Salt Marsh Harvest Mouse

Investigator: Mark Statham

Co-Investigator: Ben Sacks

Ph.D. Researcher: Cody Aylward

Collaborators: Laureen Barthman-Thompson (CDFW), Sarah Estrella (CDFW), Rachel Tertes (USFWS), Meg Marriott (USFWS), Katie Smith (UCD, CDFW, WRA), Isa Woo (USGS), Doug Kelt (UCD), and others.

Funding: CDFW, USFWS, DWR.

The salt marsh harvest mouse (SMHM, Reithrodontomys raviventris) is a state and federally listed endangered species that is only found in salt and brackish marshes of the Greater San Francisco Bay. The decline of the species is mainly attributed to human induced fragmentation and loss of habitat, which is anticipated to increase with the advent of rising sea levels due to climate change. Throughout much of its range the SMHM is sympatric with morphologically similar western harvest mouse (WHM, R. megalotis), which makes accurate field identification difficult, especially in the range of the southern subspecies.

We are working on a variety of different questions broadly related to improving the conservation of the species. Previous research has involved the development genetic tools (through the use of next generation sequencing and other means) for molecular species identification as well as the investigation of population substructure within the species. Currently we are conducting a landscape genetic study of the SMHM in the Suisun Bay to investigate how populations are structured and how this relates to vegetation cover and topographic features. We are also conducting a combined morphological and genetic study with the aim of producing an improved field method for differentiating between harvest mouse species. Additionally we have a number of other on-going SMHM related projects.


Aylward CM, Grahn R, Barthman-Thompson L, Kelt D, Sacks BN, Statham MJ. A Novel Non-Invasive Genetic Survey Technique for Small Mammals.  Statham M. Journal of Mammalogy. June 2022.

Aylward CM, Statham MJ, Barthman-Thompson L, Kelt D, Sacks BN. Dietary characterization of the Endangered Salt Marsh Harvest Mouse and Sympatric Rodents using DNA Metabarcoding. Ecology and Evolution. July 2022.

Statham MJ, Aylward CM, Barthman-Thompson L, Kierepka EM, Sacks BN. Landscape genetics of an endangered salt marsh endemic: identifying population continuity and barriers to dispersal. Conservation Genetics.

Statham MJ, Barthman-Thompson L, Fresquez S, Sacks BN. Development of a morphological key for the southern salt marsh harvest mouse using genetically verified individuals. California Fish and Wildlife, CESA Special Issue. 367-381.

Harvest mouse ventral coloration photographs. Supporting information for the California Fish and Wildlife Journal.

Final report: Statham MJ, Fresquez S, Sacks BN. (2019) Genetic and Morphological Investigation of Harvest Mice (genus Reithrodontomys) in the Southern San Francisco Bay. Report to the U.S. Fish and Wildlife Service.

Final report: Statham MJ, Sacks BN. (2019) Salt Marsh Harvest Mouse Landscape Genetics and Connectivity within the Suisun Bay Area Recovery Unit. Report to the California Dept. of Water Resources.

Smith KR, Riley MK, Barthman-Thompson L, Woo I, Statham MJ, Estrella S, Kelt DA. (2018) Toward Salt Marsh Harvest Mouse Recovery: A Review. San Francisco Estuary and Watershed Science. 16: 1-24?.

Smith KR, Riley MK, Barthman-Thompson L, Statham MJ, Estrella S, Kelt DA. (2018) Toward Salt Marsh Harvest Mouse Recovery: Research Priorities. San Francisco Estuary and Watershed Science. 16: 1-6?.

Statham MJ, Aamoth S, Barthman-Thompson L, Estrella S, Fresquez S, Hernandez LD, Tertes R, Sacks BN. Conservation genetics of the endangered San Francisco Bay endemic salt marsh harvest mouse (Reithrodontomys raviventris). Conservation Genetics, 17: 1055-1066.

Final report: Statham MJ, Sacks BN (2014) Cooperative ecosystem study of the endangered salt marsh harvest mouse (Reithrodontomys raviventris) population genetics. Report to the California Department of Fish and Wildlife, August 4th, 2014.

Reponen SEM, Statham MJ*, Barthman-Thompson L, Sacks BN (2014) Microsatellite primer development for the salt marsh harvest mouse (Reithrodontomys raviventris) and cross-amplification in the western harvest mouse (R. megalotis). Conservation Genetics Resources, 6: 285-287.