Integrating remote sensing and ground-based spectral analysis to investigate biodiversity of archaeological sites in Amazonia

Lead Research Organisation: University of St Andrews
Department Name: Biology

Abstract

There is growing evidence and awareness that human impacts on ecosystems and biodiversity are leading to significant implications for sustainability. Amazonia is a critically important biome in terms of: potential impacts of development (e.g. deforestation), sustainability of indigenous peoples and their livelihood, and sustainability of biodiversity and ecosystem services with global impact. Modern land uses such as urbanization, intensive agriculture or extensive conversion to pasture is already showing devastating effects on Amazonian biodiversity. Until recently, the Amazon was considered to be pristine forest, barely occupied by people in the past. Researchers have now come to agree that at least the riverine areas of the basin were densely occupied While there is keen awareness of contemporary anthropic effects, Amazonia is in fact a laboratory for investigation of long-term impacts of anthropic influence. Emerging technologies will shed light on ancient human footprints on biodiversity which in turn will help us to better understand current and future anthropic impacts and potentially develop mitigation strategies which will inform national and global efforts towards biodiversity conservation and sustainability.

The overarching objective of this project is to implement and demonstrate a novel approach to investigation of anthropic impacts on biodiversity in the Amazonian rainforest. This will be achieved by developing a multidisciplinary team that includes remote sensing expertise, archaeologists, and plant biodiversity expertise. Our plan is to demonstrate the usefulness and power of integrating ground-based spectral analysis of vegetation (NIR - near infrared spectroscopy) with aerial survey data using NIR to develop a method for analysing local biodiversity that is scalable to much larger areas by remote sensing. This will enable analysis of the impact of past human activity on biodiversity, and it will also enable investigation of that human footprint across a larger landscape. The programme of work includes a UK inception workshop, a Brazilian workshop, and a field demonstration project.

This project has grown out of scientific networks established under STFC/NERC Global Challenges Network on Bioinformatics and Environmental Omics. Networking activities through these programmes have also established an interface with the "Terra Preta de Indio Network" (TPInet: http://tpinet.org).

The purpose of the present STFC Futures proposal is to consolidate a potential research network involving EOS and integrating across strengths at STFC RAL-Space (remote sensing), St Andrews (plant diversity and conservation), RBG Kew (plant diversity and conservation, remote sensing), Cardiff (TPINet)., and USP, Brazil (archaeology) to develop advanced remote sensing technologies for investigation of long-term anthropic impacts on Amazonian ecosystems.

Planned Impact

There are many aspects of this project that are topical and of inherent interest and potential use to a wide range of audiences.

Brazil is listed as an ODA country on the Organisation for Economic Cooperation and Development Assistance Committee (DAC) list. Amazonia in particular is a target for much-needed economic development. Improved understanding of historical impacts and contemporary biodiversity that would arise from this project would support integration of conservation with regional development goals.

Acre is one of only two states in the Brazilian Amazon that has legislation in place to support Payment for Ecosystem Services (PES). Rapid survey techniques to enhance and accelerate understanding of the history and diversity of Acre's forests (which still cover nearly 90% of the area of the state) will be important to ensure that the areas of greatest value (in cultural and biodiversity terms) are recognised and factored into the implementation of PES and other regional development schemes.

In terms of public engagement, almost anyone who learns about this project would find it fascinating. Archaeology, ancient civilisations, the Amazon, tropical rainforests, UAVs. We have it all. Neves and his archaeological work has been featured in the popular press as well as television documentaries. There is scope for press releases and even telejournalism through the BBC and other outlets. There are also other opportunities that might arise. RBG Kew, Museu de Arqueologia e Etnologia da USP, and the Rio de Janeiro all have a strong public interface that could provide opportunities for public presentations of this work. Meagher, through his role as Chair of Education and Outreach for the Society for the Study of Evolution has access to multiple opportunities to present scientific findings to broader audiences, in particular secondary school teachers. Mortimer has a strong track record of scientific outreach and could facilitate connections between outputs from this project and UK media and entertainment.

