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3 Stressors: Environmental Factors and Their Effects on the Bay-Delta Ecosystem THE CHALLENGE: IDENTIFYING, DISTINGUISHING, AND RANKING INTERACTING ENVIRONMENTAL FACTORS AFFECTING THE BAY-DELTA ECOSYSTEM Many environmental factors, including water diversions, affect the structure and functioning of biotic communities in the delta. Although it would be convenient if one or only a few of these factors could be identi- fied as the source of the "problem," or even ranked with some certainty, it is not possible to do that, for at least three reasons: the "problem" is not easily definable, the suite of stressors is complex and interactive, and the ecosystem and its components do not react to any stressor as a single unit. "The Problem" of the Delta Is Not a Single, Easily Definable Problem Although the ecosystem has been radically altered over the past 150 years, it nonetheless remains a biologically diverse and productive eco- system. Some species have thrived, but others, including some listed as threatened or endangered under the federal Endangered Species Act and California's Endangered Species Act, have declined dramatically. In addi- tion, species composition and environmental conditions in the delta have undergone large changes over the period. Therefore, while an immediate difficulty for some is that concern over some listed species has affected water diversions, "the problem" is harder to define biologically, and is perceived differently by various stakeholder groups, institutions, and other interests. 57

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58 SUSTAINABLE WATER MANAGEMENT IN THE DELTA The Suite of Stressors Affecting Water Quality, Habitat, and Sustainability of the San Francisco Bay Delta Is Complex and Interactive Interactions among stressors and between stressors and ecosystem pro- cesses are common. Nutrient enrichment, toxic chemicals, and temperature, for example, are affected by hydrology and hydrodynamics, that is, the way tides and freshwater flow interact to determine the temporal and spatial variability of the physical environment of the estuary. This complicates the interpretation and evaluation as to positive, negative, or neutral overall ef- fects of any single stressor on the ecosystem and its attributes. Furthermore, species differ in their individual responses to most types of stress. The result is a complex biological, spatial, and temporal mosaic of impacts from this combination of influences. To some extent, the evaluation of the impacts of these effects also depends on which ecosystem services and needs are of interest or concern, for example, safe and usable water supplies, recreational and commercial fisheries, habitat condition, or public use of the delta. Thus, while it is politically attractive to attempt to rank stressors so as to prioritize societal investments in their amelioration, that task is much more complex than it might at first seem. To some degree, priorities can be defined if the stress, species, place, and time are first prioritized or defined. The stressors dis- cussed below and shown in Figure 3-1 are highly dynamic; that is, they can quantitatively change in time and space depending on changes in human activities (including future management actions), climate, and combinations thereof. The Ecosystem and Its Components Do Not Necessarily Respond as a Single Unit to Most Environmental Factors For example, Chinook salmon (Oncorhynchus tshawytscha) spend several years at sea and then return to pass through the delta as adults to spawn; their eggs and young spend time in delta tributaries before passing through the delta on their way to the ocean to mature. Returning adult Chinook salmon always die after spawning, and so they are not susceptible to chronic environmental factors, because they die before such factors can affect them. They also are strong swimmers and therefore most changes in flow patterns in the delta are reasonably small challenges for them. The eggs and young are susceptible to conditions in the tributaries and are exposed to them for considerable periods, and the outmigrating smolts are not as strong swimmers as are the returning adults, and so probably are more sus- ceptible to changes in flow patterns. By contrast, delta smelt (Hypomesus transpacificus) spend their entire (short) lives in the delta and so they can be chronically exposed to contaminants in the water; being smaller and

