Diagnosing observation error correlations for Doppler radar radial winds in the Met Office UKV model using observation-minus-background and observation-minus-analysis statistics

With the development of convection-permitting numerical weather prediction the efficient use of high resolution observations in data assimilation is becoming increasingly important. The operational assimilation of these observations, such as Dopplerradar radial winds, is now common, though to avoid violating the assumption of un- correlated observation errors the observation density is severely reduced. To improve the quantity of observations used and the impact that they have on the forecast will require the introduction of the full, potentially correlated, error statistics. In this work, observation error statistics are calculated for the Doppler radar radial winds that are assimilated into the Met Office high resolution UK model using a diagnostic that makes use of statistical averages of observation-minus-background and observation-minus-analysis residuals. This is the first in-depth study using the diagnostic to estimate both horizontal and along-beam correlated observation errors. By considering the new results obtained it is found that the Doppler radar radial wind error standard deviations are similar to those used operationally and increase as the observation height increases. Surprisingly the estimated observation error correlation length scales are longer than the operational thinning distance. They are dependent on both the height of the observation and on the distance of the observation away from the radar. Further tests show that the long correlations cannot be attributed to the use of superobservations or the background error covariance matrix used in the assimilation. The large horizontal correlation length scales are, however, in part, a result of using a simplified observation operator.

CO2 emission estimation in the urban environment: measurement of the CO2 storage term

Eddy covariance has been used in urban areas to evaluate the net exchange of CO2 between the surface and the atmosphere. Typically, only the vertical flux is measured at a height 2–3 times that of the local roughness elements; however, under conditions of relatively low instability, CO2 may accumulate in the airspace below the measurement height. This can result in inaccurate emissions estimates if the accumulated CO2 drains away or is flushed upwards during thermal expansion of the boundary layer. Some studies apply a single height storage correction; however, this requires the assumption that the response of the CO2 concentration profile to forcing is constant with height. Here a full seasonal cycle (7th June 2012 to 3rd June 2013) of single height CO2 storage data calculated from concentrations measured at 10 Hz by open path gas analyser are compared to a data set calculated from a concurrent switched vertical profile measured (2 Hz, closed path gas analyser) at 10 heights within and above a street canyon in central London. The assumption required for the former storage determination is shown to be invalid. For approximately regular street canyons at least one other measurement is required. Continuous measurements at fewer locations are shown to be preferable to a spatially dense, switched profile, as temporal interpolation is ineffective. The majority of the spectral energy of the CO2 storage time series was found to be between 0.001 and 0.2 Hz (500 and 5 s respectively); however, sampling frequencies of 2 Hz and below still result in significantly lower CO2 storage values. An empirical method of correcting CO2 storage values from under-sampled time series is proposed.

Seasonal surface urban energy balance and wintertime stability simulated using three land-surface models in the high-latitude city Helsinki

The performance of three urban land surface models, run in offline mode, with their default external parameters, is evaluated for two distinctly different sites in Helsinki: Torni and Kumpula. The former is a dense city centre site with 22% vegetation, while the latter is a suburban site with over 50% vegetation. At both locations the models are compared against sensible and latent heat fluxes measured using the eddy covariance technique, along with snow depth observations. The cold climate experienced by the city causes strong seasonal variations that include snow cover and stable atmospheric conditions. Most of the time the three models are able to account for the differences between the study areas as well as the seasonal and diurnal variability of the energy balance components. However, the performances are not systematic across the modelled components, season and surface type. The net all-wave radiation is well simulated, with the greatest uncertainties related to snowmelt timing, when the fraction of snow cover has a key role, particularly in determining the surface albedo. For the turbulent fluxes, more variation between the models is seen which can partly be explained by the different methods in their calculation and partly by surface parameter values. For the sensible heat flux, simulation of wintertime values was the main problem, which also leads to issues in predicting near-surface stabilities particularly at the dense city centre site. All models have the most difficulties in simulating latent heat flux. This study particularly emphasizes that improvements are needed in the parameterization of anthropogenic heat flux and thermal parameters in winter, snow cover in spring and evapotranspiration in order to improve the surface energy balance modelling in cold climate cities.

