M.P. Kirkpatrick

Chromosome Inversions, Local Adaptation and Speciation

We study the evolution of inversions that capture locally adapted alleles when two populations are exchanging migrants or hybridizing. By suppressing recombination between the loci, a new inversion can spread. Neither drift nor coadaptation between the alleles (epistasis) is needed, so this local adaptation mechanism may apply to a broader range of genetic and demographic situations than alternative hypotheses that have been widely discussed. The mechanism can explain many features observed in inversion systems. It will drive an inversion to high frequency if there is no countervailing force, which could explain fixed differences observed between populations and species. An inversion can be stabilized at an intermediate frequency if it also happens to capture one or more deleterious recessive mutations, which could explain polymorphisms that are common in some species. This polymorphism can cycle in frequency with the changing selective advantage of the locally favored alleles. The mechanism can establish underdominant inversions that decrease heterokaryotype fitness by several percent if the cause of fitness loss is structural, while if the cause is genic there is no limit to the strength of underdominance that can result. The mechanism is expected to cause loci responsible for adaptive species-specific differences to map to inversions, as seen in recent QTL studies. We discuss data that support the hypothesis, review other mechanisms for inversion evolution, and suggest possible tests.

The impact of humidity above stratiform clouds on indirect aerosol climate forcing

Some of the global warming from anthropogenic greenhouse gases is offset by increased reflection of solar radiation by clouds with smaller droplets that form in air polluted with aerosol particles that serve as cloud condensation nuclei. The resulting cooling tendency, termed the indirect aerosol forcing, is thought to be comparable in magnitude to the forcing by anthropogenic CO2, but it is difficult to estimate because the physical processes that determine global aerosol and cloud populations are poorly understood. Smaller cloud droplets not only reflect sunlight more effectively, but also inhibit precipitation, which is expected to result in increased cloud water. Such an increase in cloud water would result in even more reflective clouds, further increasing the indirect forcing. Marine boundary-layer clouds polluted by aerosol particles, however, are not generally observed to hold more water. Here we simulate stratocumulus clouds with a fluid dynamics model that includes detailed treatments of cloud microphysics and radiative transfer. Our simulations show that the response of cloud water to suppression of precipitation from increased droplet concentrations is determined by a competition between moistening from decreased surface precipitation and drying from increased entrainment of overlying air. Only when the overlying air is humid or droplet concentrations are very low does sufficient precipitation reach the surface to allow cloud water to increase with droplet concentrations. Otherwise, the response of cloud water to aerosol-induced suppression of precipitation is dominated by enhanced entrainment of overlying dry air. In this scenario, cloud water is reduced as droplet concentrations increase, which diminishes the indirect climate forcing.

Evaluation of Large-Eddy Simulations via Observations of Nocturnal Marine Stratocumulus

Data from the first research flight (RF01) of the second Dynamics and Chemistry of Marine Stratocumulus (DYCOMS-II) field study are used to evaluate the fidelity with which large-eddy simulations (LESs) can represent the turbulent structure of stratocumulus-topped boundary layers. The initial data and forcings for this case placed it in an interesting part of parameter space, near the boundary where cloud-top mixing is thought to render the cloud layer unstable on the one hand, or tending toward a decoupled structure on the other hand. The basis of this evaluation consists of sixteen 4-h simulations from 10 modeling centers over grids whose vertical spacing wa s5ma t thecloud-top interface and whose horizontal spacing was 35 m. Extensive sensitivity studies of both the configuration of the case and the numerical setup also enhanced the analysis. Overall it was found that (i) if efforts are made to reduce spurious mixing at cloud top, either by refining the vertical grid or limiting the effects of the subgrid model in this region, then the observed turbulent and thermodynamic structure of the layer can be reproduced with some fidelity; (ii) the base, or native configuration of most simulations greatly overestimated mixing at cloud top, tending toward a decoupled layer in which cloud liquid water path and turbulent intensities were grossly underestimated; (iii) the sensitivity of the simulations to the representation of mixing at cloud top is, to a certain extent, amplified by particulars of this case. Overall the results suggest that the use of LESs to map out the behavior of the stratocumulus-topped boundary layer in this interesting region of parameter space requires a more compelling representation of processes at cloud top. In the absence of significant leaps in the understanding of subgrid-scale (SGS) physics, such a representation can only be achieved by a significant refinement in resolution—a refinement that, while conceivable given existing resources, is probably still beyond the reach of most centers.

DO PHYLOGENETIC METHODS PRODUCE TREES WITH BIASED SHAPES

We examine whether phylogenetic methods provide biased estimates of tree shape with respect to the random branching model. We investigate the performance of five commonly used phylogenetic methods using computer simulation: (1) maximum parsimony; (2) neighbor joining; (3) UPGMA with an outgroup taxon; (4) UPGMA without an outgroup taxon; and (5) maximum likelihood. All methods provide estimates of tree shape that are, on average, more asymmetrical than the true tree, especially when rates of evolution are high. We suggest a simple explanation for the bias and propose a modified test of tree shape that corrects for it.

Large Eddy Simulation of a Propagating Turbulent Premixed Flame

A large eddy simulation of a turbulent premixed flame propagatingthrough a chamber containing a square obstruction is presented anddiscussed. The governing equations for compressible, reacting flowsare Favre filtered and turbulence closure is achieved using thedynamic Smagorinsky subgrid model. A simple flame surface densitymodel based on the flamelet concept is employed for the subgrid scalereaction rate. The simulation gives very good agreement with experimentalresults for the speed and the shape of the flame as it propagates throughthe chamber. The peak pressures, however, are underpredicted by20–30%. Reasons for this are discussed and it is concluded that amore sophisticated combustion model is required for complex flowssuch as this one, if a more accurate prediction of the pressureis to be achieved.

