Season- and depth-dependent variability of a demersal fish assemblage in a large fjord estuary (Puget Sound, Washington)

Fjord estuaries are common along the northeast Pacific coastline, but little information is available on fish assemblage structure and its spatiotemporal variability. Here, we examined changes in diversity metrics, species biomasses, and biomass spectra (the distribution of biomass across body size classes) over three seasons (fall, winter, summer) and at multiple depths (20 to 160 m) in Puget Sound, Washington, a deep and highly urbanized fjord estuary on the U.S. west coast. Our results indicate that this fish assemblage is dominated by cartilaginous species (spotted ratfish [Hydrolagus colliei] and spiny dogfish [Squalus acanthias]) and therefore differs fundamentally from fish assemblages found in shallower estuaries in the northeast Pacific. Diversity was greatest in shallow waters (80 m) that are more common in Puget Sound and that are dominated by spotted ratf ish and seasonally (fall and summer) by spiny dogfish. Strong depth-dependent variation in the demersal fish assemblage may be a general feature of deep fjord estuaries and indicates pronounced spatial variability in the food web. Future comparisons with less impacted fjords may offer insight into whether cartilaginous species naturally dominate these systems or only do so under conditions related to human-caused ecosystem degradation. Information on species distributions is critical for marine spatial planning and for modeling energy flows in coastal food webs. The data presented here will aid these endeavors and highlight areas for future research in this important yet understudied system

The use of operational harmful algal bloom monitoring systems in South Africa to assess long term changes to bloom occurrence & impacts for aquaculture

The south coast of South Africa is a very dynamic, productive, high energy environment and is considered to be a generally challenging setting for in-water aquaculture. One of the largest environmental threats to aquaculture are harmful algal blooms (HABs), a natural ecological phenomenon often accompanied by severe impacts on coastal resources and local economies. There is a wide variety of potentially harmful blooming species in the region, with impacts resulting from both toxicity and the negative effects associated with high biomass. While HABs are fairly well documented around the southern Benguela area, the primary concern is the lack of long-term data showing if blooms are becoming more frequent, persistent or are having greater impact over the last decades, consistent with environmental change experienced in the region. For this study, high-resolution satellite remote sensing observations from 16 years of MODIS-Aqua (1 km) and one month of Sentinel-3 OLCI (300 m), using regionally optimised blended algorithms, were used to investigate the spatial distribution and temporal variability of chlorophyll-a (Chl-a) along the south coast of South Africa. A Chl-a threshold of 27 mg m−3 was used as an analytic to identify the occurrence of high biomass blooms in the remote sensing data. Phytoplankton count data from aquaculture farms are used to provide information corresponding to changes in phytoplankton community structure, and to investigate the distribution and seasonal trends of HABs along the south coast. To further explore the spatial and temporal distribution, phytoplankton species considered harmful for this study were identified and classified to their seasonal occurrence: some species were consistently present throughout the years, however each region showed contrasting seasonality. A second interest of this study is linked to assessing the capacity of the aquaculture industry to make profitable use of existing observational and early warning tools. The impact of HABs on the environment or in aquaculture facilities can be potentially mitigated by increasing the industry awareness and early warnings of HAB development. In this regard, the Fisheries and Aquaculture Decision Support Tool (DeST) was used in order to develop short term alerts on HAB development. The EO analyses conducted here specifically use the same methods used by this DeST to demonstrate the use of this tool for historical analysis in addition to real time alerting. In order to evaluate the effectiveness of the tool and how the aquaculture farmers use the ABSTRACT information provided on the DeST, an online user feedback was generated, and distributed to all stakeholders via emai

Forward Flux Sampling for rare event simulations

Rare events are ubiquitous in many different fields, yet they are notoriously difficult to simulate because few, if any, events are observed in a conventiona l simulation run. Over the past several decades, specialised simulation methods have been developed to overcome this problem. We review one recently-developed class of such methods, known as Forward Flux Sampling. Forward Flux Sampling uses a series of interfaces between the initial and final states to calculate rate constants and generate transition paths, for rare events in equilibrium or nonequilibrium systems with stochastic dynamics. This review draws together a number of recent advances, summarizes several applications of the method and highlights challenges that remain to be overcome.Comment: minor typos in the manuscript. J.Phys.:Condensed Matter (accepted for publication

