BIODIVERSITY AND LAND-USE IMPACTS ON TROPICAL ECOSYSTEM FUNCTION (BALI)
Lead Research Organisation:
University of Aberdeen
Department Name: Inst of Biological and Environmental Sci
Abstract
Anthropogenic disturbance and land-use change in the tropics is leading to irrevocable changes in biodiversity and substantial shifts in ecosystem biogeochemistry. Yet, we still have a poor understanding of how human-driven changes in biodiversity feed back to alter biogeochemical processes. This knowledge gap substantially restricts our ability to model and predict the response of tropical ecosystems to current and future environmental change. There are a number of critical challenges to our understanding of how changes in biodiversity may alter ecosystem processes in the tropics; namely: (i) how the high taxonomic diversity of the tropics is linked to ecosystem functioning, (ii) how changes in the interactions among trophic levels and taxonomic groups following disturbance impacts upon functional diversity and biogeochemistry, and (iii) how plot-level measurements can be used to scale to whole landscapes. We have formed a consortium to address these critical challenges to launch a large-scale, replicated, and fully integrated study that brings together a multi-disciplinary team with the skills and expertise to study the necessary taxonomic and trophic groups, different biogeochemical processes, and the complex interactions amongst them.
To understand and quantify the effects of land-use change on the activity of focal biodiversity groups and how this impacts biogeochemistry, we will: (i) analyse pre-existing data on distributions of focal biodiversity groups; (ii) sample the landscape-scale treatments at the Stability of Altered Forest Ecosystems (SAFE) Project site (treatments include forest degradation, fragmentation, oil palm conversion) and key auxiliary sites (Maliau Basin - old growth on infertile soils, Lambir Hills - old growth on fertile soils, Sabah Biodiversity Experiment - rehabilitated forest, INFAPRO-FACE - rehabilitated forest); and (iii) implement new experiments that manipulate key components of biodiversity and pathways of belowground carbon flux.
The manipulations will focus on trees and lianas, mycorrhizal fungi, termites and ants, because these organisms are the likely agents of change for biogeochemical cycling in human-modified tropical forests. We will use a combination of cutting-edge techniques to test how these target groups of organisms interact each other to affect biogeochemical cycling. We will additionally collate and analyse archived data on other taxa, including vertebrates of conservation concern. The key unifying concept is the recognition that so-called 'functional traits' play a key role in linking taxonomic diversity to ecosystem function. We will focus on identifying key functional traits associated with plants, and how they vary in abundance along the disturbance gradient at SAFE. In particular, we propose that leaf functional traits (e.g. physical and chemical recalcitrance, nitrogen content, etc.) play a pivotal role in determining key ecosystem processes and also strongly influence atmospheric composition. Critically, cutting-edge airborne remote sensing techniques suggest it is possible to map leaf functional traits, chemistry and physiology at landscape-scales, and so we will use these novel airborne methods to quantify landscape-scale patterns of forest degradation, canopy structure, biogeochemical cycling and tree distributions. Process-based mathematical models will then be linked to the remote sensing imagery and ground-based measurements of functional diversity and biogeochemical cycling to upscale our findings over disturbance gradients.
To understand and quantify the effects of land-use change on the activity of focal biodiversity groups and how this impacts biogeochemistry, we will: (i) analyse pre-existing data on distributions of focal biodiversity groups; (ii) sample the landscape-scale treatments at the Stability of Altered Forest Ecosystems (SAFE) Project site (treatments include forest degradation, fragmentation, oil palm conversion) and key auxiliary sites (Maliau Basin - old growth on infertile soils, Lambir Hills - old growth on fertile soils, Sabah Biodiversity Experiment - rehabilitated forest, INFAPRO-FACE - rehabilitated forest); and (iii) implement new experiments that manipulate key components of biodiversity and pathways of belowground carbon flux.
The manipulations will focus on trees and lianas, mycorrhizal fungi, termites and ants, because these organisms are the likely agents of change for biogeochemical cycling in human-modified tropical forests. We will use a combination of cutting-edge techniques to test how these target groups of organisms interact each other to affect biogeochemical cycling. We will additionally collate and analyse archived data on other taxa, including vertebrates of conservation concern. The key unifying concept is the recognition that so-called 'functional traits' play a key role in linking taxonomic diversity to ecosystem function. We will focus on identifying key functional traits associated with plants, and how they vary in abundance along the disturbance gradient at SAFE. In particular, we propose that leaf functional traits (e.g. physical and chemical recalcitrance, nitrogen content, etc.) play a pivotal role in determining key ecosystem processes and also strongly influence atmospheric composition. Critically, cutting-edge airborne remote sensing techniques suggest it is possible to map leaf functional traits, chemistry and physiology at landscape-scales, and so we will use these novel airborne methods to quantify landscape-scale patterns of forest degradation, canopy structure, biogeochemical cycling and tree distributions. Process-based mathematical models will then be linked to the remote sensing imagery and ground-based measurements of functional diversity and biogeochemical cycling to upscale our findings over disturbance gradients.
Planned Impact
Beneficiaries will include the policy makers associated with the development of REDD+ schemes (including the United Nations Framework Convention on Climate Change [UNCCC] and the Intergovernmental Panel on Climate Change [IPCC]), forest managers at company and State level, the oil palm industry, academic institutions in Malaysia, and the conservation sector globally.
REDD+ policy: Results from this project will provide information of key relevance to the management and monitoring of degraded forests within REDD+ schemes. In particular this work will quantify the impacts of habitat degradation and change on belowground biodiversity and processes and develop a series of robust indicators, which can be developed into effective monitoring strategies to assess forest degradation and recovery. REDD+ policy is of particular importance given UNFCCC COP negotiations in Doha in December 2012. The UNFCCC are active in developing guidance for REDD+, and REDD+ is one of the hottest topics in development of the IPCC chapter on Agriculture Forestry and Other Land Use.
Forest Managers: Belowground processes are key to sustainable forest management. The development of user-friendly survey techniques will allow timber industries to assess the impacts of existing management options more fully. |In particular the project will allow assessment of key strategies for aiding forest recovery; crucial for sustainable timber production in the region.
Oil palm industry: The increasing focus of the global oil palm industry on corporate social responsibility and the development of more sustainable management practices through schemes such as the RSPO, has precipitated a growing need for robust monitoring of belowground processes associated with sustainable oil palm production. The indicators developed in this project will be key to this and will facilitate the monitoring of these processes in a plantation context for the first time.
Academic institutions in Malaysia: Despite a growing body of biodiversity research in the region, the biodiversity of Southeast Asia, particularly that of belowground components, remains relatively little studied. Such a knowledge gap can act as a barrier for continued ecological research in the region. This project will provide detailed information on species data for belowground systems.
Conservation sector: The growth of tropical agriculture represents the major threat to biodiversity globally. However, conservation organizations are sometimes hampered in their ability to converse with government policy makers, through lack of detailed information about the impacts of habitat change. This project will fill a knowledge gap in this area and provide detailed data on the impacts of habitat change on below ground biodiversity and ecosystem processes.
REDD+ policy: Results from this project will provide information of key relevance to the management and monitoring of degraded forests within REDD+ schemes. In particular this work will quantify the impacts of habitat degradation and change on belowground biodiversity and processes and develop a series of robust indicators, which can be developed into effective monitoring strategies to assess forest degradation and recovery. REDD+ policy is of particular importance given UNFCCC COP negotiations in Doha in December 2012. The UNFCCC are active in developing guidance for REDD+, and REDD+ is one of the hottest topics in development of the IPCC chapter on Agriculture Forestry and Other Land Use.
Forest Managers: Belowground processes are key to sustainable forest management. The development of user-friendly survey techniques will allow timber industries to assess the impacts of existing management options more fully. |In particular the project will allow assessment of key strategies for aiding forest recovery; crucial for sustainable timber production in the region.
Oil palm industry: The increasing focus of the global oil palm industry on corporate social responsibility and the development of more sustainable management practices through schemes such as the RSPO, has precipitated a growing need for robust monitoring of belowground processes associated with sustainable oil palm production. The indicators developed in this project will be key to this and will facilitate the monitoring of these processes in a plantation context for the first time.
Academic institutions in Malaysia: Despite a growing body of biodiversity research in the region, the biodiversity of Southeast Asia, particularly that of belowground components, remains relatively little studied. Such a knowledge gap can act as a barrier for continued ecological research in the region. This project will provide detailed information on species data for belowground systems.
Conservation sector: The growth of tropical agriculture represents the major threat to biodiversity globally. However, conservation organizations are sometimes hampered in their ability to converse with government policy makers, through lack of detailed information about the impacts of habitat change. This project will fill a knowledge gap in this area and provide detailed data on the impacts of habitat change on below ground biodiversity and ecosystem processes.
