Section 1. Introduction

Our objective in this section is to review the status and trends of biophysical components of Puget Sound that speak to the Puget Sound Partnership's key goals: species and food webs, habitats, water quality and water quantity. Each of these goals are multi-facetted, and a nearly limitless range of topics could be covered. Indeed, one of the qualities that make Puget Sound a natural treasure is the diversity of species and habitats that it supports. This diversity precludes detailed treatment of all ecosystem components and requires thoughtful selection of metrics that speak to ecological condition and policy goals.

An ideal process for selecting components would be a sequential approach allowing us to use the framework developed in Chapter 1 to evaluate multiple indicators followed by an analysis of data availability, status and trends therein. However, time constraints required that we work in parallel with the Chapter 1 effort, so our choice of focal components and our reporting is largely independent of that process. We do not use the term "indicators" when referring to these components because they have not been formally vetted as such.

Lacking a formal procedure or framework to select focal biophysical components, we adopted two overarching considerations in selecting components: metrics should be ecologically or policy relevant attributes of Puget Sound, and must have been the focus of sufficient study to permit status evaluation. Consequently, species that are recognized as important in the Puget Sound ecosystem, but for which sufficient data do not exist, were excluded from this analysis. Omissions based on data insufficiencies can be used to help guide decisions regarding data collection programs in the future. Additional guiding principles and considerations included the following: 1) culturally important species for which there are clear policy goals (e.g., harvested species, iconic species such as killer whales) were included whenever possible, along with critical species and habitats upon which they rely; 2) species of particular conservation concern were incorporated; 3) water quality and water quality components were chosen to reflect the topical emphasis of scientific study in each of those disciplines; 4) species that have been specifically identified as ecosystem indicators (via peer reviewed publications) were considered whenever possible.

This set of principles provided criteria that allowed a systematic approach to selection of components to include in this analysis. However, it did result in some noteworthy exclusions. For example, the status and trends of invasive species (e.g., Spartina, Ciona) are not reported. Analysis of zooplankton community composition and trends is limited by the paucity of data. Ocean acidification, a growing concern with potentially substantial impacts on shellfish aquaculture and natural communities, is not treated here. These and other omissions are not intended to imply that these are not important issues or components of the Puget Sound ecosystem, and we anticipate that the next iteration of the Puget Sound Science update can consider a broader range of metrics.

The ecosystem components treated in this chapter clearly emphasize marine and freshwater elements of the Puget Sound Watershed. This emphasis reflects the historical focus of the Puget Sound Science Update and the specific expertise of the lead authors. Even so, we selected terrestrial topics that have some linkage to aquatic portions of the watershed. We anticipate that future iterations of the Puget Sound Science Update will take a broader view and include many more terrestrial topics than we could incorporate in the present document.

There is a growing need for ecosystem assessments to guide ecosystem-based management. While the present evaluation might be considered a contribution to such an assessment, it is not an ecosystem assessment per se. Instead, it is an assessment of several ecosystem components. A full ecosystem assessment would also include a conceptual framework that links biological, physical and chemical processes and reports on key drivers and responses of each. Moreover, a quantitative synthesis of status and trends across all ecological and policy-relevant attributes of Puget Sound will provide a substantial advance.

Throughout, we aimed to vet available information to include only those results and conclusions that had undergone prior review. We recognized in advance that maintaining a requirement of peer-reviewed publication in scientific journals would be inappropriate: much of the scientific work on Puget Sound derives from long term monitoring that is not published in such journals. We therefore considered agency documents that were part of research reporting series to be sufficiently reviewed to be included in this chapter. This process revealed considerable differences among local agencies in the transparency of review processes for reports. There is a need for consistent standards and reporting practices among these agencies to permit an assessment of the thoroughness of reviews. We generally avoided citing previous iterations of the Puget Sound Science update as primary sources, because the nature and extent of review of components of those documents is also not clear. In some cases, monitoring data were used directly provided that the procedures used in collecting them had been reviewed and published.

Given these constraints, this chapter is not intended to be the final word on indicators for evaluating the status of Puget Sound. Indeed, Chapter 1 of the 2010 Puget Sound Science Update provides a substantial advance in improving the capacity to select ecologically meaningful indicators. Future versions of the Puget Sound Science Update will clearly benefit from the foundation that the present effort provides.

This chapter is organized primarily along the four Puget Sound Partnership goals, with separate sections for each ecosystem component. Within each summary, we provide background and rationale for inclusion in the Chapter, a brief treatment of threats and drivers to give the needed context. More thorough treatment of threats and drivers is provided in Chapter 3. We include in each section a synthesis of key data gaps and uncertainties. In some cases the uncertainties are scientific: uncertainties that can be resolved through additional scientific study. In other cases the uncertainties reflect emerging concepts, hypotheses and explanations that have not yet been vetted through a formal review process.