APPENDIX 1. Expanded Discussion of Specific Institutional Gaps Several gaps in governance were identified for each jurisdiction. Eelgrass and climate change consistently emerge as components lacking acknowledgement in law and regulation. While 14 sections (four divisions) in Washington law used for this analysis refer to eelgrass, only two sections (derived from the same source document) in Oregon law and one section in California law refer to this component. No reference to the scientific name (Zostera spp.) exists in any law utilized for the analysis. U.S. federal law contains no reference to eelgrass; invariably all eelgrass links in the ecosystem are the subject of gaps at the national level of management. Especially on the federal level, this lack of emphasis on eelgrass may not reveal a problem, but rather this species and its linkages may be covered with broader terms in law, such as through the protection of marine resources in the California Coastal Act and critical habitat under various federal statutes. However, it may be notable that according to ecology literature and management plans that eelgrass has been heavily degraded in the past century as a result of inadequate protection (Short and Neckles 1999, Duffy 2006, Orth et al. 2006). Beyond the recognition of eelgrass-related linkages in an estuarine system, a number of significant gaps in management emerged. California, Oregon, and the U.S. do not have any section of law referring to both the estuary and seabird components, an omission that ignores the well established dependency of seabirds on estuaries for refuge (Litle et al. 2000, Parrish et al. 2003). While it is an issue of concern for many managers and scientists, it is not a surprise that no section of the law collection analyzed accounts for the relationships between climate change and seabirds, salmon, and estuaries. Climate change scientifically has received worldwide attention for its predicted and ongoing impacts on ecosystems, however, until recently, the United States government has failed to account for or even to recognize that such a human-driven global trend exists. On one hand, we were surprised to find the absence of explicit reference to a pesticide and estuary linkage in the State of Washington law since this has become a widely accepted relationship in policy. A high number of sections deal explicitly with the two components but separately (pesticide 84, estuary 76). This demonstrates significant management responsibility, indicating that the gap in the form of a lack of legal treatment jointly of pesticide and estuary might be contributing to the environmental degradation of Washington estuaries. On the other hand, federal level law may in fact cover this linkage; indeed seven sections of U.S. federal law contain both components. However, if this linkage were the sole responsibility of national law and federal agencies, then it would not also appear in Oregon and California analysis. Alternatively, the gap may be misleading because synonymous terms representative of the two components were not used in the text analysis. For example, the name of a specific pesticide or the general term pollution could be queried to find if it occurs in any sections of law with the keyword estuary, or a query could be done on like-terms, such as bay, brackish water, inlet, tidal marsh, or river mouth. All these possibilities can be explored using the next iteration of the technique and are presented here to show the range of complexity the method needs to accommodate. LITERATURE CITED Duffy, J. E. 2006. Biodiversity and the functioning of seagrass ecosystems. Marine Ecology Progress Series 311:233–250. [online] URL: http://www.int-res.com/articles/theme/m311_TS.pdf#page=59. Litle, K., S. Breslow, and J. K. Parrish. 2000. Pacific Northwest coastal ecosystems regional study (PNCERS) 2000 report. Submitted to Coastal Ocean Programs, NOAA. Orth, R. J., T. J. B. Carruthers, W. C. Dennison, C. M. Duarte, J. W. Fourqurean, K. L. Heck, A. R. Hughes, G. A. Kendrick, W. J. Kenworthy, S. Olyarnik, F. T. Short, M. Waycott, and S. L. Williams. 2006. A global crisis for seagrass ecosystems. BioScience 56:987–996. [online] URL: http://www.bioone.org/archive/0006-3568/56/12/pdf/i0006-3568-56-12-987.pdf. Parrish, J., R. Bailey, A. E. Copping, and J. E. Stein. 2003. The Pacific Northwest coastal ecosystems regional study. Estuaries 26:991–993. Short, F. T., and H. A. Neckles. 1999. The effects of global climate change on seagrasses. Aquatic Botany 63:169–196.