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Published journal articles by MLML faculty, staff and students. Full text is included when copyright allows.


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 General blue water diving procedures and guidelines
General blue water diving procedures and guidelines
A California Sea Grant College Program Publication, No. T-CSGCP-014
234Th:238U disequilibria within the California Current
234Th:238U disequilibria within the California Current
Profiles of dissolved and particulate 234Th were determined at several stations within the California Current. Modeling of the disequilibria between the 234Th and 23aU within the surface waters provides for estimates of the residence time of dissolved thorium with respect to particle scavenging (TP varies from 6 to 50 days), the particle residence time (TP varies from 2 to 20 days), and the particulate 234Th flux exiting the surface layer. The model-derived, first-order scavenging rate constant for dissolved thorium is observed to be proportional to the rate of primary production. Particle residence times seem to be governed by the rate of zooplankton grazing and the types of zooplankton present. Model-derived particulate 234Th fluxes are in good agreement with direct measurements by sediment traps.
A Late Pleistocene time-series of bottom-current speed in the Vema Channel
A Late Pleistocene time-series of bottom-current speed in the Vema Channel
A coarsening of the mean particle size of the carbonate-free silt fraction from sea-floor samples below 4000 m in the Vema Channel has been used to separate high-velocity Antarctic Bottom Water (AABW) from the overlying, slower North Atlantic Deep Water (NADW). A time-series of fluctuations in bottom-current speed within the modern AABW/NADW transition zone was examined by determining the particle-size distribution of sediments from eight gravity cores with a high-resolution stratigraphy for the past 250 kyrs. The bottom-current paleospeed was inferred from a correlation of particle size in seafloor samples with mean current speed from nearby current-meters. The mean bottom-current speed at depths comparable to modern AABW was highest (7-10 cm/s) during interglacial to glacial transitions corresponding to the oxygen isotopic stage 6/7 and 4/5 boundaries and at present. The mean bottom-current speed at depths comparable to modern NADW was nearly uniform for most of the past 250 kyrs except during glacial oxygen isotopic stage 2 when the speed dropped to 2 cm/s, or one-half of the present speed. The application of the "calibrated" particle-size method to examine bottom-current paleospeed allows testing of paleoceanographic models which rely on assumptions or inferences of changes in bottom-water production rate during the late Pleistocene paleoclimatic fluctuations. © 1986., Cited By (since 1996):17, CODEN: PPPYA, Oceanography
A Re-Evaluation of the Size of the White Shark (Carcharodon carcharias) Population off California, USA
A Re-Evaluation of the Size of the White Shark (Carcharodon carcharias) Population off California, USA
White sharks are highly migratory and segregate by sex, age and size. Unlike marine mammals, they neither surface to breathe nor frequent haul-out sites, hindering generation of abundance data required to estimate population size. A recent tag-recapture study used photographic identifications of white sharks at two aggregation sites to estimate abundance in ‘‘central California’’ at 219 mature and sub-adult individuals. They concluded this represented approximately one-half of the total abundance of mature and sub-adult sharks in the entire eastern North Pacific Ocean (ENP). This low estimate generated great concern within the conservation community, prompting petitions for governmental endangered species designations. We critically examine that study and find violations of model assumptions that, when considered in total, lead to population underestimates. We also use a Bayesian mixture model to demonstrate that the inclusion of transient sharks, characteristic of white shark aggregation sites, would substantially increase abundance estimates for the adults and subadults in the surveyed sub-population. Using a dataset obtained from the same sampling locations and widely accepted demographic methodology, our analysis indicates a minimum all-life stages population size of .2000 individuals in the California subpopulation is required to account for the number and size range of individual sharks observed at the two sampled sites. Even accounting for methodological and conceptual biases, an extrapolation of these data to estimate the white shark population size throughout the ENP is inappropriate. The true ENP white shark population size is likely severalfold greater as both our study and the original published estimate exclude non-aggregating sharks and those that independently aggregate at other important ENP sites. Accurately estimating the central California and ENP white shark population size requires methodologies that account for biases introduced by sampling a limited number of sites and that account for all life history stages across the species’ range of habitats., Downloaded from: http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0098078 (8 July 2014).
