A Demographic Model to Evaluate Population Declines in the Endangered Streaked Horned Lark

The Streaked Horned Lark (Eremophila alpestris strigata) is listed as endangered by the State of Washington, USA and by Canada under the Species at Risk Act and is also classified as a federal candidate for listing under the Endangered Species Act in the USA. A substantial portion of Streaked Horned Lark habitat has been lost or degraded, and range contraction has occurred in Oregon, Washington, and British Columbia. We estimate the vital rates (fecundity, adult and juvenile survival) and population growth rate (λ) for Streaked Horned Larks breeding in Washington, USA and conduct a Life-Stage Simulation Analysis (LSA) to evaluate which vital rate has the greatest influence on λ. We simulated changes in the three vital rates to examine how much they would need to be adjusted either independently or in concert to achieve a stable Streaked Horned Lark population (λ = 1). We also evaluated which fecundity component (the number of fledglings per egg laid or renesting interval) had the greatest impact on λ. The estimate of population growth suggests that Streaked Horned Larks in Washington are declining rapidly (λ = 0.62 ± 0.10) and that local breeding sites are not sustainable without immigration. The LSA results indicate that adult survival had the greatest influence on λ, followed by juvenile survival and fecundity. However, increases in vital rates led to λ = 1 only when adult survival was raised from 0.47 to 0.85, juvenile survival from 0.17 to 0.58, and fecundity from 0.91 to 3.09. Increases in breeding success and decreases in the renesting interval influenced λ similarly; however, λ did not reach 1 even when breeding success was raised to 100% or renesting intervals were reduced to 1 day. Only when all three vital rates were increased simultaneously did λ approach 1 without requiring highly unrealistic increases in each vital rate. We conclude that conservation activities need to target all or multiple vital rates to be successful. The baseline data presented here and subsequent efforts to manage Streaked Horned Larks will provide valuable information for management of other declining Horned Lark subspecies and other grassland songbirds across North America.

The counter-propagating Rossby-wave perspective on baroclinic instability. II: Application to the Charney model

The constant-density Charney model describes the simplest unstable basic state with a planetary-vorticity gradient, which is uniform and positive, and baroclinicity that is manifest as a negative contribution to the potential-vorticity (PV) gradient at the ground and positive vertical wind shear. Together, these ingredients satisfy the necessary conditions for baroclinic instability. In Part I it was shown how baroclinic growth on a general zonal basic state can be viewed as the interaction of pairs of ‘counter-propagating Rossby waves’ (CRWs) that can be constructed from a growing normal mode and its decaying complex conjugate. In this paper the normal-mode solutions for the Charney model are studied from the CRW perspective. Clear parallels can be drawn between the most unstable modes of the Charney model and the Eady model, in which the CRWs can be derived independently of the normal modes. However, the dispersion curves for the two models are very different; the Eady model has a short-wave cut-off, while the Charney model is unstable at short wavelengths. Beyond its maximum growth rate the Charney model has a neutral point at finite wavelength (r=1). Thereafter follows a succession of unstable branches, each with weaker growth than the last, separated by neutral points at integer r—the so-called ‘Green branches’. A separate branch of westward-propagating neutral modes also originates from each neutral point. By approximating the lower CRW as a Rossby edge wave and the upper CRW structure as a single PV peak with a spread proportional to the Rossby scale height, the main features of the ‘Charney branch’ (0model where the positive PV gradient exists only at the tropopause

Examination of Relationships between Clear-Sky Longwave Radiation and Aspects of the Atmospheric Hydrological Cycle in Climate Models, Reanalyses, and Observations

Relationships between clear-sky longwave radiation and aspects of the atmospheric hydrological cycle are quantified in models, reanalyses, and observations over the period 1980-2000. The robust sensitivity of clear-sky surface net longwave radiation (SNLc) to column-integrated water vapor (CWV) of 1-1.5 Wm(-2) mm(-1) combined with the positive relationship between CWV and surface temperature (T-s) explains substantial increases in clear-sky longwave radiative cooling of the atmosphere (Q(LWc)) to the surface over the period. Clear-sky outgoing longwave radiation (OLRc) is highly sensitive to changes in aerosol and greenhouse gas concentrations in addition to temperature and humidity. Over tropical ocean regions of mean descent, Q(LWc) increases with T-s at similar to 3.5-5.5 W m(-2) K-1 for reanalyses, estimates derived from satellite data, and models without volcanic forcing included. Increased Q(LWc) with warming across the tropical oceans helps to explain model ensemble mean increases in precipitation of 0.1-0.15 mm day(-1) K-1, which are primarily determined by ascent regions where precipitation increases at the rate expected from the Clausius-Clapeyron equation. The implications for future projections in the atmospheric hydrological cycle are discussed