Organisations
- University of Aberdeen (Lead Research Organisation)
- Malaysian Palm Oil Board (Collaboration)
- Swiss Federal Institute of Technology in Lausanne (EPFL) (Collaboration)
- Saebo (Collaboration)
- The Royal Society (Collaboration)
- Forest Research Centre (Collaboration)
- SE Asia Rainforest Research Partnership (Collaboration)
- The National University of Malaysia (MUM) (Collaboration)
- Malaysian University of Sabah (Collaboration)
Publications
Aanen DK
(2017)
Symbiogenesis: Beyond the endosymbiosis theory?
in Journal of theoretical biology
Aguirre-GutiƩrrez J
(2021)
Pantropical modelling of canopy functional traits using Sentinel-2 remote sensing data
in Remote Sensing of Environment
Aguirre-GutiƩrrez J
(2022)
Functional susceptibility of tropical forests to climate change.
in Nature ecology & evolution
Ashton LA
(2019)
Termites mitigate the effects of drought in tropical rainforest.
in Science (New York, N.Y.)
Blonder B
(2018)
Extreme and Highly Heterogeneous Microclimates in Selectively Logged Tropical Forests
in Frontiers in Forests and Global Change
Blonder B
(2020)
Linking functional traits to multiscale statistics of leaf venation networks.
in The New phytologist
Blonder B
(2019)
Leaf venation networks of Bornean trees: images and hand-traced segmentations.
in Ecology
Bloom A
(2020)
Lagged effects regulate the inter-annual variability of the tropical carbon balance
in Biogeosciences
Bolas C
(2020)
iDirac: a field-portable instrument for long-term autonomous measurements of isoprene and selected VOCs
in Atmospheric Measurement Techniques
Title | BALI logo |
Description | Designed and contributed ideas towards the BALI consortium logo. |
Type Of Art | Image |
Year Produced | 2014 |
Impact | Promoting the project and its aims. |
URL | http://www.bali.hmtf.info |
Title | HMTF film |
Description | A short film specifically focusing on the Malaysian part of the Human Modified Tropical Forests Programme (i.e. incorporating the work of the BALI, LOMBOK and SAFE projects) has been developed and is now available on the HMTF website (www.hmtf.info). |
Type Of Art | Film/Video/Animation |
Year Produced | 2017 |
Impact | The video has helped to showcase our research and objectives to the general public and to raise awareness. |
URL | http://www.hmtf.info |
Description | BALI plant trait campaign: The BALI plant trait field campaign started in July 2015 and was completed six months later in December 2015. The campaign, led by Dr Sabine Both, successfully measured 32 functional plant traits on 651 trees in eight 1ha permanent forest plots: in the Maliau Basin Conservation Area (MBCA, two plots) and the Danum Valley Conservation Area (DVCA, two plots), and four plots embedded in the Kalabakan Forest Reserve (SAFE project). In 2017 all laboratory analyses of plant material were finalised, with leaf nutrient concentrations being measured at the Forest Research Centre Sepilok and leaf isotope concentrations determined in the University of Aberdeen, UK. In addition, tree species identification has been completed in all 1ha permanent plots. The first scientific manuscript discussing the effects of logging disturbance and soil properties on plant functional trait expression has been published in New Phytologist. This manuscript, with co-authors Dr Noreen Majalap-Lee and researchers from Lancaster University, University of Oxford and The University of Manchester, is shedding light on the shift from structural and persistence traits in unlogged tree communities to greater trait values that drive carbon capture and growth in selectively logged forest. This observation is crucial for the prediction and likely implications for ecosystem functions across human-modified tropical forests in Sabah. In another manuscript, we will analyse and compare traits of leaves that have been affected by herbivory. During the BALI plant trait campaign we quantified the herbivory damage on leaves and subsequently analysed the chemical composition of affected leaves. We hypothesise that tree individuals may relocate their leaf nutrients and secondary components in response to damage by herbivores. This study will give insight into herbivore load in old-growth and logged forests and potential consequences for nutrient cycling. Masters student, Mrs Palasiah Jotan, at the School of International Tropical Forestry, Universiti Malaysia Sabah (UMS) has been analysing wood anatomical traits on samples derived from the BALI plant trait campaign. She has measured a wide selection of anatomical traits, for example vessel area (determined by the average of cross-sectional area of all vessel lumens excluding vessel walls in the wedge-shaped transect), vessel diameter, hydraulically weighted diameter, vessel number per area, and the vessel area to number ratio. These traits will be compared for trees in old-growth and selectively logged forests in order to discuss their changes in the light of land use change in Sabah. In addition to the study of plant functional traits, we currently are preparing a publication to describe the tree species composition in old-growth and selectively logged forest communities. We expect a shift in species occurrences based on their functional traits and interaction with environmental conditions following logging. Microclimate dynamics and venation networks: Work investigating microclimate dynamics in disturbed tropical forests has been completed and published in Frontiers in Forests and Global Change and Global Change Biology. Research investigating venation networks and the drivers of their geometrical variation in Malaysian tree species is still in progress. We have finished preparing high resolution images of all of our samples and have finished hand-tracing representative areas of each image. We are now almost finished developing neural network methods for automatically tracing the remainder of each image with collaborators at Oxford (Hao Xu, Mark Fricker). We hope to publish a methods paper on this topic in the coming 2-3 months, and a paper on the ecology of these species in the next 3-5 months. Hyperspectral data: Airborne hyperspectral data was obtained over the key BALI sites and the Sepilok Forest Reserve in a series of flights in 2014 as part of the BALI Remote Sensing component led by Prof. David Coomes at the University of Cambridge. While several technical challenges had to be overcome before the data could be used for scientific analysis, we have now finished all the necessary pre-processing steps and are actively working on upscaling field measurements to landscape-level analysis. Dr. Tommaso Jucker, who was previously employed as a Post-Doctoral Research Assistant for the BALI project, has recently completed analysis looking at topographic controls of forest structure in the Sepilok Forest Reserve and published these findings in Ecology Letters. Work led by Dr. Tom Swinfield builds upon the traits campaign dataset to look at forest-wide responses to disturbance across Danum, Maliau and SAFE. The analysis has been completed and the manuscript submitted to Global Change Biology. He is also working directly with Dr David Milowdowski (University of Edinburgh) and a number of PhD students under the supervision of Dr Matthew Struebig to develop high definition habitat metrics to predict animal response to forest degradation; this work is now published in the Journal of Applied Ecology. A methodological paper is in review and a number of other projects are at an analytical stage. PhD student Boris Bongalov has been utilising the airborne dataset to look at drivers of community dissimilarity in the Sepilok Forest Reserve, the analysis is complete and a manuscript is being prepared. The LiDAR data obtained in 2014 over the SAFE landscape has also been used to develop carbon prediction models in oil palm plantations. On that note, we have published a paper in August 2017 comparing different methods to estimate carbon density in terms of accuracy. PhD student Matheus Nunes is now working on a project using repeat LiDAR to track the dynamics in the SAFE landscape to understand human impacts on carbon emissions. The project has been carried out in cooperation with the Carnegie Airborne Observatory (CAO) led by Dr. Greg Asner, who has provided a 2016 LiDAR data over the same landscape. The repeat measurements allow us to investigate how selective logging and fragmentation contribute to carbon balance and develop insights on how to reduce carbon emissions from forest conversion to oil palm agriculture. The analyses are at an advanced stage and a manuscript is being prepared. Assessment of the impact of selective logging on soil microbial diversity and function: We are studying the effects of land degradation (deforestation and conversion of forest to oil palm plantation) on soil microbial diversity and function. A soil survey was carried out across plots at SAFE, Maliau Basin and Danum Valley. Soil samples were analysed for physical and chemical properties and microbial community structure was determined using next generation sequencing techniques. These data have been analysed in combination with plant traits metrics and a publication is currently in preparation explaining observed patterns in community structure. Variation in soil bacterial communities appeared to be driven predominantly by soil chemistry whilst ectomycorrhizal and saprophytic fungal communities were shaped by a combination of variation in plant traits and soil chemistry. Logged forests had a significantly lower species richness of ectomycorrhizal fungi reflecting the removal of dipterocarp trees, which associate almost exclusively with ectomycorrhizae. To test whether these changes in belowground community had an impact upon litter decomposition process rates a controlled reciprocal litter transplant experiment was conducted in the laboratory. This suggested that there is functional redundancy in terms of litter decomposition as no differences were detected in decomposition rates between forest types. Neither was there evidence to support the "home field advantage" hypothesis that states that communities should be specialised to decompose