The Yerba Buena mud member of the San Antonio Formation is an upper Pleistocene estuarine deposit that records a marine transgression during the last interglacial into the valley today filled by San Francisco Bay. These sediments now lie between 25-70 m below mean sea level and are not exposed subaerially. Foraminifers, sand-sized diatoms, seeds, fish elements, molluscan shells, and other microfossils preserved in core samples trace environmental changes that occurred as sea level rose. This multitaxon approach permits biostratigraphic analysis of subsurface units even when core samples have undergone extended storage and consequent deterioration of calcareous microfossils. Foraminifers are preserved in only 22% of the Yerba Buena mud samples, but more than 70% of the samples contain diatoms or other taxa useful for paleoenvironmental analyses.

In the Yerba Buena mud, 32 species of foraminifers are present. These species are predominantly estuarine and nearshore marine fauna. Seven species make up more than 98% of the population in all samples: Ammonia beccarii, Buccella frigida, Buliminella elegantissima, Elphidiella hannai, Elphidium excavatum, Elphidium gunteri, and Elphidium magellanicum. Foraminifers and sand-sized diatoms define five biofacies that indicate changing environmental conditions during a single transgression into the Yerba Buena bay. Biofacies present in the lower portion of the unit indicate environments ranging from brackish, such as those prevailing in the upper reaches of the present estuary, to the higher salinity of the present central Bay. Biofacies in the upper part of the unit indicate coastal-marine salinity and lower water temperature, conditions unlike those in the present estuary but prevalent along the outer-central California coast today

The transgressional record in the Yerba Buena mud is a useful example of environmental changes that might result from the effect of sea-level rise in major Holocene estuaries.

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