Quantifying the impact of woodland restoration on rodent communities and their pathogens

Global environmental change and alteration of natural habitats by human activity (e.g., urbanisation, agricultural intensification) increase exposure to animal viruses. Concurrently, accelerated human population growth and movement have enabled zoonotic viruses to spread faster and further.

Land use change is an important driver of emerging infectious diseases in human populations. 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. Climate and land use change are affecting ecosystem functioning at an unprecedented scale that has consequences for human well-being. Environmental change is an ongoing process that is dominant 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, but the implications of these efforts have not been formally tested.

This project will investigate how woodland restoration affects rodent communities and their viruses by combining fieldwork, high resolution mapping of rodent contact networks, and next generation sequencing of virus communities. Field sites will be chosen from an existing network of woodland creation sites (e.g. from the WrEN and TreE_PlaNat projects) to examine how rodent communities and infections differ between woodlands of different ages and degree of connectivity to other broadleaf forests in the landscape. The aim of this study is to improve our understanding of how reforestation and woodland creation can be leveraged to improve wildlife health and reduce risk of zoonotic disease in human populations.

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Image Captions

Small mammal traps used for monitoring rodents and their pathogens


To achieve the objectives, the PhD student will use a mixture of field, laboratory and quantitative methods to characterise rodent communities and viral infections across a gradient of woodland restoration:
1) Small rodent trapping and individual rodent tagging to quantify abundance and species of rodents across woodlands of different ages and landscape connectivity.
2) State-of-the-art minimally invasive techniques for tracking small mammal movement across months to establish social contact networks and identify key opportunities for transmission.
3) Analysis of spatial data to infer home range and contact networks.
4) Collection of faecal samples and quantification virus communities through RNA extraction, library preparation and next generation sequencing.
5) Statistical modelling to detect differences in rodent community diversity, social contact structure, and infection risk between different restored woodlands.

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 analysis (nucleic acid extraction and library preparation) of archived samples. First field season to set up trapping grids, collect baseline data and trial movement tracking at a single site. Attend conference to present preliminary results and network.

Year 2

Field data collection continues – completion of first field season and start of second field season. Initial laboratory analysis of collected samples. Write up detailed methods for publication and thesis.

Year 3

Finalize laboratory processing and analyze infection and social network data collected in the field. Continue writing up results as individual research papers and for thesis data chapters. Attend conference to present results.

Year 3.5

Writing and analysis for publication and thesis.

& Skills

The student will be trained in molecular laboratory techniques, small mammal live trapping and fine-scale tracking, and analysis of next generation sequencing and social network datasets.

References & further reading

Creating a natural experiment to assess the long-term effects of woodland creation: https://onlinelibrary.wiley.com/doi/full/10.1002/ece3.2066 ; Influence of forest restoration on rodent communities : https://esajournals.onlinelibrary.wiley.com/doi/full/10.1002/eap.2028; Measuring social contact networks in rodents: https://www.nature.com/articles/s41396-021-00949-3

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