The influence of bottom topography on the decay of modeled Agulhas rings

The influence of a large meridional submarine ridge on the decay of Agulhas rings is investigated with a 1 and 2-layer setup of the isopycnic primitive-equation ocean model MICOM. In the single-layer case we show that the SSH decay of the ring is primarily governed by bottom friction and secondly by the radiation of Rossby waves. When a topographic ridge is present, the effect of the ridge on SSH decay and loss of tracer from the ring is negligible. However, the barotropic ring cannot pass the ridge due to energy and vorticity constraints. In the case of a two-layer ring the initial SSH decay is governed by a mixed barotropic–baroclinic instability of the ring. Again, radiation of barotropic Rossby waves is present. When the ring passes the topographic ridge, it shows a small but significant stagnation of SSH decay, agreeing with satellite altimetry observations. This is found to be due to a reduction of the growth rate of the m = 2 instability, to conversions of kinetic energy to the upper layer, and to a decrease in Rossby-wave radiation. The energy transfer is related to the fact that coherent structures in the lower layer cannot pass the steep ridge due to energy constraints. Furthermore, the loss of tracer from the ring through filamentation is less than for a ring moving over a flat bottom, related to a decrease in propagation speed of the ring. We conclude that ridges like the Walvis Ridge tend to stabilize a multi-layer ring and reduce its decay.

The role of nonhydrostatic dynamics in controlling development of a surface ocean front

Numerical studies of surface ocean fronts forced by inhomogeneous buoyancy loss show nonhydrostatic convective plumes coexisting with baroclinic eddies. The character of the vertical overturning depends sensitively on the treatment of the vertical momentum equation in the model. It is less well known how the frontal evolution over scales of O(10 km) is affected by these dynamics. Here, we compare highly resolved numerical experiments using nonhydrostatic and hydrostatic models and the convective-adjustment parametrization. The impact of nonhydrostatic processes on average cross-frontal transfer is weak compared to the effect of the O(1 km) scale baroclinic motions. For water-mass distribution and formation rate nonhydrostatic dynamics have similar influence to the baroclinic eddies although adequate resolution of the gradients in forcing fluxes is more important. The overall implication is that including nonhydrostatic surface frontal dynamics in ocean general circulation models will have only a minor effect on scales of O(1 km) and greater.

An integrated model of soil-canopy spectral radiances, photosynthesis, fluorescence, temperature and energy balance

This paper presents the model SCOPE (Soil Canopy Observation, Photochemistry and Energy fluxes), which is a vertical (1-D) integrated radiative transfer and energy balance model. The model links visible to thermal infrared radiance spectra (0.4 to 50 μm) as observed above the canopy to the fluxes of water, heat and carbon dioxide, as a function of vegetation structure, and the vertical profiles of temperature. Output of the model is the spectrum of outgoing radiation in the viewing direction and the turbulent heat fluxes, photosynthesis and chlorophyll fluorescence. A special routine is dedicated to the calculation of photosynthesis rate and chlorophyll fluorescence at the leaf level as a function of net radiation and leaf temperature. The fluorescence contributions from individual leaves are integrated over the canopy layer to calculate top-of-canopy fluorescence. The calculation of radiative transfer and the energy balance is fully integrated, allowing for feedback between leaf temperatures, leaf chlorophyll fluorescence and radiative fluxes. Leaf temperatures are calculated on the basis of energy balance closure. Model simulations were evaluated against observations reported in the literature and against data collected during field campaigns. These evaluations showed that SCOPE is able to reproduce realistic radiance spectra, directional radiance and energy balance fluxes. The model may be applied for the design of algorithms for the retrieval of evapotranspiration from optical and thermal earth observation data, for validation of existing methods to monitor vegetation functioning, to help interpret canopy fluorescence measurements, and to study the relationships between synoptic observations with diurnally integrated quantities. The model has been implemented in Matlab and has a modular design, thus allowing for great flexibility and scalability.

Understanding mixing efficiency in the oceans. Do the nonlinearities of the equation of state matter?

