A .pdf version of this CV can be downloaded here .
Current employment
Nov 2021 - Present
Post-Doctoral Research Associate, School of GeoSciences, The University of Edinburgh
SECO: Resolving the current and future carbon dynamics of the dry tropics
Education
Sep 2017 - Sep 2021
PhD: Atmospheric and Environmental Sciences
The University of Edinburgh
Thesis: Biodiversity - Ecosystem Function Relationships in Southern African Woodlands
Used the SEOSAW plot network for a regional-scale study of the interaction of tree diversity, canopy structure, woody biomass, environmental processes, and disturbance regime across southern Africa. Terrestrial LiDAR of tree canopy structure in Angola and Tanzania to investigate neighbourhood community composition and ecosystem structure. Used MODIS data and plot data from the Zambian Integrated Land Use Assessment to investigate how species composition and species diversity affects land-surface phenology. I manage 15 permanent woodland monitoring plots in Bicuar National Park, Angola.
Sep 2012 - Jun 2016
BSc Hons: Ecological and Environmental Sciences - 1st Class
The University of Edinburgh
Dissertation: Forest structure along an Amazon-Andes elevation gradient drives tree seedling trait acclimation.
Sep 2009 - Jul 2011
A-Levels: Geology (A*), Geography (A), Biology (A)
Queen Elizabeth Sixth Form College, Darlington, County Durham
Manuscripts and Published Work
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Godlee J. L. … - Structural diversity and tree density drives variation in the biodiversity-ecosystem function relationship of woodlands and savannas - New Phytologist - 2021
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Godlee J. L., … - Diversity and Structure of an Arid Woodland in Southwest Angola, with Comparison to the Wider Miombo Ecoregion - Diversity - Special issue: Biodiversity of Vegetation and Flora in Tropical Africa - 2020
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The SEOSAW partnership incl. Godlee J. L. - A network to understand the changing socio-ecology of the southern African woodlands (SEOSAW): Challenges, benefits, and methods - Plants People Planet - 2020
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Panzou G. J. L. … Godlee J. L. … - Pantropical variability in tree crown allometry - Global Ecology and Biogeography - 2020
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Daskalova G., … Godlee J. L. - Rare and common vertebrates span a wide spectrum of population trends - Nature Communications - 2020
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Rowland, L. … Godlee J. L. - Drought stress and tree size determine stem CO~2~ efflux in a tropical forest - New Phytologist - 2018
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Esquivel-Muelbert A. … Godlee J. L. … - Bridging scales in monitoring global tree mortality globally - Nature Communications - in prep. July 2021
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Tchamba J. J., Godlee J. L. … - Tree species diversity and composition of the woodlands in the municipality of Chipindo, Huila, Angola. - African Journal of Ecology - in prep. July 2021
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Godlee J. L., … - Variation in forest canopy structure along an Andean elevation gradient causes species-specific stress responses in tree seedlings - Plant Biology - in prep. July 2021
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Godlee J. L., … - Geographically and genetically distinct populations of scots pine (Pinus sylvestris) differ in resistance to damage by the large pine weevil (Hylobius abietis): a common garden translocation study - Agricultural and Forest Entomology - in prep. July 2021
Research profile
My research interests lie in the complex interactions between ecological communities and their environment, and how this determines ecosystem structure. Through my PhD I have particularly developed an interest in how community composition influences ecosystem function. My thesis focusses on tree species diversity in southern African savannas and its multiple effects on canopy structure, phenology, biomass accumulation, and disturbance regime.
My PhD project straddles multiple spatial scales. I answer macro-ecological biodiversity-ecosystem function questions by integrating large collaborative plot datasets and remote sensing products, but have also conducted my own plot-based field campaigns to investigate canopy structure and diversity patterns both in Angola and Tanzania. I have a strong data science background, with broad skills in ecological data analysis, which combine with my extensive theoretical knowledge of dry tropical ecosystems to produce ambitious projects with high-impact and novel research outcomes.
