Effects of taxonomic uncertainty on species diversity indices

As a result of taxonomic uncertainty, generic and higher taxonomic ranks (family, order, class or phylum) are often treated as units in calculating diversity indices, instead of species. In this paper, the errors introduced by such practices are examined for various diversity indices (Shannon - Wiener Index, Maximum Information Index, Evenness, Margalef's Species Richness Index and Hurlbert's Probability of Interspecific Encounter). The use of higher taxonomic ranks may invalidate comparison of diversity indices. In a single study, substantial error and erroneous conclusion may arise, even if consistent practices are adopted.     

Measuring and modelling temporal trends of 226Ra in waters of a Spanish estuary affected by the phosphate industry

The presence and temporal evolution (1990-2001) of (226)Ra in a tidal estuary affected by the phosphate industry has been investigated. Water samples collected in the course of four separate sampling campaigns were analysed for (226)Ra content using a gas flow proportional counter following Ba coprecipitation. Two (226)Ra sources have been identified: direct discharges from the industrial complex and run-off from a phosphogypsum pile. Although activity levels are similar, or even higher, than those found in other environments affected by the phosphate industry, there has been a general decrease in contamination since direct discharges ceased in 1998 due to new regulations from the EU. However, sediments are now acting as a source of Ra to the water column due to redissolution processes. A numerical model of the estuary has been developed to describe quantitatively the experimental results. The model solves the hydrodynamics and the dispersion equation of (226)Ra including interactions with sediments. Model results are, in general, in good agreement with observations.     

Using ocean ambient noise for array self-localization and self-synchronization

Estimates of the travel times between the elements of a bottom hydrophone array can be extracted from the time-averaged ambient noise cross-correlation function (NCF). This is confirmed using 11-min-long data blocks of ambient noise recordings that were collected in May 1995 near the southern California coast at an average depth of 21 m in the 150-700 Hz frequency range. Coherent horizontal wavefronts emerging from the time derivative of the NCF are obtained across the array's aperture and are related to the direct arrival time of the time-domain Green's function (TDGF). These coherent wavefronts are used for array element self-localization (AESL) and array element self-synchronization (AESS). The estimated array element locations are used to beamform on a towed source.     

Copepod grazing during spring blooms: Can Pseudocalanus newmani induce trophic cascades?

During late winter and spring of 2002 and 2003, 24 two- to three-day cruises were conducted to Dabob Bay, Washington State, USA, to examine the grazing, egg production, and hatching success rates of adult female Calanus pacificus and Pseudocalanus newmani. Here, we discuss the results of our grazing experiments for P. newmani. Each week, we conducted traditional microzooplankton dilution experiments and “copepod dilution” experiments, each from two different layers. Grazing was measured by changes in chlorophyll concentration and direct cell counts. Clearance rates on individual prey species, as calculated by cell counts, showed that Pseudocalanus are highly selective in their feeding, and may have much higher grazing rates on individual taxa than calculated from bulk chlorophyll disappearance. The grazing rates of the copepods, however, are typically an order of magnitude lower than the grazing rates of the microzooplankton community, or the growth rates of the phytoplankton. P. newmani ingested diatoms, but, at certain times fed preferentially on microzooplankton, such as ciliates, tintinnids, and larger dinoflagellates. Removal of the microzooplankton may have released the other phytoplankton species from grazing pressure, allowing those species’ abundance to increase, which was measured as an apparent “negative” grazing on those phytoplankton species. The net result of grazing on some phytoplankton species, while simultaneously releasing others from grazing pressure resulted in bulk chlorophyll-derived estimates of grazing which were essentially zero or slightly negative; thus bulk chlorophyll disappearance is a poor indicator of copepod grazing. Whether copepods can significantly release phytoplankton from the grazing pressure by microzooplankton in situ, thus causing a trophic cascade, remains to be verified, but is suggested by our study.     

