Clonal Interference, Multiple Mutations, and Adaptation in Large Asexual Populations

Two important problems affect the ability of asexual populations to accumulate beneficial mutations, and hence to adapt. First, clonal interference causes some beneficial mutations to be outcompeted by more-fit mutations which occur in the same genetic background. Second, multiple mutations occur in some individuals, so even mutations of large effect can be outcompeted unless they occur in a good genetic background which contains other beneficial mutations. In this paper, we use a Monte Carlo simulation to study how these two factors influence the adaptation of asexual populations. We find that the results depend qualitatively on the shape of the distribution of the effects of possible beneficial mutations. When this distribution falls off slower than exponentially, clonal interference alone reasonably describes which mutations dominate the adaptation, although it gives a misleading picture of the evolutionary dynamics. When the distribution falls off faster than exponentially, an analysis based on multiple mutations is more appropriate. Using our simulations, we are able to explore the limits of validity of both of these approaches, and we explore the complex dynamics in the regimes where neither are fully applicable.Comment: 24 pages, 5 figure

On the Rates of Type Ia Supernovae in Dwarf and Giant Hosts with ROTSE-IIIb

We present a sample of 23 spectroscopically confirmed Type Ia supernovae that were discovered in the background of galaxy clusters targeted by ROTSE-IIIb and use up to 18 of these to determine the local (z = 0.05) volumetric rate. Since our survey is flux limited and thus biased against fainter objects, the pseudo-absolute magnitude distribution (pAMD) of SNeIa in a given volume is an important concern, especially the relative frequency of high to low-luminosity SNeIa. We find that the pAMD derived from the volume limited Lick Observatory Supernova Search (LOSS) sample is incompatible with the distribution of SNeIa in a volume limited (z<0.12) sub sample of the SDSS-II. The LOSS sample requires far more low-luminosity SNeIa than the SDSS-II can accommodate. Even though LOSS and SDSS-II have sampled different SNeIa populations, their volumetric rates are surprisingly similar. Using the same model pAMD adopted in the SDSS-II SNeIa rate calculation and excluding two high-luminosity SNeIa from our sample, we derive a rate that is marginally higher than previous low-redshift determinations. With our full sample and the LOSS pAMD our rate is more than double the canonical value. We also find that 5 of our 18 SNeIa are hosted by very low-luminosity (M_B > -16) galaxies, whereas only 1 out 79 nearby SDSS-II SNeIa have such faint hosts. It is possible that previous works have under-counted either low luminosity SNeIa, SNeIa in low luminosity hosts, or peculiar SNeIa (sometimes explicitly), and the total SNeIa rate may be higher than the canonical value.Comment: 18 pages; accepted for publication in The Astronomical Journa

Effect of permittivity and frequency on induced velocity in ac-DBD surface and channel plasma actuators

Plasma actuators have attracted interest for use as active flow control devices due to their many benefits; they have no moving parts and are lightweight, can be flush mounted, and require low power. In this study, the performance of plasma actuators are experimentally characterized with dielectric material, dielectric thickness, and operating frequency for surface and channel actuator geometries. The channel height, changing the effective dielectric constant, is also varied. Induced velocities were measured using a pitot tube and PIV, and power consumption levels were recorded. For the surface plasma actuator, PTFE and GRE dielectric materials show similar performance, with Kapton producing the highest induced velocity jet. Higher plasma ionization tends to occur with operating frequencies of 5 and 10 kHz, with a minimum at 7 kHz – possibly related to a change to streamer discharge from corona discharge. Power consumption was also higher at frequencies of 5 and 10 kHz. Thinner dielectric materials outperformed thicker ones for a given high voltage input. GRE, which has the highest dielectric constant of the tested materials, resulted in higher induced velocities than PTFE and Kapton for the same dielectric thickness. For the channel actuator, the smallest air gap corresponding to the lowest permittivity generated the highest peak induced velocity at 12 kHz. Different air gap heights do not seem to affect the induced velocities for frequencies above 14 kHz. A high gradient of velocity reduction with streamwise distance from the exposed electrode of the channel actuators was also observed

