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IntroductionUnderstanding how abundance, productivity and distribution of individual species may respond to climate change is a critical first step towards anticipating alterations in marine ecosystem structure and function, as well as developing strategies to adapt to the full range of potential changes.MethodsThis study applies the NOAA (National Oceanic and Atmospheric Administration) Fisheries Climate Vulnerability Assessment method to 64 federally-managed species in the California Current Large Marine Ecosystem to assess their vulnerability to climate change, where vulnerability is a function of a species’ exposure to environmental change and its biological sensitivity to a set of environmental conditions, which includes components of its resiliency and adaptive capacity to respond to these new conditions.ResultsOverall, two-thirds of the species were judged to have Moderate or greater vulnerability to climate change, and only one species was anticipated to have a positive response. Species classified as Highly or Very Highly vulnerable share one or more characteristics including: 1) having complex life histories that utilize a wide range of freshwater and marine habitats; 2) having habitat specialization, particularly for areas that are likely to experience increased hypoxia; 3) having long lifespans and low population growth rates; and/or 4) being of high commercial value combined with impacts from non-climate stressors such as anthropogenic habitat degradation. Species with Low or Moderate vulnerability are either habitat generalists, occupy deep-water habitats or are highly mobile and likely to shift their ranges.DiscussionAs climate-related changes intensify, this work provides key information for both scientists and managers as they address the long-term sustainability of fisheries in the region. This information can inform near-term advice for prioritizing species-level data collection and research on climate impacts, help managers to determine when and where a precautionary approach might be warranted, in harvest or other management decisions, and help identify habitats or life history stages that might be especially effective to protect or restore.

The expression of anadromy in partially migratory salmonid populations is influenced by sex-specific interactions among an individual’s genotype, condition, and environment, but genotype–phenotype relationships prior to the expression of migratory type are poorly understood. We examined whether juvenile growth and condition differed with respect to sex and a migration-associated genomic region (Omy05) in a coastal California population of steelhead and rainbow trout (Oncorhynchus mykiss). Sex and Omy05 genotype had additive effects on annual growth from age 0+ to age 1+ (∼6–18 months old), with higher growth in males and individuals with copies of the rearranged–resident haplotype. Condition at age 1+ increased with the number of copies of the rearranged–resident haplotype, with similar support for additive or interactive effects with sex; additive effects suggested that genotype differences occurred in both sexes and also that condition was slightly higher in males, while interactive effects suggested that the genotype differences occurred only in males. Our results indicate that phenotypic differences related to sex and Omy05 genotype occur well in advance of anadromous migration or freshwater maturation in this southern O. mykiss population.

Steelhead (Oncorhynchus mykiss) are a species of conservation concern in California’s Sacramento River, and their poor status is hypothesized to be due in significant part to poor survival in freshwater. We used acoustic telemetry to examine the migratory survival of hatchery reared steelhead smolts through five contiguous regions of the Sacramento River and its estuary (upper river, lower river, delta, north bays, central San Francisco Bay) from 2006 to 2011. We consistently observed the highest losses in the upper river with only 20.5%, 33.7%, 43.3%, 21.3%, and 29.0% of the tagged population successfully passing through the 210-km region in years one through five respectively. Average migratory success was similar among the other regions with reduced rates of loss in the lower river (139.5-km, 8.4% ± 4.2), delta (99-km, 7.9% ± 3.4), and Estuary (69.5-km, 6.8% ± 2.9). The average survival through the Sacramento River to the Pacific Ocean across all five years was 5.6% ±3.6 SE. In the first study year we observed tagged steelhead responding to an increase in river discharge. Sixty-seven percent of all steelhead that successfully migrated to the entrance to the Pacific Ocean began their migration during an increased discharge event. A similar pattern was observed in years two, four and five (77.8%, 77.8%, and 84%). Steelhead survival rates to the Pacific Ocean were highest in year five of the study (9.3% in January and 8.0% in December) when the largest discharges in the Sacramento River were observed (2200 m3 s−1).

