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Salt marsh mice can now be identified using a “decision tree”

The first thing conservation biologists need if they are to protect an endangered species is the ability to identify it accurately. Until recently, this has been a problem with the endemic salt marsh harvest mouse (Reithrodontomys raviventris) which is found only in the tidal marshes of the San Francisco Estuary.

“If people misidentify the species, they have a false impression that they’re doing well,” said Mark Statham, lead author and researcher with the Mammalian Ecology and Conservation Unit within the UC Davis School of Veterinary Medicine.

These small rodents have lost three-quarters of their habitat to human expansion as the marshes have been drained for housing developments. Along with rising sea levels, this has left salt marsh harvest mice with few options. They have been listed as endangered under both the California and U.S. Endangered Species Acts.

Two subspecies of salt marsh harvest mice occur in the San Francisco Bay area, with the southern subspecies being the more endangered. Conservation work has, thus far, proven difficult because the mice look very similar to the western harvest mouse, a non-endangered species that lives in the same area. 

But now, scientists from UC Davis have used DNA analysis, along with body measurements and other physical characteristics to develop an identification tool that can be used in the field. They collected data from 204 harvest mice trapped in the southern species’ population range. Overall, 48 were endangered salt marsh harvest mice and the rest were western harvest mice.   

The team then used a statistical analysis to identify the most useful characteristics to distinguish between the two species. These turned out to be the color of the belly hair and the hair underneath the tail. Results of the DNA analysis were used to verify each individual’s species. 

A “decision tree,” or dichotomous key, was then drawn up to assist biologists with identification in the field. When tested against a sample of harvest mice of known species, the key was able to identify 94 percent of 179 harvest mice to species level with 99 percent accuracy.

Accurate identification will allow conservationists to understand the range, habitat, abundance, demography, and population trends of the endangered species, and this information will inform conservation efforts. 

“Now field researchers can go in the field and identify the animal immediately,” said Statham. “Without something like this, you don’t really know what you’ve got.”

Details of the study were published this month in a special issue of the journal California Fish and Wildlife.

By Alison Bosman, Staff Writer

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