Identifying adaptive genetic divergence among populations from genome scans

The identification of signatures of natural selection in genomic surveys has become an area of intense research, stimulated by the increasing ease with which genetic markers can be typed. Loci identified as subject to selection may be functionally important, and hence (weak) candidates for involvement in disease causation. They can also be useful in determining the adaptive differentiation of populations, and exploring hypotheses about speciation. Adaptive differentiation has traditionally been identified from differences in allele frequencies among different populations, summarised by an estimate of F-ST. Low outliers relative to an appropriate neutral population-genetics model indicate loci subject to balancing selection, whereas high outliers suggest adaptive (directional) selection. However, the problem of identifying statistically significant departures from neutrality is complicated by confounding effects on the distribution of F-ST estimates, and current methods have not yet been tested in large-scale simulation experiments. Here, we simulate data from a structured population at many unlinked, diallelic loci that are predominantly neutral but with some loci subject to adaptive or balancing selection. We develop a hierarchical-Bayesian method, implemented via Markov chain Monte Carlo (MCMC), and assess its performance in distinguishing the loci simulated under selection from the neutral loci. We also compare this performance with that of a frequentist method, based on moment-based estimates of F-ST. We find that both methods can identify loci subject to adaptive selection when the selection coefficient is at least five times the migration rate. Neither method could reliably distinguish loci under balancing selection in our simulations, even when the selection coefficient is twenty times the migration rate.

Application of Gaussian multi-scale representation to feature tracking in meteorological satellite imagery

Gaussian multi-scale representation is a mathematical framework that allows to analyse images at different scales in a consistent manner, and to handle derivatives in a way deeply connected to scale. This paper uses Gaussian multi-scale representation to investigate several aspects of the derivation of atmospheric motion vectors (AMVs) from water vapour imagery. The contribution of different spatial frequencies to the tracking is studied, for a range of tracer sizes, and a number of tracer selection methods are presented and compared, using WV 6.2 images from the geostationary satellite MSG-2.

Sensitivity of large-scale atmospheric analyses to humidity observations and its impact on the global water cycle and tropical and extratropical weather systems in ERA40

Reanalysis data obtained from data assimilation are increasingly used for diagnostic studies of the general circulation of the atmosphere, for the validation of modelling experiments and for estimating energy and water fluxes between the Earth surface and the atmosphere. Because fluxes are not specifically observed, but determined by the data assimilation system, they are not only influenced by the utilized observations but also by model physics and dynamics and by the assimilation method. In order to better understand the relative importance of humidity observations for the determination of the hydrological cycle, in this paper we describe an assimilation experiment using the ERA40 reanalysis system where all humidity data have been excluded from the observational data base. The surprising result is that the model, driven by the time evolution of wind, temperature and surface pressure, is able to almost completely reconstitute the large-scale hydrological cycle of the control assimilation without the use of any humidity data. In addition, analysis of the individual weather systems in the extratropics and tropics using an objective feature tracking analysis indicates that the humidity data have very little impact on these systems. We include a discussion of these results and possible consequences for the way moisture information is assimilated, as well as the potential consequences for the design of observing systems for climate monitoring. It is further suggested, with support from a simple assimilation study with another model, that model physics and dynamics play a decisive role for the hydrological cycle, stressing the need to better understand these aspects of model parametrization. .

A comparison of recent reanalysis datasets using objective feature tracking: Storm tracks and tropical easterly waves

Data from four recent reanalysis projects [ECMWF, NCEP-NCAR, NCEP - Department of Energy ( DOE), NASA] have been diagnosed at the scale of synoptic weather systems using an objective feature tracking method. The tracking statistics indicate that, overall, the reanalyses correspond very well in the Northern Hemisphere (NH) lower troposphere, although differences for the spatial distribution of mean intensities show that the ECMWF reanalysis is systematically stronger in the main storm track regions but weaker around major orographic features. A direct comparison of the track ensembles indicates a number of systems with a broad range of intensities that compare well among the reanalyses. In addition, a number of small-scale weak systems are found that have no correspondence among the reanalyses or that only correspond upon relaxing the matching criteria, indicating possible differences in location and/or temporal coherence. These are distributed throughout the storm tracks, particularly in the regions known for small-scale activity, such as secondary development regions and the Mediterranean. For the Southern Hemisphere (SH), agreement is found to be generally less consistent in the lower troposphere with significant differences in both track density and mean intensity. The systems that correspond between the various reanalyses are considerably reduced and those that do not match span a broad range of storm intensities. Relaxing the matching criteria indicates that there is a larger degree of uncertainty in both the location of systems and their intensities compared with the NH. At upper-tropospheric levels, significant differences in the level of activity occur between the ECMWF reanalysis and the other reanalyses in both the NH and SH winters. This occurs due to a lack of coherence in the apparent propagation of the systems in ERA15 and appears most acute above 500 hPa. This is probably due to the use of optimal interpolation data assimilation in ERA15. Also shown are results based on using the same techniques to diagnose the tropical easterly wave activity. Results indicate that the wave activity is sensitive not only to the resolution and assimilation methods used but also to the model formulation.

