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3 The Life Histories of the Fishes INTRODUCTION Chinook salmon (Oncorhynchus tshawytscha), steelhead (Oncorhynchus mykiss), and green sturgeon (Acipenser medirostris) are anadromous species; that is, they spawn in freshwater but spend a portion of their life in saltwater. Delta smelt (Hypomesus transpacificus) are resident within the brackish and freshwater habitats of the delta. In both anadromous and resident life-history strategies the fish migrate from their natal habitat into their adult habitat and then back to the spawning habitat, completing the life cycle. The fish do not simply drift between their habitats, but have evolved specific life-stage behav- iors to meet the challenges they confront. These behaviors are cued by the fishes’ physiology and by environmental conditions, which together drive the timing and movement of the individuals through their life cycle. Because all species spend time in the delta, they share some environmental conditions and challenges, but their different life histories cause them also to face unique chal- lenges. Many of the challenges are the result of anthropogenic modifications to the delta and river habitats, and these challenges are of particular concern (see Chapter 5). Some, but not all, of them are addressed in the RPAs. The informa- tion on the fishes’ life histories presented below illustrates the complexity of their interactions with their environments and the potential importance of appar- ently small changes in the timing, direction, and magnitude of variations in flow, salinity, turbidity, water temperature, and other environmental conditions. FISHES OF THE SALMON FAMILY The delta provides habitat for two species of Pacific salmon, Chinook salmon (hereafter “salmon”) and the rainbow trout-steelhead complex. Pacific salmon typically are anadromous. There are many exceptions, however, such as rainbow trout, which although apparently genetically identical to steelhead, are 22

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The Life Histories of the Fishes 23 not anadromous; and there is a great deal of variation in their life histories (Wil- liams, 2006). When adult salmon, steelhead, and sturgeon return from the ocean and be- gin their upriver migration, they experience several challenges, including physi- cal and water-quality blockages. Here the delta water system has had a great impact on populations, for 80 percent of the historical spawning habitat for Chi- nook salmon (Clark, 1929) and much of it for the other species has been blocked by the storage reservoirs of the Central Valley (Lindley et al., 2006). Summer temperatures in the Central Valley waterways can reach potentially lethal levels for salmon, increasing their susceptibility to disease and decreasing metabolic efficiency (Myrick and Cech, 2001, 2004). The timing of adult salmon runs leads them to avoid most of the detrimental effects of high summer temperatures because they enter the delta and swim upriver to their spawning habitats and hatcheries in the spring, autumn, and winter. Wild spawning fish excavate redds in stream reaches with loose gravel in shallow riffles or along the margins of deeper runs (NMFS, 2009), where temperatures are cooler and eggs buried in the gravel receive a sufficient flux of oxygenated water through interstitial flow. The eggs incubate for several months and after emerging the young fry either immediately begin their migration back to the ocean or spend several weeks to a year in freshwater before migrating. Because of this diversity, juvenile salmon and steelhead pass through the delta throughout the year; however, the timing and size of the migrants generally corresponds to specific runs (Lindley et al., 2006; Williams, 2006). Salmon and steelhead undergo a complex set of physiological changes in preparation for their migration to the ocean known as “smoltification,” after which the young fish are known as “smolts.” The alteration of the fish’s physi- ology to successfully osmoregulate in saltwater after beginning life in freshwater is a significant challenge that can be exacerbated by human-caused environ- mental changes (e.g., NRC, 2004b). Most Central Valley Chinook salmon mi- grate to the ocean within a few months of hatching and the smolts are less than 10 cm long, although some remain in freshwater for up to a year. Juvenile steelhead migrate to sea after one to three years in freshwater, and can be as large as 25 cm in length. Young migrating Chinook are much more vulnerable to entrainment in adverse flows than the stronger-swimming steelhead smolts. Juvenile salmon migrants experience predation during their downstream migration through the Sacramento River or through the interior delta on their way to the sea. Fish that enter the central delta, driven by the strong tidal and pumping-induced flows, are moved through a labyrinth of channels, which fur- ther delays their migration and exposes them to additional predators (Perry et al., 2010). Finally, fish that enter the Old and Middle Rivers (OMR) can be drawn