My research skills are broad, ranging from phylogenetics and pest resistance in Scots Pine, to fire disturbance and tree mortality dynamics in Congolese Savanna, to terrestrial LiDAR of savanna tree canopies, to global investigation of species population trends with respect to rarity. My varied previous research experience places me well to conduct collaborative whole-system science which incorporates cutting edge methodologies.
I have a deep interest in developing rigorous and accessible field protocols for phyto-demographic plot data. Through my research assistant position with SEOSAW and in constructing permanent survey plots in Angola, I am keenly aware of the value of a precise and considered field methodology that is well documented, easily accessible and built for collaboration, to ensure that data has a legacy befitting the effort expended to collect it.
I support the development of effective teaching in higher education and aim to remain active within the academic teaching community as I progress through my career. Particularly I am interested in teaching research design and data analysis in an ecological science context. I aim to equip students with transferable skills for research management that will form the foundation of a successful career. In the future I hope to forge an academic career in a university as I enjoy researching alongside other academics, sharing knowledge for the greater good, and writing robust science.
Research & Outreach Grants
- Feb 2019 - Davis Expedition Fund - £4000 - Terrestrial LiDAR assessment of canopy structure and ecosystem processes in southern Tanzania
- Jan 2019 - National Geographic Beginning Investigators Grant - $10,000 - Co-I with PI Francisco Maiato. How resilient are the carbon stocks and biodiversity of miombo woodlands to degradation and fuelwood harvesting?
- Jun 2018 - NERC bursary - £980 - Funding to attend Applied Plant Taxonomy and Field Survey Skills course at Kew Gardens
- May 2018 - Principals Go Abroad Fund - £350 - Funding to attend Mozambique SEOSAW Network Meeting funding
- Feb 2018 - School of GeoSciences Facilities Committee Research Equipment Grant - £2810 - Funding to buy Camera equipment for hemispherical tree canopy photography for the School of GeoSciences
- Nov 2017 - James Rennie Bequest - £170 - Funding to run Coding Club workshop at the British Ecological Society Annual Meeting
- Nov 2017 - Centenary Agroforestry 89 Fund - £984 - Construction of permanent woodland monitoring plots in Bicuar National Park, Angola
- Nov 2017 - British Ecological Society Small Grant - £1500 - Funding to run Scottish Tropical Ecology and Biology Student Meeting
- Nov 2017 - Institute for Academic Development Action Fund Small Grant - £470 - Funding to run Scottish Tropical Ecology and Biology Student Meeting
- Mar 2016 - Royal Society of Biology Travel Grant - £500 - Research expedition for Canadian Arctic herbivory study
- Dec 2015 - Friends of Roslin Glen Outreach Fund - £900 - Funding to design an interpretation panel about Roslin Glen’s industrial history
- Nov 2015 - Lothian Conservation Volunteers Outreach Fund - £500 - Funding to install an interpretation panel about Roslin Glen’s industrial history.
- May 2015 - Principal’s Go Abroad Fund - £350 - Research expedition for Peruvian Andes seedling competition study (undergraduate dissertation)
- Apr 2015 - British Travel Association Fund - £1000 - Research expedition for Peruvian Andes seedling competition study (undergraduate dissertation)
Academic and Research Experience
- Apr-Sep 2020 - Research assistant - University of Edinburgh - Dr. Casey Ryan
- Developed the SEOSAW database through production of an R package for cleaning and analysing SEOSAW data. I wrote documentation and a created a robust data management system for the SEOSAW database. I created educational research-focussed tools to facilitate collection and management of plot data such as advanced ODK XForms for digital data collection, data sheets, a field manual and a data analysis manual. I facilitated fieldwork by in-country partners in Angola (ISCED Huila), Democratic Republic of Congo (University of Lubumbashi) and Zimbabwe (Zimbabwe Forestry Commission), with the aim of expanding SEOSAW’s permanent plot coverage to under-represented bioclimatic regions. I provided support for other researchers using the SEOSAW dataset to create floristic maps and estimate carbon dynamics.