In terms of policy, outputs of this project will have relevance to government policy related to conservation as well as UK and Brazilian negotiations with regard to international conservation efforts. These potential impacts will be facilitated through connections to DEFRA (Meagher, Nic Lughadha) in the UK and to Reflora (Nic Lughadha and Zappi) in Brazil. Meagher in his current Scottish Government role as Trustee of the Royal Botanic Garden Edinburgh) has a network of professional connections with which he will facilitate awareness of project outputs and their policy implications through Scottish RERAD. There is also substantial potential for direct uptake in practice and organisational policies by conservation NGOs, which will be facilitated through connections to RBG Kew (Nic Lughadha) and the Rio de Janeiro Botanic Garden (Zappi).

Publications

10 25 50
 
Description The project supported exciting field trials (UAV surveys, ground-based NIR and LIDAR) on archaeological sites in Acre (Oct 2017). While in the field, individuals from across a broad spectrum of disciplines (e.g., plant biodiversity, invertebrate biodiversity, physics, planetary science, archaeology, social anthropology, remote sensing, forestry) felt first-hand the intellectual excitement of interdisciplinary discovery.

An example outcome from this field trial, now the basis for future funding to implement these trials at full project level, is the use of UAV multispectral imaging to isolate and analyze spectral properties of individual trees from forest canopies (sadly, images representing this work would not paste into this window).
Exploitation Route An additional URL for the box above is http://environmentalomics.org/wp-content/uploads/2018/06/09-Hussain-ali-15.06.2018-Sao-Paulo.pdf.

Our trial studies have demonstrated the potential for use of high-resolution UAV surveys to expand the scope of biodiversity analysis in remote or difficult terrain. We are now scaling that up to full project level to further consolidate this methodology and also to implement at full project level.

This methodology will be an effective tool in ecosystem modeling to inform conservation as well as biodiversity and land-use management.
Sectors Aerospace, Defence and Marine,Agriculture, Food and Drink,Environment,Culture, Heritage, Museums and Collections,Other

URL http://environmentalomics.org/wp-content/uploads/2018/06/Whats-the-point.pdf
 
Description Workshop outputs from this project informed stakeholder engagement and development for a GCRF HUB application. Collaborations established under this project were also key to the development of a successful application to a British Council Researcher Links LATAM call. The Researcher Links LATAM workshop took place at Instituto Nacional de Pesquisas Espaciais, São José dos Campos, SP, Brazil 13-15 June 2018 and was co-organised by Prof Thomas Meagher, University of St Andrews, UK, and Dr Jean Ometto, Director, Earth System Science Center, INPE, SP, Brazil. Several preseantations at the workshop were direct outputs from this project, including talks by Thomas Meagher, Justin Moat (Royal Botanic Gardens, Kew), and Ali Hussain (STFC RAL-Space). More details can be found on our post-workshop web page, http://environmentalomics.org/researcher-links-workshop/. Trial studies and networking funded by this grant have enabled consolidation of research and impact networks through Brazil and UK collaborators and project partners at the University of St Andrews, the Royal Botanic Gardens Kew, STFC RAL Space, the University of São Paulo, the Instituto Nacional de Pesquisas Espaciais (Brazil), the Instituto Tecnológico Vale (Brazil) and Embrapa (national environmental and agricultural research institute, Brazil). Moreover, this project jhas facilited establishment of stakeholder networks, including the Joint Nature Conservation Committee (Defra, UK) and Instituto Socioambiental (Brazil). Outputs from this project, refined during the LATAM workshop, were the bases for three grant proposal submissions in autumn 2019: NERC LATAM, STFC GCRF, STFC Network+. Of these, the STFC GCRF application was successful (a 33% success rate!) and is currently listed in my awards profile. This new award will enable implementation of the trial technologies from 'Integrating remote sensing and ground-based spectral analysis to investigate biodiversity of archaeological sites in Amazonia' to be implemented as a full-scale research project, and it will also serve to consolodate St Andrews-STFC-Kew-Brazil collaborations and scientific networking.
First Year Of Impact 2017
Sector Aerospace, Defence and Marine,Environment,Culture, Heritage, Museums and Collections,Other
Impact Types Cultural,Policy & public services

