3.5.5 Nonindigenous Species 
Taxa were classified as native, nonindigenous, cryptogenic, indeterminate, 
or unclassified. Cryptogenic species are species of uncertain origin (Carlton, 
1996) and may include potential introductions, sibling species, or species that 
have yet to be sufficiently well resolved taxonomically over their global range. 
Indeterminate taxa are those not identified with sufficient taxonomic resolution to 
classify as native, nonindigenous, or cryptogenic (Lee et al. 2003). Unclassified 
species are those that have yet to be analyzed sufficiently to render a final 
classification. The classifications used here follow the Pacific Ecosystem 
Information System (PCEIS), a geo-referenced database of native and 
nonindigenous species of the Northeast Pacific being developed by the EPA and 
USGS (Lee and Reusser 2008). 
Of the 1,108 taxa identified to species, 13 species are currently classified 
as nonindigenous (Table 3.5.6), though there are uncertainties about the 
taxonomic resolution of several of these species. In addition, another 121 
species are classified as cryptogenic and 208 species are unclassified. The 
taxonomic uncertainties with the putative nonindigenous species and the large 
number of cryptogenic and unclassified species reflect both the lack of detailed 
analysis of the invasion status of shelf species as well as the difficulties inherent 
in harmonizing taxonomy on a global scale. Thus the present analysis should be 
considered preliminary until additional information becomes available on the 
taxonomy and classification of these uncertain species. 
The 13 nonindigenous species constitute only 1.2% of the taxa that were 
identified to species or, excluding the cryptogenic and unclassified species, 1.7% 
of the native species. Even with the uncertainty over the classification of some 
species, the number of nonindigenous species appears to be much lower on the 
shelf than in the estuarine ecosystems of the Pacific Coast. For example, 42 
nonindigenous species were found in the probabilistic survey of tidal wetlands of 
the Pacific Coast (Nelson et al. 2007a), while over 200 nonindigenous species 
have been found in the San Francisco Estuary (Cohen and Carlton 1995). 
Additionally, the nonindigenous species were in low abundance. None of the 
nonindigenous species were included in the 50 most abundant taxa (Table 
3.5.4), and combined they constituted only 0.4% of the total individuals or 0.7% 
of the abundance of the natives. This is in contrast to many Pacific Coast 
estuaries, where nonindigenous species constitute a substantial if not major 
portion of the total abundance (Nelson et al. 2005), and from the San Francisco 
Estuary in particular, where nonindigenous species are the numerical dominants 
in most of the benthic assemblages (Lee et al. 2003). The most abundant 
nonindigenous species were the spionid polychaete Laonice cirrata and the 
ampharetid polychaete Anobothrus gracilis, which had average abundances of 
0.40 and 0.29 individuals per grab, respectively (Table 3.5.6). While neither of 
these species was abundant, both were moderately frequent, occurring in 23% 
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