A biooptical model of irradiance distribution and photosynthesis in seagrass canopies
A biooptical model of irradiance distribution and photosynthesis in seagrass canopies
Although extremely vulnerable to coastal eutrophication, seagrasses represent important structuring elements and sources of primary production in shallow waters. They also generate an optical signature that can be tracked remotely. Accurate knowledge of light absorption and scattering by submerged plant canopies permits the calculation of important plant- and ecosystem-level properties, including rates of photosynthesis, vegetation abundance, and distribution. The objectives of this study were to develop a realistic, yet simply parameterized two-flow model of plane irradiance distribution through a seagrass canopy submerged in an optically active water column, to evaluate its performance against in situ measurements, and to explore the impacts of variations in canopy architecture on irradiance distribution and photosynthesis within the canopy. Allometric functions derived from leaf length-frequency data enabled simple parameterization of canopy architecture. Model predictions of downwelling spectral irradiance distributions in seagrass canopies growing in both oligotrophic and eutrophic waters were within 15% of field measurements. Thus, the model provides a robust tool for investigating photosynthetic performance of seagrass canopies as functions of water quality, depth distribution, canopy architecture, and leaf orientation. Model predictions of upwelling irradiance were less reliable, particularly in the upper half of the canopies. The model was more sensitive to leaf orientation than leaf optical properties, seabed reflectance, or the average cosine of downwelling irradiance. Better knowledge of leaf orientation appears to be a fruitful avenue for improving our understanding of the interaction between seagrasses and the submarine light environment., Cited By (since 1996):36, Seaweeds, CODEN: LIOCA
A captive feeding study with the Pacific harbor seal (Phoca vitulina richardii)
A captive feeding study with the Pacific harbor seal (Phoca vitulina richardii)
Seven prey species (ntotal > 2,700) were fed to seven captive male Pacific harbor seals (Phoca vitulina richardii) in 177 experimental meals to quantify biases associated with scat analysis and current consumption models. Hard parts from an individual meal were recovered in an average of 3.8 ± 1.8 scats (range 1-10; mean ± SD). Overall, 57.7 ± 33.2% of otoliths and 89.5 ± 15.5% of squid beaks were recovered. Recovery rates varied, and prey with smaller, fragile otoliths were recovered in lesser quantities than prey with larger, robust otoliths. Recovery rates of all prey except pink salmon were improved by a mean of 31.7% when all diagnostic structures were included in estimates. Estimated recovery of pink salmon was 9.5 times that fed seals based on the all-structure technique. Mean length reduction of recovered otoliths was 20.4 ± 10.1%. Correction factors calculated from average length reduction improved length estimates for all fish species. Grade-specific length correction factors (gLCFs) reduced variability in all of the estimates and significantly improved estimates of prey with highly eroded otoliths including Pacific hake and shortbelly rockfish. The Biomass Reconstruction (BR) model accurately predicted biomass consumption within 4% of known consumption, whereas estimates based on frequency of occurrence were inaccurate. © 2009 by the Society for Marine Mammalogy., Cited By (since 1996):8, Marine Mammals, Birds and Turtles, CODEN: MMSCE
A classification scheme for deep seafloor habitats
A classification scheme for deep seafloor habitats
A standard, universally useful classification scheme for deepwater habitats needs to be established so that descriptions of these habitats can be accurately and efficiently applied among scientific disciplines In recent years many marine benthic habitats in deep water have been described using geophysical and biological data. These descriptions can vary from one investigator to another, which makes it difficult to compare habitats and associated biological assemblages among geographic regions. Using geophysical data collected with a variety of remote sensor systems and in situ biological and geologic observations, we have constructed a classification scheme that can be used in describing marine benthic habitats in deep water., Cited By (since 1996):117, Rocks and Cores, CODEN: OCACD
A closer look at regime shifts based on coastal observations along the eastern boundary of the North Pacific
A closer look at regime shifts based on coastal observations along the eastern boundary of the North Pacific