litter derived from their home environment. The Borneo rainforest girdling experiment: responses in structure and ecophysiology: The overall aim of the BALI Girdling research project is to assess how the termination of the transport of sugars and defoliation alter forest ecosystem functioning and structure using girdling as a treatment approach. The experiment was conducted in an area destined to be converted into oil palm plantation and targeted trees were girdled by removing a strip of bark (including cambium and phloem, but leaving the xylem intact) from around the tree trunk to stop sugar transport to the belowground zone of the trees (i.e. roots and soil, rhizosphere). Pre- and post- girdling sampling work has been completed and our researchers are analysing the data for publication. Former PhD student, Muhammad Firdaus Karim's research focused on the impact of reduced plants' root derived carbon (photosynthates) via girdling treatment on nitrous oxide (N2O) emission and soil nitrogen pool at genus level i.e. between Macaranga and Parashorea species. Soil cores placed around targeted trees were labelled with 15-potassium nitrate (15KNO3) at 20 atom %, giving a unique isotopic 15N-deposition signature rate of 10 kg ha-1 to study the N-mineralisation pathway between the two genera. Here, we hypothesised that reduced fresh tree roots' labile carbon supply to soil will result in a reduction of nitrifiers and denitrifiers activity, shifting the dynamics of N-mineralisation pathway thus reducing soil N2O emissions. Muhammad Firdaus Karim successfully passed his PhD viva and is now making corrections to his PhD thesis. Impacts of logging and forest restoration on soil biodiversity and function in Borneo: All soil physical and chemical data have been obtained from FRC for assessing differences in soil properties between forest and gap plots. Hemispherical photographs have been analysed for relative canopy cover in order to assess canopy gap structure in relation to soil characteristics. PLFA laboratory analysis is also now complete and awaiting statistical analysis. Preliminary analysis of newly-obtained soil microbial DNA sequencing data from gap survey (alpha diversity and community similarity of 16S and ITS amplicons for bacteria and eukaryotes) have found differences in the composition of fungal communities between treatments. Sam Robinson has completed field work (March 2018) for collection of environmental data and litterbags. The protocol for a controlled drought (drying-rewetting) incubation experiment is now finalised, including addition of 13C labelled glucose for investigating priming effects. A 21-day experiment was conducted in Lancaster during April-May 2018 after fresh cores were collected from logging gap survey plots in SAFE B North and B South. Statistical analysis of all soil biological, chemical and physical characteristics and vegetation/environmental metrics commenced in April 2018 and papers are currently being prepared for publication. Ant & termite exclusion experiment, Maliau: Continued collaboration with the BALI Ant and Termite research team is ongoing with the aim of producing a synthetic paper on the effects of ecosystem engineers on soil microbiome. Hyphal volume measurements have been calculated for all plots for use in structural equation modelling. So far, this work has been highly successful, resulting in papers on ant impacts on resource use (Journal of Animal Ecology) and a recent high profile paper in Science (DOI: 10.1126/science.aau9565) on the role of termites in mitigating the ecosystem-scale effects of drought . Soil microbial communities and function in restored forest: A soil survey was conducted at the INFAPRO restoration site during March 2018, and in adjacent unrestored and primary forest for comparison. Sampling was spatially explicit for distance decay analysis of soil microbial community turnover across multiple scales. Soil samples were transported to UK for biological, chemical and physical analysis in April-July 2018. |
Exploitation Route | We aim to disseminate of project results by: Supporting public outreach activities and skill transfer to local institutions and wider audiences through workshops, educational events and training in the lab and field. Dissemination of information via our project website, film documentaries, at local and international conferences and through publications in scientific journals. Provide detailed feedback to stakeholders, including landholders, relevant industries and local and national governmental departments. |
Sectors | Agriculture Food and Drink Environment Government Democracy and Justice |
URL | http://bali.hmtf.info/ |
Description | PUBLIC POLICY Members of the BALI consortium have also contributed to the development of sustainable management strategies for the oil palm industry. For example, PIs Burslem and Teh provided expert opinions, input, and advice on a technical report for the RSPO which helps define best-practice guidelines for conserving carbon in oil palm landscapes and mitigating climate change. The final report is entitled "The High Carbon Stock Science Study: Independent Report from the Technical Committee." PUBLIC OUTREACH Researchers from BALI have participated in a number of public outreach events, including presentations to the general public, primary and secondary schools, and training (capacity building) events within their host countries. For example, BALI team members were involved in a Nature Live Public Lecture at the Natural History Museum, open day events throughout the UK (e.g. Doors Open Day in Aberdeen, NERC UnEarthed in Edinburgh), guest lectures at primary and secondary schools in Malaysia and elsewhere, and training of local research assistants and volunteers on invertebrate identification and dung beetle sampling (BALI and LOMBOK). MULTIMEDIA Members of the BALI consortium, LOMBOK, and SEARRP have jointly produced a short film specifically focusing on the Malaysian part of the HMTF programme to showcase our research and objectives. Educational videos on biogeochemical cycling, mammals, invertebrate dispersal, leeches, dung beetles, and birds are also being developed. The films are geared towards the general public and will be displayed on the HMTF consortia websites and disseminated via social networks (www.hmtf.info). |
First Year Of Impact | 2015 |
Sector | Agriculture, Food and Drink,Education,Environment |
Impact Types | Societal Economic |
Description | Development of new protected areas in Sabah |
Geographic Reach | Asia |
Policy Influence Type | Influenced training of practitioners or researchers |
Description | Implementation of UNFCCC REDD+ protocols in Sabah |
Geographic Reach | Local/Municipal/Regional |
Policy Influence Type | Influenced training of practitioners or researchers |
Impact | Members of the BALI consortia hosted a training workshop for forestry department staff, NGOs, industry consultants and other stakeholders to further develop the capacity of the state of Sabah to implement UNFCCC REDD+ protocols. This included a wider discussion about REDD+ strategy, links between biodiversity and C, and a discussion of how to process remote sensing imagery and interpret the remote sensing products. This workshop further enhanced stakeholders' skills in handling remote sensing data and enabled relevant stakeholders to make more informed decisions about how to implement REDD+ protocols. |
Description | Prevented spurious carbon offset proposal |
Geographic Reach | Asia |
Policy Influence Type | Contribution to a national consultation/review |
Impact | The briefing note influenced the decision of the Sabah State Government to reject a spurious proposal to sign away the rights of indigenous Sabah citizens to benefits from forest carbon assets. |
URL | https://www.nst.com.my/news/nation/2022/02/772617/sabah-carbon-deal-not-certifiable-saleable-or-prof... |
Description | Training of local research assistants the methodology of dung beetle sampling and invertebrate identification |
Geographic Reach | Local/Municipal/Regional |
Policy Influence Type | Influenced training of practitioners or researchers |
Description | Combining long-term field data and remote sensing to test how tree diversity influences aboveground biomass recovery in logged tropical forests |
Amount | Ā£650,416 (GBP) |
Funding ID | NE/X000281/1 |
Organisation | Natural Environment Research Council |
Sector | Public |
Country | United Kingdom |
Start | 06/2023 |
End | 12/2026 |
Description | Ecosystem Carbon and Nitrogen Dynamics of Tropical Peatland: A Comprehensive Assessment of Carbon Dynamics of Forest Conversion to Oil Palm Plantation (PHASE II) |
Amount | RM7,500,000 (MYR) |
Organisation | Malaysian Palm Oil Board |
Sector | Public |
Country | Malaysia |
Start | 03/2018 |
End | 12/2022 |
Description | Leverhulme |
Amount | Ā£300,000 (GBP) |
Organisation | The Leverhulme Trust |
Sector | Charity/Non Profit |
Country | United Kingdom |
Start | 11/2017 |
End | 10/2020 |
Description | Malaysia Palm Oil Board Research Grant |
Amount | RM6,520,000 (MYR) |
Organisation | Malaysian Palm Oil Board |
Sector | Public |
Country | Malaysia |
Start | 06/2014 |
End | 06/2017 |
Description | NERC Do riparian zones conserve biodiversity and ecofunctioing in oil palm-dominated landscapes |
Amount | Ā£607,678 (GBP) |
Organisation | Natural Environment Research Council |
Sector | Public |
Country | United Kingdom |
Start |
Description | NI: FOR-RESTOR - A network for evidence-based tropical FORest RESTORation |
Amount | Ā£98,558 (GBP) |
Funding ID | NE/T005092/1 |
Organisation | Natural Environment Research Council |
Sector | Public |
Country | United Kingdom |
Start | 12/2019 |
End | 12/2022 |
Description | Newton Advanced Fellowship |
Amount | Ā£74,000 (GBP) |
Funding ID | NAF\R1\201192 |
Organisation | Newton Fund |
Sector | Public |
Country | United Kingdom |
Start | 03/2020 |
End | 09/2023 |
Description | Spatio-TEmporal Dynamics of Forest Response to ENSO Drought (STEED) |
Amount | Ā£255,076 (GBP) |
Funding ID | NE/P004806/1 |
Organisation | Natural Environment Research Council |
Sector | Public |
Country | United Kingdom |
