PhD: Utilising digital technologies to map river thermal habitat availability for key indicator freshwater species: a decision-support conservation tool for best-practice riparian woodland management

University of Glasgow

Glasgow, UK 🇬🇧

This PhD will explore the use of digital technologies (drone-based unmanned aerial vehicles (UAVs) for thermal and habitat imagery, remotely sensed satellite data, GIS) as conservation tools for investigating best-practice riparian woodland management for moderating river temperatures and improving thermal habitat availability for keystone species such as the Freshwater Pearl Mussel (FPM) and their host salmonids, and identification of high-risk populations. The project will work with Forestry and Land Scotland (FLS), NatureScot, SEPA and local fishery trusts.

Climate change and biodiversity loss are the most significant global challenges we face today. Freshwater biodiversity provides essential ecosystem services fundamental for human well-being. However, global freshwater biodiversity has declined by >80% since the 1970s. Impacts of climate change, through increased water temperature and frequency of extreme flow events (floods/droughts), are key drivers of decline.

River water temperature is a key aspect of rivers’ ecological functioning. Water temperature influences physicochemical processes and biological activity (Caisse, 2006), with rivers exhibiting patches of warm and cool water habitat, highly variable through space and time (Dugdale et al, 2019). This heterogeneity exerts considerable influence on distribution, behaviour, and abundance of aquatic species. However, river temperature regimes are changing due to climate change and there remains uncertainty over how biological communities will respond.

It is suggested temperatures in Scottish rivers could increase by an average 2.2°C by 2050, and the high degree of exposure of large tracts of Scottish rivers (forest cover in Scotland is only 17.1% means that such a warming could have serious impacts on Scotland’s fluvial ecosystems, including ecologically and economically important salmonid fish species such as Atlantic salmon (Salmo salar) and brown trout (Salmo trutta)(Jackson et al, 2021). In 2018, ~ 70% of Scottish rivers experienced temperatures exceeding the threshold for thermal stress in juvenile Atlantic salmon (23oC). Research is therefore needed to help understand and mitigate river temperature extremes and this PhD seeks to do this.

Riparian treescape expansion is a potential solution to delivering multiple local benefits, not just environmental benefits such as providing shade and reducing river temperature, stabilising riverbanks, reducing erosion, increasing riparian biodiversity, Natural Flood Management, reducing greenhouse gas emissions, reducing pollution, and enhancing water quality, but societal benefits such as providing an attractive environment which inspires, encourages recreation, well-being and boosts physical and mental health. Riparian restoration is a key element in this PhD’s CASE partner Forestry and Land Scotland’s (FLS) land management planning. Over the next 50 years FLS plans to restore 10,000 hectares of plantation forestry to riparian woodlands.

We need, however, to improve the evidence-base, to provide practitioners with a decision support framework to help inform best-practice riparian treescape expansion. Little is known about the relative ability of different riparian forest types to moderate stream temperatures. Further research is therefore necessary. A clear need has been highlighted for more information into combinations of tree species, size and buffer spacing that are most effective in generating shade to moderate water temperature (Orr et al, 2015). This PhD will extend the knowledge base informing treescape expansion, by assessing evidence-based impacts of different riparian woodland/forest forms and types on river water temperature heterogeneity using digital technologies, remote sensing and in-stream measurements, and assess how that heterogeneity impacts key indicator species. By targeting key indicator species, riparian woodland management decisions that benefit those species, will have additional benefits, or environmental net gains, to other species due to the ecosystem services they provide. This project will focus on the critically endangered freshwater pearl mussels and their host salmonids as key indicator species (Atlantic salmon and brown trout are functional hosts for a parasitic phase of the mussel life cycle)(Skinner et al 2003).

