Habitat of the endangered salt marsh harvest mouse (Reithrodontomys raviventris) in San Francisco Bay

Bruce G. Marcot, Isa Woo, Karen M. Thorne, Chase M. Freeman, Glenn R. Guntenspergen

Research output: Contribution to journalArticlepeer-review

Abstract

Understanding habitat associations is vital for conservation of at-risk marsh-endemic wildlife species, particularly those under threat from sea level rise. We modeled environmental and habitat associations of the marsh-endemic, Federally endangered salt marsh harvest mouse (Reithrodontomys raviventris, RERA) and co-occurrence with eight associated small mammal species from annual trap data, 1998–2014, in six estuarine marshes in North San Francisco Bay, California. Covariates included microhabitat metrics of elevation and vegetation species and cover; and landscape metrics of latitude–longitude, distance to anthropogenic features, and habitat patch size. The dominant cover was pickleweed (Salicornia pacifica) with 86% mean cover and 37 cm mean height, and bare ground with about 10% mean cover. We tested 38 variants of Bayesian network (BN) models to determine covariates that best account for presence of RERA and of all nine small mammal species. Best models had lowest complexity and highest classification accuracy. Among RERA presence models, three best BN models used covariates of latitude–longitude, distance to paved roads, and habitat patch size, with 0% error of false presence, 20% error of false nonpresence, and 20% overall error. The all-species presence models suggested that within the pickleweed marsh environment, RERA are mostly habitat generalists. Accounting for presence of other species did not improve prediction of RERA. Habitat attributes compared between RERA and the next most frequently captured species, California vole (Microtus californicus), suggested substantial habitat overlap, with RERA habitat being somewhat higher in marsh elevation, greater in percent cover of the dominant plant species, closer to urban areas, further from agricultural areas, and, perhaps most significant, larger in continuous size of marsh patch. Findings will inform conservation management of the marsh environment for RERA by identifying best microhabitat elements, landscape attributes, and adverse interspecific interactions.

Original languageEnglish (US)
Pages (from-to)662-677
Number of pages16
JournalEcology and Evolution
Volume10
Issue number2
DOIs
StatePublished - Jan 1 2020
Externally publishedYes

Bibliographical note

Funding Information:
We thank John Y. Takekawa and Susan De La Cruz as programmatic leads for USGS San Francisco Bay Estuary Field Station (SFBEFS) wetland restoration studies, and James Cronin for a review of the manuscript. All salt marsh harvest mouse trapping and handling for USGS SFBEFS was led by I. Woo and conducted under California Department of Fish and Wildlife Memorandum of Understanding (PI: J. Takekawa and S. Wainwright-De La Cruz), and California Scientific Colleting Permit (Woo: 005749), and Federal permits (PI: J. Takekawa and S. Wainwright-De La Cruz; TE020548). Data from Tolay Creek and Tubbs Island Setback was a collaborative effort including: Michael Bias and USFWS San Pablo Bay National Wildlife Refuge (SPB NWR; Giselle Block and Meg Marriott). We thank SPB NWR for site permission to conduct small mammal surveys at Tolay Creek and Tubbs Island Setback. We thank CA Department of Fish and Wildlife for site permission for Fagan Slough and Corte Madera Marsh and CA Department of Transportation for site permission on Guadalcanal and Benicia-Martinez wetland mitigation sites. We also thank numerous USGS employees and volunteers who helped conduct field work at these sites. BGM acknowledges funding support from USDA Forest Service, Pacific Northwest Research Station, Portland Oregon. GRG acknowledges funding support from the USGS Land Change Science and Ecosystems Programs. All other authors acknowledge funding support from their respective programs and institutions. Any use of trade, product, or firm names in this publication is for descriptive purposes only and does not imply endorsement by the US Government.

Funding Information:
We thank John Y. Takekawa and Susan De La Cruz as programmatic leads for USGS San Francisco Bay Estuary Field Station (SFBEFS) wetland restoration studies, and James Cronin for a review of the manuscript. All salt marsh harvest mouse trapping and handling for USGS SFBEFS was led by I. Woo and conducted under California Department of Fish and Wildlife Memorandum of Understanding (PI: J. Takekawa and S. Wainwright‐De La Cruz), and California Scientific Colleting Permit (Woo: 005749), and Federal permits (PI: J. Takekawa and S. Wainwright‐De La Cruz; TE020548). Data from Tolay Creek and Tubbs Island Setback was a collaborative effort including: Michael Bias and USFWS San Pablo Bay National Wildlife Refuge (SPB NWR; Giselle Block and Meg Marriott). We thank SPB NWR for site permission to conduct small mammal surveys at Tolay Creek and Tubbs Island Setback. We thank CA Department of Fish and Wildlife for site permission for Fagan Slough and Corte Madera Marsh and CA Department of Transportation for site permission on Guadalcanal and Benicia‐Martinez wetland mitigation sites. We also thank numerous USGS employees and volunteers who helped conduct field work at these sites. BGM acknowledges funding support from USDA Forest Service, Pacific Northwest Research Station, Portland Oregon. GRG acknowledges funding support from the USGS Land Change Science and Ecosystems Programs. All other authors acknowledge funding support from their respective programs and institutions. Any use of trade, product, or firm names in this publication is for descriptive purposes only and does not imply endorsement by the US Government.

Publisher Copyright:
Published 2019. This article is a U.S. Government work and is in the public domain in the USA. Ecology and Evolution published by John Wiley & Sons Ltd

Keywords

  • Bayesian network models
  • California vole
  • Microtus californicus
  • Reithrodontomys raviventris
  • San Francisco Bay
  • San Pablo Bay
  • habitat use
  • occupancy
  • salt marsh harvest mouse
  • small mammal assemblage

PubMed: MeSH publication types

  • Journal Article

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