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STRESSORS 59 FIGURE 3-1Conceptual diagram showing the interactive stressors affecting San Francisco Bay Delta water quality, habitat condition, and overall ecosystem struc- ture and functioning. While this figure is focused on key fish species (e.g., salmo- nids), these are intimately linked to other biotic components of the ecosystem, including planktonic and benthic primary producers, grazers, larval, and juvenile and mature invertebrate and fish species. SOURCE: Courtesy of A. Joyner, University of North Carolina. R02208 Figure 3-1 bitmapped weaker swimmers than even salmonraster image smolts, they likely are more suscep- tible to changes in flow than salmon are. In addition, the behaviors, food, distribution in the water column, and physiologies of salmon and smelt are different, so even if they are exposed for a time to the same adverse envi- ronmental conditions, their responses to them almost certainly are different. The above discussion compared only two species, but other species are important as well, including those that are not listed. Other biotic components, ranging from phytoplankton to fish, are part of the ecological community and yet they, too, differ in behavior, distribution, physiology, and susceptibility to a wide variety of environmental conditions, including contaminants. Thus most attempts to identify and rank single environ- mental factors as stressors are very likely to fail, unless the factors can be specifically related to a particular aspect of a species' life history. Even such

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60 SUSTAINABLE WATER MANAGEMENT IN THE DELTA factors as dams, which would appear at first glance to adversely affect only or mainly migratory species like salmon, steelhead (Oncorhynchus mykiss), and green sturgeon (Acipenser medirostris), also affect flow patterns, water temperature and quality, food availability, and so on, and they differentially affect many species, even those that do not migrate. There is a complex in- terplay between key water quality, habitat, and sustainability issues and the drivers affecting them. Furthermore, uncertainties and scientific gaps exist that further compound the problem (Table 3-1). Indeed, the delta prob- lem is a "wicked" problem in the sense of Rittel and Webber (1973) and Conklin (2005): the problem is hard to define objectively and the nature of the problem depends on the values of those who define it. For all the above reasons, the committee concludes that only a syn- thetic, integrated, analytical approach to understanding the effects of suites of environmental factors on the ecosystem and its components is likely to provide important and useful insights that can lead to enhancement of the delta ecosystem and its species. ECOSYSTEM STRESSORS Although the committee recommends a synthetic, integrated approach to assessing environmental factors, such an approach first requires a de- scription of the individual factors separately. Therefore, we provide such descriptions, covering a variety of environmental factors that are important or potentially important in the following sections. The current set of stress- ors discussed is not an exhaustive list; rather, they are the most prominent stressors in the delta system in the committee's judgment. Following this, the committee provides its assessment of each stressor individually. Physical Environment: Geomorphology and Delta Geometry Changes in geomorphology of the delta in the last 150 years have been dramatic. Alteration of tidal channels and drainage of wetlands within the delta began for agricultural purposes, but eventually, as new centers of com- merce and shipping developed, the drained lands supported urban develop- ment. Levees surrounding delta islands isolate most land in the delta from tidal or riverine flooding. Historically, periodic flooding of floodplains and wetlands provided habitat for many species and reduced the risk of down- stream flooding. The delta absorbed flood flows to become a vast shallow lake. At its greatest extent prior to the transition to agriculture, the delta covered 1,931 square miles of tidally influenced open water, intertidal flat, and marsh. By 1930, however, 35 percent of the delta had been converted (Thompson 1957), leading a trend of land conversion that established the channel geometry and variability that is present today.

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STRESSORS 61 TABLE 3-1 Examples of the Interplay Among Ecosystem Processes (Drivers), Stressors, Science Needs, and Policy Uncertainties and Science Driversa Stressors Water Policy Issues Needs Anthropogenic Canals. Effects: benefits vs. Predicting influences of new infrastructure Removing more adverse implications water routing? Implications changes water from the for ecosystems of population growth, resulting in system. water use or conservation? changes in Reservoirs. Impediments and benefits freshwater flow to fish passage. and turbidity Climate Temperature: Will future habitats Can we manage habitats to change Changing ocean be suitable for create refuges and sustain conditions. Changing species of concern? optimal carbon, nutrient, hydrology. Can we save and and oxygen cycling? manage sensitive species? Exports Entrainment. How to balance Effects on fish populations Indirect effects on supply reliability vs. individuals? Quantifying hydrodynamics. with ecosystem indirect effects? Nutrient and carbon requirements. Quantifying effects of loadings. upstream diversions? Upstream diversions. Food quality Nutrients: N,P,C. Declining quality Relative importance of Flow. of food for grazers bottom-up vs. top-down Grazing. and higher trophic controls on food web. levels. Influence of habitat changes. Feasibility of management? Habitat loss Nutrients. Can restoration of Restoration uncertainties: Freshwater flows. habitat facilitate What is manageable against Light, turbidity. recovery of key a changing baseline [climate Physical disturbance processes and native change, invasive species, and elimination. species? declining sediment inputs]? Harvest and Top-down Implications for How to manage harvest for fishing fisheries. sustainable populations and to avoid top-down effects on ecosystems [sustainable production, desirable water quality, and habitat]. Introduced Alteration of food Survival and Predicting success of species webs and nutrient management of invaders and their cycling. native species. ecological implications? Alteration of food Fate of restoration Life cycle of invasive availability. actions. species: can vulnerabilities Changes in be found? predation. Controlling inputs and Change in physical managing habitat for habitat from optimal production of macroflora. native species. continued