- May-Jun 2017 - Fieldwork coordinator - University of Edinburgh - Dr. Edward Mitchard
- Managed the fieldwork of a long term experiment in collaboration with the US Forest Service, the Wildlife Conservation Society and Paula Nieto-Quintano, a PhD student at the University of Edinburgh. Fieldwork conducted in remote and logistically challenging Beteke Plateau of the Republic of Congo. I supervised students from Marien Ngouabi University, Brazzaville, and maintenance workers responsible for creating firebreaks. Fieldwork involved a tree growth and mortality census, with herbaceous biomass measurements in four 25 ha plots, followed by controlled burning of the plots.
- Sep-Dec 2016 - Research assistant - University of Exeter - Dr. Lucy Rowland
- Six weeks fieldwork at the Caxiuana Esecaflor drought experiment followed by work at the University of Exeter. Extensive experience with the Li-COR 6400XT Portable Photosynthesis System, collection and analysis of leaf traits. Lab work in Exeter included use of CAN-EYE Leaf Area Index analysis software and developing a method for the analysis of foliar fungal infections from scanned leaf images. I worked with a 10 year time series of leaf traits to analyse the effects of experimentally induced drought on tree growth and photosynthetic capacity.
- Mar-Aug 2016 - Field assistant - University of Edinburgh - Dr. Isla Myers-Smith
- Two months fieldwork at Kluane Lake Research Station and Herschel Island (Qikiqtaruk) in the Yukon Territory, Canada. I conducted an experiment investigating elevation-dependent patterns of seed herbivory, the data from which form part of a larger latitudinal study (Hargreaves et al. 2019 ). Other work included the collection of plant traits, monitoring of vegetation cover, and investigating soil decomposition rates with the International Tea Bag Index .
- Jul-Sep 2015 - Field assistant - University of Edinburgh - Dr. Pippa Stone
- Part of a five person field team for two months on an elevational plot transect in Manu National Park, Peru. Physiological and morphological measurements of seedling and adult trees, as well as competition measurements among tree seedlings for which I designed and executed the methodology. Experience using a MINIPAM-II portable chlorophyll fluorescence meter and analysing ecophysiological data.
- May-Dec 2015 - Research assistant - Centre for Ecology & Hydrology - Dr. Stephen Cavers
- Research assistant and data analyst for a common garden experiment investigating differentiation in Scots pine seed stock in terms of growth, phenology and environmental resistance. I conducted a study investigating the resistance of seedlings to pine weevils, an economically important pest of Scots pine.
Teaching & Outreach Experience
- Sep 2018, 2019 - Field demonstrator - Ecological Sciences Field Course - University of Edinburgh
- I taught 4th year undergraduate students on a week long field course near Oban Scotland. I designed a student research project brief and mentored 5 students in their experimental design data collection and analysis. I ran clinics on the operation of hemispherical photography equipment for measuring tree canopy structure.
- Sep-Dec 2017, 2018 - Demonstrator - Principles of Ecology - University of Edinburgh
- I led two groups of 2nd year ecology undergraduates through the research design process, data collection, and analysis of a plant fungal pathology project looking at tar-spots on sycamore. I also tutored students in basic statistics and translated older Minitab statistics practicals into modern R.
- Oct 2017-Present - Web developer for SEOSAW - University of Edinburgh
- I designed and currently maintain the SEOSAW network website
using Jekyll Bitbucket Pipelines and Github-Pages. Notably I implemented an interactive Javascript
leaflet
map of study sites using geoJSON compiled from the SEOSAW dataset.
