Ecology
A diversity of aquatic and terrestrial organisms populate Sonoma Creek and its riparian zone. Winter-run Chinook salmon (Oncorhynchus tsawytscha), Delta smelt (Hypomesus transpacificus) and steelhead (Onchorhynchus mykiss) are the most prominent fishes. Anadromous fish movements in Sonoma Creek have been studied extensively not only in the mainstem Sonoma Creek, but in some of the tributaries. These investigations have demonstrated a historical decline in spawning and habitat value for these species, primarily due to sedimentation and secondarily to removal of riparian vegetation since the 1800s.
A variety of salamanders, snakes and frogs are also present. The federally listed as threatened California red-legged frog is present in the northern reach draining the south slopes of Annadel State Park. Several endangered species (mostly associated with the marshy discharge area) present include California clapper rail (Rallus longirostris), California Black Rail (Laterallus jamaicensis), California brown pelican (Pelicanus occudentalis), California freshwater shrimp (Syncaris pacifica), Salt marsh harvest mouse (Reithrodontomys raviventris ), Suisun Shrew (Sorex ornatus sinuosus), Sacramento splittail (Pogonichtys macrolepidotus). The above are endangered species with the exception of the splittail, steelhead and black rail, which species are federally designated as Threatened.
California Golden Beaver ("Castor canadensis subauratus") were historically abundant along Sonoma Creek but were trapped out in the California Fur Rush of the late eighteenth and early nineteenth centuries. In 1828 fur trapper Michel La Framboise travelled from the Bonaventura River to San Francisco and then the missions of San José, San Francisco Solano and San Rafael Arcángel. La Framboise stated that "the Bay of San Francisco abounds in beaver", and that he "made his best hunt in the vicinity of the missions". The beaver were likely wiped out by the mid-nineteenth century but returned to Sonoma Creek, likely from the Delta, in the 1990s. In 1996 a beaver family developed a taste for merlot grapevine bark in a vineyard beside the creek and were exterminated, leading to civic uproar and a shift to accommodate beaver resettlement. Sonoma Ecology Center executive director Richard Dale reports that although beavers fell trees and dam culverts, on balance they perform nearly "perfect stream restoration," because they cause the creation of deep pools, slowing the flow of flood water and enhancing fishery habitat. New beavers have recolonized Sonoma Creek and are currently located in both Sonoma and Glen Ellen. A "keystone species", the beaver have created habitat that has, in turn, led to the return of river otter ("Lontra canadensis") which have been sighted recently in the beaver pond below the Boyes Boulevard bridge in Boyes Hot Springs.
Upland ecosystems drained include mixed California oak woodland, chaparral and savannah woodland, In these upland reaches one finds plentiful Black-tailed Deer, coyote, skunk, raccoon, opossum, wild turkey, turkey vulture, red-tailed hawk and occasionally bobcat and mountain lion. Prominent higher elevation trees include: Coast live oak, Garry Oak, Pacific madrone, California Buckeye, Douglas fir, whereas Valley oak is prevalent on the Sonoma Valley floor.
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