Microsatellite primer development for the salt marsh harvest mouse (Reithrodontomys raviventris) and cross-amplification in the western harvest mouse (R. megalotis)

The salt marsh harvest mouse (SMHM, Reithrodontomys raviventris) only exists in a patchwork of salt marshes scattered throughout the San Francisco, San Pablo, and Suisun Bays of California. The species has declined significantly from its historical distribution due to habitat loss and fragmentation and is categorized as an endangered species under the US Endangered Species Act and by the IUCN. We identified ten microsatellite loci that amplify in the SMHM and the western harvest mouse [western harvest mouse (WHM); R. megalotis], a sympatric congener. Screening in 30 SMHM identified eight polymorphic loci, with an average of 4.6 alleles per locus, an observed heterozygosity of 0.45, and an expected heterozygosity of 0.55. Four of these loci and an additional one amplified in the WHM, of which two were polymorphic and three enabled species differentiation. We amplified all markers in two multiplexes, which will provide important tools for the conservation and monitoring of this flagship endangered species.