A new method for detecting spikes in acoustic Doppler velocimeter data sequences is suggested. The method combines three concepts: (1) that differentiation enhances the high frequency portion of a signal, (2) that the expected maximum of a random series is given by the Universal threshold, and (3) that good data cluster in a dense cloud in phase space or Poincare maps. These concepts are used to construct an ellipsoid in three-dimensional phase space, then points lying outside the ellipsoid are designated as spikes. The new method is shown to have superior performance to various other methods and it has the added advantage that it requires no parameters. Several methods for replacing sequences of spurious data are presented. A polynomial fitted to good data on either side of the spike event, then interpolated across the event, is preferred by the authors.

Despiking Acoustic Doppler Velocimeter Data

Reductive genomic evolution, driven by genetic drift, is common in endosymbiotic bacteria. Genome reduction is less common in free-living organisms, but it has occurred in the numerically dominant open-ocean bacterioplankton Prochlorococ- cus and "Candidatus Pelagibacter," and in these cases the reduction appears to be driven by natural selection rather than drift. Gene loss in free-living organisms may leave them dependent on cooccurring microbes for lost metabolic functions. We present the Black Queen Hypothesis (BQH), a novel theory of reductive evolution that explains how selection leads to such dependen- cies; its name refers to the queen of spades in the game Hearts, where the usual strategy is to avoid taking this card. Gene loss can provide a selective advantage by conserving an organism's limiting resources, provided the gene's function is dispensable. Many vital genetic functions are leaky, thereby unavoidably producing public goods that are available to the entire community. Such leaky functions are thus dispensable for individuals, provided they are not lost entirely from the community. The BQH predicts that the loss of a costly, leaky function is selectively favored at the individual level and will proceed until the production of public goods is just sufficient to support the equilibrium community; at that point, the benefit of any further loss would be offset by the cost. Evolution in accordance with the BQH thus generates "beneficiaries" of reduced genomic content that are dependent on leaky "helpers," and it may explain the observed nonuniversality of prototrophy, stress resistance, and other cellular functions in the microbial world.

The Black Queen Hypothesis: Evolution of Dependencies through Adaptive Gene Loss

▪ Abstract The direct effects of marine habitat disturbance by commercial fishing have been well documented. However, the potential ramifications to the ecological function of seafloor communities and ecosystems have yet to be considered. Soft-sediment organisms create much of their habitat's structure and also have crucial roles in many population, community, and ecosystem processes. Many of these roles are filled by species that are sensitive to habitat disturbance. Functional extinction refers to the situation in which species become so rare that they do not fulfill the ecosystem roles that have evolved in the system. This loss to the ecosystem occurs when there are restrictions in the size, density, and distribution of organisms that threaten the biodiversity, resilience, or provision of ecosystem services. Once the functionally important components of an ecosystem are missing, it is extremely difficult to identify and understand ecological thresholds. The extent and intensity of human disturbance to ...

/pdf/disturbance-to-marine-benthic-habitats-by-trawling-and-1p5bzlbz50.pdf

Disturbance to Marine Benthic Habitats by Trawling and Dredging: Implications for Marine Biodiversity

Field data are used to study the size distribution of bedload in paved gravel-bed streams. Similarity analysis yields the results that all grain size ranges are of approximately equal transportability when the critical condition for breaking the pavement is exceeded. This result is only approximately correct due to deviations from similarity. However, it is adequate to justify development of a method for calculating total bedload, which requires only the subpavement median grain size rather than the size distribution. A method for calculating bedload size distribution that accounts for deviation from similarity is also developed.