The large‐scale freshwater cycle of the Arctic

This paper synthesizes our understanding of the Arctic\u27s large‐scale freshwater cycle. It combines terrestrial and oceanic observations with insights gained from the ERA‐40 reanalysis and land surface and ice‐ocean models. Annual mean freshwater input to the Arctic Ocean is dominated by river discharge (38%), inflow through Bering Strait (30%), and net precipitation (24%). Total freshwater export from the Arctic Ocean to the North Atlantic is dominated by transports through the Canadian Arctic Archipelago (35%) and via Fram Strait as liquid (26%) and sea ice (25%). All terms are computed relative to a reference salinity of 34.8. Compared to earlier estimates, our budget features larger import of freshwater through Bering Strait and larger liquid phase export through Fram Strait. While there is no reason to expect a steady state, error analysis indicates that the difference between annual mean oceanic inflows and outflows (∼8% of the total inflow) is indistinguishable from zero. Freshwater in the Arctic Ocean has a mean residence time of about a decade. This is understood in that annual freshwater input, while large (∼8500 km3), is an order of magnitude smaller than oceanic freshwater storage of ∼84,000 km3. Freshwater in the atmosphere, as water vapor, has a residence time of about a week. Seasonality in Arctic Ocean freshwater storage is nevertheless highly uncertain, reflecting both sparse hydrographic data and insufficient information on sea ice volume. Uncertainties mask seasonal storage changes forced by freshwater fluxes. Of flux terms with sufficient data for analysis, Fram Strait ice outflow shows the largest interannual variability

Review of recent research on Southern Resident Killer Whales to detect evidence of poor body condition in the population

Prepared for: The SeaDoc Society, Karen C. Drayer Wildlife Health Center, Eastsound, WA 98245This review was commissioned by the SeaDoc Society in light of major concern for the population trajectory of the SRKW population. The review focuses on identifying evidence for poor body condition in the SRKW population from information presented in Seattle, March 6 2017 (see Appendix 1 Agenda). Body condition can be influenced by food availability (quantity and quality), energy balance, disease, toxin exposure, physiological status, genetics and stress from noise and vessel traffic, amongst other factors, although food availability is the most common cause in wild mammalian populations. For SRKW, food availability to individuals is determined by both prey availability and time to find, catch, share and consume prey. Anthropogenic disturbance will reduce food consumption and thus influence body condition. The small population size and complex social structure of SRKW complicate detection of associations between measures of body condition and population dynamics. Stochastic events can skew population-wide trends substantially. Therefore, individual cases must be considered rather than analyses of trends and correlations on limited-sample-sizes. The small sample size problem hinders many analyses of this population's ecology. A recent shift in distribution of Northern Resident Killer Whales (NRKW) into offshore SRKW range complicates choice of a control population. NRKW could compete for space and prey, and may be influenced by environmental variables that influence SRKW. Thus when using a case control approach, and comparing parameters between SRKW and a reference population, care should be taken when using the NRKW, and another population should be used such as the southern Alaskan residents

Density functional theory and DFT+U study of transition metal porphines adsorbed on Au(111) surfaces and effects of applied electric fields

We apply Density Functional Theory (DFT) and the DFT+U technique to study the adsorption of transition metal porphine molecules on atomistically flat Au(111) surfaces. DFT calculations using the Perdew-Burke-Ernzerhof (PBE) exchange correlation functional correctly predict the palladium porphine (PdP) low-spin ground state. PdP is found to adsorb preferentially on gold in a flat geometry, not in an edgewise geometry, in qualitative agreement with experiments on substituted porphyrins. It exhibits no covalent bonding to Au(111), and the binding energy is a small fraction of an eV. The DFT+U technique, parameterized to B3LYP predicted spin state ordering of the Mn d-electrons, is found to be crucial for reproducing the correct magnetic moment and geometry of the isolated manganese porphine (MnP) molecule. Adsorption of Mn(II)P on Au(111) substantially alters the Mn ion spin state. Its interaction with the gold substrate is stronger and more site-specific than PdP. The binding can be partially reversed by applying an electric potential, which leads to significant changes in the electronic and magnetic properties of adsorbed MnP, and ~ 0.1 Angstrom, changes in the Mn-nitrogen distances within the porphine macrocycle. We conjecture that this DFT+U approach may be a useful general method for modeling first row transition metal ion complexes in a condensed-matter setting.Comment: 14 pages, 6 figure

