Biological Invasions 5: 85–102, 2003. © 2003 Kluwer Academic Publishers. Printed in the Netherlands. Estuarine and scalar patterns of invasion in the soft-bottom benthic communities of the San Francisco Estuary Henry Lee II 1,∗ , Bruce Thompson 2 & Sarah Lowe 2 1 US Environmental Protection Agency, ORD, NHEERL, Western Ecology Division, 2111 S.E. Marine Science Drive, Newport, OR 97365, USA; 2 San Francisco Estuary Institute, 7770 Pardee Lane, Oakland, CA 94621-1424, USA; ∗ Author for correspondence (e-mail: lee.henry@epa.gov; fax: 541 867 4049) Received 4 October 2001; accepted in revised form 9 July 2002 Key words: estuarine gradients, invasion metrics, invasion patterns, nonindigenous species, San Francisco Estuary, soft-bottom communities, spatial scales Abstract 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 ecological interpretation of the metrics is discussed. Overall, the estuarine transition community located in the estuarine turbidity maximum zone (mean 5 practical salinity unit (psu)), main estuarine community (mean 16 psu), and marine muddy community (mean 28 psu) were more invaded than two fresh-brackish communities (mean <1 psu) and a marine sandy community (mean 27 psu). 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. Introduction Increasingly, nonindigenous species represent a major environmental threat to nearly every aquatic and ter- restrial ecosystem (e.g. Westbrooks 1998; Mack et al. 2000; Pimentel et al. 2000). Among coastal ecosys- tems, the San Francisco Bay-Delta (the ‘San Francisco Estuary’) has become the archetype for an invaded estuary. Cohen and Carlton (1998) reported 234 nonindigenous species from the Bay area, substan- tially more than reported from other North American bays and estuaries (Ruiz et al. 1997, 2000). Even with this plethora of introduced species, the rate of new invasions has increased from one new species every 55 weeks prior to 1960 to one every 14 weeks (Cohen and Carlton 1998). Many of these invaders have been successful and have become the numerical or biomass dominants in a number of habitats (e.g. Nichols and Thompson 1985a; Nichols and Pamatmat 1988; Carlton et al. 1990; Meng et al. 1994; Cohen and Carlton 1995). Taken together, these observations sug- gest that the San Francisco Estuary ‘may be the most invaded estuary in the world’ (Cohen and Carlton 1998).