Sturgeon diet and feeding habitats are notoriously difficult to document. We mapped the locations of feeding pits in Willapa Bay, Washington, to characterize estuarine habitats used by sub-adult and adult sturgeon for infaunal feeding. Monthly summer surveys of intertidal plots revealed that feeding pit density was highest in July and August, when sturgeon occupy Willapa Bay. The ephemeral nature of feeding pits and high daily densities (> 1000 pits/ha) indicated intensive sturgeon feeding over unvegetated littoral mud flats during high tide. Feeding pit density was lowest in subtidal areas, over sand (grain sizes primarily >63 μ), and at sites with dense stands of non-indigenous seagrass, Zostera japonica. Sub-adult and adult sturgeon apparently used these habitats significantly less than would be predicted based on their availability. Feeding pit formation was negatively correlated with Z. japonica shoot dry weight and positively correlated with the abundance of thalassinid shrimp burrows. Experimental removal of Z. japonica resulted in increased sturgeon feeding, but experimental removal of burrowing shrimp did not significantly affect feeding pit formation. Aquaculture activities that harden substrate and proliferation of invasive seagrass both appear to produce estuarine substrates that are unsuitable for benthic feeding by sturgeon.

There is currently only a limited understanding of the relationship between water quality and predation on Pacific salmon Oncorhynchus spp. smolts. We addressed the hypothesis that poor water quality will decrease a smolt’s swimming performance and presumably its predator evasion capabilities. Predation is a major factor affecting salmon smolt survival throughout the San Joaquin River and the Sacramento–San Joaquin Delta of California. Prior studies have quantified predation rates, but the effect of water quality on predator evasion capability has not previously been evaluated. We quantified the swimming performance of juvenile Chinook Salmon O. tshawytscha in relation to water quality variables. The maximum swim speeds (Umax) of 45 hatchery-reared smolts (7.1–9.9 cm FL) were measured in controlled (laboratory) and field environments by using a mobile swim tunnel respirometer; measurements were obtained before and after the fish received a 2-d exposure to the lower San Joaquin River while being he...

Summary Green Sturgeon (GRS) Acipenser medirostris is one of the most marine-oriented of all sturgeons. It primarily spawns in the Sacramento, Klamath, and Rogue Rivers, yet lives most of its life in estuarine and coastal waters along the West Coast of North America. Spawning is only known to occur in the Rogue, Klamath and Sacramento rivers and optimal temperatures for egg incubation and larval growth are not always maintained in these dammed and highly-regulated systems. Genetic analysis and acoustic telemetry have confirmed the presence of two genetically distinct populations; the southern population is listed as “threatened” under the ESA. Adults only enter natal rivers to spawn every 1–4 years. They make extensive coastal migrations in depths

Outmigration survival of acoustic-tagged, hatchery-origin, late-fall-run Chinook salmon (Oncorhynchus tshawytscha) smolts from the Sacramento River was estimated for 5 years (2007–2011) using a receiver array spanning the entire outmigration corridor, from the upper river, through the estuary, and into the coastal ocean. The first 4 years of releases occurred during below-average river flows, while the fifth year (2011) occurred during above-average flows. In 2011, overall outmigration survival was two to five times higher than survival in the other 4 years. Regional survival estimates indicate that most of the improved survival seen in 2011 occurred in the riverine reaches of the outmigration corridor, while survival in the brackish portions of the estuary did not significantly differ among the 5 years. For the 4 low-flow years combined, survival rate in the river was lower in the less anthropogenically modified upper reaches; however, across all regions, survival rate was lowest in the brackish portion of the estuary. Even in the high-flow year, outmigration survival was substantially lower than yearling Chinook salmon populations in other large rivers. Potential drivers of these patterns are discussed, including channelization, water flow, and predation. Finally, management strategies are suggested to best exploit survival advantages described in this study.

