PCR‐based techniques to determine diet of the Australian sea lion (Neophoca cinerea): a comparison with morphological analysis

Comprehensive dietary information for the endangered Australian sea lion (Neophoca cinerea) is currently limited by the deficiency and poor quality of identifiable prey remains recovered from regurgitate and faeces and the difficulty of observing feeding in the wild. In this study, we investigated DNA‐based prey detection methods using conventional (end‐point) and quantitative real‐time PCR (qPCR) on faeces collected from two captive Australian sea lions fed experimental diets of whole teleost fish, squid and shark tissue. PCR prey detection methods using the mitochondrial cytochrome oxidase subunit I (COI) and 16S genes combined with clone sequencing were compared with prey identified using traditional hard part analysis. The molecular results indicated that prey DNA was degraded. However, prey amplification was successful by targeting short (71 bp) DNA fragments. Both conventional PCR and qPCR techniques significantly increased prey detection compared with analysis of hard parts. For both sea lions, the hard part analysis was constrained by sporadic and extremely low recovery of fish otoliths (<2%), and cephalopod beaks were not recovered from the 116 squid fed. Comparisons between PCR techniques indicated comparable prey detection frequencies for all species tested; however, the sensitivity and greater resolution of qPCR improved prey detection by ~25% in one sea lion fed the experimental squid and perch. The detection of squid DNA ≤ 6 day post‐ingestion by qPCR further exhibits the ability and potential of this method to detect low concentrations of infrequent or pulse prey. This study highlights the use of DNA‐based analysis to detect prey taxa in the absence of identifiable hard prey remains.     

Verification of RASS-measured temperature profiles using a radio-controlled model glider

Potential sonic temperature profiles from a continuous electromagnetic, pulsed acoustic, radio acoustic sounding system (RASS) were compared with profiles recorded by a commercially available temperature, relative humidity and pressure recorder mounted in a radio-controlled model motor-glider. The glider profiles covered the period of the morning transition in the lowest 200 m of an initially stably stratified boundary layer. Comparison of the profiles shows that the sonic temperature can be calculated based on the average speed of sound in the boundary layer; this removes the need to correct for vertical velocity in each temperature profile, thus avoiding the possibility of contaminating the temperatures with measurement noise from the vertical velocity profiles. Further, the low-level cold bias that occurs with the spatially separated transmit and receive antennas of a bistatic RASS system was not significant for the present measurements as the separation between the antennas was minimised. The comparison of RASS and glider temperatures gives confidence in the use of RASS-derived temperatures for investigating the performance of boundary layer models.     

Influence of road network and population demand assumptions in evacuation modeling for distant tsunamis

Tsunami evacuation planning in coastal communities is typically focused on local events where at-risk individuals must move on foot in a matter of minutes to safety. Less attention has been placed on distant tsunamis, where evacuations unfold over several hours, are often dominated by vehicle use and are managed by public safety officials. Traditional traffic simulation models focus on estimating clearance times but often overlook the influence of varying population demand, alternative modes, background traffic, shadow evacuation, and traffic management alternatives. These factors are especially important for island communities with limited egress options to safety. We use the coastal community of Balboa Island, California (USA), as a case study to explore the range of potential clearance times prior to wave arrival for a distant tsunami scenario. We use a first-in–first-out queuing simulation environment to estimate variations in clearance times, given varying assumptions of the evacuating population (demand) and the road network over which they evacuate (supply). Results suggest clearance times are less than wave arrival times for a distant tsunami, except when we assume maximum vehicle usage for residents, employees, and tourists for a weekend scenario. A two-lane bridge to the mainland was the primary traffic bottleneck, thereby minimizing the effect of departure times, shadow evacuations, background traffic, boat-based evacuations, and traffic light timing on overall community clearance time. Reducing vehicular demand generally reduced clearance time, whereas improvements to road capacity had mixed results. Finally, failure to recognize non-residential employee and tourist populations in the vehicle demand substantially underestimated clearance time.     