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62 SUSTAINABLE WATER MANAGEMENT IN THE DELTA TABLE 3-1 Continued Uncertainties and Science Driversa Stressors Water Policy Issues Needs Nutrients Nitrogen/phosphorus Nutrient input Determine nutrient input (nitrogen and loads. reductions. and flow thresholds for phosphorus) Flows. eutrophication and algal Temperature. bloom formation and macroflora. Roles of ratios and forms of nutrients in determining community composition. Passage Dams. Inability of species What species most affected impediments Migration barriers. to utilize former by diversions? Water diversions. habitats. Feasibililty of management? Toxic chemicals Inputs of selenium, Concentrations not Selenium: San Joaquin mercury, pesticides. declining and could River inputs to the Bay? increase. Mercury: methylation increase from wetland restoration? Pesticides: How many areas of high concentration and where? Improved management. aDrivers listed in alphabetical order. SOURCE: Modified from Healey et al. (2008a). The Bay Delta Conservation Plan (BDCP) Independent Science Advi- sors (BDCP 2007) identified two fundamental environmental gradients that control physical characteristics of habitat for various species (Figure 3-2). While the salinity gradient has always been oriented along the axes of the major rivers flowing through the delta, elevation gradients existed at a number of spatial scales. At the largest scale, there is a decrease in elevation and slope along the river channels and banks from upstream as they enter the delta, toward the bay. At the reach scale, the high natural river levees resulted in a decrease in elevation away from the channel into floodplain (upstream) and tidal marsh (downstream), and these "cross-channel" gra- dients were multiplied by the complex system of river and tidal drainage channels that previously occupied the delta. Today, the network of delta levees has substantially reduced the area exposed to the tides to about 618 square miles (Culberson et al. 2008). The drainage density within the delta has been reduced and is restricted to deep subtidal channels, resulting in a limited array of environmental gradients within the delta. Natural high land (e.g., river levees) has been essentially eliminated, as have shallow channels. Tidal and riverine flow,

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STRESSORS 63 FIGURE 3-2 Horizontal and vertical gradients that control environmental condi- tions in the delta. SOURCE: BDCP (2007). across the salinity gradient, is confined to channels that do not drain at low tide. Flooded delta islands (e.g., Franks Tract, Mildred Island, and Liberty Island) are now lower than the marshes R02208 and channels in those areas would have been prior to drainage. Figure 3-2 bitmapped Isolated areas of naturally raster inundated image wetland still exist in the delta (most of the wetlands in Suisun marsh are actually semi-impounded and their inundation regime does not therefore reflect the environmental condi- tions of naturally inundated wetlands). Forested floodplain with natural inundation regime is now limited to the Cosumnes River, and Rush Ranch in Suisun Bay is remnant salt marsh at the lower end of the system. Because tules (Schaoenoplectus spp.) do not require substrate drainage and can grow at elevations as low as ~0.5 m mean lower low water, tule patches ex- ist in remnant midchannels islands and around the margins of some flooded islands. Tules have a low salt tolerance, but current water management that keeps the delta fresh for conveyance purposes allows tule wetlands to ex- tend to the margins of Suisun Bay. Their ability to colonize into the subtidal