Preferred structures in large-scale circulation and the effect of doubling greenhouse gas concentration in HadCM3

Preferred structures in the surface pressure variability are investigated in and compared between two 100-year simulations of the Hadley Centre climate model HadCM3. In the first (control) simulation, the model is forced with pre-industrial carbon dioxide concentration (1×CO2) and in the second simulation the model is forced with doubled CO2 concentration (2×CO2). Daily winter (December-January-February) surface pressures over the Northern Hemisphere are analysed. The identification of preferred patterns is addressed using multivariate mixture models. For the control simulation, two significant flow regimes are obtained at 5% and 2.5% significance levels within the state space spanned by the leading two principal components. They show a high pressure centre over the North Pacific/Aleutian Islands associated with a low pressure centre over the North Atlantic, and its reverse. For the 2×CO2 simulation, no such behaviour is obtained. At higher-dimensional state space, flow patterns are obtained from both simulations. They are found to be significant at the 1% level for the control simulation and at the 2.5% level for the 2×CO2 simulation. Hence under CO2 doubling, regime behaviour in the large-scale wave dynamics weakens. Doubling greenhouse gas concentration affects both the frequency of occurrence of regimes and also the pattern structures. The less frequent regime becomes amplified and the more frequent regime weakens. The largest change is observed over the Pacific where a significant deepening of the Aleutian low is obtained under CO2 doubling.

New insights on growth mechanisms of protein clusters at surfaces: an AFM and simulation study

Despite its relevance to a wide range of technological and fundamental areas, a quantitative understanding of protein surface clustering dynamics is often lacking. In inorganic crystal growth, surface clustering of adatoms is well described by diffusion-aggregation models. In such models, the statistical properties of the aggregate arrays often reveal the molecular scale aggregation processes. We investigate the potential of these theories to reveal hitherto hidden facets of protein clustering by carrying out concomitant observations of lysozyme adsorption onto mica surfaces, using atomic force microscopy. and Monte Carlo simulations of cluster nucleation and growth. We find that lysozyme clusters diffuse across the substrate at a rate that varies inversely with size. This result suggests which molecular scale mechanisms are responsible for the mobility of the proteins on the substrate. In addition the surface diffusion coefficient of the monomer can also be extracted from the comparison between experiments and simulations. While concentrating on a model system of lysozyme-on-mica, this 'proof of concept' study successfully demonstrates the potential of our approach to understand and influence more biomedically applicable protein-substrate couples.

Perturbation growth at the convective scale for CSIP IOP18

The Met Office Unified Model is run for a case observed during Intensive Observation Period 18 (IOP18) of the Convective Storms Initiation Project (CSIP). The aims are to identify the physical processes that lead to perturbation growth at the convective scale in response to model-state perturbations and to determine their sensitivity to the character of the perturbations. The case is strongly upper-level forced but with detailed mesoscale/convective-scale evolution that is dependent on smaller-scale processes. Potential temperature is perturbed within the boundary layer. The effects on perturbation growth of both the amplitude and typical scalelength of the perturbations are investigated and perturbations are applied either sequentially (every 30 min throughout the simulation) or at specific times. The direct effects (within one timestep) of the perturbations are to generate propagating Lamb and acoustic waves and produce generally small changes in cloud parameters and convective instability. In exceptional cases a perturbation at a specific gridpoint leads to switching of the diagnosed boundary-layer type or discontinuous changes in convective instability, through the generation or removal of a lid. The indirect effects (during the entire simulation) are changes in the intensity and location of precipitation and in the cloud size distribution. Qualitatively different behaviour is found for strong (1K amplitude) and weak (0.01K amplitude) perturbations, with faster growth after sunrise found only for the weaker perturbations. However, the overall perturbation growth (as measured by the root-mean-square error of accumulated precipitation) reaches similar values at saturation, regardless of the perturbation characterisation.

