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Transferable Ecology for a changing world (TREE)

Lead Research Organisation: UNIVERSITY OF READING
Department Name: Sch of Biological Sciences

Abstract

Global-scale sustainability transformations are urgently required to address catastrophic climate change and biodiversity loss. In practice, however, the conservation, restoration and management actions to combat these crises will be applied at local scales: to individual forests, fields, lakes, and grasslands. Practitioners, policymakers and ecologists have long-recognised the futility of silver bullet, 'one-size-fits-all' strategies, and the importance of targeting and tailoring actions to specific or individual contexts, and developing action plans for specific species, or individual sites. For example, the UK government's ambitious tree planting initiatives emphasise the importance of 'the right tree in the right place' to achieving Net Zero, because the wrong trees planted in the wrong place may fail to establish, or worse still, lead to net carbon emissions that persist for decades. However, despite the need for context-specific information for individual sites, ecology has traditionally focused on average effects, rather than individual effects, undermining the ultimate goal of applied ecology: the application of ecological science to the real-world.

To do science that can truly inform on-the-ground policies, ecology can capitalise on methods developed by the rapidly advancing field of 'precision medicine', which similarly rests on the premise that the effect of a given drug or treatment may be different for each individual patient, necessitating personalised healthcare plans. The application of precision medicine methodologies, which require 'big data', is now possible due to the increasing availability of vast quantities of ecological data from multiple sources, including remote sensors, citizen scientists and environmental monitoring networks. In this exploratory project, we will adapt the use of precision medicine approaches to applied ecological problems and develop novel approaches that help guide the next generation of applied ecologists into the big-data era. We will develop frameworks and tools for sampling and modelling big data in a way that yields accurate and practicable knowledge that can inform on-the-ground actions.

This project will achieve this using a 'virtual ecology' approach using an existing computer model - 'iLand' - that simulates real, forested landscapes in Europe, the U.S.A and Japan. First, we will use iLand to virtually implement forest restoration actions to individual forests across these landscapes. The forests in these landscapes will then be subjected to virtual sampling, thus mimicking the collection of data by ecologists, citizen scientists and remote sensing technologies. For example, we will mimic surveyors that measure forest biodiversity as part of a national environmental monitoring campaigns. We will then apply different modelling methods to analyse the virtually sampled data, including methods developed in the field of precision medicine as well as methods that are commonly used in ecology. By comparing the results of these analyses against the 'true' simulated data, we will be able to evaluate how different sampling and modelling decisions influence the accuracy of our results. Specifically, we will assess the accuracy of predictions individual forest responses to restoration actions across a range of environmental conditions (i.e., elevation, climate, soil types). We will use this understanding to develop guidelines for designing future environmental monitoring surveys, and modelling of big data, that maximises the accuracy of these predictions.

By shifting applied ecology's focus away from average effects, towards actionable, individual-level effects, our guidelines will enable policymakers to target and prioritise restoration actions to areas where desired effects are greatest, thus maximising efficacy of limited resources for addressing climate change and biodiversity loss.

Publications

10 25 50
 
Description In this exploratory project, we have begun to adapt the use of precision medicine approaches to an applied ecological problem - identifying forest management actions that can maximise soil carbon at individual locations across an environmentally variable region. We are in the process of developing a set of guidelines for fitting models to large ecological datasets (specifically, National Forest Inventories [NFIs]) in a way that yields accurate and practicable knowledge that can inform on-the-ground action - i.e., what management regime to implement, and where. We are coding up a reproducible workflow that uses a 'virtual ecology' approach applied to existing simulated data from forest dynamic models - 'Heureka' - that simulates forest dynamics in real forest landscapes in Europe.
We are comparing the predictive accuracy of alternative analytical workflows and modelling decisions to evaluate how different sampling and modelling decisions influence the accuracy of our results. Specifically, we are assessing the accuracy of predictions of individual NFI plot responses to restoration actions across a range of environmental conditions (i.e., elevation, climate, soil types). We are using this understanding to develop guidelines for designing future modelling of NFI data, that maximises the accuracy of predictions.
Exploitation Route Too early to say (the manuscript and workflows have not been published yet).
We will soon submit the manuscript and workflows to a scientific journal.
Sectors Environment

 
Description Collaboration with Dr Matt grainger at the Norwegian Institute for Nature Research 
Organisation Norwegian Institute for Nature Research
Country Norway 
Sector Public 
PI Contribution E Jackson and R Spake approached Matt Grainger at NINA to collaborate on Project TREE. We have developed a manuscript together, a Perspective piece about machine learning in applied ecology.
Collaborator Contribution Matt Grainger has provided his expertise on applied ecology and causal inference to this project.
Impact Manuscript under revision.
Start Year 2023
 
Description Collaboration with Swedish University of Agricultural Sciences 
Organisation Swedish University of Agricultural Sciences
Country Sweden 
Sector Academic/University 
PI Contribution EJ and RS approached Tord for his expertise.
Collaborator Contribution The TREE team collaborated with Tord Snall at Swedish University of Agricultural Sciences. He provided us with a simulated National Forest Inventory dataset and his time.
Impact Manuscript in prep
Start Year 2023
 