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24 Threatened and Endangered Fishes in California’s Bay-Delta towards the SWP and CVP pumps (Kimmerer, 2008a). Juvenile salmon that successfully pass through the delta enter the ocean and spend one or more years there before returning to freshwater to spawn. Ocean survival is particularly de- pendent on the conditions the fish experience during the first few months they enter the saltwater (Lindley et al., 2009). Fish that are drawn into the central and southern delta by reverse flows are more vulnerable to predation than those that take a more direct path to the ocean, and other aspects of changed environ- mental conditions also expose them to predators (for more detail, see Chapter 5). GREEN STURGEON The Central Valley green sturgeon (Acipenser medirostris) is an anadro- mous fish that can reach 270 cm (nearly nine feet) in length with a maximum age of 60 to 70 years (Moyle et al., 2002). The historical distribution of green sturgeon is poorly documented, but they may have been distributed above the locations of present-day dams on the Sacramento and Feather Rivers (Beames- derfer et al., 2007). Information on the distribution of green sturgeon in the San Joaquin River is lacking. Mature green sturgeon enter the Sacramento River from the ocean in March and April. The Red Bluff Diversion Dam can impede their migrations (Heublein et al., 2009). After spawning, green sturgeon may immediately leave the river or hold over in deep pools until the onset of winter rains (Erikson et al., 2002; Heublein et al., 2009). Individuals then migrate back to the ocean and return to freshwater to spawn every two to four years (Erickson and Webb, 2007; Lindley et al., 2008) Based on adult spawning behavior and the habitats required for green stur- geon embryo development, reproductive females likely select spawning areas with turbulent, high velocities near low-velocity resting areas. Green sturgeon spawning areas are presumed to be characterized by coarser substrates upstream of lower gradient reaches, which usually have slower velocities. Eggs and milt are released in turbulent water above deep, complex habitats; fertilized eggs drift into deeper areas and stick onto the substrate. Eggs require cool temperatures for development and hatch after approximately a week. Larval and juvenile green sturgeons are bottom-oriented and nocturnally active until a few months of age (Kynard et al., 2005). Juvenile green sturgeon migrate into seawater portions of natal estuaries as early as one and a half years old (Allen and Cech, 2007), and eventually emigrate to nearshore coastal waters by three years old. Subadults are migratory, spending their next 12 to16 years foraging in the coastal ocean and entering western estuaries during the summer (Moser and Lindley, 2007). In the ocean, green sturgeon inhabit the coastal shelf out to 100m depth with occa-

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The Life Histories of the Fishes 25 sional, rapid vertical ascents near or to the surface (Erickson and Hightower, 2006). DELTA SMELT The delta smelt is a near-annual species; most individuals complete their life cycle in one year, but some survive for two years and reproduce again. Delta smelt reside in brackish waters around the western delta and Suisun Bay region of the estuary, being commonly found in salinities of 2 to 7, but the range they occupy extends from 0 (freshwater) to 15 or more (Moyle, 2002). In the winter (December to April), pre-spawning delta smelt migrate to tidal freshwater habitats for spawning, and larvae rear in these areas before emigrating down to the brackish water (Bennett, 2005). Delta smelt inhabit open waters away from the bottom and shore-associated structural features. Although delta smelt spawn- ing has never been observed in the wild, information about related members of the smelt family suggests that delta smelt use bottom substrate and nearshore features during spawning. Juvenile and adult stages, 20-70 mm in length, are generally caught in the western delta and Suisun Bay in the landward margin of the brackish salinity zone, which may extend upstream of the confluence zone of the Sacramento and San Joaquin Rivers. Historically pre- and post-spawned fish were observed throughout the delta. In wet years, spawning adults often were observed in the channels and sloughs in Suisun Marsh and the lower Napa River. In the brackish habitat of the western delta the flow is tidal with a net sea- ward movement, and so to maintain position, the juvenile fish appear to coordi- nate swimming behavior with the tides, occurring near the surface on the flood tides and at depth on the ebbs. However, in other regions, adaptive tidal behav- ior has not been observed and fish simply move with the tides, which may pro- mote horizontal exchange to adjacent shallow water habitats. The FWS biologi- cal opinion emphasizes the complexity of this behavior (p. 651) and thus the above description is a general one that does not capture details that might be important. The brackish zone also has higher densities of other fishes and zooplankton, suggesting that it may serve as a nursery habitat for delta smelt and other fishes (Bennett, 2005). The spawning movement of adults from their brackish habitat in the western delta landward to the freshwater portions of the delta is triggered by high flows and turbidity pulses. This diversity of paths from the low-salinity (brackish) zone to the freshwa- ter spawning habitats suggests that delta smelt do not have fidelity to specific