At least six regime shifts have been reported in the North Pacific since 1920. They occurred in 1925, 1939, 1946, 1976-1977, 1989 and 1999. The major change in 1976-1977 corresponds to a regime shift that is now widely accepted as a canonical event since it had a significant impact on virtually all climatic and ecosystem indicators. We seek to determine if daily sea surface temperature (SST) from Pacific Grove, in central California, and Scripps Pier, in southern California, and coastal observations from several other locations along the west coast of North America can be used to detect and resolve these events. Cumulative sums (CUSUMs) were initially calculated to enhance the detection process. The CUSUM trajectories during the 1976-1977 event at Pacific Grove and Scripps Pier were distinctive, highly correlated, and in phase. The turning point patterns from this event were then used to search for other events that have been reported since 1920. Turning point patterns very similar to the 1976-1977 event were detected in 1946 and 1989. The events in 1925 and 1939 were generally similar, but the CUSUM patterns for the event in 1999 departed significantly from the other events. Further examination of the 1976 and 1989 events revealed inflection points in the CUSUMs near the beginning and end of each transition that correspond to critical values or extrema in the original data. The inflection points and/or critical values provide an improved basis for determining the duration of these events. The robustness of the CUSUM approach for detecting regime shifts was examined by posing the inverse problem to determine if other possible regime changes could be detected that have not been previously reported. The period between 1946 and 1976 was examined, and one match in 1972 was found, which coincided with a large shift in the Aleutian Low Pressure Index. The CUSUM patterns associated with well-defined regime shifts may be essentially unique and thus useful in searching for other events. Whether the temperature ultimately increases or decreases following a regime shift is well-predicted by the sign of the CUSUM slope during an event. Testing regime shifts for statistical significance may be problematic, but our results suggest that when CUSUMs are employed, the detection problem becomes one that is more closely related to pattern recognition where other tests could be applied. CUSUMs often produce a distinct pattern that appears to be characteristic of regime shifts. During well-defined events such as those that occurred in 1946, 1976, and 1989, the CUSUM trajectories from Pacific Grove and Scripps Pier were highly synchronized and nearly identical in form. The CUSUM transformation allows us to identify, localize and observe how these events evolve. We have only been able to examine these events in such detail because daily observations from single locations were used. Based on the events we have examined, they have time scales that range from about 4-9 months. Salinity and sea level data were also employed in this study and were found to be less sensitive to the changes associated with regime shifts than SST. Regime shifts detected in CUSUMs of SST at two locations off Vancouver Island were found to be weaker in amplitude and less well-defined than those detected at Pacific Grove and Scripps Pier. However, they were in phase with the events observed further south. Establishing the connection between these results, and changes in the ecosystems of the North Pacific, should be given a high priority. Finally, the results of this study are related to decadal climate variability and provide additional insight into the nature of this phenomenon. © 2007 Elsevier Ltd. All rights reserved., Cited By (since 1996):8, Oceanography
A comparison of age and growth of the Bering skate, Bathyraja interrupta (Gill and Townsend, 1897), from two Alaskan large marine ecosystems
A comparison of age and growth of the Bering skate, Bathyraja interrupta (Gill and Townsend, 1897), from two Alaskan large marine ecosystems
The Bering skate, Bathyraja interrupta, is commonly found in both the Bering Sea and Gulf of Alaska, where skates are a regular bycatch in commercial long line and bottom trawl fisheries. This is the first study to examine the age and growth of B. interrupta, and one of the few studies to directly compare growth parameters of a skate species between management regions. Ages were estimated based on band counts using the standard gross-sectioning method of vertebral centra preparation. Additionally, a preliminary investigation was conducted into the utility of the histological method. Several growth models were compared and the best-fit model for both regions was identified as the logistic model using the Akaike's Information Criterion approach. No significant difference was detected between sexes for any model in either region; however, a slight but significant difference was found between regions. The parameters of the logistic growth model based on the gross-sectioned preparation were L∞=82.80cm TL and k-1yr=0.23 for the eastern Bering Sea and L∞=86.94cm TL and k-1yr=0.20 for the Gulf of Alaska. Age estimates from the gross sectioned vertebral centra provided a minimum longevity of 19 years and 21 years, respectively. Estimates based on the histologically prepared samples provide overall slightly higher age estimates, but the same maximum age of 21 years. © 2014 Elsevier B.V.