 
Description British Council Research Links award - "Remote Sensing for Biodiversity and Ecosystem Services Inventory", co-investigator Dr Jean Ometto, INPE, Brazil
Amount £48,500 (GBP)
Funding ID 2017-RLWK9-359477089 
Organisation British Council 
Sector Charity/Non Profit
Country United Kingdom
Start 03/2018 
End 08/2018
 
Description DEFRA Captial bid, UAV (Unmanned Aerial Vehicle) PI Justin Moat
Amount £24,000 (GBP)
Organisation Department For Environment, Food And Rural Affairs (DEFRA) 
Sector Public
Country United Kingdom
Start 03/2019 
End 12/2019
 
Description DEFRA Captial bid, UAV (Unmanned Aerial Vehicle), Handheld Terrestrial Laser Scanner, Tree sensors - sonic tomography. PI Justin Moat
Amount £121,000 (GBP)
Organisation Department For Environment, Food And Rural Affairs (DEFRA) 
Sector Public
Country United Kingdom
Start 03/2017 
End 06/2018
 
Description Equipment- Hyper spectral camera and LiDAR for UAV
Amount £131,000 (GBP)
Organisation Department For Environment, Food And Rural Affairs (DEFRA) 
Sector Public
Country United Kingdom
Start 05/2020 
End 03/2021
 
Description NERC Field Spectroscropy
Amount £70,000 (GBP)
Organisation Natural Environment Research Council 
Sector Public
Country United Kingdom
Start 01/2017 
End 01/2018
 
Description Nature-based Solutions for Climate Change at the Landscape Scale
Amount £12,500,000 (GBP)
Organisation Natural England 
Sector Charity/Non Profit
Country United Kingdom
Start 09/2021 
End 03/2024
 
Description Remote Sensing for sustainable use of seasonally dry tropical forests - Learning to live with the forest
Amount £395,374 (GBP)
Funding ID ST/S003215/1 
Organisation Science and Technologies Facilities Council (STFC) 
Sector Public
Country United Kingdom
Start 03/2019 
End 03/2021
 
Description 12-14 October 2017 workshop - "Amazonia at Rio Branco" 
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 This workshop was directed towards onsite planning for fieldwork that immediately followed. The meeting took place in Rio Branco, Acre State, Brazil, and was organised by PI Prof Thomas Meagher and hosted by Embrapa-Acre. There were 9 participants from Brazil and 8 from the UK. The workshop included a day dedicated to identification of stakeholders for inclusion in GCRF project development.
Year(s) Of Engagement Activity 2017
 
Description 13 November 2017 presentation to CNPq, Brasilia, Brazil 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Supporters
Results and Impact Presentation on "STFC/NERC Bioinformatics & Environmental 'Omics Synthesis: Adventures in meta-science - from cloud computing to remote sensing" to programme officers and others at CNPq. This was an engagement meeting to assist CNPq in the development of a future funding call.
Year(s) Of Engagement Activity 2017
 
Description 15 November 2017 seminar at Rutgers University, New Jersey, USA 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Postgraduate students
Results and Impact This was an academic seminar entitled "STFC/NERC Bioinformatics & Environmental 'Omics Synthesis: Adventures in meta-science - from cloud computing to remote sensing" and presented for the benefit of colleagues and postgraduate students at Rutgers University
Year(s) Of Engagement Activity 2018
 
