Salmon Life Histories, Habitat, and Food Webs in the Columbia River Estuary: An Overview of Research Results, 2002-2006.

From 2002 through 2006 we investigated historical and contemporary variations in juvenile Chinook salmon Oncorhynchus tshawytscha life histories, habitat associations, and food webs in the lower Columbia River estuary (mouth to rkm 101). At near-shore beach-seining sites in the estuary, Chinook salmon occurred during all months of the year, increasing in abundance from January through late spring or early summer and declining rapidly after July. Recently emerged fry dispersed throughout the estuary in early spring, and fry migrants were abundant in the estuary until April or May each year. Each spring, mean salmon size increased from the tidal freshwater zone to the estuary mouth; this trend may reflect estuarine growth and continued entry of smaller individuals from upriver. Most juvenile Chinook salmon in the mainstem estuary fed actively on adult insects and epibenthic amphipods Americorophium spp. Estimated growth rates of juvenile Chinook salmon derived from otolith analysis averaged 0.5 mm d-1, comparable to rates reported for juvenile salmon Oncorhynchus spp. in other Northwest estuaries. Estuarine salmon collections were composed of representatives from a diversity of evolutionarily significant units (ESUs) from the lower and upper Columbia Basin. Genetic stock groups in the estuary exhibited distinct seasonal and temporal abundance patterns, including a consistent peak in the Spring Creek Fall Chinook group in May, followed by a peak in the Western Cascades Fall Chinook group in July. The structure of acanthocephalan parasite assemblages in juvenile Chinook salmon from the tidal freshwater zone exhibited a consistent transition in June. This may have reflected changes in stock composition and associated habitat use and feeding histories. From March through July, subyearling Chinook salmon were among the most abundant species in all wetland habitat types (emergent, forested, and scrub/shrub) surveyed in the lower 100 km of the estuary. Salmon densities within wetland habitats fell to low levels by July, similar to the pattern observed at mainstem beach-seining sites and coincident with high water temperatures that approached or exceeded 19 C by mid-summer. Wetland habitats were used primarily by small subyearling Chinook salmon, with the smallest size ranges (i.e., rarely exceeding 70 mm by the end of the wetland rearing season) at scrub/shrub forested sites above rkm 50. Wetland sites of all types were utilized by a diversity of genetic stock groups, including less abundant groups such as Interior Summer/Fall Chinook

Salmon at River\u27s End: The Role of the Estuary in the Decline and Recovery of Columbia River salmon

The continued decline of Columbia River salmon (Oncorhynchus spp.) populations has long focused concerns on habitat changes upriver, particularly the effects of large hydroelectric dams. Increasing evidence that ocean conditions strongly influence salmon production, however, has raised questions about the importance of the estuarine environment to salmon and whether the hydropower system has affected estuarine-rearing habitats. In response to Northwest Power Planning Council recommendations, we initiated a review of what is known about the effects of the hydroelectric system on the hydrology, habitats, and ecology of the Columbia River estuary. Our goal was to develop recommendations for improving estuarine conditions or to identify research that may be needed before appropriate salmon-management changes can be defined. Our review and analyses addressed four major questions: (1) What habitats and processes support native salmon populations during the estuarine phase of their life cycle? (2) Have changes to the estuary had a significant role in salmon decline? (3) What have been the impacts of flow regulation on the hydrology, habitat, and biological interactions in the estuarine ecosystem? (4) What estuarine conditions are necessary to maintain salmonid diversity in the Columbia River basin

Correspondence between Scale Morphometrics and Scale and Otolith Chemistry for Interpreting Juvenile Salmon Life Histories

Fish scales have long been used to reconstruct fine-scale habitat transitions such as the movement of juvenile fish from freshwater, estuary, and ocean environments. Despite the importance of life history information to fisheries management and conservation, few studies have validated that scale morphology accurately describes fish movement between these habitats. Therefore, we tested the accuracy of using scale morphometric criteria to identify the movement of juvenile Chinook Salmon Oncorhynchus tshawytscha from freshwater to marine portions of the Columbia River estuary by comparing scale morphometric classification, scale chemistry, and otolith chemistry. Nearly one-half of all fish collected in the saline portion of the estuary and approximately one-quarter in the freshwater portion exhibited morphometric patterns (i.e., scale checks and intermediate growth) often associated with periods of estuary rearing. Depending upon the criteria used to define scale checks, otolith chemical results indicated that 33–53% of fish would have been misclassified as estuary residents based solely on their scale patterns. Moreover, many individuals who had resided in strontium-rich estuary water did not form a visible check (37%) on their scales to coincide with estuary entry. We estimated from otolith chemistry that these fish had either entered at or near the size at which scale formation occurs (35–42 mm) or had recently migrated to the saline portion of the estuary (<30 d) before new scale material could be formed and calcified. Scale chemistry alone was a good indicator of entrance into the saline portion of the estuary. Scale chemistry responded to the strontium-enriched salt water, and explained 86% of the variation found in otolith chemistry. Scale morphometric classification did not provide the fine-scale resolution that scale and, even more so, otolith chemistry provided for describing the proportion of juvenile Chinook salmon using the saline portion of the Columbia River estuary