Implicit equal-weights particle filter

Filter degeneracy is the main obstacle for the implementation of particle filter in non-linear high-dimensional models. A new scheme, the implicit equal-weights particle filter (IEWPF), is introduced. In this scheme samples are drawn implicitly from proposal densities with a different covariance for each particle, such that all particle weights are equal by construction. We test and explore the properties of the new scheme using a 1,000-dimensional simple linear model, and the 1,000-dimensional non-linear Lorenz96 model, and compare the performance of the scheme to a Local Ensemble Kalman Filter. The experiments show that the new scheme can easily be implemented in high-dimensional systems and is never degenerate, with good convergence properties in both systems.

Relational architecture and relational capability: organisational levers to support strategic supplier relationships

The resource based view of strategy suggests that competitiveness in part derives from a firms ability to collaborate with a subset of its supply network to co-create highly valued products and services. This relational capability relies on a foundational intra and inter-organisational architecture, the manifestation of strategic, people, and process decisions facilitating the interface between the firm and its strategic suppliers. Using covariance-based structural equation modelling we examine the relationships between internal and external features of relational architecture, and their relationship with relational capability and relational quality. This is undertaken on data collected by mail survey. We find significant relationships between both internal and external relational architecture and relational capability and between relational capability and relational quality. Novel constructs for internal and external elements of relational architecture are specified to demonstrate their positive influence on relational capability and relationship quality.

Surface Urban Energy and Water Balance Scheme (SUEWS): development and evaluation at two UK sites

The Surface Urban Energy and Water Balance Scheme (SUEWS) is evaluated at two locations in the UK: a dense urban site in the centre of London and a residential suburban site in Swindon. Eddy covariance observations of the turbulent fluxes are used to assess model performance over a twoyear period (2011-2013). The distinct characteristics of the sites mean their surface energy exchanges differ considerably. The model suggests the largest differences can be attributed to surface cover (notably the proportion of vegetated versus impervious area) and the additional energy supplied by human activities. SUEWS performs better in summer than winter, and better at the suburban site than the dense urban site. One reason for this is the bias towards suburban summer field campaigns in observational data used to parameterise this (and other) model(s). The suitability of model parameters (such as albedo, energy use and water use) for the UK sites is considered and, where appropriate, alternative values are suggested. An alternative parameterisation for the surface conductance is implemented, which permits greater soil moisture deficits before evaporation is restricted at non-irrigated sites. Accounting for seasonal variation in the estimation of storage heat flux is necessary to obtain realistic wintertime fluxes.

Sparse density estimation on multinomial manifold combining local component analysis

A new sparse kernel density estimator is introduced based on the minimum integrated square error criterion combining local component analysis for the finite mixture model. We start with a Parzen window estimator which has the Gaussian kernels with a common covariance matrix, the local component analysis is initially applied to find the covariance matrix using expectation maximization algorithm. Since the constraint on the mixing coefficients of a finite mixture model is on the multinomial manifold, we then use the well-known Riemannian trust-region algorithm to find the set of sparse mixing coefficients. The first and second order Riemannian geometry of the multinomial manifold are utilized in the Riemannian trust-region algorithm. Numerical examples are employed to demonstrate that the proposed approach is effective in constructing sparse kernel density estimators with competitive accuracy to existing kernel density estimators.