Description 2-4 May 2017, project workshop "Amazonia at St Andrews" 
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 The purpose of this workshop was to assemble an inclusive group of collaborators on this project to develop plans for field research to take place later in the calendar year and also to explore and develop project concepts for further funding applications, including GCRF. There were 6 Brazilian and 10 UK participants.
Year(s) Of Engagement Activity 2017
 
Description 26 September 2017 RCUK GCRF event, St Andrews, UK 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Supporters
Results and Impact Presentation on STFC 21st Century Global Challenges project "Integrating remote sensing and ground-based spectral analysis to investigate biodiversity of archaeological sites in Amazonia". The purpose of this presentation was to highlight results from an ongoing GCRF project and to obtain feedback for an upcoming GCRF HUB application.
Year(s) Of Engagement Activity 2017
 
Description 4-5 September 2017 NERC GCRF event, London, UK 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Supporters
Results and Impact Elevator pitch "Sustainable land use in Amazonia, past impacts and prospects for the future" to obtain feedback for an upcoming GCRF Hub application.
Year(s) Of Engagement Activity 2017
 
Description 7-9 March 2018, presentation to CNPq wokshop on "CENTRO DE SÍNTESE EM BIODIVERSIDADE E SERVIÇOS ECOSSISTÊMICOS" 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Policymakers/politicians
Results and Impact Presentation on "Perspectives on communication strategy and stakeholder dialogue". This talk included findings from fieldwork that took place in October 2017. The talk was designed to inform development of an upcoming call for proposals from CNPq for a programme with potential for collaborative UK Newton Fund collaboration.
Year(s) Of Engagement Activity 2018
 
Description Applications of Drones in Environmental Regulation and Monitoring. Drones in Pursuit of Plants Conservation and Science: Real World Experiences. 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Discussion and presentation to DEFRA and other government organisations, on the use of UAV for research etc. - 29th January 2019, North Wales, UK. Applications of Drones in Environmental Regulation and Monitoring.
Year(s) Of Engagement Activity 2019
URL http://www.ukeof.org.uk/news/drone-conf-2019
 
Description Brazil Year of Science Workshop: CSSP Brazil: Annual Workshop, 25 June 2018 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Policymakers/politicians
Results and Impact I was invited by the Newton Fund to participate in this workshop (Met Office, Exeter, UK), which was exploring a joint climate research initiative between INPE (Brazil) and the Met Office (UK). Neworking opportunities included meetings with the head of the Newton Fund for Brazil, the Director of the Brazilian Soace Research Institute (INPE), and the Director of the Brazilian Amazonian REsearch Institute (INPA).
Year(s) Of Engagement Activity 2018
 
Description British Ecological Society: Unifying tropical ecology: strengthening collaborative science. British Ecological Society: Unifying tropical ecology: strengthening collaborative science. What's the Point? Point clouds for Restoration monitoring: in A view from the top - using drones in tropical ecology and conservation. 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact British Ecological Society: Unifying tropical ecology: strengthening collaborative science. What's the Point? Point clouds for Restoration monitoring: in A view from the top - using drones in tropical ecology and conservation. Talk and discussion of new ideas and outcomes.
Year(s) Of Engagement Activity 2019
URL https://www.britishecologicalsociety.org/events/ute2019/
 
Description Guest lecture in a University of Sao Paulo - Harvard field course, Rio Branco, State of Acre, Brazil, 16 June 2018 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Undergraduate students
Results and Impact I presented a guest lecture onsite for a field course run jointly by USP (Brazil) and Harvard (USA). The title of my presentation was 'Long-term human impacts on plant biodiversity in Amazonia'.
Year(s) Of Engagement Activity 2018
 
Description Kew Science Festival. Measure trees in 3d 
Form Of Engagement Activity Participation in an open day or visit at my research institution
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Public/other audiences
Results and Impact We used the results and activities as examples of our work and why measuring and quantifying trees are important. Also teaching child that simple math can help to measure trees and landscapes
Year(s) Of Engagement Activity 2019
URL https://www.kew.org/about-us/press-media/kew-science-festival-returns-for-2019
 
Description Kew drone pilots map deforestation and fire damage around the world 
Form Of Engagement Activity A press release, press conference or response to a media enquiry/interview
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Public/other audiences
Results and Impact Press article which mentions this project and others. plus associated paper
Year(s) Of Engagement Activity 2021
URL https://www.telegraph.co.uk/environment/2021/02/21/kew-drone-pilots-map-deforestation-fire-damage-ar...
 
