Geographic patterns in cover of major plant groups may be attributed to differences in 
habitat types among states. Over 80% of Washington sites were classified as tidal flat 
and no sites were classified as marsh (Figure 3.1.2). In contrast, approximately 40% of 
sites in California and San Francisco Bay were classified as marsh. Oregon sites were 
a mixture of habitat sites, with more sites in the submerged aquatic vegetation (SAV) 
habitat class than other states. 
Taxa occurrence and mean relative cover of common emergent taxa also 
displayed geographic patterns (Appendix Table 5). The greatest number of emergent 
macrophyte species were observed in California (n = 11) and San Francisco Bay (n = 
17). Six emergent macrophyte species were observed in Oregon. The quadrats of only 
three sites in Washington had emergent macrophyte cover and only one species, S. 
alterniflora, was present in these quadrats. Because most taxa only occurred at a few 
sites, average percent cover of taxa was calculated as the average cover at sites where 
the taxa occurred and not across all sites. Mean cover of S. virginica was 39% in 
California sites and 70% in San Francisco Bay sites (Figure 3.3.8). This species 
occurred at one site in Oregon and was not present in Washington. Mean cover of J. 
carnosa was 43% in California sites and 30% in San Francisco Bay. This species was 
not present in Oregon or Washington sites. The three remaining species occurring at 
more than five sites, Batis maritima, Distichlis spicata, and Spartina foliosa, were only 
encountered in California and San Francisco Bay sites. Geographic patterns in 
occurrence and cover of common emergent macrophyte species may again be 
attributed to differences in habitat types among states. While tidal marsh macrophytes 
can tolerate inundation, these species can not tolerate the prolonged periods of 
inundation experienced on tidal flats and therefore are restricted to habitats receiving 
less inundation. 
Seagrass species were observed in the quadrats of California, Oregon and 
Washington sites. Zostera marina was present in the vegetation quadrats of all three 
states (Appendix Table 5). Mean relative cover of Z. marina was highest for 
Washington sites (Figure 3.3.9). For Washington sites, mean relative cover of the 
invasive seagrass, Z. japonica, was higher than that of Z. marina, 44% and 27%, 
respectively. Zostera japonica did not occur in California or San Francisco Bay (Figure 
3.3.10). Mean relative cover of green algae was highest in California (70%). Green 
algae did not occur in San Francisco Bay sites (Figure 3.3.11). 
Nonindigenous species (emergent macrophytes and seagrass) were 
encountered in the quadrats at 29 sites throughout the study area. Spartina alterniflora 
was observed at three sites in Washington and Z. japonica was observed at sites in 
both Oregon and Washington. Lepidium latifolium was found at one site in San 
Francisco Bay. Mean relative cover of nonindigenous species was low (8%) throughout 
the West (Figure 3.3.12). Mean cover by nonindigenous species was highest in 
Washington (21%), with nonindigenous species being found at 20 sites. Sites in 
44 