A comparison of reproductive parameters of the Bering skate, Bathyraja interrupta, from two Alaskan large marine ecosystems
A comparison of reproductive parameters of the Bering skate, Bathyraja interrupta, from two Alaskan large marine ecosystems
Estimates of size at maturity are crucial to fisheries stock assessments and may change spatially and temporally. This study directly compares life-history characteristics of a skate species in two large marine ecosystems in a region where there is both a directed fishery and considerable skate by-catch in other fisheries. The Bering skate, Bathyraja interrupta, is one of the most common skate species in Alaskan waters, occurring in two large marine ecosystems, the eastern Bering Sea (EBS) and the Gulf of Alaska (GOA), but little is known about its life history. Skates were sampled from both regions between 2004 and 2007. In the GOA, the size at maturity was estimated to be 69cm total length(TL) for males and 71cmTL for females, while in the EBS size at maturity was estimated as 70cm and 72cmTL for males and females, respectively. Median size at maturity differed by sex but not by region. Our results indicate that B. interrupta shows late maturity, typical of most skate species, suggesting that more detailed monitoring of skate populations and precautionary management is warranted as skate fisheries expand. © CSIRO 2011., Cited By (since 1996):2, Fish and Fisheries, CODEN: AJMFA
A cross-shelf gradient in δ15N stable isotope values of krill and pollock indicates seabird foraging patterns in the Bering Sea
A cross-shelf gradient in δ15N stable isotope values of krill and pollock indicates seabird foraging patterns in the Bering Sea
Concurrent measurements of predator and prey δ15N isotope values demonstrated that a cross-shelf isotopic gradient can propagate through a marine food web from forage species to top-tier predators and indicate foraging areas at a scale of tens of kilometers. We measured δ13C and δ15N in muscle tissues of thick-billed murres (Uria lomvia) and black-legged kittiwakes (Rissa tridactyla), and in whole body tissues of walleye pollock (Gadus chalcogrammus) and krill (Thysanoessa spp), sampled across the continental shelf break in the Bering Sea in 2008 and in 2009. We found significant basin-shelf differences at fine scales (<100km) in δ15N among murres but not kittiwakes, and no such differences in δ13C in either seabird species at that scale. We then quantified the multi-trophic signal and spatial structure of a basin-shelf δ15Nitrogen gradient in the central and southern Bering Sea, and used it to contrast foraging patterns of thick-billed murres and kittiwakes on the open ocean. Seabird muscle δ15N values were compared to baselines created from measurements in krill and pollock tissues sampled concurrently throughout the study area. Krill, pollock, and murre tissues from northern, shallow, shelf habitat (<200m) were enriched 1-2‰ in δ15N relative to samples taken from deeper habitats (>200m) to the south and west. Krill δ15N baseline values predicted 35-42% of the variability in murre tissue values. Patterns between kittiwakes and prey were less coherent. The persistence of strong spatial autocorrelation among sample values, and a congruence of geospatial patterns in δ15N among murre and prey tissues, suggest that murres forage repeatedly in specific areas. Murre isotope values showed distinct geospatial stratification, coincident with the spatial distribution of three colonies: St. Paul, St. George, and Bogoslof. This suggests some degree of foraging habitat partitioning among colonies.
A curious relationship between the winds and currents at the western entrance of the Santa Barbara Channel
A curious relationship between the winds and currents at the western entrance of the Santa Barbara Channel
Relationships between the surface winds and Acoustic Doppler Current Profiler (ADCP) currents at 20 levels (25 to 329 m) at the western entrance of the Santa Barbara Channel (SBC) at National Data Buoy Center (NDBC) buoy 46054 are evaluated for the 1 year period from 1 June 1996 through 31 May 1997 using a relatively new technique for correlating vectors. Gaps in the data were filled and the resulting time series examined to insure that the statistical properties of the edited data had not been significantly altered. Vertical current profiles, averaged over the year, indicate that the mean signal, although well-defined, is smaller than the variability about the mean. Vertical profiles of current speed and direction suggest the possibility of at least a twolayer system of circulation in the SBC with flow between 25 and 180 m being to the SSW and flow from 260 to 329 m being to the ENE, in agreement with previous results. Because of the existing dynamical balances, the currents are oriented approximately SW/NE, and the direction of the vertical current shear (i.e., the thermal wind) is essentially constant with depth. Thus warmer waters lie to the north and west, and colder waters, essentially south of the buoy, are consistent with observed cyclonic circulation at the western entrance of the channel. Vector correlations over the entire year indicate that the winds and currents are poorly correlated,
A distinct and active bacterial community in cold oxygenated fluids circulating beneath the western flank of the Mid-Atlantic ridge
A distinct and active bacterial community in cold oxygenated fluids circulating beneath the western flank of the Mid-Atlantic ridge
The rock-hosted, oceanic crustal aquifer is one of the largest ecosystems on Earth, yet little is known about its indigenous microorganisms. Here we provide the first phylogenetic and functional description of an active microbial community residing in the cold oxic crustal aquifer. Using subseafloor observatories, we recovered crustal fluids and found that the geochemical composition is similar to bottom seawater, as are cell abundances. However, based on relative abundances and functional potential of key bacterial groups, the crustal fluid microbial community is heterogeneous and markedly distinct from seawater. Potential rates of autotrophy and heterotrophy in the crust exceeded those of seawater, especially at elevated temperatures (25 °C) and deeper in the crust. Together, these results reveal an active, distinct, and diverse bacterial community engaged in both heterotrophy and autotrophy in the oxygenated crustal aquifer, providing key insight into the role of microbial communities in the ubiquitous cold dark subseafloor biosphere., Export Date: 18 March 2016, Article
A field bioassay approach to determining tributyltin toxicity to oysters in California
A field bioassay approach to determining tributyltin toxicity to oysters in California
Field experiments were conducted with oysters, Crassostrea gigas to determine the toxicity of tributyltin (TBT). Oysters were transplanted to over one hundred stations distributed in 25 marinas usually in a transect of four or five stations along a gradient next to vessels extending to station locations distant from vessels. In almost every bay in California there are many vessels, the TBT levels in water are > 50 ng/liter (parts per trillion), and the oysters exhibit a chambering response similar to the chambering response that was indicative of the destruction of the oyster industry in France. Although oysters were transplanted to stations that had extreme environmental conditions (near sewer and petroleum refinery discharges) no evidence of chambering was observed indicating that the chambering response does not occur with every type of environmental stress. In addition, oysters transplanted to a marina that had been abandoned for 18 months did not show a chambering response, whereas those transplanted in marinas that had vessels always showed a chambering response. The use of field techniques in determining toxicity responses worked in this case but the response could have been more clearly defined if more stations were added in each marina and the dose response determined on a marina by marina basis. More TBT measurements in water would have also helped to refine the dose-response relationship. A first estimate of a toxicity value can be determined from these data to be less than 40 ng/liter.
