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Packrat (Neotoma) Midden Metagenomics

Reconstructing Paleoenvironmental and Ecological Change in the US Southwest Using DNA from Ancient Packrat Middens

Team members involved: Melanie Kuch, Angela Hornsby
Collaboration with Julio Betancourt (University of Arizona), Felisa Smith (University of New Mexico), Jim Patton (University of California, Berkeley), and Marjorie Matocq (University of Nevada, Reno)

Packrats are rather adorable little desert rodents that have a penchant for collecting and storing “stuff” in their burrows.

All manner of bio-debris (i.e. seeds, leaves, feathers, bones, bugs and hair) from the surrounding environment finds its way into packrat dens, where over time it mixes with dirt and the occupant’s urine and faeces to form what we call a packrat midden.

Untold numbers of these middens are scattered across the more arid parts of the world, and they represent a treasure trove of macro and molecular data, if you have the tools to get at it. The arid conditions of in many cases the high elevation deserts have resulted in many of these middens being wonderfully preserved at the molecular level for extensive periods of time.

We use a variety of techniques to extract and sequence DNA from these subfossil concretions. This provides a molecular snapshot of the environment that once surrounded the burrow. Combining sequence data with C14 dates, we can build a very detailed image of ancient and more recent packrat environments, and assess changes therein through time. This represents a novel method for examining climate change and select organisms’ distributions in the geologically recent past.

The area of interest in this project is the US Southwest (i.e. Arizona, New Mexico, and Nevada), where hundreds of packrat middens have been collected and dated in recent years.