Estuary/ocean exchange and tidal mixing in a Gulf of Maine Estuary: A Lagrangian modeling study

A Lagrangian particle method embedded within a 2-D finite element code, is used to study the transport and ocean–estuary exchange processes in the well-mixed Great Bay Estuarine System in New Hampshire, USA. The 2-D finite element model, driven by residual, semi-diurnal and diurnal tidal constituents, includes the effects of wetting and drying of estuarine mud flats through the use of a porous medium transport module. The particle method includes tidal advection, plus a random walk model in the horizontal that simulates sub-grid scale turbulent transport processes. Our approach involves instantaneous, massive [O(500,000)] particle releases that enable the quantification of ocean–estuary and inter-bay exchanges in a Markovian framework. The effects of the release time, spring–neap cycle, riverine discharge and diffusion strength on the intra-estuary and estuary–ocean exchange are also investigated.The results show a rather dynamic interaction between the ocean and the estuary with a fraction of the exiting particles being caught up in the Gulf of Maine Coastal Current and swept away. Three somewhat different estimates of estuarine residence time are calculated to provide complementary views of estuary flushing. Maps of residence time versus release location uncover a strong spatial dependency of residence time within the estuary that has very important ramifications for local water quality. Simulations with and without the turbulent random walk show that the combined effect of advective shear and turbulent diffusion is very effective at spreading particles throughout the estuary relatively quickly, even at low (1 m²/s) diffusivity. The results presented here show that a first-order Markov Chain approach has applicability and a high potential for improving our understanding of the mixing processes in estuaries.     

Null broadening with snapshot-deficient covariance matrices in passive sonar

Adaptive-array beamforming achieves high resolution and sidelobe suppression by producing sharp s in the adaptive beampattern. Large-aperture sonar arrays with many elements have small resolution cells; interferers may move through many resolution cells in the time required for accumulating a full-rank sample covariance matrix. This leads to "snapshot-deficient" processing. In this paper, the -broadening technique originally developed for an ideal stationary problem is extended to the snapshot-deficient problem combined with white-noise constraint (WNC) adaptive processing. Null broadening allows the strong interferers to move through resolution cells and increases the number of degrees of freedom, thereby improving the detection of weak stationary signals.     

A nitrate and silicate budget in the equatorial Pacific Ocean: a coupled physical–biological model study

A coupled physical–biological model was developed to simulate the low-silicate, high-nitrate, and low-chlorophyll (LSHNLC) conditions in the equatorial Pacific Ocean and used to compute a detailed budget in the Wyrtki box (5°N–5°S, 180–90°W) for the major sources and cycling of nitrogen and silicon in the equatorial Pacific. With the incorporation of biogenic silicon dissolution, NH₄ regeneration from organic nitrogen and nitrification of ammonia in the model, we show that silicon recycling in the upper ocean is less efficient than nitrogen. As the major source of nutrients to the equatorial Pacific, the Equatorial Undercurrent provides slightly less Si(OH)₄ than NO₃ to the upwelling zone, which is defined as 2.5°N–2.5°S. As a result, the equatorial upwelling supplies less Si(OH)₄ than NO₃ into the euphotic zone in the Wyrtki box, having a Si/N supply ratio of about 0.85 (2.5 vs. 2.96 mmolm⁻² day⁻¹). More Si(OH)₄ than NO₃ is taken up with a Si/N ratio of 1.17 (2.72 vs. 2.33 mmolm⁻² day⁻¹) within the euphotic zone. The difference between upwelling supply and biological uptake is balanced by nutrient regeneration and horizontal advection. Excluding regeneration, the net silicate and nitrate uptakes are nearly equal (1.76 vs. 1.84 mmolm⁻² day⁻¹). However, biogenic silica export production is slightly higher than organic nitrogen (1.74 vs. 1.59 mmolm⁻² day⁻¹) following a 1.1 Si/N ratio. In the central equatorial Pacific, low silicate concentrations limit diatom growth; therefore non-diatom new production accounts for most of the new production. Higher silicate supply in the east maintains elevated diatom growth rates and new production associated with diatoms dominate upwelling zone. In contrast, the new production associated with small phytoplankton is nearly constant or decreases eastward along the equator. The total new production has a higher rate in the east than in the west, following the pattern of surface silicate. This suggests that silicate regulates the diatom production, total new production, and thereby carbon cycle in this area. The modeled mean primary production is 48.4 mmolCm⁻² day⁻¹, representing the lower end of direct field measurements, while new production is 15.0 mmolCm⁻² day⁻¹, which compares well with previous estimates.     