The role of vegetation in regional climate regulation feedback processes

A thesis submitted to the Faculty of Science in fulfilment of the requirements for the degree of Doctor of Philosophy. 30 August 2016 in Johannesburg, South Africa.The presence of Portulacaria afra affects the flow of ecosystem services from the thicket landscapes of the Eastern Cape. Degraded and intact thicket ecosystems deliver different bundles of ecosystem services, and within each bundle the services are linked non-linearly, so that land-use and management decisions which seek to increase a particular service affect the delivery of other services. One of the challenges of restoring the historically degraded thicket areas is understanding the trade-offs between various objectives, including re-establishing biodiversity and critical services such as carbon sequestration, climate regulation, water provision and forage supply. This thesis uses a variety of techniques to assess some of these trade-offs at several spatial and temporal scales. The amount, rate and nature of carbon assimilation by P. afra at a variety of spatial and temporal scales are also explored. Methods At a landscape scale stream flow data from transformed and intact catchments, near Jansenville and Bucklands respectively, are used to compare the freshwater ecosystem services provided by the presence of P. afra. Similarly, at a landscape scale, the new high resolution Multi-angle Imaging SpectroRadiometer (MISR-HR) products are used to explore the differences in the surface energy budget of intact thicket and degraded ecosystems. Two simple radiative transfer models are used to assess the radiative forcing (RF) trade-off between carbon uptake-related global cooling and albedo-related global warming. From samples and measurements taken from a field site 15 km south-west of the town of Kirkwood, radiocarbon and stable carbon isotope analysis, growth ring analysis, dendrometry, infrared thermometry, water use efficiency and eddy covariance data are used to quantify the rate of carbon assimilation by P. afra, and unpack the contribution of C3- and CAM-derived carbon to total carbon sequestration. Results Intact thicket cover results in a higher total yield of water as a fraction of rainfall, fewer extreme high flow events, and a higher volume of low-flow in comparison to landscapes thought to represent transformed former thickets. Intact thickets have a lower albedo than degraded thickets. Restoring to an intact state will result in a mean albedo decrease of 5% (absolute) which constitutes a direct radiative forcing of +0.019 pW m-2 at a global scale. This warming effect overwhelms the climate benefit derived from carbon sequestration related to P. afra growth by a factor of 1.6. The growth data suggests that P. afra produces two growth rings annually on average, with the average growth increment of 0.8mm in diameter. The multi-year and multi-source aboveground relative growth rate mean is 0.006 (±0.005 SD) g DM per g DM per year, which is mean average increment about 1.1% per year. The eddy covariance data highlighted the temporal variability in the system, measuring intact P. afra thicket vegetation as a net source of carbon to the atmosphere 0.018 gC m-2 hr-1, over the three short-duration campaigns. CAM is now understood to come in several variants. The sampled stems, averaged across all rings, had a δ13C signature of -15.8±1.0 ‰ indicative of “strong CAM” behaviour. P. afra plants in the Kirkwood locality over the past decades have derived 61% of their carbon through the CAM pathway and 39% through the C3 pathway, with substantial inter-stem variation. The soil isotope data suggests 51 - 63% C3 derived carbon, with values increasing with sampling depth. There are occasional large excursions, always in a single growth ring, towards more negative δ13C values (-19.0‰); in other words towards the C3 range. Although thought to be related to water stress, it was hard to determine a single trigger for the switching between C3 and CAM modes. This is consistent with findings for other strongly CAM plants. From the dendrometers and infrared thermometry, P. afra shows flexible stomatal behaviour on a range of timescales. For the majority of the study period the stomata were open both day and night. There is variation in stomatal closure over the year, which appears strongly seasonal, and suggests a link to the bimodal rainfall pattern experienced in the region. Using decision tree to classify the photosynthetic mode, this data suggest that the individual plants being measured are spending only 4% of the time in classical CAM mode, and the majority of the time in CAM-cycling. Conclusions Restoration of transformed thicket will improve freshwater ecosystem services associated with useful water yield, sustained supply, and flood control. It is important to include land-atmosphere feedbacks other than carbon assimilation when assessing the climate service delivered by restoration. The negative and positive radiative forcing will operate over different timelines. CAM metabolism plays an important but not exclusive role in carbon gain. Contrasting patterns between plant and soil C3 fraction may relate to allocation issues and the contribution by plants other than P. afra. The growth rates of thickets are not substantially greater than similar water-limited ecosystems.LG201