Additive genetic relationships between scrotal circumference, heifer pregnancy, and stayability in Nellore cattle

Scrotal circumference data from 47,605 Nellore young bulls, measured at around 18 mo of age (SC18), were analyzed simultaneously with 27,924 heifer pregnancy (HP) and 80,831 stayability (STAY) records to estimate their additive genetic relationships. Additionally, the possibility that economically relevant traits measured directly in females could replace SC18 as a selection criterion was verified. Heifer pregnancy was defined as the observation that a heifer conceived and remained pregnant, which was assessed by rectal palpation at 60 d. Females were exposed to sires for the first time at about 14 mo of age (between 11 and 16 mo). Stayability was defined as whether or not a cow calved every year up to 5 yr of age, when the opportunity to breed was provided. A Bayesian linear-threshold-threshold analysis via Gibbs sampler was used to estimate the variance and covariance components of the multitrait model. Heritability estimates were 0.42 +/- 0.01, 0.53 +/- 0.03, and 0.10 +/- 0.01, for SC18, HP, and STAY, respectively. The genetic correlation estimates were 0.29 +/- 0.05, 0.19 +/- 0.05, and 0.64 +/- 0.07 between SC18 and HP, SC18 and STAY, and HP and STAY, respectively. The residual correlation estimate between HP and STAY was -0.08 +/- 0.03. The heritability values indicate the existence of considerable genetic variance for SC18 and HP traits. However, genetic correlations between SC18 and the female reproductive traits analyzed in the present study can only be considered moderate. The small residual correlation between HP and STAY suggests that environmental effects common to both traits are not major. The large heritability estimate for HP and the high genetic correlation between HP and STAY obtained in the present study confirm that EPD for HP can be used to select bulls for the production of precocious, fertile, and long-lived daughters. Moreover, SC18 could be incorporated in multitrait analysis to improve the prediction accuracy for HP genetic merit of young bulls.

Fluxes of CO(2) above a plantation of Eucalyptus in southeast Brazil

Eddy-covariance measurements of net ecosystem exchange of CO(2) (NEE) and estimates of gross ecosystem productivity (GEP) and ecosystem respiration (R(E)) were obtained in a 2-4 year old Eucalyptus plantation during two years with very different winter rainfall In the first (drier) year the annual NEE GEP and RE were lower than the sums in the second (normal) year and conversely the total respiratory costs of assimilated carbon were higher in the dry year than in the normal year Although the net primary production (NPP) in the first year was 23% lower than that of the second year the decrease in the carbon use efficiency (CUE = NPP/GEP) was 11% and autotrophic respiration utilized more resources in the first dry year than in the second normal year The time variations in NEE were followed by NPP because in these young Eucalyptus plantations NEE is very largely dominated by NPP and heterotrophic respiration plays only a relatively minor role During the dry season a pronounced hysteresis was observed in the relationship between NEE and photosynthetically active radiation and NEE fluxes were inversely proportional to humidity saturation deficit values greater than 0 8 kPa Nighttime fluxes of CO(2) during calm conditions when the friction velocity (u) was below the threshold (0 25 ms(-1)) were estimated based on a Q(10) temperature-dependence relationship adjusted separately for different classes of soil moisture content which regulated the temperature sensitivity of ecosystem respiration (C) 2010 Elsevier B V All rights reserved

The energy and water balance of a Eucalyptus plantation in southeast Brazil

The eddy covariance method was used to measure energy and water balance of a plantation of Eucalyptus (grandis x urophylla) hybrids over a 2 year period. The average daily evaporation rates were 5.4 (+/- 2.0) mm day(-1) in summer, but fell to 1.2 (+/- 0.3) mm day(-1) in winter. In contrast, the sensible heat flux was relatively low in summer but dominated the energy balance in winter. Evaporation accounted for 80% and 26% of the available energy, in summer and winter respectively. The annual evaporation was 82% (1124 mm) and 96% (1235 mm) of the annual rainfall recorded during the first and second year, respectively. Daily average canopy and aerodynamic conductance to water vapour were in the summer 51.9 (+/- 38.4) mm s(-1) 84.1 (+/- 25.6) mm s(-1), respectively; and in the winter 6.0 (+/- 10.5) mm s(-1) and 111.6 (+/- 24.6) mm s(-1), respectively. (C) 2010 Elsevier B.V. All rights reserved.