Identification of Burrowing Shrimp Food Sources Along an Estuarine Gradient Using Fatty Acid Analysis and Stable Isotope Ratios

Two species of burrowing shrimp occur in high densities in US West Coast estuaries, the ghost shrimp, Neotrypaea californiensis, and the blue mud shrimp, Upogebia pugettensis. Both species of shrimp are considered ecosystem engineers as they bioturbate and irrigate extensive galleries within the sediment. While their burrows comprise a dominant habitat type in west coast estuaries, little is known about these shrimps’ diet and their role in estuarine food webs. The primary goals of this study were to identify major components of burrowing shrimp diets and detect variation in these diets along an estuarine gradient using combined fatty acid (FA) and stable isotope (SI) analyses. Shrimp and potential food sources including eelgrass blades, epiphytes, Ulva, sedimentary particulate organic matter (SPOM), burrow walls, and particulate organic material (POM) were sampled at different locations within Yaquina Bay, Oregon in August 2012. Both SI and FA analyses indicated differences in food resources assimilated by shrimp along the estuarine gradient. SI values showed that diets for U. pugettensis consisted of carbon sources derived primarily from POM and SPOM, while POM and epiphytes were primary carbon sources for N. californiensis. Shrimp from lower estuarine sites had high levels of 16:1ω7 and 20:5ω3 FAs suggesting their diet is enriched with marine diatoms. Shrimp from upriver showed greater proportion of FA associated with dinoflagellates and terrestrial sources as indicated by a high percentage of C₁₈ polyunsaturated FAs (PUFAs). This is the first study to evaluate diets of these two shrimp species using complimentary FA and SI approaches.     

Measurement of Particle-Bound Reactive Oxygen Species in Rubidoux Aerosols

The diurnal variations in the concentrations of reactive oxygen species (ROS) in various size fractions were determined for ambient particles in Rubidoux, CA. Sampling of particles was conducted at 3 h intervals using a cascade impactor. The collected particles were reacted with dichlorofluorescin (DCFH), a non-fluorescent probe that fluoresces when oxidized. The factors affecting the diurnal variation in ROS concentration were also investigated with special emphasis on the relation between ROS concentration and the intensity of photochemical reactions where the ozone concentration was taken as an index. The intensity of photochemical reactions was found to be a moderate factor affecting the daytime ROS concentration. The concentration of ROS was found to be higher on the smaller particles of the ambient aerosol. An erratum to this article is available .     

Preparing for Climatic Change: The Water, Salmon, and Forests of the Pacific Northwest

The impacts of year-to-year and decade-to-decade climatic variations on some of the Pacific Northwest's key natural resources can be quantified to estimate sensitivity to regional climatic changes expected as part of anthropogenic global climatic change. Warmer, drier years, often associated with El Niño events and/or the warm phase of the Pacific Decadal Oscillation, tend to be associated with below-average snowpack, streamflow, and flood risk, below-average salmon survival, below-average forest growth, and above-average risk of forest fire. During the 20th century, the region experienced a warming of 0.8 °C. Using output from eight climate models, we project a further warming of 0.5–2.5 °C (central estimate 1.5 °C) by the 2020s, 1.5–3.2°C (2.3 °C) by the 2040s, and an increase in precipitation except in summer. The foremost impact of a warming climate will be the reduction of regional snowpack, which presently supplies water for ecosystems and human uses during the dry summers. Our understanding of past climate also illustrates the responses of human management systems to climatic stresses, and suggests that a warming of the rate projected would pose significant challenges to the management of natural resources. Resource managers and planners currently have few plans for adapting to or mitigating the ecological and economic effects of climatic change.     

Sediment resuspension and transport in Lake Michigan during the unstratified period

Instrumented moorings were deployed during the winter of 1994–95 at three depths (28, 58 and 101 m) in southern Lake Michigan. Storms during the observation period were not unusually severe, so the processes observed are typical of those that occur during an average winter. Time series observations of water temperature, beam attenuation coefficient (a measure of water transparency) and current velocity show that local resuspension of bottom sediment occurred frequently after the breakdown of the thermocline. Resuspension was most frequent close to the shore but was also observed at the 58 m station. Local resuspension did not occur at the 101 m station, but advection to the site of material resuspended at shallower sites was observed. These observations do not support the hypothesis proposed by previous investigators that local resuspension at depths of 100 m or greater occurs during the unstratified period. It is more likely that fine-grained material resuspended by storm action in intermediate water depths (≈ 30–60 m) is transported into the deeper parts of the lake by the general lake circulation.