Description Collaboration with UKCEH 
Organisation UK Centre for Ecology & Hydrology
Country United Kingdom 
Sector Public 
PI Contribution Professor James Bullock is a listed partner on project TREE. We also invited Dr Emma Gardner onto this project.
Collaborator Contribution James and Emma contribute expertise in applied ecology and quantitative modelling.
Impact Not yet
Start Year 2023
 
Description New collaboration with Prof Tord Snall at the Swedish University of Agricultural Sciences 
Organisation Swedish University of Agricultural Sciences
Country Sweden 
Sector Academic/University 
PI Contribution PDRA Eleanor Jackson and I approached Tord Snall at the Swedish University of Agricultural Sciences, to request the use of his forest datasets. He has simulations of forest growth and soil carbon following alternative management regimes from tens of thousands of National Forest Inventory plots from across Sweden. We have used his data to investigate the influence of alternate sampling and modelling decisions on the accuracy of models predicting soil carbon changes following management. Eleanor and I are leading the writing of a manuscript for this work and have invited Tord to contribute to the interpretation of the results.
Collaborator Contribution Tord Snall is providing his data (simulations of forest growth and soil carbon following alternative management regimes from tens of thousands of National Forest Inventory plots from across Sweden). He is also providing his expertise in how the simulations worked. As an applied ecologist, he is also providing valuable insights on how applicable to methodological approaches are, and utility for informing policies.
Impact We currently have a manuscript in preparation, which we will aim to submit in the next few months. Tord also contributed to my fellowship proposal (Future Leaders Fellowship proposal), and I put him down as a Visiting Researcher.
Start Year 2023
 
Title Towards causal predictions of site-level treatment effects in applied ecology 
Description This repository contains the code and data for our in-prep manuscript: Towards causal predictions of site-level treatment effects in applied ecology. E. E. Jackson, T. Snäll, E. Gardner, J. M. Bullock & R. Spake Contents: code/ The code/ directory contains these subdirectories: scripts/ contains action scripts, i.e. all the code for cleaning, combining, and analysing the data. All paths in the scripts are relative to the root directory (where the .Rproj file lives). Each .R script has a summary at the top of what it does. The scripts are numbered in the order in which they would typically be run. functions/ contains R functions which are called by scripts in the code/scripts/ directory. Note that functions were designed to be used only within this project. notebooks/ contains .Rmd files that were used for exploratory analysis and note-taking. Notebooks are not intended to be reproducible but the .md files can be viewed as rendered html (with output) on GitHub. data/ The original data is stored in the data/raw/ subdirectory. Any data that is produced using code is stored in data/derived/.  output/ The output/ directory contains the subdirectory figures/, which contains the figures used in the paper. docs/ The docs/ directory contains the data dictionary / metadata.  Usage To reproduce results and figures from this project in the RStudio IDE, first open the .Rproj file and call renv::restore() to restore the project's R package library. Then, run the .R scripts in code/scripts/ in the order in which they are labelled, starting from 02_identify-test-plots.R. Note that the first two scripts which clean and filter the data are for reference only, since we will be providing the cleaned data in this repository. 
Type Of Technology Software 
Year Produced 2024 
Open Source License? Yes  
URL https://zenodo.org/doi/10.5281/zenodo.13269917
 
Title Towards causal predictions of site-level treatment effects in applied ecology 
Description This repository contains the code and data for our in-prep manuscript: Towards causal predictions of site-level treatment effects in applied ecology. E. E. Jackson, T. Snäll, E. Gardner, J. M. Bullock & R. Spake Contents: code/ The code/ directory contains these subdirectories: scripts/ contains action scripts, i.e. all the code for cleaning, combining, and analysing the data. All paths in the scripts are relative to the root directory (where the .Rproj file lives). Each .R script has a summary at the top of what it does. The scripts are numbered in the order in which they would typically be run. functions/ contains R functions which are called by scripts in the code/scripts/ directory. Note that functions were designed to be used only within this project. notebooks/ contains .Rmd files that were used for exploratory analysis and note-taking. Notebooks are not intended to be reproducible but the .md files can be viewed as rendered html (with output) on GitHub. data/ The original data is stored in the data/raw/ subdirectory. Any data that is produced using code is stored in data/derived/.  output/ The output/ directory contains the subdirectory figures/, which contains the figures used in the paper. docs/ The docs/ directory contains the data dictionary / metadata.  Usage To reproduce results and figures from this project in the RStudio IDE, first open the .Rproj file and call renv::restore() to restore the project's R package library. Then, run the .R scripts in code/scripts/ in the order in which they are labelled, starting from 02_identify-test-plots.R. Note that the first two scripts which clean and filter the data are for reference only, since we will be providing the cleaned data in this repository. 
Type Of Technology Software 
Year Produced 2024 
Open Source License? Yes  
URL https://zenodo.org/doi/10.5281/zenodo.13269918