A framework for investigating general patterns of benthic β-diversity along estuaries
A framework for investigating general patterns of benthic β-diversity along estuaries
The description of major patterns in beta (. β) diversity is important in order to understand changes in community composition and/or richness at different spatial and temporal scales, and can interrogate processes driving species distribution and community dynamics. Human impacts have pushed many estuarine systems far from their historical baseline of rich, diverse, and productive ecosystems. Despite the ecological and social importance of estuaries, there has not yet been an attempt to investigate patterns of β-diversity and its partitioning along estuarine systems of different continents. We aimed to evaluate if benthic assemblages would show higher turnover than nestedness in tropical than in temperate systems, if well-known impacted estuaries would show greater nestedness than less polluted systems, and to propose a conceptual framework for studying benthic macrofauna beta diversity along estuaries. We analyzed subtidal benthic macrofaunal data from estuaries in Brazil, USA and France. We estimated alpha (. α), beta (. β) and gamma (. γ) diversity for each sampling time in each system, investigated patterns of β -diversity as multivariate dispersion and the partitioning (nestedness and replacement) of β-diversity along each estuary. There was a decrease in the α-diversity along marine to freshwater conditions at most of the estuaries and sampling dates. Beta diversity as multivariate dispersion showed high variability. Most of the estuaries showed a greater proportion of the β-diversity driven by replacement than nestedness. We suggest a conceptual framework for estuaries where relatively pristine estuaries would have their β-diversity mostly driven by replacement while impacted estuaries subjected to several anthropogenic stressors would show total nestedness or total replacement, depending on the stress.
A large-scale categorization of sites in San Francisco Bay, USA, based on the sediment quality triad, toxicity identification evaluations, and gradient studies
A large-scale categorization of sites in San Francisco Bay, USA, based on the sediment quality triad, toxicity identification evaluations, and gradient studies
Sediment quality was assessed in San Francisco Bay, California, USA, using a two-tiered approach in which 111 sites were initially screened for sediment toxicity. Sites exhibiting toxicity were then resampled and analyzed for chemical contamination, recurrent toxicity, and, in some cases, benthic community impacts. Resulting data were compared with newly derived threshold values for each of the metrics in a triad-based weight-of-evidence evaluation. Sediment toxicity test results were compared with tolerance limits derived from reference site data, benthic community data were compared with threshold values for a relative benthic index based on the presence and abundance of pollution-tolerant and -sensitive taxa, and concentrations of chemicals and chemical mixtures were compared with sediment quality guideline-based thresholds. A total of 57 sites exceeded threshold values for at least one metric, and each site was categorized based on triad inferences. Nine sites were found to exhibit recurrent sediment toxicity associated with elevated contaminant concentrations, conditions that met program criteria for regulatory attention. Benthic community impacts were also observed at three of these sites, providing triad evidence of pollution-induced degradation. Multi- and univariate correlations indicated that chemical mixtures, heavy metals, chlordanes, and other organic compounds were associated with measured biological impacts in the Bay. Toxicity identification evaluations indicated that metals were responsible for pore-water toxicity to sea urchin larvae at two sites. Gradient studies indicated that the toxicity tests and benthic community metrics employed in the study predictably tracked concentrations of chemical mixtures in Bay sediments., Cited By (since 1996):36, CODEN: ETOCD, Rocks and Cores

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