidisciplinary - maths, ecology, biodiversity, evolutionary biology |
Start Year | 2012 |
Description | Diversity |
Organisation | University of Edinburgh |
Department | Centre for Integrative Physiology |
Country | United Kingdom |
Sector | Academic/University |
PI Contribution | We have provided an understanding of the links between the fundamental mathematics studied by the mathematicians with whom we collaborate and the applied biodiversity problems that the ecologists we work with wish to understand. |
Collaborator Contribution | Tom Leinster at the University of Edinburgh has been providing mathematical expertise to understand the fundamental properties of diversity measures. Jill Thompson at CEH and Neil Brummitt at NHM have been providing practical assistance in understanding the underlying biodiversity that we are studying. Michael Krabbe Borregaard at NHMD has been working on development of Julia code to help with analyses. |
Impact | How to partition diversity (arXiv paper) multidisciplinary - maths, ecology, biodiversity BB/P004202/1 Mathematical Theory and Biological Applications of Diversity (further funding) multidisciplinary - maths, ecology, biodiversity, evolutionary biology |
Start Year | 2012 |
Description | Dr Anna Harper, JULES |
Organisation | University of Exeter |
Department | Climate Change and Sustainable Futures |
Country | United Kingdom |
Sector | Academic/University |
PI Contribution | We will develop our simulations to make comparisons with the Joint UK Land Environment Simulator (JULES), the land component of the Met Office UK Earth Systems Model (UKESM1). This involves the comparison of specific UK species to the Plant Functional Types (PFTs) simulated in JULES. |
Collaborator Contribution | Dr Anna Harper, one of the developers of JULES and an expert in vegetation-climate modelling, has provided guidance on the simulation of plant functional types and the development of the model system. In the future, Anna will provide outputs from JULES runs at a finer UK scale to facilitate comparisons with the plant biodiversity simulator. |
Impact | This collaboration is multidisciplinary, involving botany, ecology, biodiversity assessment, mathematics, computer science (high performance computing) and policy. |
Start Year | 2019 |
Description | Peatland ACTION |
Organisation | NatureScot |
Country | United Kingdom |
Sector | Public |
PI Contribution | We are developing our diversity framework and biodiversity simulation environment to target peatland environments to help Peatland ACTION (a part of SNH) better target their peatland restoration work. |
Collaborator Contribution | Peatland ACTION have provided us with expert advice and guidance on modelling of the peatland environment as well as a detailed understanding of how they operate, and data that they have collected in Scotland. |
Impact | One grant at the moment - NE/T010355/1 - which is multidisciplinary, involving botany, ecology, biodiversity assessment, mathematics, computer science (high performance computing) and policy. |
Start Year | 2019 |
Description | Wales |
Organisation | Natural Resources Wales |
Country | United Kingdom |
Sector | Public |
PI Contribution | We are working with Jon Walker at Swansea as part of his Landscape Decisions fellowship and our Landscape Decisions large maths grant to develop simulations of peatland in Wales that he is studying, and with Natural Resources Wales who manage the peatland and host the relevant data. |
Collaborator Contribution | We are working with Wales peatland experts to expand the potential application of our work to Wales. |
Impact | None yet. |
Start Year | 2020 |
Description | Wales |
Organisation | Swansea University |
Country | United Kingdom |
Sector | Academic/University |
PI Contribution | We are working with Jon Walker at Swansea as part of his Landscape Decisions fellowship and our Landscape Decisions large maths grant to develop simulations of peatland in Wales that he is studying, and with Natural Resources Wales who manage the peatland and host the relevant data. |
Collaborator Contribution | We are working with Wales peatland experts to expand the potential application of our work to Wales. |
Impact | None yet. |
Start Year | 2020 |
Title | EcoSISTEM.jl package in Julia |
Description | Simulation is a Julia package that provides functionality for simulating species undergoing dynamic biological processes such as birth, death, competition and dispersal, as well as environmental changes in climate and habitat. |
Type Of Technology | Software |
Year Produced | 2020 |
Open Source License? | Yes |
Impact | This has allowed us to reconstruct plant biodiversity from historic climate reconstructions and plant records. |
URL | https://boydorr.github.io/Simulation.jl/dev |