There exist two central measures of turbulent mixing in turbulent stratified fluids that are both caused by molecular diffusion: 1) the dissipation rate D(APE) of available potential energy APE; 2) the turbulent rate of change Wr, turbulent of background gravitational potential energy GPEr. So far, these two quantities have often been regarded as the same energy conversion, namely the irreversible conversion of APE into GPEr, owing to the well known exact equality D(APE)=Wr, turbulent for a Boussinesq fluid with a linear equation of state. Recently, however, Tailleux (2009) pointed out that the above equality no longer holds for a thermally-stratified compressible, with the ratio ξ=Wr, turbulent/D(APE) being generally lower than unity and sometimes even negative for water or seawater, and argued that D(APE) and Wr, turbulent actually represent two distinct types of energy conversion, respectively the dissipation of APE into one particular subcomponent of internal energy called the "dead" internal energy IE0, and the conversion between GPEr and a different subcomponent of internal energy called "exergy" IEexergy. In this paper, the behaviour of the ratio ξ is examined for different stratifications having all the same buoyancy frequency N vertical profile, but different vertical profiles of the parameter Υ=α P/(ρCp), where α is the thermal expansion coefficient, P the hydrostatic pressure, ρ the density, and Cp the specific heat capacity at constant pressure, the equation of state being that for seawater for different particular constant values of salinity. It is found that ξ and Wr, turbulent depend critically on the sign and magnitude of dΥ/dz, in contrast with D(APE), which appears largely unaffected by the latter. These results have important consequences for how the mixing efficiency should be defined and measured in practice, which are discussed.

Climate entropy budget of the HadCM3 atmosphere-ocean general circulation model and of FAMOUS, its low resolution version

The entropy budget is calculated of the coupled atmosphere–ocean general circulation model HadCM3. Estimates of the different entropy sources and sinks of the climate system are obtained directly from the diabatic heating terms, and an approximate estimate of the planetary entropy production is also provided. The rate of material entropy production of the climate system is found to be ∼50 mW m−2 K−1, a value intermediate in the range 30–70 mW m−2 K−1 previously reported from different models. The largest part of this is due to sensible and latent heat transport (∼38 mW m−2 K−1). Another 13 mW m−2 K−1 is due to dissipation of kinetic energy in the atmosphere by friction and Reynolds stresses. Numerical entropy production in the atmosphere dynamical core is found to be about 0.7 mW m−2 K−1. The material entropy production within the ocean due to turbulent mixing is ∼1 mW m−2 K−1, a very small contribution to the material entropy production of the climate system. The rate of change of entropy of the model climate system is about 1 mW m−2 K−1 or less, which is comparable with the typical size of the fluctuations of the entropy sources due to interannual variability, and a more accurate closure of the budget than achieved by previous analyses. Results are similar for FAMOUS, which has a lower spatial resolution but similar formulation to HadCM3, while more substantial differences are found with respect to other models, suggesting that the formulation of the model has an important influence on the climate entropy budget. Since this is the first diagnosis of the entropy budget in a climate model of the type and complexity used for projection of twenty-first century climate change, it would be valuable if similar analyses were carried out for other such models.

Modelling the movement and survival of the root-feeding clover weevil, Sitona lepidus, in the root-zone of white clover

White clover (Trifolium repens) is an important pasture legume but is often difficult to sustain in a mixed sward because, among other things, of the damage to roots caused by the soil-dwelling larval stages of S. lepidus. Locating the root nodules on the white clover roots is crucial for the survival of the newly hatched larvae. This paper presents a numerical model to simulate the movement of newly hatched S. lepidus larvae towards the root nodules, guided by a chemical signal released by the nodules. The model is based on the diffusion-chemotaxis equation. Experimental observations showed that the average speed of the larvae remained approximately constant, so the diffusion-chernotaxis model was modified so that the larvae respond only to the gradient direction of the chemical signal but not its magnitude. An individual-based lattice Boltzmann method was used to simulate the movement of individual larvae, and the parameters required for the model were estimated from the measurement of larval movement towards nodules in soil scanned using X-ray microtomography. The model was used to investigate the effects of nodule density, the rate of release of chemical signal, the sensitivity of the larvae to the signal, and the random foraging of the larvae on the movement and subsequent survival of the larvae. The simulations showed that the most significant factors for larval survival were nodule density and the sensitivity of the larvae to the signal. The dependence of larval survival rate on nodule density was well fitted by the Michealis-Menten kinetics. (c) 2005 Elsevier B.V All rights reserved.

Simulating the spatial variation of soil mineral N within fields using the model SUNDIAL

Variable rate applications of nitrogen (N) are of environmental and economic interest. Regular measurements of soil N supply are difficult to achieve practically. Therefore accurate model simulations of soil N supply might provide a practical solution for site-specific management of N. Mineral N, an estimate of N supply, was simulated by the model SUNDIAL (Simulation of Nitrogen Dynamics In Arable Land) at more than 100 locations within three arable fields in Bedfordshire, UK. The results were compared with actual measurements. The outcomes showed that the spatial patterns of the simulations of mineral N corresponded to the measurements but the range of values was underestimated.