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This study considered whether different population viability analyses give similar estimates of extinction risk across management contexts. We compared the performance of population viability analyses developed by numerous scientific teams to estimate extinction risk of anadromous Pacific salmonids listed under the U.S. Endangered Species Act and challenged each analysis with data from 34 populations. We found variation in estimated extinction risk among analytical techniques, which was driven by varying model assumptions and the inherent uncertainty of risk forecasts. This result indicates that the scientific teams developed techniques that perform differently. We recommend that managers minimize uncertainty in risk estimates by using multiple models tailored to the local ecology. Assessment of relative extinction risk was less sensitive to model assumptions than was assessment of absolute extinction risk. Thus, the former method is better for comparing population status and raises caution about...

Steelhead trout, Oncorhynchus mykiss, are known to expel acoustic tags which can negatively bias population survival estimates. Tag burden may also affect the development and behavior of smolts, thereby impacting the results of population and behavioral studies. We monitored the growth, condition, and tag expulsion rate of steelhead trout in similar-sized individuals and used these data to adjust survival rates from an acoustic telemetry study conducted in the Sacramento River. Eighty fish were surgically implanted with tags—40 with cylindrical tags of 9 mm diameter and 21 or 24 mm length (V9, Vemco Ltd) and 40 with a 7 mm diameter and 20 mm length tag (V7, Vemco Ltd)—to examine the impact of tag size on peritoneal retention and survival rate of juvenile steelhead trout. A total of 20 % (16/80) of all tags were expelled by smolts during the 143-day study. Ten V9 tags were expelled between day 18 and day 66. Six V7 tags were expelled between day 21 and day 143. A statistical difference was found for retention rate by surgeon even though the surgeons were of equal experience and received the same training. There were no significant differences in the tag retention rate in relation to the tag/body weight ratio, or in growth (weight or fork length) among the control, V7 or V9 treatment groups over the duration of the study. All individuals survived throughout the experiment. Two methods were used to adjust the survival estimates of an acoustic telemetry data set from the Sacramento River based on the tag retention study. First, a simple individual censorship approach in Program MARK was utilized and next ATLAS, a software program designed to compensate for bias in survival estimates caused by tag failures was used. The results of the adjusted survival estimates were not significantly different from the unadjusted rates suggesting that it may be more important to focus on improving surgical techniques to reduce tag expulsion rather than adjusting survival estimates dependent on the study. The surgical techniques utilized in this study did not have significant impacts on the growth rates of either of the tag treatment groups compared to the control. However, tag retention was an issue regardless of the size and weight of the implanted tag and the size of the steelhead.

Understanding smolt migration dynamics is a critical step in the preservation and conservation of imperiled salmonids in California's Sacramento River system. Late-fall run Chinook salmon yearling smolts were acoustically tagged and tracked during their out- migration through California's Sacramento River and San Francisco Estuary during 2007-2009. Migration rates were 14.3 km·day -1 (± 1.3 S.E.) to 23.5 km day -1 (± 3.6 S.E.), similar to rates published for other West Coast yearling Chinook salmon smolt emigrations. Region-specific movement rates were fastest through the upper river regions, and slowest in the Sacramento/ San Joaquin River Delta. River travel times were recorded for smolts travelling through a series of ten monitor-delimited reaches. Using these, a smolt travel time model determined by two parameters (movement rate and rate of population spreading) was then used to determine the influence of different factors on the model's fit, using model selection with Akaike's In- formation Criterion. The model that allowed for both year and reach to be expressed additively for both travel time and population spreading rate estimates, while accounting for a "release" effect, was the best supported model. Finally, several models incorporated environmental data as a linear predictor of movement rates. The addition of the environmental variables, in order of importance, river width to depth ratio, river flow, water turbidity, river flow to mean river flow ratio, and water velocity all resulted in improved mod- el fit. Water temperature did not improve model fit. These environmental associations are discussed and potential improvements on the travel time model are suggested.