Water sharing for the environment and agriculture in the Broken catchment

The Commonwealth of Australia Water Act 2007 changed the priority for water use in the Murray-Darling Basin (MDB) to first ensure environmentally sustainable levels of extraction and then to maximise net economic returns to the community from water use. The Murray- Darling Basin Authority (MDBA) is expected to deliver a draft Basin Plan in 2011 providing a framework for future water planning. The Plan will include Sustainable Diversion Limits (SDLs) which define water diversions for consumption while maintaining environmental assets and ecosystem functions. The 2009 MDBA Concept Statement acknowledged that in some areas less information is available to determine the SDLs. The 2010 MDBA Guide to the Basin Plan proposed SDLs reducing the current long-term average surface water diversions to between 25 and 34% for the Goulburn-Broken region. Representative farm-level models of irrigated dairy, horticulture and viticulture, and dryland broadacre, industries were developed to determine the likely impacts on farm income and farm enterprise mix if the price and quantity of irrigation water changes. Water for ecological benefits and ecosystem functioning was determined for a range of river health levels using a bottom-up approach identifying flow requirements for fish, riparian vegetation, invertebrates, and geomorphic and nutrient processes. A novel part of the analysis is the conjunctive use of water for both purposes, e.g. wetland filling and then pumping for irrigation. The linkages between changed land use and surface/ground water outcomes are assessed using a Catchment Analysis Tool. An experimental design of different proportions of water going to the environment and consumptive uses showed potential trade-offs between agricultural, environmental and surface/ground water outcomes. These trade-offs were examined to assess the impact of alternative water management on catchment welfare, and provide information about setting SDLs.Water sharing, environment, agriculture, Murray-Darling Basin, Broken catchment, Resource /Energy Economics and Policy, Q18, Q25, Q28,

A review of flow control techniques and optimisation in S-shaped ducts

This paper is a review of significant studies in the complex flow physics in diffusive, s-shaped ducts, focusing on flow control methods employed to counteract the onset of separation, swirl formation, and non-uniformity of pressure at the duct exit plane. Passive, active, and hybrid flow control, along with optimisation techniques used to control the dominant flow features are discussed. According to the literature, tapered fin vortex generators and submerged vortex generators improve pressure loss and distortion by double digit percentages, and three-dimensional synthetic jets and pulsed micro-jets show greatest promise amongst active flow control devices. Plasma flow control methods have only sparsely been used in s-ducts with one study performing experiments with alternating-current dielectric-barrier-discharge plasma actuators. The importance of flow unsteadiness has been identified in the literature, with peak values as high as one order of magnitude different from the time-averaged properties. Despite this, very few flow control studies have used time-dependent solution methods to quantify the effect of flow control methods on the unsteadiness of the flow

Do Clouds Save the Great Barrier Reef? Satellite Imagery Elucidates the Cloud-SST Relationship at the Local Scale

Evidence of global climate change and rising sea surface temperatures (SSTs) is now well documented in the scientific literature. With corals already living close to their thermal maxima, increases in SSTs are of great concern for the survival of coral reefs. Cloud feedback processes may have the potential to constrain SSTs, serving to enforce an “ocean thermostat” and promoting the survival of coral reefs. In this study, it was hypothesized that cloud cover can affect summer SSTs in the tropics. Detailed direct and lagged relationships between cloud cover and SST across the central Great Barrier Reef (GBR) shelf were investigated using data from satellite imagery and in situ temperature and light loggers during two relatively hot summers (2005 and 2006) and two relatively cool summers (2007 and 2008). Across all study summers and shelf positions, SSTs exhibited distinct drops during periods of high cloud cover, and conversely, SST increases during periods of low cloud cover, with a three-day temporal lag between a change in cloud cover and a subsequent change in SST. Cloud cover alone was responsible for up to 32.1% of the variation in SSTs three days later. The relationship was strongest in both El Niño (2005) and La Niña (2008) study summers and at the inner-shelf position in those summers. SST effects on subsequent cloud cover were weaker and more variable among study summers, with rising SSTs explaining up to 21.6% of the increase in cloud cover three days later. This work quantifies the often observed cloud cooling effect on coral reefs. It highlights the importance of incorporating local-scale processes into bleaching forecasting models, and encourages the use of remote sensing imagery to value-add to coral bleaching field studies and to more accurately predict risks to coral reefs