New soil DNA monitoring technique provides data for better urban wildlife planning

With more than half the world now living in cities and urban land cover expected to increase by about 1.2 million square kilometers by 2030, built environments are altering ecosystems through habitat fragmentations, heat islands, and road networks. Disrupted habitats caused by urbanization can lead to invasive species, disease outbreaks, and increased human-wildlife conflict.

Using eDNA, which captures genetic material shed by organisms into their surroundings, Yale School of the Environment scientists tracked how human disturbance is impacting mammal communities. The new research published in the Journal of Animal Ecology advances novel eDNA monitoring techniques that will help scientists and city officials better manage urban biodiversity and human-wildlife interactions.

While other studies have relied on camera traps, acoustic sensors, and community science to track urban wildlife, YSE scientists  collected eDNA from soil samples across 21 urban parks in Detroit during winter and summer months. They found that urban parks show subtle, park-specific changes in community composition influenced by both ecological and anthropogenic factors and that larger parks supported more species biodiversity.

The research led by Nyeema Harris, the Knobloch Family Associate Professor of Wildlife and Land, found that eDNA can provide a dynamic understanding of seasonal shifts and human presence in urban green spaces, which can inform more responsive urban planning and management. Harris and postdoctoral associate Jane Hallam, who co-authored the study, collected soil samples from the urban parks in Detroit, Michigan, during February and July 2023 and identified 23 mammal species, including humans. They corroborated the findings with wildlife sightings submitted to the iNaturalist app.

“My Applied Wildlife Ecology (AWE) lab has been monitoring wildlife in urban parks for almost a decade using remotely triggered cameras,” Harris said. “Thanks to Dr. Hallam's molecular expertise, we've added eDNA to our toolkit, allowing for a more robust sampling technique for small mammals, which are not as easily detected with cameras.”

The DNA samples revealed seasonal shifts in mammal presence. DNA traces of hibernating animals, such as groundhogs and muskrats, were absent from winter soils. The authors noticed that animals were clustered together during winter, likely due to competition for limited resources.

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In the summer, often a time of resource abundance, eDNA patterns showed species were more dispersed across landscapes, with fewer opportunities for cross-species interaction, Hallam said.

Park size, as expected, influenced the kinds of mammals detected, the authors noted. For example, coyotes were only found at parks larger than 14.4 hectares, reflecting their need for larger home ranges.

Human DNA comprised around one-third of all DNA samples at all parks, demonstrating the constant human presence in these shared spaces. Harris said that the presence of DNA from domesticated animals, including cats, dogs, pigs, and cattle, marked urban parks as undeniably shared socio-ecological ecosystems. The presence of people also shaped biodiversity by altering mammal community composition. More generalist and human-tolerant species were found in areas of high human activity, with more sensitive species less frequently detected.

The researchers advocated for expanding green spaces and creating wildlife corridors – networks of connected parks – to better support biodiversity, particularly for animals with larger home ranges. As cities grow, these strategies may be vital for sustaining healthy, resilient ecosystems that benefit people and nature, they said. 

This research was supported by National Science Foundation grant 2140322.