We used ultrasonic telemetry to describe the movement patterns of late-fall run Chinook salmon (Oncorhynchus tshawytscha) and steelhead trout (O. mykiss) smolts during their entire emigration down California’s Sacramento River, through the San Francisco Bay Estuary and into the Pacific Ocean. Yearling hatchery smolts were tagged via intracoelomic surgical implantation with coded ultrasonic tags. They were then released at four upriver locations in the Sacramento River during the winters of 2007 through 2010. Late-fall run Chinook salmon smolts exhibited a nocturnal pattern of migration after release in the upper river. This is likely because individuals remain within a confined area during the day, while they become active at night and migrate downstream. The ratio between night and day detections of Chinook salmon smolts decreased with distance traveled downriver. There was a significant preference for nocturnal migration in every reach of the river except the Estuary. In contrast, steelhead smolts, which reside upriver longer following release, exhibited a less pronounced diel pattern during their entire migration. In the middle river, Delta, and Estuary, steelhead exhibited a significant preference for daytime travel. In the ocean Chinook salmon preferred to travel at night, yet steelhead were detected on the monitors equally during the night and day. These data show that closely related Oncorhynchus species, with the same ontogenetic pattern of out-migrating as yearlings, vary in migration tactic.

– Differential rates of anadromy between males and females are common in partially migratory salmonid populations, but this pattern is not fully clear for Oncorhynchus mykiss (rainbow trout/steelhead) from the limited but mixed data available. In particular, there are very few data on sex ratios of juvenile and nonanadromous (resident) fish to help assess sex composition of various life stages and life-history types. We used a recently developed Y-chromosome genetic marker to assess sex ratio of stream-dwelling (i.e., juvenile and nonanadromous) O. mykiss in a small coastal basin in central California, USA. We analysed 384 samples collected from three contiguous study reaches over 3 years. Sex ratio was 1:1 among juvenile-sized O. mykiss (

Green sturgeon Acipenser medirostris spend much of their lives outside of their natal rivers, but the details of their migrations and habitat use are poorly known, which limits our understanding of how this species might be affected by human activities and habitat degradation. We tagged 355 green sturgeon with acoustic transmitters on their spawning grounds and in known nonspawning aggregation sites and examined their movement among these sites and other potentially important locations using automated data-logging hydrophones. We found that green sturgeon inhabit a number of estuarine and coastal sites over the summer, including the Columbia River estuary, Willapa Bay, Grays Harbor, and the estuaries of certain smaller rivers in Oregon, especially the Umpqua River estuary. Green sturgeon from different natal rivers exhibited different patterns of habitat use; most notably, San Francisco Bay was used only by Sacramento River fish, while the Umpqua River estuary was used mostly by fish from the Kla...

Summary Conservation of the threatened green sturgeon Acipenser medirostris in the Sacramento River of California is impeded by lack of information on its historical distribution and an understanding of how impassable dams and altered hydrographs are influencing its distribution. The habitat preferences of green sturgeon are characterized in terms of river discharge, velocity, channel gradient, and air temperature associated with 2590 sightings of green sturgeon in the Klamath and Rogue rivers using the Mahalanobis distance D2, a multivariate measure of distance from the mean habitat conditions associated with the sightings. D2 was then calculated for reaches of the Sacramento and San Joaquin rivers and their tributaries under historic and current (2007) hydrographs to assess where and when habitat conditions in the Sacramento–San Joaquin basin are similar to those known to support green sturgeon. The model for current habitat conditions was validated with observations of acoustically-tagged green sturgeon at large in the basin in 2007. The model predicts that in the absence of impassable dams and altered hydrographs, green sturgeon would utilize the mainstem Sacramento and San Joaquin rivers, and several major tributaries including portions of the lower Feather River, American River, and Yuba River. While dams block access to about 9% of historically available habitat, it is likely that the blocked areas contained relatively high amounts of spawning habitat because of their upstream position in the river network. Flow regulation below the reservoirs has mixed effects on habitat suitability for green sturgeon, with many reaches showing increased suitability in winter and spring, but with some reaches showing decreased suitability in many months, particularly late spring through early autumn. Overall, it appears that the main effect of construction of large water-storage reservoirs in the Sacramento–San Joaquin river basin has been to curtail the distribution of green sturgeon within this basin.