A Study of Dynamical and Emission Variabilities in Pulsars

Pulsars are rapidly rotating highly magnetized neutron stars thought to have been formed in the core-collapse supernova of massive stars. Ever since their discovery, pulsars have shown complex behaviors. This is certainly true for their emission mechanism, which is still not fully understood. This is primarily because of the abrupt changes that appear in the pulse profile. Recent discoveries have shown that these emission changes effect the spin dynamics, particularly the spin-down rate. This indicates that pulsar emissions are even more complex than previously thought. The goal of this thesis is to apply new analysis techniques to help shed light on the pulsar emission problem.;Over the past decade, it has become apparent that a class of `bursting pulsars\u27 exist with the discovery of PSR J1752+2359 and PSR J1938+2213. In these pulsars, a sharp increase in the emission intensity is observed that then tends to systematically drop-off from pulse-to-pulse. We describe the discovery of such a relationship in high-sensitivity observations of the young (characteristic age of 90; 000 yrs) 0.33 s pulsar B0611+22 at both 327 MHz and 1400 MHz with the Arecibo observatory. While it was previously shown that B0611+22 has mode-switching properties, the data presented here show that this pulsar emits bursts with characteristic time-scales of several hundred seconds. At 327 MHz, the pulsar shows steady behavior in one emission mode which is enhanced by bursting emission slightly offset in pulse phase from this steady emission. Contrastingly at 1400 MHz, the two modes appear to behave in a competing operation while still offset in phase. Using a uctuation spectrum analysis, we also investigate each mode independently for sub-pulse drifting. Neither emission mode (i.e. during bursts or persistent emission) shows the presence of the drifting sub-pulse phenomenon. While further examples of this behavior and studies at different wavelengths are required, it appears that this phenomenon may be quite common among the pulsar population.;Until now, PSR J1752+2359 is the only one of the three bursting pulsars that has not been accompanied by a lower energy level normal emission mode. Rather, it has appeared to null between bursting events. We have been able to show through the pulse-energy distribution that PSR J1752+2359 does indeed have a normal mode with a peak flux at 0.17+/-0.3 mJy with a pulse energy of 1.0+/-0.1 muJy-s. It is also shown that PSR J1752+2359 presents no evidence for the drifting sub-pulse phenomenon in either emission mode. This is consistent with what has been seen in PSR B0611+22.;We also present techniques that searched for chaotic behaviors within the spin dynamics of 17 pulsars. These techniques allow us to re-sample the original spin-down rate estimates without losing structural information, and to search for evidence of a strange attractor within these frequency derivative time series. We demonstrate the effectiveness of our methods by applying them to a component of the Lorenz and Rossler attractors that were sampled with similar cadence to the pulsar time series. Our measurements of correlation dimension and Lyapunov exponent show that the underlying behavior appears to be driven by a strange attractor with approximately three governing non-linear differential equations. This is particularly apparent in the case of PSR B1828--11 where a correlation dimension of 2.06+/-0.03 and a Lyapunov exponent of (4.0+/-) x 10-4 inverse days were measured. These results provide an additional diagnostic for testing future models of this behavior.;Lastly, we introduce future plans to further improve our understanding of the bursting phenomena and spin-down rate changes seen here. Simultaneous observations at different frequencies will help determine how a burst is propagating through different emission regions. Along with this, a recent analogous discovery to bursting implies that bursting events may be accompanied by X-ray changes. Scheduled X-ray observations will soon determine if this is true. As data sets cover even larger amounts of time, the non-linear analysis will improve and can be utilized to test theoretical models. We also present data provided by Andrew Lyne that hints at a connection between bursting and spin-down changes