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64 SUSTAINABLE WATER MANAGEMENT IN THE DELTA zone means that bare intertidal flats, which may have historically existed throughout the delta in areas periodically influenced by salinity incursion, have essentially been eliminated except in Suisun Bay. Tules can effectively dampen wave action (e.g., Augustin et al. 2009) and thus limit resuspension of sediment in shallow subtidal areas within the delta. Accordingly, the only areas where wind waves routinely resuspend sediments and provide high turbidity levels are in Suisun Bay. Ruhl and Schoelhammer (2004) found that this effect was accentuated by the storage of highly erodible sediments on mudflats in Honker Bay. If such sediments are deposited in areas colo- nized by tules, resuspension would be limited. Thus, the changes in eleva- tion gradients within the delta have limited the occurrence of wetlands of various types and shallow turbid subtidal environments. Physical Environment: Flows and Salinity The committee's first report, A Scientific Assessment of Alternatives for Reducing Water Management Effects on Threatened and Endangered Fishes in California's Bay Delta (NRC 2010), dealt with aspects of flows, notably Old and Middle River (OMR) flows and X21 positioning that are specific to two biological opinions issued by the Fish and Wildlife Service (FWS) and the National Marine Fisheries Service (NMFS) to protect listed fish species, the delta smelt, and Chinook salmon. In what follows, we discuss flow ef- fects on the aquatic resources of the bay delta more generally, aiming to set existing knowledge about these flow effects in the same framework as other stressors such as contaminants, nutrient inputs, and invasive species. To do so requires that one consider first how flow affects organisms and processes, in which cases it is anthropogenic changes to flows, volumes, timing, and paths that are the stressor(s). As discussed below, flow volumes and timing (i.e., the hydrograph) affect the temporal and spatial variability of the physical environment, a term we use to mean environmental variables like salinity, turbidity, turbulence level, as well as elements of habitat con- nectivity associated with horizontal transport (Cloern 2007, Cowen et al. 2006) and vertical turbulent mixing (Lucas et al. 1998). By flow paths we mean transport of organisms and materials through various regions of the bay delta, including the entrainment of listed species by the water project pumps. The issue of entrainment is dealt with below. The distinction between these two types of flow effects on organisms, the food web, and thus on the ecosystem more generally is important in that sustainable approaches to reducing the effects of flow stressors may be quite different. In particular, the issue of flow paths appears amenable to engineering solutions: With the correct water engineering, entrainment 1 See page 20 for a definition of X2.

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STRESSORS 65 effects might be eliminated, allowing the maintenance of current diversion volumes, or possibly even permitting increased diversions. In a similar fash- ion, the problem some fish species have because of altered flow paths might be solved via strategies such as using information about when specific fish species (at various life stages) are at risk of entrainment and, with the aid of modeling, modify pump operations to reduce entrainment. In contrast, the effects of flow on the physical-chemical environment, most notably the salinity field and its concomitant influences on circulation and transport (Monismith et al. 2002, MacCready and Geyer 2010), do not appear amenable to engineering solutions other than to use specific flow standards tied to water year type and variability, that is, standards like the X2 standard developed by the Environmental Protection Agency in 1995,2 which has subsequently been used as a basis for developing a variety of standards, including the recently proposed and litigated Fall X2 standard as well as X2 rules as described in State Water Resources Control Board (SWRCB) decision 1641.3 In this case, the development of regulations to maintain salinity gradients relies on the central hypothesis that the environ- mentally optimum approach is to try and mimic the shape of the natural hydrograph albeit at a lower level--in other words, to make the system slightly drier than it would be naturally, but maintain the overall pattern of flow. The key conceptual model on which this hypothesis is based is that the current ecosystem is adapted to the presence of a particular seasonal variability in flow, which certainly has varied on evolutionary time scales (Ingram et al. 1996), as discussed by Moyle et al. (2010). As a consequence, many species have life strategies that depend on particular features of flow variability, such as the transport of eggs into suitable habitat at the correct time or the aggregation of ichthyoplankton into regions of higher food availability by gravitational circulation (Arthur and Ball 1979, Kimmerer et al. 1998). Also, the California SWRCB has recently been actively engaged in de- veloping regulations for various aspects of flows and diversions,4 an effort that has been backed up by a detailed examination of the manifold ways in which flows affect bay-delta biota discussed in the technical report pre- sented by Fleenor et al. (2010) to the SWRCB. 2 Federal Register, Volume 60, Number 244. 3 D1641 was finalized in March 2001. 4 Development of Flow Criteria for the Sacramento-San Joaquin Delta Ecosystem, August 3, 2010.