KELT-11b: A Highly Inflated Sub-Saturn Exoplanet Transiting the V=8 Subgiant HD 93396

We report the discovery of a transiting exoplanet, KELT-11b, orbiting the bright ($V=8.0$) subgiant HD 93396. A global analysis of the system shows that the host star is an evolved subgiant star with $T_{\rm eff} = 5370\pm51$ K, $M_{*} = 1.438_{-0.052}^{+0.061} M_{\odot}$, $R_{*} = 2.72_{-0.17}^{+0.21} R_{\odot}$, log $g_*= 3.727_{-0.046}^{+0.040}$, and [Fe/H]$= 0.180\pm0.075$. The planet is a low-mass gas giant in a $P = 4.736529\pm0.00006$ day orbit, with $M_{P} = 0.195\pm0.018 M_J$, $R_{P}= 1.37_{-0.12}^{+0.15} R_J$, $\rho_{P} = 0.093_{-0.024}^{+0.028}$ g cm$^{-3}$, surface gravity log ${g_{P}} = 2.407_{-0.086}^{+0.080}$, and equilibrium temperature $T_{eq} = 1712_{-46}^{+51}$ K. KELT-11 is the brightest known transiting exoplanet host in the southern hemisphere by more than a magnitude, and is the 6th brightest transit host to date. The planet is one of the most inflated planets known, with an exceptionally large atmospheric scale height (2763 km), and an associated size of the expected atmospheric transmission signal of 5.6%. These attributes make the KELT-11 system a valuable target for follow-up and atmospheric characterization, and it promises to become one of the benchmark systems for the study of inflated exoplanets.Comment: 15 pages, Submitted to AAS Journal

Instrumentation and measurement strategy for the NOAA SENEX aircraft campaign as part of the Southeast Atmosphere Study 2013

Natural emissions of ozone-and-aerosol-precursor gases such as isoprene and monoterpenes are high in the southeastern US. In addition, anthropogenic emissions are significant in the southeastern US and summertime photochemistry is rapid. The NOAA-led SENEX (Southeast Nexus) aircraft campaign was one of the major components of the Southeast Atmosphere Study (SAS) and was focused on studying the interactions between biogenic and anthropogenic emissions to form secondary pollutants. During SENEX, the NOAA WP-3D aircraft conducted 20 research flights between 27 May and 10 July 2013 based out of Smyrna, TN. Here we describe the experimental approach, the science goals and early results of the NOAA SENEX campaign. The aircraft, its capabilities and standard measurements are described. The instrument payload is summarized including detection limits, accuracy, precision and time resolutions for all gas-and-aerosol phase instruments. The inter-comparisons of compounds measured with multiple instruments on the NOAA WP-3D are presented and were all within the stated uncertainties, except two of the three NO2 measurements. The SENEX flights included day- and nighttime flights in the southeastern US as well as flights over areas with intense shale gas extraction (Marcellus, Fayetteville and Haynesville shale). We present one example flight on 16 June 2013, which was a daytime flight over the Atlanta region, where several crosswind transects of plumes from the city and nearby point sources, such as power plants, paper mills and landfills, were flown. The area around Atlanta has large biogenic isoprene emissions, which provided an excellent case for studying the interactions between biogenic and anthropogenic emissions. In this example flight, chemistry in and outside the Atlanta plumes was observed for several hours after emission. The analysis of this flight showcases the strategies implemented to answer some of the main SENEX science questions.</p

Historic Habitat Opportunities and Food-Web Linkages of Juvenile Salmon in the Columbia River Estuary, Annual Report of Research.