Adult green sturgeon, Acipenser medirostris, were collected in San Pablo Bay, California, and surgically implanted with ultrasonic acoustic tags from 2004 to 2006. An array of automated acoustic monitors was maintained in the Sacramento River to record movements of these fish. We presumed movements to known spawning areas (based on previous green sturgeon egg collections) or areas with potential spawning habitat (characterized by substrate, flow, and temperature criteria) represented a “spawning migration.” Three separate annual “spawning migrations” were recorded involving 15 individuals. The majority of the Sacramento River migrants entered the system in the months of March and April. Two different patterns of “spawning migration” and out-migration were observed. Six individuals potentially spawned, over-summered and moved out of the river with the first fall flow event. This is believed to be the common behavior of the green sturgeon. Alternatively, nine individuals promptly moved out of the Sacramento River before 1 September, and any known flow or temperature cue. Some green sturgeon appeared to be impeded on their upstream movement by the 15 May closure of the Red Bluff Diversion Dam, and at least five passed under the dam gates during downstream migration. A delay in the closure of the Red Bluff Diversion Dam would likely allow upstream passage of spawning green sturgeon, further, the potential mortality affects of downstream passage beneath the Red Bluff Diversion Dam should be assessed. Specific protection should be also given to the large aggregation of green sturgeon located in the reach of the Sacramento River adjacent to the Glen Colusa Irrigation District pumping facility.

Terrestrial invertebrates are a major source of prey for salmonids in many streams. Their importance as prey appears to be related to (1) the seasonal timing of terrestrial inputs relative to the abundance of aquatic prey and (2) water temperature, which affects food demand by fish. Most studies of seasonal patterns of terrestrial inputs have come from temperate systems, and patterns in most other systems are unknown. We measured monthly biomass of aquatic invertebrates, input of terrestrial invertebrates, and diets of Oncorhynchus mykiss (non-anadromous and juvenile anadromous life history forms) for 15 months in two streams in a basin with a Mediterranean-type climate on the Big Sur coast of California. Biomass of aquatic invertebrates and terrestrial inputs followed a similar seasonal pattern; highest levels occurred in summer and early autumn and were highly correlated with water temperature. Total annual input of terrestrial invertebrates was 8.7 g·m−2·year−1, and terrestrial inputs provided...

An understanding of the distribution of North American green sturgeon Acipenser medirostris in coastal waters is crucial to minimize impacts on this vulnerable species from various fisheries. To determine migratory patterns, we tagged 213 subadult and adult green sturgeon in spawning rivers and summer aggregation areas with uniquely coded ultrasonic pingers and observed their coastal movements with arrays of automated hydrophones deployed along the West Coast of North America from southeast Alaska to Monterey Bay, California. Green sturgeon exhibited an annual migration along the continental shelf from U.S. to Canadian waters in the fall and an apparent return migration in the spring. Peak migration rates exceeded 50 km/d during the springtime southward migration. Large numbers of green sturgeon were detected near Brooks Peninsula on northwest Vancouver Island, British Columbia, during May-June and October-November. A single fish was detected in southeast Alaska in December. This pattern of detec...

Bayesian hierarchical state-space models are a means of modeling fish population dynamics while accounting for both demographic and environmental stochasticity, observation noise, and parameter uncertainty. Sequential importance sampling can be used to generate posterior distributions for parameters, unobserved states, and random effects for population models with realistic dynamics and error distributions. Such a state-space model was fit to the Sacramento River winter-run Chinook salmon Oncorhynchus tshawytscha population, where a key objective was to develop a tool for predicting juvenile out-migration based on multiple sources of data. One-year-ahead 90% prediction intervals based on 1992−2003 data, while relatively wide, did include the estimated values for 2004. Parameter estimates for the juvenile production function based on the state-space model formulation differed appreciably from Bayesian estimates that ignored autocorrelation and observation noise.