Start | 03/2016 |
End | 05/2018 |
Description | Using plant hydraulic scaling to predict the drought vulnerability of the world's tallest tropical trees |
Amount | Ā£639,294 (GBP) |
Funding ID | NE/V000071/1 |
Organisation | Natural Environment Research Council |
Sector | Public |
Country | United Kingdom |
Start | 03/2021 |
End | 09/2024 |
Description | WP2.3_OP_03: The International Research Collaboration Award 2019 - University of Malaysia-Nottingham Student Travel Award |
Amount | RM15,000 (MYR) |
Organisation | University of Nottingham |
Sector | Academic/University |
Country | United Kingdom |
Start | 07/2019 |
End | 09/2019 |
Description | WP2.3_OP_04: Integration of biochar and diverse bioenergy crops into SE Asian agriculture |
Amount | Ā£25,000 (GBP) |
Organisation | Engineering and Physical Sciences Research Council (EPSRC) |
Sector | Public |
Country | United Kingdom |
Start | 01/2018 |
End | 07/2018 |
Title | Anatomical wood traits of two tree species in old-growth and selectively logged forest |
Description | Description: Anatomical wood traits of Macaranga gigantea from selectively logged forest at SAFE and Vatica dulitensis from old-growth forest in Maliau Basin. Sampled during the BALI project traits campaignProject: This dataset was collected as part of the following SAFE research project: Biodiversity and land-use impacts on tropical ecosystem function (BALI): Quantifying functional trait distributions across the disturbance gradientFunding: These data were collected as part of research funded by: NERC (Standard grant, NE/K016253/1)This dataset is released under the CC-BY 4.0 licence, requiring that you cite the dataset in any outputs, but has the additional condition that you acknowledge the contribution of these funders in any outputs.Permits: These data were collected under permit from the following authorities:Sabah Biodiversity Centre (Research licence JKM/MBS.1000-2.2(385))XML metadata: GEMINI compliant metadata for this dataset is available hereFiles: This consists of 1 file: Jotan_wood_anatomical_traits.xlsxJotan_wood_anatomical_traits.xlsxThis file contains dataset metadata and 1 data tables:Wood_anatomical_traits (described in worksheet Wood_anatomical_traits)Description: Anatomical wood traits of Macaranga gigantea from selectively logged forest at SAFE and Vatica dulitensis from old-growth forest in Maliau Basin. Sampled during the BALI project traits campaignNumber of fields: 17Number of data rows: 12Fields: location: Location within the SAFE landscape (Field type: location)forest_type: Forest type: OG: old-growth plots, Maliau and Danum; SL: selectively logged plots at SAFE (Field type: categorical)forestplots_name: Plot name coherent with forestplots database (Field type: id)plot_name_trait_campaign: Plot name used during the BALI trait campaign (Field type: id)sample_code: Sample code referencing: plot-'T'(ree) ID-branch type (Field type: id)branch_type: Binary classification of branch sampled depending on their position in the tree crown. BS: sun branch; BSH: shade branch (Field type: id)sampling_date: Date of sampling (Field type: date)tree_id: Reference for tree tag label (Field type: id)species: Tree species (Field type: taxa)VD: Mean vessel diameter, VD (mm). Vessel diameter is determined as the mean of the maximum and minimum (lumen) diameters because vessels often are not exactly circular, and total area of all vessels in each cross-sectional image. (Field type: numeric trait)Dh: Hydraulically weighted mean diameter, Dh (mm). (Dh) was calculated as (? diameter5) / (? diameter4), which weights the importance of diameter in estimated hydraulic conductance. (Field type: numeric trait)A: Mean vessel area, A (mm2). Vessel area is determined by the average cross-sectional area of all vessel lumens (excluding vessel walls) in the wedge-shaped transect of the branch wood cross-section. (Field type: numeric trait)F: Vessel lumen fraction, F (unitless). From the vessel areas and transect areas, vessel lumen fraction (F) is calculated as the fraction of transect area filled by vessel lumens. (Field type: numeric trait)N: Vessel number per area/vessel density, N (mm-2). Vessel number per area is calculated as vessel lumen fraction in the cross-section divided by vessel area (A) (N= F/A) (Field type: numeric trait)S: Vessel area to number ratio, S (mm4), the average vessel area to number of vessels per area ratio. (S) is calculated as vessel area (A) divided by vessel number per area (N) (S= A/N) which measures the variation in vessel size composition. (Field type: numeric trait)Kp: Potential (theoretical) hydraulic conductivity, Kp (Kp) is calculated as: (Kp= (p?w/128?) × N × Dh4, where Kp is the potential (xylem area-specific) hydraulic conductivity (in kg·m-1·MPa-1·s-1), ?w is the density of water at 20 ºC (998.2 kg·m-3), and ? is the viscosity of water at 20 ºC (1.002 × 10-3 Pa·s)). (Field type: numeric trait)Wood_density: Branch wood density from branch segment without bark (bark removed prior measurement) (Field type: numeric trait)Date range: 2014-05-01 to 2018-09-01Latitudinal extent: 4.5000 to 5.0700Longitudinal extent: 116.7500 to 117.8200Taxonomic coverage: All taxon names are validated against the GBIF backbone taxonomy. If a dataset uses a synonym, the accepted usage is shown followed by the dataset usage in brackets. Taxa that cannot be validated, including new species and other unknown taxa, morphospecies, functional groups and taxonomic levels not used in the GBIF backbone are shown in square brackets. - Plantae - - Tracheophyta - - - Magnoliopsida - - - - Malpighiales - - - - - Euphorbiaceae - - - - - - Macaranga - - - - - - - Macaranga gigantea - - - - Malvales - - - - - Dipterocarpaceae - - - - - - Vatica - - - - - - - Vatica dulitensis |
Type Of Material | Database/Collection of data |
Year Produced | 2019 |
Provided To Others? | Yes |
Impact | This data-set archives the results reported in this paper: Jotan, P., Maycock, C.R., Burslem, D.F.R.P., Berhaman, A. & Both, S. (2020) Comparative vessel traits of Macaranga gigantea and Vatica dulitensis from Malaysian Borneo. Journal of Tropical Forest Science, 32, 25-34. doi: 10.26525/jtfs32.1.25. |
URL | https://zenodo.org/record/3402752 |
Title | Human Modified Tropical Forests Programme Data Management |
Description | Database for archiving of metadata across the HMTF programme. As of February 2017, Primary meta datasets have been identified. In total, there are approx. 82 for LOMBOK, 69 for ECOFOR and 134 for BALI |
Type Of Material | Data handling & control |
Year Produced | 2016 |
Provided To Others? | No |
Impact | Central storage of metadata documents for (i) Tracking by DM of metadata information completeness (ii) Ease of metadata update by researchers (iii) Increasing awareness of available datasets between research projects The HMTF data management database can now identify datasets with environmental data across the three consortia, increasing the opportunity for collaboration between research groups and modellers. The second phase of the programme where DOI's are needed to support papers for journals (i.e. datasets needing to be uploaded to EIDC) has started. The HMTF programme website has been updated with relevant information and links to support researchers through this (available at www.hmtf.info/data/). |
URL | http://hmtf.info/data |
Title | Leaf Vein Network CNN Images |
Description | This download site contains the CNN vein network predictions and set of Matlab programs that were used for the analyses in Xu et al., (2020) and Blonder et al., (2020). These require Matlab 2020a or later. They may work on earlier versions of MatLab, but this has not been tested and cannot be guaranteed. The files are as follows: Zip files (e.g. BEL_downsampled_images.zip) containing a complete set of images of leaf vein predictions from a fully trained convolutional neural network (CNN), along with the ground truth data. Each folder in the unzipped file contains a sample represented by a CODE with format X-TY-BZ. X represents the name of a plot in the Global Ecosystems Monitoring network database (e.g. 'BEL'). Tree (T) Y indicates the number of a tree within a plot (e.g. '101') and Z represents the light stratum of the canopy where the leaf was collected (either 'S' for 'sunlit' or 'SH' for 'shaded'). A set of Matlab programs (Matlab files.zip) to compare the CNN predictions against other vein extraction approaches. A Matlab Readme file with instructions on how to run the analyses. References Software GUI: Xu, H., Blonder, B., Jodra, M., Malhi, Y. and Fricker, M.D. (2020) Automated and accurate segmentation of leaf venation networks via deep learning. New Phytol. (In press). Analysis of trait data: Blonder, B., S. Both, M. Jodra, H. Xu, M. Fricker, I. S. Matos, N. Majalap, D. F. R. P. Burslem, Y. Teh and Y. Malhi (2020) Linking functional traits to multiscale statistics of leaf venation networks. New Phytol. (In press). Original image data set and ground truths Blonder, B., Both, S., Jodra, M., Majalap, N., Burslem, D., Teh, Y. A., and Malhi, Y. (2019) Leaf venation networks of Bornean trees: images and hand-traced segmentations. Ecology 100: e02844.10.1002/ecy.2844. Available from: https://ora.ox.ac.uk/objects/uuid:de65fc07-4b8f-4277-a6c4-82836afbdeb3 |
Type Of Material | Database/Collection of data |
Year Produced | 2020 |
Provided To Others? | Yes |
URL | https://zenodo.org/record/4008613 |
Title | Leaf Vein Network CNN Images |