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66 SUSTAINABLE WATER MANAGEMENT IN THE DELTA Hydrologic Factors The term "flow" encompasses a broad range of effects in the bay-delta estuary. We define flow here as freshwater flow, something that has multiple components and in the context of the delta can best be thought of in terms of four major components:5 Sacramento River inflow; San Joaquin River inflow; net delta outflow, the total time averaged flow past Chipps Island at the western edge of the delta; and in-delta diversions, most notably the state and federal water projects. These four are not independent and are represented in an average sense (to a good degree of approximation):6 et delta outflow = Sacramento River inflow N + San Joaquin River inflow In-delta diversions Both of the river flows include the effects of reservoir operations (storage and releases) and diversions in and upstream of the delta, for example, the Hetch Hetchy Aqueduct, which transports Tuolumne River water to the San Francisco Bay Area. Because tidal flows at the eastern end of Suisun Bay are generally an order of magnitude larger than are mean flows (e.g., Walters et al. 1985, Monsen 2000), net delta outflow is a calculated rather than measured quantity. One can look at anthropogenic changes in the hydrology of the bay delta by comparing measured hydrographs with the "unimpaired" hy- drograph, that is, the hydrograph that would have been observed in the absence of the water projects, but including the present delta configura- tion. For example, in their presentation to the SWRCB, Chung and Ejeta (2011) more generally note that, as currently calculated, unimpaired flow is based on the hydrologic behavior of the system at present, rather than the system as it existed before dams, flood control levees, and so on were built. For this reason, the calculated unimpaired flow might actually be significantly different from what actually took place prior to development. Consequently, unimpaired flow should be treated as an approximate upper bound on the natural flow. To our knowledge, an appropriate lower bound has yet to be defined. Finally, besides a reduction in the overall volume of freshwater enter- ing the bay, the timing of flows has also been altered, with peak flows now occurring earlier in the year (February and March) than they would in the absence of water resources development. Here too, the change is not unequivocally due to water resources development: rather, it also appears 5 Besides these flows there are also the East Side streams; see http://www.water.ca.gov/ dayflow/. 6 A full water balance for the delta includes groundwatersurface water exchanges as well as evapotranspiration by delta vegetation (see, e.g., Fox 1987).

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STRESSORS 67 that precipitation in the Central Valley watersheds is increasingly taking the form of rain rather than snow (Dettinger and Cayan 1995, Cloern et al. 2011), a pattern that also tends to shift the hydrograph peak earlier in the year. Thus, to a first approximation, the flow stressor is defined by changes in hydrology, both in volumes and timing. Flow Effects on the Physical Environment In conjunction with mixing from the tides, freshwater flow determines the spatial structure of the salinity field, via the relationship between flow and the position of X2. (The position of X2 is a distance scale--kilometers upstream, or east of the Golden Gate Bridge--for salinity intrusion. Thus, if X2 is at 70 km, it is 70 km east of the Golden Gate Bridge.) The reason is that at steady state the tendency for freshwater flow to carry salt out of the estuary is balanced by the tendency for gravitational circulation and tidal dispersion to carry salt upstream toward the delta. As a result of this balance, the mean position of X2 is proportional to the net delta outflow raised to the minus one-seventh power (Monismith et al. 2002), meaning that it takes much higher flows to move X2 when X2 is farther to the west, or nearer the Golden Gate Bridge, than when it is farther to the east (Figure 3-3). For example, to position X2 at 72 km (opposite Honker Bay), a flow FIGURE 3-3 The position of X2 in kilometers east of the Golden Gate Bridge as a function of flow. SOURCE: Monismith et al. (2002). R02208 Figure 3-3 bitmapped raster image scaled for portait above, landscape below