DELETERIOUS MUTATION AND THE EVOLUTION OF GENETIC LIFE CYCLES

It is often proposed that the ability of diploids to mask deleterious mutations leads to an evolutionary advantage over haploidy. In this paper, we studied the evolution of the relative duration of haploid and diploid phases using a model of recurrent deleterious mutations across the entire genome. We found that a completely diploid life cycle is favored under biologically reasonable conditions, even when prolonging the diploid phase reduces a populations mean fitness. A haploid cycle is favored when there is complete linkage throughout the genome or when mutations are either highly deleterious or partially dominant. These results hold when loci interact multiplicatively and for synergistic epistasis. The strength of selection generated on the life cycle can be substantial because of the cumulative effect of selection against mutations across many loci. We did not find conditions that support cycles that retain both phases, such as those found in some plants and algae. Thus, selection against deleterious mutations may be an important force in the evolution of life cycles but may not be sufficient to explain all the patterns of life cycles seen in nature.

Large eddy simulation of isothermal turbulent swirling jets

Abstract This article investigates the application of the large eddy simulation (LES) technique to turbulent isothermal swirling flows. The aim was to improve our understanding of the flow physics and turbulence structure of unconfined swirling flows and examine the capability of LES to predict the formation of the vortex breakdown (VB) and recirculation zones. In this study, the filtered Navier-Stokes equations are closed using the Smagorinsky eddy viscosity model with the localized dynamic procedure of Piomelli and Liu (1995). The Sydney University swirl burner experiments are simulated as test cases. Three different test cases have been investigated covering a range of swirl numbers and stream wise annular velocities. The cases considered have swirl numbers ranging from 0 to 1.59 and Reynolds numbers from 32400 to 59000. The LES calculations confirm that the combination of lower swirl number and higher axial velocity of the primary annulus leads to the establishment of the downstream vortex breakdown region. For the cases considered, the LES calculations were successful in predicting observed recirculation zones, vortex breakdown and showed good agreement with experimentally measured mean velocities, their rms fluctuations and Reynolds shear stresses.

Effects of Swirl on Intermittency Characteristics in Non-Premixed Flames

Swirl effects on velocity, mixture fraction, and temperature intermittency have been analyzed for turbulent methane flames using large eddy simulation (LES). The LES solves the filtered governing equations on a structured Cartesian grid using a finite volume method, with turbulence and combustion modeling based on the localized dynamic Smagorinsky and the steady laminar flamelet models, respectively. Probability density function (PDF) distributions demonstrate a Gaussian shape closer to the centerline region of the flame and a delta function at the far radial position. However, non-Gaussian PDFs are observed for velocity and mixture fraction on the centerline in a region where center jet precession occurs. Non-Gaussian behavior is also observed for the temperature PDFs close to the centerline region of the flame. Due to the occurrence of recirculation zones, the variation from turbulent to nonturbulent flow is more rapid for the velocity than the mixture fraction and therefore indicates how rapidly turbulence affects the molecular transport in these regions of the flame.

Shear driven purging of negatively buoyant fluid from trapezoidal depressions and cavities

Experimental data and large eddy simulation results are analysed to investigate shear driven entrainment of a negatively buoyant fluid from trapezoidal depressions and cavities. This flow is of relevance to a number of environmentally significant applications including purging of saline pools in rivers and pollutant dispersion in cities and towns situated within topographic depressions. New scaling relations for the entrainment rate are developed based on physical arguments. Our scaling relations are shown to agree well with both experiments and numerical simulations of this flow in trapezoidal cavities with aspect ratios ranging between 7 and 17, entry beach angles between 8° and 33°, and an exit beach angle of 33°. For the numerical simulations, a sub-filter scale turbulence model is used that combines the dynamic mixed model of Zang et al. [“A dynamic mixed subgrid-scale model and its application to recirculating flows,” Phys. Fluids A 5, 3186 (1993)]10.1063/1.858675 with the dynamic localization proce...

Identification and analysis of instability in non-premixed swirling flames using LES

Large eddy simulations (LES) of turbulent non-premixed swirling flames based on the Sydney swirl burner experiments under different flame characteristics are used to uncover the underlying instability modes responsible for the centre jet precession and large scale recirculation zone. The selected flame series known as SMH flames have a fuel mixture of methane-hydrogen (50:50 by volume). The LES solves the governing equations on a structured Cartesian grid using a finite volume method, with turbulence and combustion modelling based on the localised dynamic Smagorinsky model and the steady laminar flamelet model respectively. The LES results are validated against experimental measurements and overall the LES yields good qualitative and quantitative agreement with the experimental observations. Analysis showed that the LES predicted two types of instability modes near fuel jet region and bluff body stabilised recirculation zone region. The mode I instability defined as cyclic precession of a centre jet is identified using the time periodicity of the centre jet in flames SMH1 and SMH2 and the mode II instability defined as cyclic expansion and collapse of the recirculation zone is identified using the time periodicity of the recirculation zone in flame SMH3. Finally frequency spectra obtained from the LES are found to be in good agreement with the experimentally observed precession frequencies.