Impacts of reforestation on rodent community composition, contact networks, and zoonotic pathogens


Land use change is a key driver of emerging infectious diseases. Conversion of native habitat leads to biodiversity loss, higher abundance of some zoonotic host species, and increased human-wildlife contacts, with cascading health consequences for individual humans and communities. Environmental change is a pervasive feature of landscapes globally and will disproportionately affect marginalized communities that already experience a high burden of zoonoses. Reforestation and planting of native forests has been proposed to mitigate zoonotic risk in changing landscapes, but the implications of these interventions have not been formally tested.

In Uganda, forest loss (9% since 2000) and annual human population growth (~3.5% pa) is representative of many other developing countries. Zoonoses account for >50% of severe febrile illnesses in the region. Globally, rodents are an important group of zoonotic hosts and they thrive in anthropogenic landscapes. Pilot studies in the region show high rodent host diversity and low abundance of nematode pathogens in forested ecosystems. Across the region, native woodlands are being converted to small-holder agricultural fields that also support a lower diversity of rodents but have higher burdens of zoonotic nematode pathogens. In 2012, there were several communities that planted native trees to improve soil condition and increase local biodiversity. These replanted forests have already been shown to provide important ecosystem services, but it is unknown how they impact rodent diversity and zoonotic pathogen risk in neighboring human communities.

This project will investigate how reforestation affects rodent communities and their associated nematode parasite communities by using an innovative field methodology to understand differences in contact networks and implications for pathogen transmission. Field sites will be chosen to examine how rodent communities and infections differ between three discrete land cover classes: 1) reforested plots, 2) intact native forests, and 3) converted small-holder agricultural sites. The aim of this study is to improve our understanding of how reforestation and woodland creation can be leveraged to reduce zoonotic disease risk and improve ecosystem health.


To achieve the objectives, the PhD student will use a mixture of field, laboratory and quantitative analyses to characterise rodent communities and nematode burden in different land use regimes. In this project we will undertake:
1) Small rodent trapping combined with capture-mark recapture methods to identify rodent community structure and population dynamics across a gradient of land use in eastern Uganda.
2) Fecal sample collection and laboratory analysis for detection of nematode infection status and burden.
3) RFID-tagging individual rodents and setting up a grid-logger system to track fine-scale rodent movements and quantify contact frequency and social network structures.
4) Analysis of spatial tracking data to infer home range and social networks in each land use site.
5) Statistical modelling to detect differences in rodent community diversity, social contact structure, and infection risk between different land-use types.
6) Mechanistic modelling of transmission dynamics within each rodent community/ land use type.

Project Timeline

Year 1

Overview and training in techniques used in PhD – including deploying field tracking hardware, analysis of simulated data in R, and laboratory molecular analysis (PCR and Sanger sequencing) of archived samples. Development of modelling frameworks to be used in analysis of data.

Year 2

Field data collection in Uganda – setting up sites and tracking rodents in intact native forests,newly replanted forests, and converted small-holder agricultural sites. The PhD student will benefit from an ongoing NERC- funded research project in the region starting in January 2022 and led by co-Supervisor Faust investigating spatiotemporal mechanisms driving nematode infection dynamics in small-holder agricultural fields. After collection of field data, student will run initial laboratory analysis of collected samples.

Year 3

Finalize laboratory processing and interpret results. Analyze infection and social network data collected in the field. Fit epidemiological and movement models developed in Year 1 to collected field data. Drafting of individual research papers.

Year 3.5

Writing and interpretation of results for journal publications and thesis.

& Skills

The student will develop skill sets across multiple disciplines, including basic molecular laboratory techniques, small mammal live trapping and fine-scale movement tracking, and analysis of molecular datasets. All field work will be conducted in collaboration with Makerere University in Uganda. The project will also deliver training in modelling epidemiological dynamics using a mixture of macro-parasite epidemiological models, state-space transmission modes, and hidden Markov movement models. The skills and training received throughout the course of this PhD can be applied to answer a variety of questions in population and community ecology, conservation biology, and environmental change.

References & further reading

Overview of field location: ; Influence of forest restoration on rodent communities (data from UK):; Measuring social contact networks in rodents:

Further Information

Professor Dan Haydon
Mob: 0779 534 1626
University of Glasgow

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