In 2002 with support from the U.S. Army Corps of Engineers (USACE), an interagency research team began investigating salmon life histories and habitat use in the lower Columbia River estuary to fill significant data gaps about the estuary's potential role in salmon decline and recovery . The Bonneville Power Administration (BPA) provided additional funding in 2004 to reconstruct historical changes in estuarine habitat opportunities and food web linkages of Columbia River salmon (Onchorhynchus spp.). Together these studies constitute the estuary's first comprehensive investigation of shallow-water habitats, including selected emergent, forested, and scrub-shrub wetlands. Among other findings, this research documented the importance of wetlands as nursery areas for juvenile salmon; quantified historical changes in the amounts and distributions of diverse habitat types in the lower estuary; documented estuarine residence times, ranging from weeks to months for many juvenile Chinook salmon (O. tshawytscha); and provided new evidence that contemporary salmonid food webs are supported disproportionately by wetland-derived prey resources. The results of these lower-estuary investigations also raised many new questions about habitat functions, historical habitat distributions, and salmon life histories in other areas of the Columbia River estuary that have not been adequately investigated. For example, quantitative estimates of historical habitat changes are available only for the lower 75 km of the estuary, although tidal influence extends 217 km upriver to Bonneville Dam. Because the otolith techniques used to reconstruct salmon life histories rely on detection of a chemical signature (strontium) for salt water, the estuarine residency information we have collected to date applies only to the lower 30 or 35 km of the estuary, where fish first encounter ocean water. We lack information about salmon habitat use, life histories, and growth within the long tidal-fresh reaches of the main-stem river and many tidally-influenced estuary tributaries. Finally, our surveys to date characterize wetland habitats within island complexes distributed in the main channel of the lower estuary. Yet some of the most significant wetland losses have occurred along the estuary's periphery, including shoreline areas and tributary junctions. These habitats may or may not function similarly as the island complexes that we have surveyed to date. In 2007 we initiated a second phase of the BPA estuary study (Phase II) to address specific uncertainties about salmon in tidal-fresh and tributary habitats of the Columbia River estuary. This report summarizes 2007 and 2008 Phase II results and addresses three principal research questions: (1) What was the historic distribution of estuarine and floodplain habitats from Astoria to Bonneville Dam? (2) Do individual patterns of estuarine residency and growth of juvenile Chinook salmon vary among wetland habitat types along the estuarine tidal gradient? (3) Are salmon rearing opportunities and life histories in the restoring wetland landscape of lower Grays River similar to those documented for island complexes of the main-stem estuary? Phase II extended our analysis of historical habitat distribution in the estuary above Rkm 75 to near Bonneville Dam. For this analysis we digitized the original nineteenth-century topographic (T-sheets) and hydrographic (H-sheets) survey maps for the entire estuary. Although all T-sheets (Rkm 0 to Rkm 206) were converted to GIS in 2005 with support for the USACE estuary project, final reconstruction of historical habitats throughout the estuary requires completion of the remaining H-sheet GIS maps above Rkm 75 and their integration with the T-sheets. This report summarizes progress to date on compiling the upper estuary H-sheets above Rkm 75. For the USACE estuary project, we analyzed otoliths from Chinook salmon collected near the estuary mouth in 2003-05 to estimate variability in estuary residence times among juvenile out migrants. In Phase II we expanded these analyses to compare growth and residency among individuals collected in tidal-fresh water wetlands of the lower main-stem estuary. Although no known otolith structural or chemical indicators currently exist to define entry into tidal fresh environments, our previous analyses indicate that otolith barium concentrations frequently increase before individuals encounter salt water. Here we evaluate whether otolith barium levels may provide a valid indicator of tidal fresh water entry by Columbia River Chinook salmon. We also examine otolith growth increments to quantify and compare recent (i.e., the previous 30 d) growth rates among individuals sampled in different wetland habitats along the estuarine tidal gradient

Reconnecting Social and Ecological Resilience in Salmon Ecosystems

Fishery management programs designed to control Pacific salmon (Oncorhynchus spp.) for optimum production have failed to prevent widespread fish population decline and have caused greater uncertainty for salmon, their ecosystems, and the people who depend upon them. In this special feature introduction, we explore several key attributes of ecosystem resilience that have been overlooked by traditional salmon management approaches. The dynamics of salmon ecosystems involve social-ecological interactions across multiple scales that create difficult mismatches with the many jurisdictions that manage fisheries and other natural resources. Of particular importance to ecosystem resilience are large-scale shifts in oceanic and climatic regimes or in global economic conditions that unpredictably alter social and ecological systems. Past management actions that did not account for such changes have undermined salmon population resilience and increased the risk of irreversible regime shifts in salmon ecosystems. Because salmon convey important provisioning, cultural, and supporting services to their local watersheds, widespread population decline has undermined both human well-being and ecosystem resilience. Strengthening resilience will require expanding habitat opportunities for salmon populations to express their maximum life-history variation. Such actions also may benefit the "response diversity" of local communities by expanding the opportunities for people to express diverse social and economic values. Reestablishing social-ecological connections in salmon ecosystems will provide important ecosystem services, including those that depend on clean water, ample stream flows, functional wetlands and floodplains, intact riparian systems, and abundant fish populations

Estimating Common Growth Patterns in Juvenile Chinook Salmon (Oncorhynchus tshawytscha) from Diverse Genetic Stocks and a Large Spatial Extent.

Life history variation in Pacific salmon (Oncorhynchus spp.) supports species resilience to natural disturbances and fishery exploitation. Within salmon species, life-history variation often manifests during freshwater and estuarine rearing, as variation in growth. To date, however, characterizing variability in growth patterns within and among individuals has been difficult via conventional sampling methods because of the inability to obtain repeated size measurements. In this study we related otolith microstructures to growth rates of individual juvenile Chinook salmon (O. tshawytscha) from the Columbia River estuary over a two-year period (2010-2012). We used dynamic factor analysis to determine whether there were common patterns in growth rates within juveniles based on their natal region, capture location habitat type, and whether they were wild or of hatchery origin. We identified up to five large-scale trends in juvenile growth rates depending on month and year of capture. We also found that hatchery fish had a narrower range of trend loadings for some capture groups, suggesting that hatchery fish do not express the same breadth of growth variability as wild fish. However, we were unable to resolve a relationship between specific growth patterns and habitat transitions. Our study exemplifies how a relatively new statistical analysis can be applied to dating or aging techniques to summarize individual variation, and characterize aspects of life history diversity