Description | This download site contains the CNN vein network predictions and set of Matlab programs that were used for the analyses in Xu et al., (2020) and Blonder et al., (2020). These require Matlab 2020a or later. They may work on earlier versions of MatLab, but this has not been tested and cannot be guaranteed. The files are as follows: Zip files (e.g. BEL_downsampled_images.zip) containing a complete set of images of leaf vein predictions from a fully trained convolutional neural network (CNN), along with the ground truth data. Each folder in the unzipped file contains a sample represented by a CODE with format X-TY-BZ. X represents the name of a plot in the Global Ecosystems Monitoring network database (e.g. 'BEL'). Tree (T) Y indicates the number of a tree within a plot (e.g. '101') and Z represents the light stratum of the canopy where the leaf was collected (either 'S' for 'sunlit' or 'SH' for 'shaded'). A set of Matlab programs (Matlab files.zip) to compare the CNN predictions against other vein extraction approaches. A Matlab Readme file with instructions on how to run the analyses. References Software GUI: Xu, H., Blonder, B., Jodra, M., Malhi, Y. and Fricker, M.D. (2020) Automated and accurate segmentation of leaf venation networks via deep learning. New Phytol. (In press). Analysis of trait data: Blonder, B., S. Both, M. Jodra, H. Xu, M. Fricker, I. S. Matos, N. Majalap, D. F. R. P. Burslem, Y. Teh and Y. Malhi (2020) Linking functional traits to multiscale statistics of leaf venation networks. New Phytol. (In press). Original image data set and ground truths Blonder, B., Both, S., Jodra, M., Majalap, N., Burslem, D., Teh, Y. A., and Malhi, Y. (2019) Leaf venation networks of Bornean trees: images and hand-traced segmentations. Ecology 100: e02844.10.1002/ecy.2844. Available from: https://ora.ox.ac.uk/objects/uuid:de65fc07-4b8f-4277-a6c4-82836afbdeb3 |
Type Of Material | Database/Collection of data |
Year Produced | 2020 |
Provided To Others? | Yes |
URL | https://zenodo.org/record/4008614 |
Title | Leaf Vein Network CNN Results |
Description | Results for leaf vein networks extracted using the LeafVeinCNN software package. The original image data set is available from Blonder et al. (2019) https://doi.org/10.1002/ecy.2844. The LeafVeinCNN software used in the analysis is available at https://doi.org/10.5281/zenodo.4007731. The Results_xxx.zip files contain all the Excel results spreadsheets separated by the code for each field site. results.xls provides a summary of all the network metrics for each file that was analysable Results_figures.pdf provides a summary image of the processing steps and results for each leaf segment Network_images.pdf contains a colour-coded image of each network superimposed on the leaf segment HLD_plots shows the binary tree following Hierarchical Network Decomposition PR_results.zip contains the Excel spreadsheets for evaluation of different enhancement methods for each leaf segment. PR_summary.xls provides a summary of the performance of each enhancement method. PR_F1_images.pdf and PR_FBeta2_images.pdf show the pixel classification for each enhancement and segmentation method compared to the manual ground-truth using two different optimum criteria (F1 and FBeta2). PR_fullwidth_plots show the full Precision-Recall plots for the full-width binary image compared to the manual ground-truth using the FBeta2 metric. PR_skeleton_plots show the full Precision-Recall plots for the skeletonised binary image compared to the manual ground-truth using the FBeta2 metric. PR_threshold_plots.pdf show how a set of network metrics vary with the segmentation threshold for each enhancement method. |
Type Of Material | Database/Collection of data |
Year Produced | 2020 |
Provided To Others? | Yes |
URL | https://zenodo.org/record/4008361 |
Title | Leaf Vein Network CNN Results |
Description | Results for leaf vein networks extracted using the LeafVeinCNN software package. The original image data set is available from Blonder et al. (2019) https://doi.org/10.1002/ecy.2844. The LeafVeinCNN software used in the analysis is available at https://doi.org/10.5281/zenodo.4007731. The Results_xxx.zip files contain all the Excel results spreadsheets separated by the code for each field site. results.xls provides a summary of all the network metrics for each file that was analysable Results_figures.pdf provides a summary image of the processing steps and results for each leaf segment Network_images.pdf contains a colour-coded image of each network superimposed on the leaf segment HLD_plots shows the binary tree following Hierarchical Network Decomposition PR_results.zip contains the Excel spreadsheets for evaluation of different enhancement methods for each leaf segment. PR_summary.xls provides a summary of the performance of each enhancement method. PR_F1_images.pdf and PR_FBeta2_images.pdf show the pixel classification for each enhancement and segmentation method compared to the manual ground-truth using two different optimum criteria (F1 and FBeta2). PR_fullwidth_plots show the full Precision-Recall plots for the full-width binary image compared to the manual ground-truth using the FBeta2 metric. PR_skeleton_plots show the full Precision-Recall plots for the skeletonised binary image compared to the manual ground-truth using the FBeta2 metric. PR_threshold_plots.pdf show how a set of network metrics vary with the segmentation threshold for each enhancement method. |
Type Of Material | Database/Collection of data |
Year Produced | 2020 |
Provided To Others? | Yes |
URL | https://zenodo.org/record/4008360 |
Title | Leaf venation networks of Bornean trees: images and hand-traced segmentations |
Description | The data set contains images of leaf venation networks obtained from tree species in Malaysian Borneo. The data set contains 726 leaves from 295 species comprising 50 families, sampled from eight forest plots in Sabah. Image extents are approximately 1 × 1 cm, or 50 megapixels. All images contain a region of interest in which all veins have been hand traced. The complete data set includes over 30 billion pixels, of which more than 600 million have been validated by hand tracing. These images are suitable for morphological characterization of these species, as well as for training of machine-learning algorithms that segment biological networks from images. Data are made available under the Open Data Commons Attribution License. You are free to copy, distribute, and use the database; to produce works from the database; and to modify, transform, and build upon the database. You must attribute any public use of the database, or works produced from the database, in the manner specified in the license. For any use or redistribution of the database, or works produced from it, you must make clear to others the license of the database and keep intact any notices on the original database. |
Type Of Material | Database/Collection of data |
Year Produced | 2019 |
Provided To Others? | Yes |
Impact | This data-set archives the results presented in the following paper: Blonder, B., Both, S., Jodra, M., Xu, H., Fricker, M., Matos, I.S., Majalap, N., Burslem, D.F.R.P., Teh, Y.A. & Malhi, Y. (2020) Linking functional traits to multiscale statistics of leaf venation. New Phytologist, 228, 1796-1810. doi.org/10.1111/nph.16830. |
Title | RapidEye and Landsat remote sensing measures for Sabah Biodiversity Experiment plots |
Description | Experiments under controlled conditions have established that ecosystem functioning is generally positively related to levels of biodiversity but it is unclear how widespread these effects are in real-world settings and whether they can be harnessed for ecosystem restoration. We used a long-term, field-scale tropical restoration experiment to test how the diversity of planted trees affected recovery of a 500-ha area of selectively logged forest measured using multiple sources of satellite data. Replanting using species-rich mixtures of tree seedlings with higher phylogenetic and functional diversity accelerated restoration of remote sensing estimates of aboveground biomass, canopy cover and Leaf Area Index. Our results are consistent with a positive relationship between biodiversity and ecosystem functioning in the lowland dipterocarp rainforests of SE Asia and demonstrate that using diverse mixtures of species can enhance their initial recovery after logging. |
Type Of Material | Database/Collection of data |
Year Produced | 2023 |
Provided To Others? | Yes |
URL | https://datadryad.org/stash/dataset/doi:10.5061/dryad.8w9ghx3rs |
Title | Soil properties across primary forest, logged forest and oil palm plantation in Sabah, Malaysia |
Description | Data comprise soil properties and soil nutrients across unlogged and logged tropical forests in Sabah, Malaysia. Soil properties (ID, Site, Land_Use, Plot_Name, Subplot, Horizon, pH, Total_C, Total_N, Total_P, inorganic_P, C:N, Sand, Silt, Clay) measured in soil samples and soil nutrients (Identifier, Site, Land_Use, Plot_Name, Subplot, NO3_N, NH4_N, Total_N, Ca, Mg, K, P, Fe, Mn Cu, Zn, B, S, Pb, Al, Cd) extracted from buried ion exchange membranes sampled between March and April 2015 and measured at Forest Research Centre, Sabah, Malaysia. This data is a contribution from the UK NERC-funded Biodiversity And Land-use Impacts on Tropical Ecosystem Function (BALI) consortium (http://bali.hmtf.info). |
Type Of Material | Database/Collection of data |
Year Produced | 2018 |
Provided To Others? | Yes |
Description | Antarctic Circumnavigation Experiment |
Organisation | Swiss Federal Institute of Technology in Lausanne (EPFL) |
Department | Swiss Polar Institute |
Country | Switzerland |
Sector | Academic/University |
PI Contribution | We provided an instrument to measure isoprene automatically during a circus-Antarctic cruise. This novel instrument was developed by us in the NERC BALI project and was operated byron-specialist staff. Over 60 days of measurements will be made in all in a region where few measurements have been previously made. |
Collaborator Contribution | Access to the research ship was provided for 4-5 months. A wide range of instruments were also on board which are looking at new particle formation over the Southern Ocean |
Impact | No scientific outputs yet. |
Start Year | 2016 |
Description | Biotechnology Research Institute, Universiti of Malaysia Sabah |
Organisation | Malaysian University of Sabah |
Department | Biotechnology Research Institute |
Country | Malaysia |
Sector | Academic/University |
PI Contribution | Discussion and support of PhD students working on projects aligned to our research. |
Collaborator Contribution | Access to laboratories and infrastructure for analysis of plant and soil material in Sabah. |
Impact | No outputs yet. |
Start Year | 2015 |
