Endangered California Ridgway’s rails once had access to salt marshes that encircled the San Francisco Bay. Land-use changes, particularly urban development concentrated along the Central Bay, diminished and fragmented these birds’ available habitat.

Feb. 3, 2017 – A new study analyzes the genetic diversity and population structure of the California Ridgway’s rail, Rallus obsoletus, a state and federally-listed endangered bird. The results demonstrate that the so-called “rails” are experiencing negative genetic effects following more than a century of salt marsh habitat loss from agriculture, commercial salt production and urban development.

“Genetic diversity is an important part of ensuring that populations are able to withstand and adapt to disturbance like disease or sea level rise,” said Dustin Wood, lead author and geneticist with the U.S. Geological Survey. “When small, fragmented populations experience genetic bottlenecks, they can be vulnerable to inbreeding population depression or localized extinction, which can mean trouble for the species in the future unless connectivity among populations can be restored.”

Once bordered by wetlands, the San Francisco Bay now retains less than 10 percent of its original marsh habitat. The fragmented marshes that remain lie amid urban and agricultural areas scattered around the Bay. To determine the current genetic diversity and population structure of rails inhabiting these marshes, researchers genotyped 107 rails and inferred gene flow patterns between the North, Central and South Bay.

Study results showed evidence for significant genetic differences among geographically-separated populations across San Francisco Bay. In addition, the researchers uncovered low genetic diversity within populations, small effective population sizes and overall low connectivity among marshes.

The findings also indicated the presence of genetic bottlenecks in some sites in the Central Bay, where salt marsh habitat is most fragmented. Historically, intact marshes may have acted as “bridges” for rails to migrate and pass genes from the South to North Bay. The study’s findings indicate that restoring this area could support genetic diversity and increase connectivity between isolated populations of California’s Ridgway’s rails and other vulnerable species that depend on the Bay’s wetlands.

Scientists from the USGS, University of California, Davis and Audubon California contributed to this study and published their results in “Conservation Genetics.”