- I designed and currently maintain the SEOSAW network website
using Jekyll Bitbucket Pipelines and Github-Pages. Notably I implemented an interactive Javascript
- Jan 2017-May 2019 - Copy writer - Agricology sustainable farming magazine
- I wrote summaries of online resources on the Agricology website . Articles had a focus on soil enrichment and enhancing pollinator services on British farms. Experience writing for an informed non-academic audience.
- Oct 2016-Jan 2019 - Co-founder, tutorial designer, tutor - Coding Club, programming proficiency initiative - University of Edinburgh
- Founding member of Coding Club , a peer-to-peer learning environment to overcome statistics anxiety and provide training in programming for the life sciences. I created online tutorials and delivered workshops to classes of up to 30 students/staff. Focusses include Shiny web-apps, hierarchical modelling, reproducible research using R Markdown. Co-organised and delivered two Coding Club workshops at international conferences: the SEECC conference in Aberdeen the British Ecology Society Annual Meeting.
- Sep 2015 - Apr 2016 - Interpretation resources designer - Midlothian Ranger Service
- I designed an interpretation panel that was installed at Roslin Glen, a Midlothian Country Park. The panel demonstrates historical land use of the Glen and the resulting landscape features. I designed factsheets for use in secondary schools and a QR code enabled walking route through the Glen.
Academic Service Positions
- Mar 2018 - Organiser of the Scottish Tropical Ecology and Biology Student Meeting
- I led organisation of this conference hosted by the Royal Botanic Gardens Edinburgh and the University of Edinburgh. Attended by ~50 people, 17 speakers and a midday skills workshop on creating academic posters. Secured funding from the British Ecological Society, University of Edinburgh Institute for Academic Development and the Royal Botanic Gardens Edinburgh.
- Sep 2013-Jul 2016 - Ecological and Environmental Sciences Student Representative
- Year wide degree programme representative. Liaison for student issues on course content, deadlines, and pastoral care.
- Sep 2015-Jul 2016 - School of GeoSciences Convenor
- Elected student association position at Edinburgh University Student’s Association, representing the School of GeoSciences at Student Council and various committees including the architectural board for the construction of a new GeoSciences faculty building. Skills developed in project planning, effective representation, creative problem solving, committee chairing.
- Sep 2013-Jul 2016 - Project Co-ordinator, Edinburgh University Conservation Volunteers
- Liaison with park rangers to direct weekly group excursions for between 10 and 40 students, focussed on practical conservation. Developed skills in logistics and team supervision. More practical skills in forestry, wooden construction and tool maintenance.
Awards
- Mar 2019 - Edinburgh Teaching award
- Completed a programme to improve teaching skills in higher education. Worked with a mentor over the course of an academic year to produce a series of reflective essays, drawing on pedagogical practitioner literature and personal teaching experiences. As part of the award I was inducted as an Associate Fellow of the Higher Education Academy.
- Jun 2017 - SEECC Conference - Best Long Presentation
- Best 15 minute talk from a group of 24 at the Scottish Ecology, Environment and Conservation Conference, hosted by the University of Aberdeen. The talk presented research on forest structure and climate induced range shifts in the Peruvian Andes.
- Apr 2017 - STEB Conference - Best Presentation
- Best 15 minute talk from a group of 13 at the Scottish Tropical Ecology and Biology Student Meeting, hosted by the University of Stirling. The talk presented research on tree seedling competition interactions and climate induced range shifts in the Peruvian Andes.
- 2015 - Edinburgh Award
- Professional development course at the University of Edinburgh aimed at improving graduate skills. Attended seminars and wrote reflective essays on: public speaking, academic writing and project leadership. Kept self-evaluative blog over the course of an academic year.
Quantitative, Programming and Technical Skills
- R
- Structural Equation Modelling with
lavaan
andsemPlot
. Generalised linear mixed effects models withlme4
/nlme
, model selection withMuMIn
. Manipulation of large datasets, including SEOSAW, Living Planet Index and GBIF databases. Spatial analyses of large datasets usingsf
andraster
. Authoring of R packages. Advanced data presentation withggplot2
.R Markdown
andSweave
to produce reproducible reports.Shiny
HTML5 web-apps for science communication.