Description | Forest Research Centre Sepilok |
Organisation | Forest Research Centre |
Country | Malaysia |
Sector | Learned Society |
PI Contribution | We have engaged with the Forest Research Centre, which is part of the Sabah Forestry Department, for work on soil chemistry and collaboration on pot experiments involving tropical tree seedlings. Members of our research team have visited the centre, conducted training and implemented experiments in collaboration with local scientists. |
Collaborator Contribution | Staff at the Forest Research Centre have provided access to nursery space, laboratory infrastructure and advice on species and sites for research. |
Impact | 1. Data-sets on plant and soil chemistry. 2. Experiments on responses of tree seedlings to experimental P addition.3. Publications. |
Start Year | 2016 |
Description | Forest Research Centre, Sepilok, Malaysia |
Organisation | Saebo |
Country | United States |
Sector | Private |
PI Contribution | BALI consortium research project. |
Collaborator Contribution | Use of facilities and expertise in analytical chemistry including support for research permit applications to the Sabah Biodiversity Council. |
Impact | Research is underway. |
Start Year | 2014 |
Description | ITBC, Universiti Malaysia Sabah |
Organisation | Malaysian University of Sabah |
Country | Malaysia |
Sector | Academic/University |
PI Contribution | Research for the BIODIVERSITY AND LAND-USE IMPACTS ON TROPICAL ECOSYSTEM FUNCTION (BALI) project. |
Collaborator Contribution | Use of facilities and expertise including support for research permit applications to the Sabah Biodiversity Council. |
Impact | Still active |
Start Year | 2014 |
Description | Institute for Tropical Biology and Conservation (ITBC), Malaysia |
Organisation | Malaysian University of Sabah |
Country | Malaysia |
Sector | Academic/University |
PI Contribution | Research expertise and training of researchers in the field and laboratory. |
Collaborator Contribution | Laboratory facilities and research expertise including support for research permit applications to the Sabah Biodiversity Council. |
Impact | 4 postgraduate studentships awarded to scholars through Universiti Malaysia Sabah, working in collaboration with the SAFE project and SEARRP. Research is underway. |
Start Year | 2013 |
Description | Palm oil plantation measurements |
Organisation | Malaysian Palm Oil Board |
Country | Malaysia |
Sector | Public |
PI Contribution | We provided one of our new isoprene instruments which was used by UKM staff to make measurements for 6 weeks in a palm oil plantation operated by the MPOB |
Collaborator Contribution | UKM provided the personnel to operate the instrument and are leading on the interpretation. MPOB provided the site and local support. A paper on these results is being prepared with a lead author from UKM. |
Impact | None yet |
Start Year | 2016 |
Description | Palm oil plantation measurements |
Organisation | The National University of Malaysia (MUM) |
Country | Malaysia |
Sector | Academic/University |
PI Contribution | We provided one of our new isoprene instruments which was used by UKM staff to make measurements for 6 weeks in a palm oil plantation operated by the MPOB |
Collaborator Contribution | UKM provided the personnel to operate the instrument and are leading on the interpretation. MPOB provided the site and local support. A paper on these results is being prepared with a lead author from UKM. |
Impact | None yet |
Start Year | 2016 |
Description | Southeast Asia Rainforest Research Partnership |
Organisation | SE Asia Rainforest Research Partnership |
Country | United Kingdom |
Sector | Public |
PI Contribution | Designing and implementing research projects, including data collection, analysis and preparation of manuscripts. |
Collaborator Contribution | Logistics and support in Malaysia, including assistance with permit applications, site access and provisions of local infrastructure and personnel. |
Impact | Multiple presentations, presentations, policy documents and funding applications, as detailed elsewhere in the ResearchFish archive. |
Description | The South East Asia Rainforest Research Partnership (SEARRP) |
Organisation | The Royal Society |
Country | United Kingdom |
Sector | Charity/Non Profit |
PI Contribution | Our scientists have been closely working with the Royal Society Southeast Asia Rainforest Research Programme (SEARRP) to recruit and train local research assistants and students in the laboratory and field. We are also working closely with the Assistant Director of SEARRP for Science and Knowledge Exchange, to help with dissemination of project results to relevant stakeholders. |
Collaborator Contribution | Research assistance and operational support in the field including training. |
Impact | Studentships and further funding applications. |
Start Year | 2010 |
Title | Leaf Vein Network CNN Analysis Software |
Description | Software to extract and analyse leaf vein networks using convolutional neural networks. LeafVeinCNN.mlappinstall - installs the software and trained CNN models as a matlab app (requires Matlab 2020a or later). Note the Deep Learning Toolbox and Image Processing Toolbox are required. In addition, the support package importKerasNetwork needs to be installed using the Add-On Explorer LeafVeinCNN.exe - installs the software and trained CNN models as a standalone package for Windows 10. This will automatically download the Matlab runtime library from the web during installation. (Jan 2021 - Please note we are aware of installation problems with this release on some systems and are currently working on a workaround). LeafVeinCNN_Manual.pdf - A user manual describing installation and use of the software. |
Type Of Technology | Software |
Year Produced | 2020 |
Open Source License? | Yes |
URL | https://zenodo.org/record/4007730 |
Title | Leaf Vein Network CNN Analysis Software |
Description | Software to extract and analyse leaf vein networks using convolutional neural networks. LeafVeinCNN.mlappinstall - installs the software and trained CNN models as a matlab app (requires Matlab 2020a or later). Note the Deep Learning Toolbox and Image Processing Toolbox are required. In addition, the support package importKerasNetwork needs to be installed using the Add-On Explorer LeafVeinCNN.exe - installs the software and trained CNN models as a standalone package for Windows 10. This will automatically download the Matlab runtime library from the web during installation. (Jan 2021 - Please note we are aware of installation problems with this release on some systems and are currently working on a workaround). LeafVeinCNN_Manual.pdf - A user manual describing installation and use of the software. |
Type Of Technology | Software |
Year Produced | 2020 |
Open Source License? | Yes |
URL | https://zenodo.org/record/4007731 |
Description | "Introduction to the BALI Consortium - Biodiversity And Land-use Impacts on Tropical Ecosystem Function" at the University of Malaysia Sabah |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Other academic audiences (collaborators, peers etc.) |
Results and Impact | Talked encourage collaboration among Malaysian academics/researchers and UK academics. New collaborative relationships developed. |
Year(s) Of Engagement Activity | 2014 |
Description | "Introduction to the BALI Consortium - Biodiversity And Land-use Impacts on Tropical Ecosystem Function" at the Malaysian Palm Oil Board in Kuala Lumpur |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Professional Practitioners |
Results and Impact | Talk lead to in-depth discussion. Strengthening of existing research collaborations |
Year(s) Of Engagement Activity | 2013 |
Description | Aberdeen University Doors Open Day 2017 |
Form Of Engagement Activity | Participation in an open day or visit at my research institution |
Part Of Official Scheme? | No |
Geographic Reach | Local |
Primary Audience | Study participants or study members |
Results and Impact | University of Aberdeen opened its doors to members of the public, 9th September 2017. Following last year's success, BALI researchers set up another 'tropical forests' themed stall to help showcase our work and talk to visitors about our research. We displayed photos from our field trips as well as tropical seeds, insect and animal specimens. We had ~1400 visitors throughout the day including visitors to the Zoology Museum and Biodiversity Centre. Main impact: Knowledge exchange |
Year(s) Of Engagement Activity | 2017 |
Description | Ants dominate rainforest clean-up articles |
Form Of Engagement Activity | A magazine, newsletter or online publication |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Media (as a channel to the public) |
Results and Impact | The BALI project's ant and termite work was featured in nature's research highlights. The article titled "Ants dominate rainforest clean-up" show that more than half of scavenging on forest floors is done by insects. This work was published in the Journal of Animal Ecology and covered by the Daily Mail, Phys.org and The Daily Ant. Main impact: public engagement and knowledge exchange. |
Year(s) Of Engagement Activity | 2017 |
URL | https://www.nature.com/articles/d41586-017-02500-x |
Description | Biodiversity and Land-use Impacts on Tropical Ecosystem Function, Chicheley |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Professional Practitioners |
Results and Impact | Gave a talk titled Biodiversity And Land-use impacts on Tropical Ecosystem Function at the Royal Society Southeast Asia Rainforest Research Programme Meeting, Chicheley Hall, Chicheley. |
Year(s) Of Engagement Activity | 2014 |
Description | Bioenergy Presentation at the University of Brawijaya, Indoensia |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Postgraduate students |
Results and Impact | A seminar series from CEH and an Indonesian Government Regional Planning Authority in Java. The purpose was to exchange knowledge and ideas around sustainable agriculture in SE Asia. The audience comprised University Staff, postgrad students and some members of government. An active collaboration is now on-going with the University of Brawijaya through NERC ODA Award NE/R000131/1. Part of the CEH lecture is now used by university lecturers. |
