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A century of landscape disturbance and urbanization of the San Francisco Bay region affects the present-day genetic diversity of the California Ridgway’s rail (Rallus obsoletus obsoletus)

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Abstract

Fragmentation and loss of natural habitat have important consequences for wild populations and can negatively affect long-term viability and resilience to environmental change. Salt marsh obligate species, such as those that occupy the San Francisco Bay Estuary in western North America, occupy already impaired habitats as result of human development and modifications and are highly susceptible to increased habitat loss and fragmentation due to global climate change. We examined the genetic variation of the California Ridgway’s rail (Rallus obsoletus obsoletus), a state and federally endangered species that occurs within the fragmented salt marsh of the San Francisco Bay Estuary. We genotyped 107 rails across 11 microsatellite loci and a single mitochondrial gene to estimate genetic diversity and population structure among seven salt marsh fragments and assessed demographic connectivity by inferring patterns of gene flow and migration rates. We found pronounced genetic structuring among four geographically separate genetic clusters across the San Francisco Bay. Gene flow analyses supported a stepping stone model of gene flow from south-to-north. However, contemporary gene flow among the regional embayments was low. Genetic diversity among occupied salt marshes and genetic clusters were not significantly different. We detected low effective population sizes and significantly high relatedness among individuals within salt marshes. Preserving genetic diversity and connectivity throughout the San Francisco Bay may require attention to salt marsh restoration in the Central Bay where habitat is both most limited and most fragmented. Incorporating periodic genetic sampling into the management regime may help evaluate population trends and guide long-term management priorities.

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Acknowledgments

We are grateful for the valuable comments from the associate editor and three anonymous reviewers and that helped improve a previous version of the manuscript. The microsatellite data and associated metadata used for this study can be obtained from ScienceBase (http://dx.doi.org/10.5066/F7HD7SQ0) and ND2 mtDNA sequences were deposited in GENBANK (KU505148-KU505209). We thank our field crews including A. Merritt, E. Schultz, K. Barry, L. Koenig, K. Sawyer, and J. Burton for collecting samples and locality information. We thank S. Bobzien, M. Taylor, and R. Trujillo for assistance and access to East Bay Regional Park District properties; and the U.S. Geological Survey San Francisco Bay Field Station staff for assistance with field work. We also thank the California Department of Fish and Wildlife, Don Edwards National Wildlife Refuge, Marin County Parks, and Las Gallinas Valley Sanitary District for granting us access to their properties. This project was funded by the U. S. Geological Survey Western Ecological Research Center and grants from the U.S. Fish and Wildlife Service, Region 8, Coastal Programs and Recovery Branches and by the California State Coastal Conservatory and Department of Fish and Wildlife. The blood and tissue samples were collected under U.S. Fish and Wildlife Service endangered species permit TE-020548, California Department of Fish and Wildlife Memorandum of Understanding and scientific collecting permits, U.S. Geological Survey Bird Banding Laboratory permit 21142, and the U.S. Geological Survey Western Ecological Research Center Animal Care and Use Committee. Any use of trade, product, or firm names is for descriptive purposes only and does not imply endorsement by the U.S. Government.

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  1. U.S. Geological Survey, Western Ecological Research Center, San Diego Field Station, 4165 Spruance Road, Suite 200, San Diego, CA, 92101, USA

    Dustin A. Wood & Amy G. Vandergast

  2. U.S. Geological Survey, Western Ecological Research Center, Dixon Field Station, 800 Business Park Drive, Suite D, Dixon, CA, 95620, USA

    Thuy-Vy D. Bui, Cory T. Overton & Michael L. Casazza

  3. Department of Animal Science, Meyer Hall, University of California, Davis, One Shields Avenue, Davis, CA, 95616, USA

    Joshua M. Hull

  4. U.S. Geological Survey, Western Ecological Research Center, San Francisco Bay Estuary Field Station, 505 Azuar Drive, Vallejo, CA, 94592, USA

    John Y. Takekawa

  5. Audubon California, 376 Greenwood Beach Road, Tiburon, CA, 94920, USA

    John Y. Takekawa

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Wood, D.A., Bui, TV.D., Overton, C.T. et al. A century of landscape disturbance and urbanization of the San Francisco Bay region affects the present-day genetic diversity of the California Ridgway’s rail (Rallus obsoletus obsoletus). Conserv Genet 18, 131–146 (2017). https://doi.org/10.1007/s10592-016-0888-4

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