Conservation genetics of the endangered San Francisco Bay endemic salt marsh harvest mouse (Reithrodontomys raviventris)

M. J. Statham, S. Aamoth, L. Barthman-Thompson, S. Estrella, S. Fresquez, L. D. Hernandez, R. Tertes, Benjamin Sacks

Research output: Contribution to journalArticlepeer-review

8 Scopus citations


The salt marsh harvest mouse (SMHM, Reithrodontomys raviventris) is an endangered species endemic to the San Francisco Bay region of California, USA, where habitat loss and fragmentation over the past century have reduced the mouse’s distribution to <25 % of its historical range. To aid in conservation prioritization, we first investigated the possibility of hybridization with the morphologically similar western harvest mouse (WHM, R. megalotis) in areas of sympatry and developed genetic tools to differentiate the two species. We then investigated the phylogeography and genetic structure of the SMHM, including support for currently recognized SMHM subspecies designations. Lastly, we evaluated the morphological criteria currently used for the identification of species in the field. Analyses using mtDNA cytochrome b sequences and 11 microsatellites from 142 mice indicated complete and substantial separation of the SMHM and WHM, with no evidence of hybridization. These genetic markers as well as the mtDNA control region also identified a deep genetic division within the SMHM concordant with the current subspecies designations, R. r. raviventris and R. r. halicoetes. We identified the lowest genetic diversity within the southern subspecies, which inhabits a much reduced and highly fragmented portion of the species range. Morphological field identification of harvest mouse species was more successful at identifying SMHM (92 %) than WHM (44 %), with a large portion of WHM being incorrectly identified as SMHM. Field identification of harvest mouse species in the range of the southern SMHM subspecies was just above 50 %, indicating that current methods for morphological differentiation of species in that area are insufficient. Our confirmation of genetically distinct SMHM subspecies highlights the importance of determining the status and genetic composition of relict populations in the remaining patches of marshland in the central San Francisco Bay where the two subspecies may occur, as well as developing better tools for the discrimination of species, particularly in the range of the southern subspecies

Original languageEnglish (US)
Pages (from-to)1055-1066
Number of pages12
JournalConservation Genetics
Issue number5
StatePublished - Oct 1 2016


  • Field identification
  • Management
  • Morphology
  • Population subdivision
  • Species identification
  • Subspecies

ASJC Scopus subject areas

  • Ecology, Evolution, Behavior and Systematics
  • Genetics


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