Description London DEFRA computing group, 
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 Talk was given to DEFRA policymakers, on the computing power needed for the next generation of data to be captured. Details of these projected used to show data capture and potiental.
Year(s) Of Engagement Activity 2019
 
Description London DEFRA computing group, Kew Spatial Analysis for Plant Conservation and Science 
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 Demostration to DEFRA and policy makers of high level computing from spatial data. 26th July 2019, London DEFRA computing group, Kew Spatial Analysis for Plant Conservation and Science
Year(s) Of Engagement Activity 2019
 
Description Music Planet presents 'Xerxes in the Garden': Byre Opera and Botanic Garden Study Day, 2 June 2018, St Andrews, UK 
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 I was an invited panelist and presenter for a presentation to the general public. The title of my presenation was 'Long-term human impacts on plant biodiversity in Amazonia'
In association with Music Planet, University researchers and performers involved in Byre Opera's 'Xerxes' offered a stimulating exploration of human interactions with the natural environment and the role of gardens in encouraging biodiversity.

The day included a chance to hear some of the music from the opera and discussions about the production's engagement with environmental themes.
Year(s) Of Engagement Activity 2018
 
Description Natural Capital Evidence to Application: Building multi-disciplinary partnerships, 22-25 May 2018, Punta Arenas, Chile 
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 I was an in vited contributtor to a JNCC workshop to explore potential for development of research collaborations on Natural Capital in South America and adjacent British Overseas Territories. The title of my presentation at the workshop was 'Integrating remote sensing and ground-based spectral analysis to investigate biodiversity of archaeological sites in Amazonia'.
To establish the Sustainability Partnership Network, the 'Natural Capital: Evidence to Application' workshop was co-hosted by UK's Joint Nature Conservation Committee (JNCC) and the University of Magallanes to develop these links.
The JNCC is an authority on national and global nature conservation, and a statutory advisor to the UK Government. Through our scientific expertise and high-quality evidence we deliver innovative solutions to governments, businesses and society to realise the value of nature. We have a strong record of convening multi-disciplinary partnerships, including through international collaboration.
Within the South Atlantic region, JNCC has a 10-year record of supporting research and nature conservation in the UK South Atlantic Overseas Territories (UKOTs). In late 2016, JNCC began a 2-year project focussed on the evidence needed to support sustainable management and natural capital1 assessment and valuation in the Territories. An important part of the project is to reach out beyond the UKOTs to the wider South Atlantic region to create a network of sustainability practitioners from which international partnerships can emerge, and to encourage the transferability of processes and knowledge exchange. The establishment of the Sustainability Partnerships' Network is funded by the UK Department for Environment, Food and Rural Affairs (Defra) through the Conflict, Security and Stability Fund (CSSF), which includes promoting the role of the natural environment in underpinning long-term economic prosperity.
Year(s) Of Engagement Activity 2018
 
Description Newton Fund / British Council / FAPESP LATAM Researcher Links Workshop: Remote Sensing for Biodiversity and Ecosystem, 12-14 June 2018 
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 The purpose of this workshop was to provide a forum for development of concepts towards interdisciplinary research proposals for an upcoming call under the Newton Fund Regional Latin America Biodiversity Programme. Participants werre drawn from the UK, Brazil, Peru, Chile, Colombia, Argentina and Mexico. The workshop took place at INPE, SP, Brazil, 12-14 June, 2018.
Year(s) Of Engagement Activity 2018
URL http://environmentalomics.org/researcher-links-workshop/