Endangered Mouse Study Shares No-Contact Sampling Method


From marmots to moles, shrews and mice, many of the world’s endangered mammals are small. Genetic sampling is important to understand how to conserve and protect their populations. However, finding efficient, non-invasive ways to collect genetic samples from small animals can be challenging.

A study from the University of California, Davis describes a new, non-invasive genetic screening technique for the endangered salt marsh pygmy mouse, which lives exclusively in the tidal marshes of the San Francisco Bay estuary.

Scientists often collect fecal samples from larger mammals, but the feces of small animals can be so small that they are difficult to see in the wild.

The new technique, published in the Journal of Mammalogy, uses a combination of bait stations and genetics to sample and identify salt marsh harvest mice, or “salties” as researchers affectionately call them. The species has lost more than 90% of its habitat to evolution and is also threatened by rising sea levels. Because of this, it is imperative that the remaining populations are identified accurately and efficiently, the authors note.

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Cody Aylward checks a bait station during field work to study the endangered salt marsh pygmy mouse, found only in the mouth of the San Francisco Bay. (Mark Statham/UC Davis)

dine and dash

The technique is simple: scientists bait boxes with a snack made from seeds, millet and oats and lay out cotton litter. Mice can come and go. A researcher returns a week later to collect the fecal pellets for genetic samples in the lab. There, a unique species identification test distinguishes samples of salt marsh harvest mice from those of other rodents that may have used the bait box.

Contrast this process with the more common and intensive method of live trapping: a team of three to five researchers check traps at sunrise and sunset for several consecutive days. To prevent animals from drowning, these traps must be placed above the tide line, excluding several areas of the tidal marsh habitat. But with the new, non-invasive technique, mice can leave at any time, allowing researchers to safely and efficiently monitor more swamps and more mice.

I Hopefully someone somewhere studying an endangered small animal will read this study and say, ‘This is something I can do.’ – Cody Aylward

“Our genetic identification method is simple, inexpensive, and adaptable to other small mammalian systems,” said lead author Cody Aylward, a recent graduate and former PhD student in the Mammalian Ecology and Conservation Unit at UC Davis School of Veterinary Medicine. “I I hope someone somewhere studying an endangered small animal reads this study and says, ‘This is something I can do.’”

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A bait station is located on the flooded tidal marsh of Corte Madera. The bait station attracts but doesn’t capture endangered salt marsh harvest mice, allowing scientists to collect feces for genetic samples without harming the mice or other visiting animals as the tides rise and fall. (Cody Aylward/UC Davis)

Little wonder

Little is known about salt marsh harvest mice, so the implications of their possible loss are also unclear. Scientists know that the species is unusual in several respects. For example, salties are strong swimmers, can drink seawater, and have a unique genetic lineage, as Aylward explains:

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Genetic data say they are 3.5 million years apart from their closest relative,” he said. “So if we lose them, 3.5 million years of evolutionary history are lost.”

The critically endangered salt marsh harvest mouse is endemic to the San Francisco Bay Area and is easily confused with the harvest mouse, which is widespread in the West. (William Thein)

Co-authors include principal investigator Mark Statham, Robert Grahn and Benjamin Sacks of UC Davis School of Veterinary Medicine; Douglas Kelt of the UC Davis Department of Wildlife, Fish and Conservation Biology; and Laureen Barthman-Thompson of the California Department of Fish and Wildlife.

The research was funded by the California Department of Water Resources and the USDA National Institute of Food and Agriculture.



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