Aims of the PhD are therefore to:
1. Assess thermal habitat availability for keystone species FPM and host salmonids at key sites with different riparian woodland management using a combination of drone-based UAVs, remotely sensed satellite data and in-stream measurements.
2. Develop a decision-support framework that determines best-practice riparian woodland management strategies for moderating river temperatures and improving thermal habitat availability for FPM and host salmonids, directly addressing UK/International Biodiversity policy and Scottish Government’s Forest Strategy..
3. Identify at-risk FPM and host salmonid populations across Scotland, categorized as high, medium, and low risk, based on remotely-sensed satellite data of riparian land use, environmental secondary data (river flow and temperature, FPM and host salmonid population status) thus prioritizing remedial actions.

This will be achieved by working with the CASE partner FLS and end users of this research, including NatureScot, SEPA, Marine Scotland and relevant fishery trusts.


1. With CASE partner FLS, who have approved access to the entire national forest estate, and NatureScot, who hold data on FPM population location, functionality and specific host salmonids, identify 10 field sites of existing but different riparian woodlands/forests/plantations for river reaches with similar morphology, with FPM populations. This will be achieved using a combination of satellite-based geospatial remotely sensed data and GIS, and FLS’ extensive working knowledge of the national forest estate. Working with FLS, in the field identify characteristics of riparian woodland at each site, e.g. tree species, degree of species mixing, stand height, size, spacing, distance from riverbanks, and ground-truth satellite data on land cover type. Using novel drone-based UAVs, conduct thermal imagery (TIR) mapping in conjunction with red-green-blue-band (RGB) imagery mapping of river reach (UoG equipment) to identify and characterize river temperature heterogeneity at each field site, thus classifying key riverscape habitats and associated thermal properties. Conduct in-stream measurements of river temperature to ground-truth UAV data. Using NatureScot’s FPM survey data, confirm previously mapped locations/distributions of FPM using Leica GPS total station. Collate river flow data (SEPA) to characterize annual flow variability, host salmonid data on functionality and density (local Fishery Trusts) and any existing stream temperature data (Marine Scotland SRTMN database) for each site. Conduct satellite-based remote sensing, UAV mapping and instream measurements twice a year (summer/winter) to account for seasonal changes.

Intended datasets: for each site, a GIS-based site-catalogued layered dataset comprising a supervised classification of fluvial mesohabitats based on spectral properties (RGB), a thermal heterogeneity assessment linked to thermal properties (TIR) of classified habitats, satellite-based remotely sensed geospatial data, in-stream temperature measurements, mapped distribution of FPM populations and identified characteristics of associated riparian woodlands. Outputs will establish spatial thermal/habitat availability linked to riparian woodland type, using established optimal habitat requirements for key indicator species FPM and host salmonids (either Atlantic salmon or brown trout), thus determining best-practice riparian woodland management strategies for moderating river temperatures and improving thermal habitat availability.

2.Identification and prioritisation of at-risk FPM and host salmonid populations will be achieved by collating environmental data from rivers across Scotland with FPM populations (~115 rivers) to determine those most at risk of declines in current and future optimal thermal habitat availability. Using GIS and geospatial remotely sensed satellite data on riparian land/tree cover presence/absence and type (working with FLS), in combination with river flow regime and temperature data (SEPA, Marine Scotland), functionality of FPM populations (NatureScot) and functionality and density of host salmonid population (local Fishery Trusts), FPM populations will be categorized as high, medium and low risk.

Intended dataset: an evidence-based national prioritization of FPM rivers into high, medium and low risk to aid in guiding best-practice targeted riparian woodland planting strategies to improve thermal habitat for keystone species FPM, Atlantic salmon and brown trout.

Project Timeline

Year 1

Conduct literature reviews of i) thermal regimes of rivers; ii) habitat requirements of FPM, Atlantic salmon, brown trout; iii) use of drone-based UAVs to map habitat/thermal properties, and iv) influence of riparian tree cover on habitat/river temperatures.
Attend training courses.
Spend up to 4 weeks with Case Partner FLS, with advice from NatureScot, identifying possible field sites.
Desk-based collation of satellite data of land cover, FPM and host salmonid population status, and environmental data (river flow variability, any existing stream temperature) for chosen field sites.