MJO Simulation Diagnostics

The Madden–Julian oscillation (MJO) interacts with and influences a wide range of weather and climate phenomena (e.g., monsoons, ENSO, tropical storms, midlatitude weather), and represents an important, and as yet unexploited, source of predictability at the subseasonal time scale. Despite the important role of the MJO in climate and weather systems, current global circulation models (GCMs) exhibit considerable shortcomings in representing this phenomenon. These shortcomings have been documented in a number of multimodel comparison studies over the last decade. However, diagnosis of model performance has been challenging, and model progress has been difficult to track, because of the lack of a coherent and standardized set of MJO diagnostics. One of the chief objectives of the U.S. Climate Variability and Predictability (CLIVAR) MJO Working Group is the development of observation-based diagnostics for objectively evaluating global model simulations of the MJO in a consistent framework. Motivation for this activity is reviewed, and the intent and justification for a set of diagnostics is provided, along with specification for their calculation, and illustrations of their application. The diagnostics range from relatively simple analyses of variance and correlation to more sophisticated space–time spectral and empirical orthogonal function analyses. These diagnostic techniques are used to detect MJO signals, to construct composite life cycles, to identify associations of MJO activity with the mean state, and to describe interannual variability of the MJO.

A multi-scale framework for strategic management of diffuse pollution

A multi-scale framework for decision support is presented that uses a combination of experiments, models, communication, education and decision support tools to arrive at a realistic strategy to minimise diffuse pollution. Effective partnerships between researchers and stakeholders play a key part in successful implementation of this strategy. The Decision Support Matrix (DSM) is introduced as a set of visualisations that can be used at all scales, both to inform decision making and as a communication tool in stakeholder workshops. A demonstration farm is presented and one of its fields is taken as a case study. Hydrological and nutrient flow path models are used for event based simulation (TOPCAT), catchment scale modelling (INCA) and field scale flow visualisation (TopManage). One of the DSMs; The Phosphorus Export Risk Matrix (PERM) is discussed in detail. The PERM was developed iteratively as a point of discussion in stakeholder workshops, as a decision support and education tool. The resulting interactive PERM contains a set of questions and proposed remediation measures that reflect both expert and local knowledge. Education and visualisation tools such as GIS, risk indicators, TopManage and the PERM are found to be invaluable in communicating improved farming practice to stakeholders. (C) 2008 Elsevier Ltd. All rights reserved.

A contour-advective semi-lagrangian numerical algorithm for simulating fine-scale conservative dynamical fields

This paper describes a novel numerical algorithm for simulating the evolution of fine-scale conservative fields in layer-wise two-dimensional flows, the most important examples of which are the earth's atmosphere and oceans. the algorithm combines two radically different algorithms, one Lagrangian and the other Eulerian, to achieve an unexpected gain in computational efficiency. The algorithm is demonstrated for multi-layer quasi-geostrophic flow, and results are presented for a simulation of a tilted stratospheric polar vortex and of nearly-inviscid quasi-geostrophic turbulence. the turbulence results contradict previous arguments and simulation results that have suggested an ultimate two-dimensional, vertically-coherent character of the flow. Ongoing extensions of the algorithm to the generally ageostrophic flows characteristic of planetary fluid dynamics are outlined.

The triggering of orographic rainbands by small-scale topography

The triggering of convective orographic rainbands by small-scale topographic features is investigated through observations of a banded precipitation event over the Oregon Coastal Range and simulations using a cloud-resolving numerical model. A quasi-idealized simulation of the observed event reproduces the bands in the radar observations, indicating the model’s ability to capture the physics of the band-formation process. Additional idealized simulations reinforce that the bands are triggered by lee waves past small-scale topographic obstacles just upstream of the nominal leading edge of the orographic cloud. Whether a topographic obstacle in this region is able to trigger a strong rainband depends on the phase of its lee wave at cloud entry. Convective growth only occurs downstream of obstacles that give rise to lee-wave-induced displacements that create positive vertical velocity anomalies w_c and nearly zero buoyancy anomalies b_c as air parcels undergo saturation. This relationship is quantified through a simple analytic condition involving w_c, b_c, and the static stability N_m^2 of the cloud mass. Once convection is triggered, horizontal buoyancy gradients in the cross-flow direction generate circulations that align the bands parallel to the flow direction.

The simulation of peak and delayed ENSO teleconnections

There is much evidence that El Niño and La Niña lead to significant atmospheric seasonal predictability across much of the globe. However, despite successful predictions of tropical Pacific SSTs, atmospheric seasonal forecasts have had limited success. This study investigates model errors in the Hadley Centre Atmospheric Model version 3 (HadAM3) by analyzing composites of similar El Niño and La Niña events at their peak in December–January–February (DJF) and through their decay in March–April–May (MAM). The large-scale, tropical ENSO teleconnections are modeled accurately by HadAM3 during DJF but the strongest extratropical teleconnection, that in the North Pacific during winter, is modeled inaccurately. The Aleutian low is frequently observed to shift eastward during El Niño but the modeled response always consists of a deepening of the low without a shift. This is traced to small errors in the sensitivity of precipitation to SST in the tropical Pacific, which does not display enough variability so that the precipitation is always too high over the warmest SSTs. This error is reduced when vertical resolution is increased from 19 to 30 levels but enhanced horizontal resolution does not improve the simulation further. In MAM, following the peak of an El Niño or La Niña, atmospheric anomalies are observed to decay rapidly. The modeled ENSO response in DJF persists into MAM, making the extratropical anomalies in MAM too strong. This inaccuracy is again likely to be due to the high modeled sensitivity of tropical Pacific precipitation to SST, which is not significantly improved with enhanced vertical or horizontal resolution in MAM.