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26 Threatened and Endangered Fishes in California’s Bay-Delta structural habitats as do salmon. Instead, their upstream movement is directed by a combination of physiological and environmental cues that involve salinity, turbidity, and both net and tidal flows through the channels of the delta and its tributaries. Additionally, since 2005, approximately 42 percent of the current delta smelt population is in the Cache Slough complex north of the delta, and may represent an alternative life-history strategy in which the fish remain up- stream through maturity (Sommer et al., 2009). Historically, the complete delta-smelt life cycle occurred unobstructed throughout the delta. Human-caused changes in delta water quality and hydro- dynamics have disrupted the cycle and since 2005, delta-smelt population densi- ties have been extremely low in the traditional habitats in the central and south delta (http://www.dfg.ca.gov/delta/data/), and pump salvage1 also has been ex- tremely low, about four percent of the 50-year average index (http://www.dfg.ca. gov/delta/data/townet/indices.asp?species=3). Analyses seeking causes for the declines to the present condition have focused on relationships between abun- dance, salvage, water exports, delta flows, turbidity, and food. Kimmerer (2008b) found that delta-smelt survival between summer (juvenile) and fall (adult) was related to zooplankton biomass, suggesting that high zooplankton abundances contributed to delta-smelt abundance and residence time in the southern delta, and thus increased entrainment risk at the pumps. Grimaldo et al. (2009) found that between 1995 and 2005 the inter-annual variation in adult delta-smelt salvage was best correlated with turbidity and the interaction of OMR2 flows and X23. The annual salvage of age-0 delta smelt (fish hatched in that year, around 27 mm in length) was best correlated with spring abundance of zooplankton, OMR flows, and turbidity. Additionally, Grimaldo et al. suggested that differences in temporal patterns of entrainment of delta smelt between years may be a measure of the degree to which their physical habitat overlapped with the hydrodynamic footprint of negative OMR flows towards the pumps. How- ever, the year-class strength of adult delta smelt was not related to salvage, al- 1 “Salvage” refers to fish caught in the pumps and retrieved alive to be released elsewhere in the system. It often is used as a surrogate estimate for “take” by the pumps. 2 The term “OMR flows” refers to flows in the Old and Middle Rivers (see Figure 1-1), which are affected by the pumping of water for export. At high negative flows, that is, flows away from the sea towards the pumps in the south, the normal seaward flow associated with ebb tides can be completely eliminated. 3 “X2” refers to the salinity isohaline of salinity 2 (a contour line of equal salinity). Some- times X2 is used as shorthand for the mean position of that isohaline, measured in kilome- ters upstream from the Golden Gate Bridge over the outlet of San Francisco Bay. Manag- ing the position of X2 is a major aspect of the delta smelt Biological Opinion and RPA; it is managed by adjusting flows of fresh water from delta reservoirs, as well as by adjusting pumping rates.

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The Life Histories of the Fishes 27 though the position of X2 was correlated with salvage at an intra-annual scale when OMR flows were negative. Other analyses showed a similar correlation (e.g., FWS, 2008). While the correlation between OMR flows and salvage is substantial (Kimmerer, 2008b), their effect on population dynamics is not clear (Bennett, 2005; Grimaldo et al., 2009). Indirect factors could have contributed to popula- tion declines through a reduction in the size and abundance of food in the brack- ish zone. Overall zooplankton abundance is correlated with delta smelt survival (Feyrer et al., 2007; Grimaldo et al., 2009; Kimmerer, 2008b). Zooplankton abundance has been reduced through several factors, including the introduction of the overbite clam (Corbula amurensis), an efficient grazer of zooplankton in the low-salinity zone, and changes in nutrients that have altered the phytoplank- ton population so that cyanobacteria, which can reduce the food supply for zoo- plankton, have increased while diatoms have declined (FWS, 2008). The change in zooplankton species, associated with the success of invasive species in changed environmental conditions, also is probably important. It has been sug- gested that the position of X2 affects the size of delta smelt habitat and thus it affects the susceptibility of juvenile and adult delta smelt to pump entrainment (Feyrer et al., 2007, Kimmerer, 2008a). Furthermore, the mean position of X2 has moved inland about 10 km over the past 15 years (FWS, 2008, p. 180). However, there is no direct evidence relating these indirect effects to population numbers of smelt (Bennett, 2005; Kimmerer, 2002). In addition, delta smelt are now largely absent from the central and southern delta, while a significant por- tion of the remaining population exists in the Cache Slough complex to the north. These changes increase the uncertainty surrounding current estimates of delta smelt population changes in response to alterations in delta hydraulics.