The land-atmosphere water flux in the tropics

Tropical vegetation is a major source of global land surface evapotranspiration, and can thus play a major role in global hydrological cycles and global atmospheric circulation. Accurate prediction of tropical evapotranspiration is critical to our understanding of these processes under changing climate. We examined the controls on evapotranspiration in tropical vegetation at 21 pan-tropical eddy covariance sites, conducted a comprehensive and systematic evaluation of 13 evapotranspiration models at these sites, and assessed the ability to scale up model estimates of evapotranspiration for the test region of Amazonia. Net radiation was the strongest determinant of evapotranspiration (mean evaporative fraction was 0.72) and explained 87% of the variance in monthly evapotranspiration across the sites. Vapor pressure deficit was the strongest residual predictor (14%), followed by normalized difference vegetation index (9%), precipitation (6%) and wind speed (4%). The radiation-based evapotranspiration models performed best overall for three reasons: (1) the vegetation was largely decoupled from atmospheric turbulent transfer (calculated from X decoupling factor), especially at the wetter sites; (2) the resistance-based models were hindered by difficulty in consistently characterizing canopy (and stomatal) resistance in the highly diverse vegetation; (3) the temperature-based models inadequately captured the variability in tropical evapotranspiration. We evaluated the potential to predict regional evapotranspiration for one test region: Amazonia. We estimated an Amazonia-wide evapotranspiration of 1370 mm yr(-1), but this value is dependent on assumptions about energy balance closure for the tropical eddy covariance sites; a lower value (1096 mm yr(-1)) is considered in discussion on the use of flux data to validate and interpolate models.

Reliability of orbital fits for resonant extrasolar planetary systems: the case of HD82943

We perform a statistical study of the process of orbital determination of the HD82943 extrasolar planetary system, using the current observational data set of N = 165 radial velocity (RV) measurements. Our aim is to analyse the dispersion of possible orbital fits leading to residuals compatible with the best solution, and to discuss the sensitivity of the results with respect to both the data set and the error distribution around the best fit. Although some orbital parameters (e.g. semimajor axis) appear well constrained, we show that the best fits for the HD82943 system are not robust, and at present it is not possible to estimate reliable solutions for these bodies. Finally, we discuss the possibility of a third planet, with a mass of 0.35M(Jup) and an orbital period of 900 d. Stability analysis and simulations of planetary migration indicate that such a hypothetical three-planet system could be locked in a double 2/1 mean-motion resonance, similar to the so-called Laplace resonance of the three inner Galilean satellites of Jupiter.

Skull Modularity in Neotropical Marsupials and Monkeys: Size Variation and Evolutionary Constraint and Flexibility

An organism is built through a series of contingent factors, yet it is determined by historical, physical, and developmental constraints. A constraint should not be understood as an absolute obstacle to evolution, as it may also generate new possibilities for evolutionary change. Modularity is, in this context, an important way of organizing biological information and has been recognized as a central concept in evolutionary biology bridging on developmental, genetics, morphological, biochemical, and physiological studies. In this article, we explore how modularity affects the evolution of a complex system in two mammalian lineages by analyzing correlation, variance/covariance, and residual matrices (without size variation). We use the multivariate response to selection equation to simulate the behavior of Eutheria and Metharia skulls in terms of their evolutionary flexibility and constraints. We relate these results to classical approaches based on morphological integration tests based on functional/developmental hypotheses. Eutherians (Neotropical primates) showed smaller magnitudes of integration compared with Metatheria (didelphids) and also skull modules more clearly delimited. Didelphids showed higher magnitudes of integration and their modularity is strongly influenced by within-groups size variation to a degree that evolutionary responses are basically aligned with size variation. Primates still have a good portion of the total variation based on size; however, their enhanced modularization allows a broader spectrum of responses, more similar to the selection gradients applied (enhanced flexibility). Without size variation, both groups become much more similar in terms of modularity patterns and magnitudes and, consequently, in their evolutionary flexibility. J. Exp. Zool. (Mol. Dev. Evol.) 314B:663-683, 2010. (C) 2010 Wiley-Liss, Inc.