Year 2

Fieldwork, minimum 10 weeks, hosted by FLS, to visit half of field sites, ground-truth satellite land cover data, collect drone-based UAV imagery and in-stream temperature measurements in both summer and winter field campaign, confirm FPM locations from previous NatureScot surveys.
Process and analyse images to produce site-based thermal habitat availability for FPM and host salmonids.
Attend UK conference to present research topic and preliminary results via a poster presentation at the end of Yr2.
Organise and attend research update/progress workshops/meetings at i) CASE partner FLS venue, ii) NatureScot venue, and iii) SEPA venue.
Write up desk-based and fieldwork methodology as draft thesis chapter.

Year 3

Repeat summer/winter field campaigns for remaining half of chosen field sites as per Yr2.
Processing and analysis of all data to produce GIS-based site-catalogued layered dataset and linked decision-support management tool for best-practice riparian planting strategies to increase thermal resilience of rivers containing FPM and host salmonids.
Identification of high, medium and low risk FPM and salmonid populations.
Write up draft data analysis methods as part of methodology chapter.
Attend International conference and give oral presentation to present research findings to date.
Organise and attend research update/progress workshops/meetings at i) CASE partner FLS venue, ii) NatureScot venue, and iii) SEPA venue.
Start write up of results chapters.

Year 3.5

Continuation of, and completion of thesis write-up.
Co-write paper with candidate as first author to submit to peer-reviewed journal.

Training & Skills

Project-specific Internal University of Glasgow Training:
The candidate will undertake training in field operation of drone-based UAVs, Leica GPS and field measurements, attend training courses including Principles of GIS, Remote Sensing of the Environment, which will include image processing and analyses, and Introduction to Statistics for Environmental Analysis.
Training in academic writing, research ethics and communication/presentation skills via attending Academic & Professional Skills course.
First Aid and field safety training.

The candidate will be part of a supportive learning environment with access to the Earth Systems Research Group, including completion of a researcher development log as part of an Annual Progress Review and established Graduate School training programme.

The candidate will have access to all IAPETUS2 training programmes and events.

External Training:
UKCEH training course: Using drones to map habitat.

Time spent with external organisations (FLS, NatureScot, SEPA, Marine Scotland, Fishery Trusts) will enable networking opportunities that will benefit the candidate’s career development and provide an interdisciplinary research and training experience. The supervisory team has a mix of gender and career stages.

References & further reading

Caissie, D. (2006). The thermal regime of rivers: a review. Freshwater Biology 51, 1389–1406.
Dugdale, S.J., Kelleher, C.A., Malcolm, I.A., Caldwell, S. & Hannah, D.M. (2019). Assessing the potential of drone‐based thermal infrared imagery for quantifying river temperature heterogeneity. Hydrological Processes, 33:1152–1163.
Jackson, F.L., Hannah, D.M, Oullet, V. & Malcolm, I.A. (2021). A deterministic river temperature model to prioritize management of riparian woodlands to reduce summer maximum river temperatures. Hydrological Processes. 2021;35.
Orr, H.G., Johnson, M.F., Wilby, R.L., Hatton-Ellis, T., Broadmeadow, S. (2015). What else do managers need to know about warming rivers? A United Kingdom perspective. WIRES 2, 55–64.
Skinner, A., Young, M., and Hastie, L. (2003). Ecology of the freshwater pearl mussel, Conserv. Nat., 2000, Rivers Ecol. Ser., 2003, no. 2.

Supervisory Team

  • Dr Rhian Thomas (University of Glasgow)
  • Prof. Nigel Willby (University of Stirling)
  • Dr Edward Curley (University of Glasgow)

Case partners

Dr Kenny Kortland (Forestry and Land Scotland)

Lead Institution

University of Glasgow (School of Geographical and Earth Sciences)

Further Information

for informal enquiries, contact:

Dr Rhian Thomas

University of Glasgow

Key Words

  • Climate change
  • river thermal habitats
  • biodiversity
  • digital technologies





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