Evaluation of a large-eddy model simulation of a mixed-phase altocumulus cloud using microwave radiometer, lidar and Doppler radar data

Using the Met Office large-eddy model (LEM) we simulate a mixed-phase altocumulus cloud that was observed from Chilbolton in southern England by a 94 GHz Doppler radar, a 905 nm lidar, a dual-wavelength microwave radiometer and also by four radiosondes. It is important to test and evaluate such simulations with observations, since there are significant differences between results from different cloud-resolving models for ice clouds. Simulating the Doppler radar and lidar data within the LEM allows us to compare observed and modelled quantities directly, and allows us to explore the relationships between observed and unobserved variables. For general-circulation models, which currently tend to give poor representations of mixed-phase clouds, the case shows the importance of using: (i) separate prognostic ice and liquid water, (ii) a vertical resolution that captures the thin layers of liquid water, and (iii) an accurate representation the subgrid vertical velocities that allow liquid water to form. It is shown that large-scale ascents and descents are significant for this case, and so the horizontally averaged LEM profiles are relaxed towards observed profiles to account for these. The LEM simulation then gives a reasonable. cloud, with an ice-water path approximately two thirds of that observed, with liquid water at the cloud top, as observed. However, the liquid-water cells that form in the updraughts at cloud top in the LEM have liquid-water paths (LWPs) up to half those observed, and there are too few cells, giving a mean LWP five to ten times smaller than observed. In reality, ice nucleation and fallout may deplete ice-nuclei concentrations at the cloud top, allowing more liquid water to form there, but this process is not represented in the model. Decreasing the heterogeneous nucleation rate in the LEM increased the LWP, which supports this hypothesis. The LEM captures the increase in the standard deviation in Doppler velocities (and so vertical winds) with height, but values are 1.5 to 4 times smaller than observed (although values are larger in an unforced model run, this only increases the modelled LWP by a factor of approximately two). The LEM data show that, for values larger than approximately 12 cm s(-1), the standard deviation in Doppler velocities provides an almost unbiased estimate of the standard deviation in vertical winds, but provides an overestimate for smaller values. Time-smoothing the observed Doppler velocities and modelled mass-squared-weighted fallspeeds shows that observed fallspeeds are approximately two-thirds of the modelled values. Decreasing the modelled fallspeeds to those observed increases the modelled IWC, giving an IWP 1.6 times that observed.

Mesoscale simulations of organized convection: importance of convective equilibrium

The validity of convective parametrization breaks down at the resolution of mesoscale models, and the success of parametrized versus explicit treatments of convection is likely to depend on the large-scale environment. In this paper we examine the hypothesis that a key feature determining the sensitivity to the environment is whether the forcing of convection is sufficiently homogeneous and slowly varying that the convection can be considered to be in equilibrium. Two case studies of mesoscale convective systems over the UK, one where equilibrium conditions are expected and one where equilibrium is unlikely, are simulated using a mesoscale forecasting model. The time evolution of area-average convective available potential energy and the time evolution and magnitude of the timescale of convective adjustment are consistent with the hypothesis of equilibrium for case 1 and non-equilibrium for case 2. For each case, three experiments are performed with different partitionings between parametrized and explicit convection: fully parametrized convection, fully explicit convection and a simulation with significant amounts of both. In the equilibrium case, bulk properties of the convection such as area-integrated rain rates are insensitive to the treatment of convection. However, the detailed structure of the precipitation field changes; the simulation with parametrized convection behaves well and produces a smooth field that follows the forcing region, and the simulation with explicit convection has a small number of localized intense regions of precipitation that track with the mid-levelflow. For the non-equilibrium case, bulk properties of the convection such as area-integrated rain rates are sensitive to the treatment of convection. The simulation with explicit convection behaves similarly to the equilibrium case with a few localized precipitation regions. In contrast, the cumulus parametrization fails dramatically and develops intense propagating bows of precipitation that were not observed. The simulations with both parametrized and explicit convection follow the pattern seen in the other experiments, with a transition over the duration of the run from parametrized to explicit precipitation. The impact of convection on the large-scaleflow, as measured by upper-level wind and potential-vorticity perturbations, is very sensitive to the partitioning of convection for both cases. © Royal Meteorological Society, 2006. Contributions by P. A. Clark and M. E. B. Gray are Crown Copyright.