Formaldehyde over the central Pacific during PEM-Tropics B

Formaldehyde, CH2O, mixing ratios are reported for the central Pacific troposphere from a series of 41 flights, which took place in March-April 1999 as part of the NASA Pacific Exploratory Mission (PEM) -Tropics B mission. Ambient CH2O was collected in aqueous media and quantified using an enzyme-derivatization fluorescence technique. Primary calibration was performed using aqueous standards and known flow rates. Occasionally, CH2O gas standard additions to ambient air were performed as a secondary calibration. Analytical blanks were determined by replacing ambient air with pure air. The estimated precision was ±30 pptv and the estimated accuracy was the sum of ±30 parts per trillion by volume (pptv) ±15% of the measured value. Approximately 25% of the observations were less than the instrumental detection limit of 50 pptv, and 85% of these occurred above 6 km. CH2O mixing ratios decreased with altitude; for example, near the equator the median value in the lowest 2 km was 275 pptv, decreased to 150 pptv by 6 km and was below 100 pptv above 8 km. Between 130 and 170 W and below 1km, a small variation of CH2O mixing ratio with latitude was noted as near-surface median mixing ratios decreased near the equator (275 pptv) and were greater on either side (375 pptv). A marked decrease in near-surface CH2O (200 pptv) was noted south of 23° S on two flights. Between 3° and 23° S, median CH2O mixing ratios were lower in the eastern tropical Pacific than in the western or central Pacific; nominal differences were >100 pptv near the surface to ∼100 pptv at midaltitude to ∼50 pptv at high altitude. Off the coast of Central America and Mexico, mixing ratios as high as 1200 pptv were observed in plumes that originated to the east over land. CH2O observations were consistently higher than the results from a point model constrained by other photochemical species and meteorological parameters. Regardless of latitude or longitude, agreement was best at altitudes above 4 km where the difference between measured and modeled CH2O medians was less than 50 pptv. Below 2 km the model median was approximately 150 pptv less than the measured median. Copyright 2001 by the American Geophysical Union

Markovian Dynamics on Complex Reaction Networks

Complex networks, comprised of individual elements that interact with each other through reaction channels, are ubiquitous across many scientific and engineering disciplines. Examples include biochemical, pharmacokinetic, epidemiological, ecological, social, neural, and multi-agent networks. A common approach to modeling such networks is by a master equation that governs the dynamic evolution of the joint probability mass function of the underling population process and naturally leads to Markovian dynamics for such process. Due however to the nonlinear nature of most reactions, the computation and analysis of the resulting stochastic population dynamics is a difficult task. This review article provides a coherent and comprehensive coverage of recently developed approaches and methods to tackle this problem. After reviewing a general framework for modeling Markovian reaction networks and giving specific examples, the authors present numerical and computational techniques capable of evaluating or approximating the solution of the master equation, discuss a recently developed approach for studying the stationary behavior of Markovian reaction networks using a potential energy landscape perspective, and provide an introduction to the emerging theory of thermodynamic analysis of such networks. Three representative problems of opinion formation, transcription regulation, and neural network dynamics are used as illustrative examples.Comment: 52 pages, 11 figures, for freely available MATLAB software, see http://www.cis.jhu.edu/~goutsias/CSS%20lab/software.htm

The cultural evolution of adaptive-trait diversity when resources are uncertain and finite

In this paper, we seek to build on existing mathematical studies of cultural change by exploring how the diversity of adaptive cultural traits evolves by innovation and cultural transmission when the payoff from adopting traits is both uncertain and frequency dependent. The model is particularly aimed at understanding the evolution of subsistence trait diversity, since the payoff from exploiting particular resources is often variable and subject to diminishing returns as a result of overexploitation. We find that traits that exploit the same shared resource evolve most quickly when intermediate rates of cultural transmission promote fluctuation in trait diversity. Higher rates of cultural transmission, which promote predominantly low diversity, and lower rates, which promote predominantly high diversity, both retard the adoption of traits offering higher payoff. We also find that the distribution of traits that exploit independent resources can evolve towards the theoretical Ideal Free Distribution so long as the rate of cultural transmission is low. Increasing the rate of cultural transmission reduces trait diversity, so that a more limited number of "niches" are occupied at any given time