Year(s) Of Engagement Activity | 2017 |
Description | British Ecological Society Annual meeting, Liverpool, 11-14th December 2016 |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | National |
Primary Audience | Other audiences |
Results and Impact | BALI researchers, David Coomes, Tommaso Jucker, Louise Ashton, Sam Robinson and Stephanie Law gave presentations at the British Ecological Society Meeting in Liverpool, 11-14th December 2016. |
Year(s) Of Engagement Activity | 2016 |
Description | Consultancy report on inventory methods for estimating carbon storage in High Carbon stock forests |
Form Of Engagement Activity | A formal working group, expert panel or dialogue |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Industry/Business |
Results and Impact | Contribution to an evaluation and summary of methodologies for estimating carbon storage in High Carbon Stock (HCS) forests under the Roundtable on Sustainable Palm Oil, an industry-led body seeking to improve the environmental and social sustainability of oil palm production. |
Year(s) Of Engagement Activity | 2015 |
URL | http://www.simedarby.com/sustainability/clients/simedarby_sustainability/assets/contentMS/img/templa... |
Description | Convenor, Annual Conference of the European Society for Tropical Ecology 2016 |
Form Of Engagement Activity | Participation in an activity, workshop or similar |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Professional Practitioners |
Results and Impact | Co-convener for the session Human-modified tropical forests - Impacts of forest degradation and biodiversity loss on tropical ecosystem functioning at the Annual Conference of the Society for Tropical Ecology, Gottingen, Germany |
Year(s) Of Engagement Activity | 2016 |
URL | http://www.soctropecol.eu |
Description | Convenor, Annual Conference of the European Society for Tropical Ecology 2017 |
Form Of Engagement Activity | Participation in an activity, workshop or similar |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Professional Practitioners |
Results and Impact | Convened a session on Human-modified tropical forests - Impacts of forest degradation and biodiversity loss on tropical ecosystem functioning. The aim of the session was to explore what is known about the linkages between forest degradation and biodiversity loss, and investigate the consequences of these concomitant phenomena for ecosystem processes and trace gas exchange. Knowledge gaps and means of addressing them, including inter-disciplinary or multi-disciplinary modes of problem solving were discussed. |
Year(s) Of Engagement Activity | 2017 |
URL | http://www.soctropecol.eu |
Description | Development of a bespoke display in the Museum of Zoology, Cambridge |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Public/other audiences |
Results and Impact | We have developed a small permanent display in the University Museum of Zoology, Cambridge illustrating the impacts of forest conversion to oil palm on biodiversity and the importance of more sustainable oil palm management. Since the Museum reopened in 2018, it has received over 100,000 visitors. |
Year(s) Of Engagement Activity | 2018,2019 |
Description | Educational film |
Form Of Engagement Activity | A broadcast e.g. TV/radio/film/podcast (other than news/press) |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Public/other audiences |
Results and Impact | The BALI consortium has teamed up with the South East Asia Rainforest Research Programme (SEARRP) and the LOMBOK project to produce a joint film specifically focusing on the Malaysian part of the HMTF programme to showcase our research and objectives. The is geared towards the general public and will be displayed on the HMTF consortia websites and disseminated via social networks (www.hmtf.info). |
Year(s) Of Engagement Activity | 2017 |
Description | Friends of Borneensis, 11-13th March 2016 |
Form Of Engagement Activity | Participation in an activity, workshop or similar |
Part Of Official Scheme? | No |
Geographic Reach | Local |
Primary Audience | Schools |
Results and Impact | BALI researchers, Hannah Griffiths, Louise Ashton and Terhi Riutta and LOMBOK researchers Eleanor Slade and Sol Milne gave talks at the Friends Of Borneensis, an educational event for local secondary school pupils organised by the Institute for Tropical Biology and Conservation at Universiti Malaysia Sabah, 11-13 March 2016. During Friends of Borneensis, students learn different aspects of rainforest ecology and field-based ecological methods, including collecting insects, flying drones and tree climbing skills. |
Year(s) Of Engagement Activity | 2016 |
Description | Guest speaker at United World College of Southeast Asia |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | Local |
Primary Audience | Schools |
Results and Impact | Guest speaker. Gave a talk titled "Day in the life of a tropical ecologist". |
Year(s) Of Engagement Activity | 2015 |
Description | Human-modified Tropical Forests Science Day |
Form Of Engagement Activity | Participation in an activity, workshop or similar |
Part Of Official Scheme? | No |
Geographic Reach | Regional |
Primary Audience | Postgraduate students |
Results and Impact | The HMTF Programme organised a science day at the University of Malaysia Sabah showcasing the research conducted so far by the Programme. |
Year(s) Of Engagement Activity | 2018 |
Description | Implementation of UNFCCC REDD+ protocols in Sabah |
Form Of Engagement Activity | Participation in an activity, workshop or similar |
Part Of Official Scheme? | No |
Geographic Reach | National |
Primary Audience | Professional Practitioners |
Results and Impact | The BALI consortium organised a workshop focusing on implementation of UNFCCC REDD+ protocols in Sabah. |
Year(s) Of Engagement Activity | 2018 |
Description | International Conference of Heart of Borneo, 8-9 November 2016 |
Form Of Engagement Activity | Participation in an activity, workshop or similar |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Study participants or study members |
Results and Impact | LOMBOK and BALI team members attended the International Conference of Heart of Borneo, 8th - 9th November, organised by the Sabah Forestry Department. Eleanor Slade helped organise a science-policy workshop with South East Asia Rainforest Research Programme (SEARRP) at the meeting and ran a break-out group on science-policy interface for riparian areas. Jake Bicknell led a break-out group for oil palm high conservation value areas. |
Year(s) Of Engagement Activity | 2016 |
URL | http://www.heartofborneo.org |
Description | International Year of Soils (seminar in Aberdeen) |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | Regional |
Primary Audience | Professional Practitioners |
Results and Impact | Presentation to about 50 trainee school teachers on the subject of soils and my research, connected the International Year of Soils |
Year(s) Of Engagement Activity | 2015 |
Description | International webinar on Forest Conservation in Malaysia. Universiti Malaysia Kelantan, Malaysia |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Postgraduate students |
Results and Impact | Invited presentation and discussion on the topic of forest conservation in Malaysia |
Year(s) Of Engagement Activity | 2020 |
Description | International webinar on The Role of Forests in Mitigating Climate Change through Nature-Based Solutions |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Professional Practitioners |
Results and Impact | Invited presentation to researchers in Iran |
Year(s) Of Engagement Activity | 2021 |
Description | Interview for NERC Planet Earth Magazine |
Form Of Engagement Activity | A magazine, newsletter or online publication |
Part Of Official Scheme? | No |
Geographic Reach | National |
Primary Audience | Media (as a channel to the public) |
Results and Impact | Paul Hallett and I were interview by Julia Horton in the lead-up to the NERC UnEarthed Event in Edinburgh (17-19 November 2017) on the topic of how our consumption of tropical food and food products impacts natural ecosystems, agricultural activity, and rural livelihoods in tropical countries. |
Year(s) Of Engagement Activity | 2017 |
URL | http://www.nerc.ac.uk/planetearth/stories/1879/ |
Description | Introduction to the BALI consortium at the Science@SAFE 2014 meeting |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Study participants or study members |
Results and Impact | Presentation on the Impacts of biodiversity loss and land-use change on biogeochemical cycling and trace gas fluxes across a forest degradation gradient in northern Borneo. The presentation gave an overview of BALI consortium activities and an update on current research progress. A HMTF programme management team meeting was also held at this event. |
Year(s) Of Engagement Activity | 2014 |
URL | http://www.safeproject.net/workshop/schedule.php |
Description | Keynote Address at World Biodiversity Forum, Davos, February 2020 |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Professional Practitioners |
Results and Impact | Keynote presentation at a major international conference designed to contribute evidence to the post-2020 review of the Convention on Biological Diversity, attended by policy-makers and biodiversity practitioners as well as academic researchers. |
Year(s) Of Engagement Activity | 2020 |
Description | NERC UnEarthed, Edinburgh, 17-20 November 2017 |
Form Of Engagement Activity | Participation in an activity, workshop or similar |
Part Of Official Scheme? | No |
Geographic Reach | National |
Primary Audience | Study participants or study members |
Results and Impact | University of Aberdeen Researchers and members of the BALI project held an exhibit at the NERC Unearthed event at Dynamic Earth, Edinburgh, 17th - 20th November 2017. The theme of our stall focused on soil health and food security in tropical regions. We wanted to show how what we eat affects the world and how our research may tackle these issues. The day was hugely successful and we are planning to set up our exhibit again for Climate Week Fun Day at Hazelhead Park, Aberdeen, 24th March. |