Inter-annual variability in larval supply to populations of three invertebrate taxa in the northern California Current

We investigated sources of inter-annual variability in larval supply to crab and sea urchin populations at Bodega Head and Point Reyes in northern California. During the spring and summer upwelling seasons of the years 1992 through 1997 we monitored the weekly settlement rates of nine species of crabs and two species of sea urchins. As observed in previous studies, daily values of alongshore windstress, temperature and salinity provided evidence for the poleward flow of relatively warm, low salinity water from south of Point Reyes, an apparent retention zone, during upwelling relaxation events. In years dominated by these events (1992, 1993, 1995 and 1996) we observed that alongshore windstress, temperature and salinity were coherent and temperature was significantly correlated with cancrid crab settlement. During these years the magnitude of cancrid crab settlement and the fraction of cancrid crabs relative to other crab species settling were high. Over four years of concurrent sampling there was consistently greater cancrid crab settlement at the Point Reyes site, within the retention zone, than at Bodega Head. Settlement of non-cancrid crabs (porcellanids, grapsids, pagurids and majids) was not as closely linked to intra-annual patterns of upwelling and relaxation, possibly due to the shorter seasonal availability of larvae allowing for the influence of fewer relaxation events. Settlement of this group among years was positively correlated with environmental indicators of strong seasonal upwelling; high salinity, Bakun upwelling index and low temperature. Sea urchin settlement events were observed in June and July of 1992, 1994 and 1997 during warming periods when salinity and temperature were increasing and alongshore windstress was low. Across the six years of the study, we found that cancrid crab larvae had a more even seasonal availability than larvae of non-cancrid species, which settled in greatest numbers during the early portion of the upwelling season. Sea urchins settled in greatest numbers during the later part of the upwelling season. Together these patterns demonstrate the taxon-specific way that inter-annual variability in larval supply is forced by the coincidence of larval availability with favorable physical transport mechanisms.     

Modeling bed-load transport of coarse sediments in the Great Bay Estuary, New Hampshire

Current, sea level and bed-load transport are investigated in the Lower Piscataqua River section of the Great Bay Estuary, New Hampshire, USA—a well-mixed and geometrically complex system with low freshwater input, having main channel tidal currents ranging between 0.5 and 2 m s⁻¹. Current and sea level forced by the M₂M₄M₆ tides at the estuarine mouth are simulated by a vertically averaged, non-linear, time-stepping finite element model. The hydrodynamic model uses a fixed boundary computational domain and accounts for flooding–drying of tidal flats by making use of a groundwater component. Inertia terms are neglected in comparison with pressure gradient and bottom friction terms, which is consistent with the observed principal dynamic balance for this section of the system. The accuracy of hydrodynamic predictions in the study area is demonstrated by comparison with four tidal elevation stations and two cross-section averaged current measurements. Simulated current is then used to model bed-load transport in the vicinity of a rapidly growing shoal located in the main channel of the lower system. Consisting of coarse sand and gravel, the shoal must be dredged every five to eight years. Two approaches are taken—an Eulerian parametric method in which nodal bed-load flux vectors are averaged over the tidal cycle and a Lagrangian particle tracking approach in which a finite number of sediment particles are released and tracked. Both methods yield pathways and accumulations in agreement with the observed shoal formation and the long-term rate of sediment accumulation in the shoal area.