Green sturgeon, Acipenser medirostris, are the most marine-oriented of North American sturgeons. However, their estuarine/marine distribution and the seasonality of estuarine use are largely unknown. We used acoustic telemetry to document the timing of green sturgeon use of Washington estuaries. In the summers of 2003 and 2004, uniquely coded acoustic transmitters were surgically implanted in green sturgeon captured using commercial gillnets. All sturgeon tagged were greater than 1.2 m total length. They were caught, tagged, and released in both Willapa Bay (n = 49) and Columbia River (n = 11) estuaries. We deployed an array of four fixed- site acoustic receivers in Willapa Bay to detect the estuarine entry and exit of these and any of over 100 additional green sturgeon tagged in other systems during 2003 and 2004. Green sturgeon occurred in Willapa Bay in summer when estuarine water temperatures exceeded coastal water temperatures by at least 2°C. They exhibited rapid and extensive intra- and inter- estuary movements and green sturgeon from all known spawning populations were detected in Willapa Bay. We hypothesize that green sturgeon optimize their growth potential in summer by foraging in the relatively warm, saline waters of Willapa Bay and we caution that altering the quality of estuarine habitats could negatively affect this species throughout its range.

The National Marine Fisheries Service (NMFS) is charged with restoring and protecting anadromous Pacific salmon stocks in all habitats of U.S. waters, including their period of residence in estuarine and oceanic waters. Recent studies have implicated the estuarine and coastal phase of the salmon life cycle as being of equal importance to the freshwater phase in determining production. Evaluation of the freshwater phase of salmon has yielded a better understanding of the factors limiting production in this environment; however, a comparable understanding in the marine environment is lacking. Currently, some marine salmon research is being conducted at various NMFS labs on the West Coast, but there has been little attempt to coordinate activities among the different regions. In response, we propose a comprehensive plan to address ocean and estuarine survival of salmon by identifying research needs and suggesting ways to meet these needs. We recommend that NMFS research focus on (1) distribution and...

We report rates of gross and net O2 production measured in vitro during JGOFS cruises in the equatorial Pacific in spring and fall, 1992. We scale O2 productivities to net and gross C production. We then compare the calculated rates with 14C production and with new/export production measured by various techniques. 14C productivities in samples incubated for 24 h are about 45% of gross carbon production rates calculated from gross O2 production. The difference is compatible with expected rates of the Mehler reaction, photorespiration, excretion, and community mitochondrial respiration. 14C production rates are similar to net carbon production rates in the upper half of the euphotic zone. At lower irradiances, where net C production can be zero or less, 14C productivities lie between net community production and gross primary production. Net carbon production rates in vitro are a factor of =4–20 times greater than estimates from drifting sediment trap and tracer transport studies. This difference probably reflects anomalous accumulation of POC in bottles because of the exclusion of grazers.

Recent studies in the central equatorial Pacific allow a comprehensive assessment of phytoplankton regulation in a high-nutrient, low-chlorophyll (HNLC) ecosystem. Elemental iron enters the euphotic zone principally via upwelling and is present at concentrations (530 PM) well below the estimated half-saturation constant (120 PM) for the large cells that bloom with iron enrichment. In addition, the meridional trend in quantum yield of photosynthesis suggests that even the dominant small phytoplankton are held below their physiological potential by iron deficiency. Grazing by microzooplankton dominates phytoplankton losses, accounting for virtually all of the measured phytoplankton production during El Nina conditions and -66% during normal upwelling conditions, with mesozooplankton grazing and lateral advection closing the balance. Nitrate uptake is strongly correlated with the pigment biomass of diatoms, which increase in relative abundance during normal upwelling conditions. Nonetheless, the f-ratio remains low (0.07-0.12) under all conditions. Iron budgets are consistent with the notions that new production is determined by the rate of new iron input to the system while total production depends on efficient iron recycling by grazers. Although the limiting substrates differ, the interactions of resource limitation and grazing in HNLC regions are conceptually similar to the generally accepted view for oligotrophic subtropical regions. In both systems, small dominant phytoplankton grow at rapid, but usually less than physiologically maximal, rates; they are cropped to low stable abundances by microzooplankton; and their sustained high rates of growth depend on the remineralized by-products of grazing.

