UC Davis

The salt marsh harvest mouse (Reithrodontomys raviventris) is an endangered species endemic to coastal wetland habitat in the San Francisco Estuary (SFE). It is >3.5 million years diverged from its extant sister species and is the only mammalian species completely restricted to salt marsh habitat. Over the past 150 years, the SFE has lost over 90% of its historical tidal marsh habitat. Habitat loss and fragmentation has been more pronounced in the central and southern parts of salt marsh harvest mouse range, where the southern subspecies (R. r. raviventris) occurs, whereas habitat in the range of the northern subspecies (R. r halicoetes) appears to be more stable. The evolutionary history of the salt marsh harvest mouse is poorly understood, as is its contemporary distribution in the highly fragmented central and southern SFE. In the north, large populations persist on brackish, diked wetlands, where the effects of non-native and upland vegetation are potentially concerns for salt marsh harvest mice. To this end, I applied genomic techniques to aid our understanding of salt marsh harvest mouse historical and modern distribution, evolutionary and demographic history, and use of dietary resources with respect to upland competitors. I found that modern salt marsh harvest mouse distribution was significantly reduced in the central portions of the bay, where some historically occupied regions appear to be extirpated. Salt marsh harvest mouse occupancy conformed to the area-isolation paradigm of metapopulation theory, such that the probability that a marsh was occupied was positively related to its size and connectivity to nearby marsh habitat. The evolutionary history of the salt marsh harvest mouse has been closely associated with sea level. Population size increased and lineages diverged as sea level rose following the Last Glacial Maximum. Several lineages diverged as the modern SFE formed, and again as rising sea levels caused vicariance of previously continuous patches of marsh habitat. Finally, the dietary resource use by salt marsh harvest mice was driven largely by affinities for pickleweed (Salicornia) and fat-hen (Atriplex). Their diet varied seasonally in association with the phenology of their preferred plants, and their dietary niche breadth was narrower than that of three upland-associated competitors, highlighting their specialization on marsh habitat. Overall, the results of my research provided a molecular basis for subspecies delineation, highlighted the significant impact of habitat loss on this endangered species, and identified important dietary resources for salt marsh harvest mice.