Dietary characterization of the endangered salt marsh harvest mouse and sympatric rodents using DNA metabarcoding

The salt marsh harvest mouse (Reithrodontomys raviventris; RERA) is an
endangered species endemic to the coastal wetlands of the San Francisco
Estuary, California. RERA are specialized to saline coastal wetlands, and
their historical range has been severely impacted by landscape conversion
and the introduction of non-native plant and rodent species. A better
understanding of their diet is needed to assess habitat quality,
particularly in relation to potential competitors. We investigated three
questions using DNA metabarcoding with ITS2 and trnL markers: (1) Do RERA
specialize on the native plant, pickleweed (Salicornia pacifica), (2) Do
RERA consume non-native plants, and (3) What is the dietary niche breadth
and overlap with three sympatric native and non-native rodents? RERA diet
was dominated by two plants, native Salicornia and non-native salt bush
(Atriplex spp.), but included 48 plant genera. RERA diet breadth was
narrowest in fall, when they consumed the highest frequencies of
Salicornia and Atriplex, and broadest in spring when the frequencies of
these two plants were lowest. Diet breadth was slightly lower for RERA
than for co-occurring species in pairwise comparisons. All four species
consumed similarly high frequencies of wetland plants, but RERA consumed
fewer grasses and upland plants, suggesting that it may be less suited to
fragmented habitats than sympatric rodents. Diet overlap was lowest
between RERA and the native California vole (Microtis californicus). In
contrast, RERA diet overlapped substantially with the native western
harvest mouse (R. megalotis) and non-native house mouse (Mus musculus),
suggesting potential for competition if these species become sufficiently
abundant.