Thalli of the chlorophyte macroalga Ulva rotundata were acclimated to sun (100 % I,) and shade (9% I,) in outdoor tumble tanks under nutrient-sufficient conditions. Diurnal patterns were determined for area1 photosynthetic O2 exchange capacity (P,,) and quantum yleld (@), respiration (Rd) , and photosystem (PS) I1 chlorophyll fluorescence using 2 independent techniques. Net P, was maximal at midday in sun-grown thalli and at midmorning in shade-grown thalli exposed to 100 "L I,. A slight afternoon decline in net P, in shade-grown thalli exposed to 100 % I, could be explained entirely by a concurrent rise in Rd. Sun thalli exhibited a larger diurnal fluctuation of net P, which was inconsistent with photoinhibition or end product inhibition by accumulated photosynthate. This leaves endogenous control as the most likely cause, with slight modification by Rd Fluorescence data were consistent with simultaneous damage to PSI1 and photoprotection by thermal deexcitation, with sun thalli showing greater capacity for protection. Both of these processes reduced @ but apparently did not affect P,,. In that U. rotundata thalli were light-saturated in our tumble tanks for most of the day, we conclude that photoinhibition (E damage + protection) had little effect on ~ntegrated diurnal production under these conditions. Our results demonstrate the utility of fluorescence analysis and the importance of precise determination of P,, @ and Rd in ascribing mechanisms to diurnal fluctuations in photosynthetic performance. The validity of using photosynthetic light-response (P-I) curves determined at one time of day to predict integrated diurnal production will depend on the extent to which P,, @ and Rd vary. This in turn depends on species, irradiance history, and possibly other factors such as temperature and nutrition.

Protected evolutionarily significant units (ESUs) of salmonids require objective and measurable criteria for guiding their recovery. In this report, we develop a method for assessing population viability and two ways to integrate these population-level assessments into an assessment of ESU viability. Population viability is assessed with quantitative extinction models or criteria relating to population size, population growth rate, the occurrence of catastrophic declines, and the degree of hatchery influence. ESU viability is assessed by examining the number and distribution of viable populations across the landscape and their proximity to sources of catastrophic disturbance. Central Valley spring-run and winter-run Chinook salmon ESUs are not currently viable, according to the criteria-based assessment. In both ESUs, extant populations may be at low risk of extinction, but these populations represent a small portion of the historical ESUs, and are vulnerable to catastrophic disturbance. The winter-run Chinook salmon ESU, in the extreme case, is represented by a single population that spawns outside of its historical spawning range. We are unable to assess the status of the Central Valley

Effective conservation and recovery planning for Central Valley steelhead requires an understanding of historical population structure. We describe the historical structure of the Central Valley steelhead evolutionarily significant unit using a multi-phase modeling approach. In the first phase, we identify stream reaches possibly suitable for steelhead spawning and rearing using a habitat model based on environmental envelopes (stream discharge, gradient, and temperature) that takes a digital elevation model and climate data as inputs. We identified 151 patches of potentially suitable habitat with more than 10 km of stream habitat, with a total of 25,500 km of suitable habitat. We then measured the distances among habitat patches, and clustered together patches within 35 km of each other into 81 distinct habitat patches. Groups of fish using these 81 patches are hypothesized to be (or to have been) independent populations for recovery planning purposes. Consideration of climate and elevation differences among the 81 habitat areas suggests that there are at least four major subdivisions within the Central Valley steelhead ESU that correspond to geographic regions defined by the Sacramento River basin, Suisun Bay area tributaries, San Joaquin tributaries draining the Sierra Nevada, and lower-elevation streams draining to the Buena Vista and Tulare basins, upstream of the San Joaquin River. Of these, it appears that the Sacramento River basin was the main source of steelhead production. Presently, impassable dams block access to 80% of historically available habitat, and block access to all historical spawning habitat for about 38% of the historical populations of steelhead.