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Lee II, H., B. Thompson, and S. Lowe. 2003. Estuarine and scalar patterns of invasion in the soft-bottom benthic communities of the San Francisco Estuary. Biological Invasions 5:85-102. WED-02-120.

The spatial patterns of nonindigenous species in seven subtidal soft-bottom communities in the San Francisco Estuary were quantified. Sixty nonindigenous species were found out of the 533 taxa enumerated (11%). Patterns of invasion across the communities were evaluated using a suite of invasion metrics based on the abundance or species richness of nonindigenous species. Patterns of invasion along the estuarine gradient varied with the invasion metric used, and the factors affecting the metrics and their ecological interpretations are discussed. Overall, the estuarine transition community located in the estuarine turbidity maximum zone (mean 5 practical salinity unit (psu)), main estuarine community (mean psu = 16), and marine muddy community (mean psu = 28) were more invaded than two fresh-brackish communities (mean psu <1) and a marine sandy community (mean psu = 27). Nonindigenous species were numerically dominant over much of the Estuary, making up more than 90% of the individuals in two communities. The percentage of the total species composed of nonindigenous species increased at smaller spatial scales: 11% at the estuary (gamma) scale, 21% at the community (alpha) scale, and 42% at the grab (point) scale. Wider spatial distributions of nonindigenous species and a relatively greater percentage of rare native species may have resulted in this pattern. Because of this scale dependency, comparisons among sites need to be made at the same spatial scale. Native species were positively correlated with nonindigenous species in several of the communities, presumably due to similar responses to small-scale differences in habitat quality. The rate of invasion into the soft-bottom communities of the San Francisco Estuary appears to have increased over the last one to two decades and many of the new introductions have become numerically dominant.

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