A Century of Landscape Disturbance and Urbanization of the San Francisco Bay Region affects the Present-day Genetic Diversity of the California Ridgways Rail (Rallus obsoletus obsoletus).

Fragmentation and loss of natural habitat have important consequences for wild populations. Reductions in population size, density and connectivity can disrupt the distribution of genetic diversity within species and negatively impact long-term viability and resilience to environmental change. Genetic assessments of population structure, diversity and gene flow can provide important insights into conservation for rare and at-risk species. The California Ridgways rail (Rallus obsoletus obsoletus) is a state and federally endangered saltmarsh obligate that occurs within tidal wetlands of the highly urbanized San Francisco Bay region. On the basis of microsatellite genotyping and mitochondrial sequencing analyses, we estimated population structure among saltmarsh fragments currently occupied by the California Ridgways rail, and assessed demographic connectivity by inferring patterns of historical and contemporary gene flow. We found four geographically separate genetic clusters across the San Francisco Bay. Historical gene flow analyses supported a stepping stone pattern of gene flow from south-to-north and highest mitochondrial diversity was observed in the Central and South embayments. However, contemporary gene flow among the regional embayments appears less intact. Our results indicate the California Ridgways rail may be losing diversity and undergoing genetic differentiation induced by low gene flow and genetic drift, as a consequence of urbanization and small population sizes. Given these genetic findings, we present management and restoration actions for recovery of the California Ridgways rail.