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142 SUSTAINABLE WATER MANAGEMENT IN THE DELTA Healey, M., M. Dettinger, and R. Norgaard. 2008a. New perspectives on science and policy in the Bay-Delta. Pp. 1-18 in The State of Bay-Delta Science: 2008, edited by M. Healey. Sacramento, CA: CALFED Science Program. Available at http://www.science.calwater. ca.gov/publications/sbds.html. Accessed July 17, 2012. Healey, M. C., M. D. Dettinger, and R. B. Norgaard, eds. 2008b. The State of Bay-Delta Sci- ence, 2008. Sacramento, CA: CALFED Science Program. Heinz Center. 2002. Dam Removal: Science and Decision Making. Washington, DC: The John Heinz III Center for Science, Economics, and the Environmnent. Heppell, S. S. 2007. Elasticity analysis of green sturgeon life history. Environmental Biology of Fishes 79:357-368. Herren, J. R., and S. S. Kawasaki. 2001. Inventory of water diversions in four geographic areas in California's Central Valley. Pp. 343-355 in Contributions to the Biology of Central Valley Salmonids, edited by R. L. Brown. Volume 2. California Fish and Game, Fish Bulletin 179. Heublein, J. C., J. T. Kelly, C. E. Croker, A. P. Klimley, and S. T. Lindley. 2009. Migration of green sturgeon, Acipenser medirostris in the Sacramento River. Environmental Biology of Fishes 84:245-258. Hillman, T. W., and J. W. Mullan. 1989. Effect of hatchery releases on the abundance and behavior of wild juvenile salmonids. Pp. 265-285 in Summer and Winter Ecology of Ju- venile Chinook Salmon and Steelhead Trout in the Wenatchee River, Washington, edited by Don Chapman Consultants. Final Report to Chelan County Public Utility District. Hoekstra, J. M., K. K. Bartz, M. H. Ruckelshaus, J. M. Moslemi, and T. K. Harms. 2007. Quantitative threat analysis for management of an imperiled species: Chinook salmon (Oncorhynchus tshawytscha). Ecological Applications 17:2061-2073. Hornberger, M.I., S. N. Luoma, A. van Geen, C. Fuller, and R. Anima. 1999. Historical trends of metals in the sediments of San Francisco Bay, California. Marine Chemistry 64:39-55. Hornberger, M. I., S. N. Luoma, D. J. Cain, F. Parchaso, C. L. Brown, R. M. Bouse, C. Wellise, and J. K. Thompson. 2000. Linkage of bioaccumulation and biological effects to changes in pollutant loads in South San Francisco Bay. Environmental Science Tech- nology 34:2401-2409. HSRG (Hatchery Scientific Review Group). 2009. System-Wide Report on Columbia River Hatchery Reform. Available at http://hatcheryreform.us/hrp/reports/system/welcome_ show.action Accessed July 16, 2012. Hunt, J. W., B. S. Anderson, B. M. Phillips, R. S. Tjeerdema, K. M. Taberski, C. J. Wilson, H. M. Puckett, M. Stephenson, R. Fairey, and J. Oakden. 2001. A large-scale categori- zation of sites in San Francisco Bay, USA, based on the sediment quality triad, toxicity identification evaluations, and gradient studies. Environmental Toxicology and Chemistry 20:1252-1265. IEP (Interagency Ecological Program for the San Francisco Estuary). 2006. Interagency Eco- logical Program Synthesis of 2005 Work to Evaluate the Pelagic Organism Decline (POD) in the Upper San Francisco Estuary. Available at http://www.water.ca.gov/iep/docs/pod/ synthesis_report_111405.pdf. Accessed July 25, 2012. Ihde, T. F., M. J. Wilberg, D. L. Loewensteiner, D. H. Secor, and T. J. Miller. 2011. The increas- ing importance of marine recreational fishing in the US: Challenges for management. Fish and Fisheries 108:268-276. Ingram, B. L., J. C. Ingle, and M. E. Conrad. 1996. A 2000 yr record of Sacramento-San Joaquin River inflow to San Francisco Bay estuary, California. Geology 24:331-334. Irvine, J. 2010. 2010 Sendai Salmon Workshop on Climate Change. Newsletter of the North Pacific Marine Science Organization 18(2):22-23.

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