- Structural Equation Modelling with
- Julia
- Ecological network analysis using the
SpatialEcology.jl
package. Rapid calculation of diversity statistics from large databases. Analysing huge point cloud (10^8 points) nearest neighbour distances and estimating point clusters with a custom algorithm adapted from C++.
- Ecological network analysis using the
- Terrestrial LiDAR
- Designed sampling protocol to assess canopy structure of savanna trees and herbaceous biomass using a Leica HDS6100 scanner. Registration of point clouds using Leica Cyclone and CloudCompare. Extensive use of PDAL for point cloud processing. Use of R and Julia to extract statistical parameters from point clouds. Basic knowledge of
treeseg
for isolation of individual trees from point clouds.
- Designed sampling protocol to assess canopy structure of savanna trees and herbaceous biomass using a Leica HDS6100 scanner. Registration of point clouds using Leica Cyclone and CloudCompare. Extensive use of PDAL for point cloud processing. Use of R and Julia to extract statistical parameters from point clouds. Basic knowledge of
- ImageJ
- Advanced knowledge of the ImageJ macro language for leaf area analysis and processing hemispherical tree canopy photographs. I designed a routine to identify fungal growths on leaves from droughted trees in the Brazilian Amazon. I wrote a manual on hemispherical tree canopy photography which covers use of ImageJ to analyse images.
- Python
- Processing spatial data with the Google Earth Engine Python API. Collection and processing of climate data using the ECMWF Python API. Knowledge of
numpy
andmatplotlib
for simple data visualisation and data wrangling.
- Processing spatial data with the Google Earth Engine Python API. Collection and processing of climate data using the ECMWF Python API. Knowledge of
- QGIS
- Experience creating maps for publication and using GDAL both within QGIS and on the command line to manipulate spatial data.
- LaTeX
- Construction of long documents with tabular and graphical elements for myself and others. Integration of citation management software, custom BibTeX stylesheets and templating with custom .sty. Creation of custom Beamer presentation templates.
- Git
- Experience managing collaborative research, websites and teaching resources. Branch management with multiple collaborators, pull requests, troubleshooting with
git diff
. I currently maintain the SEOSAW Bitbucket repository which holds resources and data for the SEOSAW project and involves a number of collaborators. In 2018 I ran two workshops at the University of Edinburgh on using Git on the command line.
- Experience managing collaborative research, websites and teaching resources. Branch management with multiple collaborators, pull requests, troubleshooting with
- Web development
- I created the Coding Club and SEOSAW websites using Jekyll, Markdown, HTML, CSS, and Javascript, hosted using Github Pages.
- Off-road driving and field vehicle maintenance
- Completed an off-road driving and 4x4 vehicle maintenance course. Training in basic 4x4 field mechanicking, oil changes, radiator repair, tyre replacement, axle alignment, identifying faults. Extensive experience driving and maintaining 4x4 vehicles in Angola, Tanzania, and the UK.
- Fieldwork First Aid, Expedition Medical Skills & Advanced First Aid Qualifications
- Four day intensive first aid training with Marlin Training Ltd, valid until June 2021. Trained in: AED/O2, airways, trauma care, spinal injury care, suturing wounds, injections, pain relief drugs, recognition of expedition illness and antibiotic therapy in remote locations.
Languages
- Portuguese: Basic-intermediate reading and writing, basic speaking.
- Spanish: Basic reading, writing and speaking.
Professional Associations
- Higher Education Academy (Associate Fellow)
- Botanical Society of Scotland (Student Member)
- Royal Society of Biology (Affiliate Member)
- British Ecological Society (Student Member)
- Royal Scottish Geographical Society
- EdinbR R User Group
curl
my contact card
:
curl -sL https://johngodlee.xyz/files/card