Closure of "Bedload and Size Distribution in Paved Gravel-Bed Streams"

/pdf/analysis-of-observed-chaotic-data-3spe9uweeb.pdf

Analysis of observed chaotic data

Characteristics of turbulence structure in quasi-2D flows with static and weakly mobile gravel beds are presented. Three sets of measurements with acoustic Doppler velocimeters in an irrigation canal were used: two with subcritical bed shear stress (static beds) and one with the bed shear stress τo close to critical τoc (weakly mobile bed). The analyses included vertical distributions of local mean velocities, turbulence intensities, turbulent shear stresses, velocity auto- and cross-spectra, the quadrant method, and high-order velocity moments. A number of properties of turbulence intensities, high-order moments, streamwise bursting parameters, and velocity spectra appeared to be similar for all three flows, but some properties were different. The most important one was an observed reduction in the von Karman constant for the flow with weakly mobile bed. Comparison of these results with other studies and analogies with drag-reducing flows suggest that at τo/τoc ≈ 1 the drag on the bed for a given granula...

Flow Turbulence over Fixed and Weakly Mobile Gravel Beds

Previous studies have shown major differences in the way biomass of stream periphyton is controlled by spatial variations in velocity. We hypothesize that these differences may be the result of different growth forms within the community. Some dense and coherent growth forms (e.g. mucilaginous diatom/cyanobacterial mats) may be resistant to diffusion and also resistant to dislodgment by shear stress. Higher velocities applied to such communities could therefore be expected to enhance biomass accrual by increasing rates of mass transfer, but without greatly increasing losses through sloughing. Conversely, other growth forms (e.g. long filamentous green algae) have an open matrix, and high rates of diffusion into the mats can potentially occur even at low velocity. However, as velocities increase, high skin friction and form drag should lead to higher rates of sloughing. The overall result of these processes should be that maximum biomass occurs at low velocities. This “subsidy-stress” hypothesis was tested twice with each of three different periphytal growth forms: a coherent, mucilaginous, diatom community; a moderately coherent, stalked/ short, filamentous diatom community; and an open-weave, long, filamentous green algal community. A monotonic increase in chl a biomass occurred as a function of near-bed velocities for the first of the two mucilaginous diatom communities investigated. No biomass-velocity relationship was found, however, with the second mucilaginous community, probably because the waters were highly enriched and mass transfer driven by molecular diffusion was probably high throughout the velocity gradient. Biomass was moderate at low velocities, peaked at near-bed velocities from 0.18 to 0.2 m·s−1 (∼0.40–0.45 m·s−1 mean column velocity), and then decreased at higher velocities in both of the stalked/ short filament communities of diatoms analyzed. With the long filamentous green algal communities, a monotonic reduction in biomass occurred as a function of increases in velocity. Proliferations greater than 100 mg·m−2 chl a occurred at low near-bed velocities (i.e. <0.2 m·s−1), after which biomass declined nearly exponentially as a function of increasing velocity to less than 10 mg·m−2 chl a at velocities greater than 0.4 m·s−1. These biomass-velocity trends support our hypothesis that community growth form determines periphytal responses to spatial variations in velocity within stream reaches.

Subsidy and stress responses of stream periphyton to gradients in water velocity as a function of community growth form

A simple technique to reduce the Doppler noise influence on measurements of turbulence using the Acoustic Doppler Velocimeter (ADV) is developed, and basic relationships to estimate turbulence characteristics using information about the Doppler noise are derived. The procedure involves, firstly, measurement of instantaneous velocities in the flow under consideration; secondly, measurement of the Doppler noise components in still water taken from the flow investigated (with the same velocity range setting that was used in turbulence measurements); and thirdly, estimation of turbulence characteristics using both sets of measurements and relationships developed in the paper. The technique was tested for three typical environments (water storage basin with silty water, laboratory flume with water containing seeding material of neutrally buoyant hollow glass spheres with a mean size around 8–10 μm, and outdoor flume with natural water containing air bubbles and organic particles). It was shown that the Doppler...

Derek G. Goring

Papers

Despiking Acoustic Doppler Velocimeter Data

Flow Turbulence over Fixed and Weakly Mobile Gravel Beds

Subsidy and stress responses of stream periphyton to gradients in water velocity as a function of community growth form

Closure of "ADV Measurements of Turbulence: Can We improve Their Interpretation?"

ADV Measurements of Turbulence: Can We Improve Their Interpretation?