SIZE AS A LINE OF LEAST RESISTANCE II: DIRECT SELECTION ON SIZE OR CORRELATED RESPONSE DUE TO CONSTRAINTS?

Evolutionary change in New World Monkey (NWM) skulls occurred primarily along the line of least resistance defined by size (including allometric) variation (g(max)). Although the direction of evolution was aligned with this axis, it was not clear whether this macroevolutionary pattern results from the conservation of within population genetic covariance patterns (long-term constraint) or long-term selection along a size dimension, or whether both, constraints and selection, were inextricably involved. Furthermore, G-matrix stability can also be a consequence of selection, which implies that both, constraints embodied in g(max) and evolutionary changes observed on the trait averages, would be influenced by selection Here, we describe a combination of approaches that allows one to test whether any particular instance of size evolution is a correlated by-product due to constraints (g(max)) or is due to direct selection on size and apply it to NWM lineages as a case study. The approach is based on comparing the direction and amount of evolutionary change produced by two different simulated sets of net-selection gradients (beta), a size (isometric and allometric size) and a nonsize set. Using this approach it is possible to distinguish between the two hypotheses (indirect size evolution due to constraints or direct selection on size), because although both may produce an evolutionary response aligned with g(max), the amount of change produced by random selection operating through the variance/covariance patterns (constraints hypothesis) will be much smaller than that produced by selection on size (selection hypothesis). Furthermore, the alignment of simulated evolutionary changes with g(max) when selection is not on size is not as tight as when selection is actually on size, allowing a statistical test of whether a particular observed case of evolution along the line of least resistance is the result of selection along it or not. Also, with matrix diagonalization (principal components [PC]) it is possible to calculate directly the net-selection gradient on size alone (first PC [PC1]) by dividing the amount of phenotypic difference between any two populations by the amount of variation in PC1, which allows one to benchmark whether selection was on size or not

The Evolution of Modularity in the Mammalian Skull I: Morphological Integration Patterns and Magnitudes

Morphological integration refers to the modular structuring of inter-trait relationships in an organism, which could bias the direction and rate of morphological change, either constraining or facilitating evolution along certain dimensions of the morphospace. Therefore, the description of patterns and magnitudes of morphological integration and the analysis of their evolutionary consequences are central to understand the evolution of complex traits. Here we analyze morphological integration in the skull of several mammalian orders, addressing the following questions: are there common patterns of inter-trait relationships? Are these patterns compatible with hypotheses based on shared development and function? Do morphological integration patterns and magnitudes vary in the same way across groups? We digitized more than 3,500 specimens spanning 15 mammalian orders, estimated the correspondent pooled within-group correlation and variance/covariance matrices for 35 skull traits and compared those matrices among the orders. We also compared observed patterns of integration to theoretical expectations based on common development and function. Our results point to a largely shared pattern of inter-trait correlations, implying that mammalian skull diversity has been produced upon a common covariance structure that remained similar for at least 65 million years. Comparisons with a rodent genetic variance/covariance matrix suggest that this broad similarity extends also to the genetic factors underlying phenotypic variation. In contrast to the relative constancy of inter-trait correlation/covariance patterns, magnitudes varied markedly across groups. Several morphological modules hypothesized from shared development and function were detected in the mammalian taxa studied. Our data provide evidence that mammalian skull evolution can be viewed as a history of inter-module parcellation, with the modules themselves being more clearly marked in those lineages with lower overall magnitude of integration. The implication of these findings is that the main evolutionary trend in the mammalian skull was one of decreasing the constraints to evolution by promoting a more modular architecture.