Year(s) Of Engagement Activity | 2017 |
Description | Nature Live public outreach event at the Natural History Museum |
Form Of Engagement Activity | Participation in an activity, workshop or similar |
Part Of Official Scheme? | No |
Geographic Reach | Local |
Primary Audience | Public/other audiences |
Results and Impact | Researchers Hannah Griffiths and Louise Ashton participated in a Nature Live public outreach event at the Natural History Museum, 27th January 2016, where they gave a talk about their research and displayed some of the invertebrates they collected and identified in the field. |
Year(s) Of Engagement Activity | 2016 |
Description | Nature Live talk to NHM visitors |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | National |
Primary Audience | Public/other audiences |
Results and Impact | Presenting an overview of work to the general public |
Year(s) Of Engagement Activity | 2017 |
Description | Press release and media engagement related to the carbon credits from forest restoration in Sabah |
Form Of Engagement Activity | A press release, press conference or response to a media enquiry/interview |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Media (as a channel to the public) |
Results and Impact | A briefing note and press release were written to respond to a proposal to erroneously register a large portion of the remaining forest in Sabah, Malaysia, as a carbon offset by a Singapore-based finance company. The press release was picked up by multiple media channels in Southeast Asia, and the briefing note was discussed by the Sabah State Government, who subsequently rejected the proposal. |
Year(s) Of Engagement Activity | 2022 |
URL | https://www.nst.com.my/news/nation/2022/02/772617/sabah-carbon-deal-not-certifiable-saleable-or-prof... |
Description | Provide expert scientific input on the High Carbon Stock (HCS) Science Study by the Roundtable for Sustainable Palm Oil |
Form Of Engagement Activity | A formal working group, expert panel or dialogue |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Industry/Business |
Results and Impact | David Burslem and Yit And Teh provided were asked to advise and provide feedback on a report commissioned by the Roundtable on Sustainable Palm Oil (RSPO) called "HCS Science Study: Draft Synthesis Report". This document, prepared by an independent scientific panel and co-chaired by Jonathon Porritt, aimed to provide expert advice and guidance to the oil palm industry on how to sustainably manage oil palm plantations and the surrounding landscapes for carbon, with the wider goal of offsetting or mitigating carbon losses from plantation development. The input provided by Burslem and Teh led to the production of a final report ("High Carbon Stock Science Study: Independent Report from the Technical Committee"), which will be used to guide the planning and management practices of the oil palm industry, and support the RSPO in reaching its sustainability and climate change mitigation targets. |
Year(s) Of Engagement Activity | 2015 |
URL | http://www.simedarby.com/sustainability/clients/simedarby_sustainability/assets/contentMS/img/templa... |
Description | REDD+ Support and Capacity Building Meeting 7-8 August 2017, Sabah Forestry Department |
Form Of Engagement Activity | A formal working group, expert panel or dialogue |
Part Of Official Scheme? | No |
Geographic Reach | Regional |
Primary Audience | Policymakers/politicians |
Results and Impact | Initial meeting with policy makers and practitioners in the Sabah Forestry Department and conservation-based NGOs to discuss how the HMTF Programme and BALI Consortium can support and help develop the skills and knowledge base in Sabah to conduct REDD+ activities |
Year(s) Of Engagement Activity | 2017 |
Description | Research seminar talk at the National University of Singapore |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Professional Practitioners |
Results and Impact | Gave a talk titled Soil-atmosphere trace gas exchange in the tropical Andes at a Research Seminar at the National University of Singapore. |
Year(s) Of Engagement Activity | 2013 |
Description | Research seminar talk at the University of Oxford, UK |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | Local |
Primary Audience | Professional Practitioners |
Results and Impact | Gave a talk titled Impacts of soil methane and nitrous oxide dynamics on ecosystem climate forcing at a Research Seminar, University of Oxford. |
Year(s) Of Engagement Activity | 2012 |
Description | SEARRP Science Meeting, 20-21 April 2017, University of Cambridge |
Form Of Engagement Activity | Participation in an activity, workshop or similar |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Professional Practitioners |
Results and Impact | BALI and LOMBOK researchers attended and gave presentations at the SEARRP Science meeting, 20-21 April, University of Cambridge. The second day included breakout group discussions to identify core objectives and experimental ideas for a new forest restoration project in Aceh, Indonesia. The main impact/outcome of this event were requests and opportunoties to get further involved in the project and knowledge exchange. |
Year(s) Of Engagement Activity | 2017 |
Description | SEnSOR meeting, Royal Over-Seas League, London, May 2016 |
Form Of Engagement Activity | Participation in an activity, workshop or similar |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Professional Practitioners |
Results and Impact | Members from BALI and LOMBOK attended a meeting with the Socially and Environmentally Sustainable Oil Palm Research (SEnSOR) project at the Royal Over-Seas League, London, 27 May 2016. The aim of the meeting was to discuss possible SEnSOR-linked research (new, existing, and expanded) that could be funded in order to test the impact of RSPO certification. BALI and LOMBOK each submitted 3 research proposals to the committee for consideration. |
Year(s) Of Engagement Activity | 2016 |
Description | Seminar on interim outputs on Prioritization with DFOs |
Form Of Engagement Activity | Participation in an activity, workshop or similar |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Professional Practitioners |
Results and Impact | A seminar was held to brief District Forest Officers of the Sabah Forestry Department on the interim outputs of a prioritization exercise for selecting new protected areas in Sabah, influenced by NERC-funded research on the distribution of functional diversity. |
Year(s) Of Engagement Activity | 2018 |
Description | Seminar presentation to International Institute of Tropical Agriculture |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Professional Practitioners |
Results and Impact | I presented a research talk to about 50 members of staff IITA broadly engaged with research on tropical forest restoration, including a question and answer session that stimulated discussion and follow-up correspondence. |
Year(s) Of Engagement Activity | 2023 |
Description | Talk at Royal Botanic Gardens Edinburgh symposium |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | National |
Primary Audience | Policymakers/politicians |
Results and Impact | A talk on biodiversity from space to a broad audience from research, policy, NGOs and education |
Year(s) Of Engagement Activity | 2020 |
Description | Training workshop on R |
Form Of Engagement Activity | Participation in an activity, workshop or similar |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Professional Practitioners |
Results and Impact | A 2-day training workshop in the use of R was held for government departments, NGOs and Universiti of Malaysia Sabah postgraduate students. |
Year(s) Of Engagement Activity | 2018 |
Description | UK Dept of Business Enterprise Innovation and Skills |
Form Of Engagement Activity | A formal working group, expert panel or dialogue |
Part Of Official Scheme? | No |
Geographic Reach | National |
Primary Audience | Policymakers/politicians |
Results and Impact | An invited visit to BEIS to discuss forest monitoring, reporting for international climate agreements |
Year(s) Of Engagement Activity | 2017 |
Description | University Malaysia Sabah, Current Topics in Conservation module for undergraduate students |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | Local |
Primary Audience | Undergraduate students |
Results and Impact | BALI researchers Boris Bongalov and Terhi Riutta and LOMBOK researcher Eleanor Slade gave talks to undergraduate Conservation students at University Malaysia Sabah (UMS), in February and April 2016. This was part of a module entitled "Current Topics in Conservation" which aimed to provide students with examples of real-life research that applied to concepts they studied during the course of their degree. |
Year(s) Of Engagement Activity | 2016 |
Description | University of Aberdeen Doors Open Day 2016 |
Form Of Engagement Activity | Participation in an open day or visit at my research institution |
Part Of Official Scheme? | No |
Geographic Reach | Local |
Primary Audience | Public/other audiences |
Results and Impact | University of Aberdeen opened its doors to members of the public, 10th September 2016. We set up a 'tropical forests' themed stall to help showcase our work and talk to visitors about our research in Malaysia. We displayed photos from our trips as well as tropical seeds, insect and animal specimens. We had 453 visitors throughout the day including visitors to the Zoology museum and Biodiversity Centre. |
Year(s) Of Engagement Activity | 2016 |
Description | Workshops at the Science@SAFE 2014 meeting |
Form Of Engagement Activity | Participation in an activity, workshop or similar |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Professional Practitioners |
Results and Impact | 3 workshops were held at the Science@SAFE meeting including 1) an overview of EarthCape platform, 2) Linking plot and satellite data 3) Soil trace gas flux measurements. |
Year(s) Of Engagement Activity | 2014 |