Identifying the critical parameters of a cyanobacterial growth and movement model by using generalised sensitivity analysis

Bloom-forming and toxin-producing cyanobacteria remain a persistent nuisance across the world. Modelling of cyanobacteria in freshwaters is an important tool for understanding their population dynamics and predicting the location and timing of the bloom events in lakes and rivers. A new deterministic-mathematical model was developed, which simulates the growth and movement of cyanobacterial blooms in river systems. The model focuses on the mathematical description of the bloom formation, vertical migration and lateral transport of colonies within river environments by taking into account the major factors that affect the cyanobacterial bloom formation in rivers including, light, nutrients and temperature. A technique called generalised sensitivity analysis was applied to the model to identify the critical parameter uncertainties in the model and investigates the interaction between the chosen parameters of the model. The result of the analysis suggested that 8 out of 12 parameters were significant in obtaining the observed cyanobacterial behaviour in a simulation. It was found that there was a high degree of correlation between the half-saturation rate constants used in the model.

Integrated Nitrogen CAtchment model (INCA) applied to a tropical catchment in the Atlantic Forest, Sao Paulo, Brazil

Stream-water flows and in-stream nitrate and ammonium concentrations in a small (36.7 ha) Atlantic Forest catchment were simulated using the Integrated Nitrogen in CAtchments (INCA) model version 1.9.4. The catchment, at Cunha, is in the Serra do Mar State Park, SE Brazil and is nearly pristine because the nearest major conurbations, Sao Paulo and Rio, are some 450 km distant. However, intensive farming may increase nitrogen (N) deposition and there are growing pressures for urbanisation. The mean-monthly discharges and NO3-N concentration dynamics were simulated adequately for the calibration and validation periods with (simulated) loss rates of 6.55 kg.ha(-1) yr(-1) for NO3-N and 3.85 kg.ha(-1) yr(-1) for NH4-N. To investigate the effects of elevated levels of N deposition in the future, various scenarios for atmospheric deposition were simulated; the highest value corresponded to that in a highly polluted area of Atlantic Forest in Sao Paulo City. It was found that doubling the atmospheric deposition generated a 25% increase in the N leaching rate, while at levels approaching the highly polluted Sao Paulo deposition rate, five times higher than the current rate, leaching increased by 240%, which would create highly eutrophic conditions, detrimental to downstream water quality. The results indicate that the INCA model can be useful for estimating N concentration and fluxes for different atmospheric deposition rates and hydrological conditions.

Impacts of forestry on nitrogen in upland and lowland catchments: a comparison of the River Severn at Plynlimon in mid-Wales and the Bedford Ouse in south-east England using the INCA Model

The impacts of afforestation at Plynlimon in the Severn catchment, mid-Wales. and in the Bedford Ouse catchment in south-east England are evaluated using the INCA model to simulate Nitrogen (N) fluxes and concentrations. The INCA model represents the key hydrological and N processes operating in catchments and simulates the daily dynamic behaviour as well as the annual fluxes. INCA has been applied to five years of data front the Hafren and Hore headwater sub-catchments (6.8 km(2) area in total) of the River Severn at Plytilimon and the model was calibrated and validated against field data. Simulation of afforestation is achieved by altering the uptake rate parameters in the model. INCA simulates the daily N behaviour in the catchments with good accuracy as well as reconstructing the annual budgets for N release following clearfelling a four-fold increase in N fluxes was followed by a slow recovery after re-afforestation. For comparison, INCA has been applied to the large (8380 km(2)) Bedford Ouse catchment to investigate the impact of replacing 20% arable land with forestry. The reduction in fertiliser inputs from arable farming and the N uptake by the forest are predicted to reduce the N flux reaching the main river system, leading to a 33% reduction in N-Nitrate concentrations in the river water.

Modelling the movement and survival of the root-feeding clover weevil, Sitona lepidus, in the root-zone of white clover

White clover (Trifolium repens) is an important pasture legume but is often difficult to sustain in a mixed sward because, among other things, of the damage to roots caused by the soil-dwelling larval stages of S. lepidus. Locating the root nodules on the white clover roots is crucial for the survival of the newly hatched larvae. This paper presents a numerical model to simulate the movement of newly hatched S. lepidus larvae towards the root nodules, guided by a chemical signal released by the nodules. The model is based on the diffusion-chemotaxis equation. Experimental observations showed that the average speed of the larvae remained approximately constant, so the diffusion-chernotaxis model was modified so that the larvae respond only to the gradient direction of the chemical signal but not its magnitude. An individual-based lattice Boltzmann method was used to simulate the movement of individual larvae, and the parameters required for the model were estimated from the measurement of larval movement towards nodules in soil scanned using X-ray microtomography. The model was used to investigate the effects of nodule density, the rate of release of chemical signal, the sensitivity of the larvae to the signal, and the random foraging of the larvae on the movement and subsequent survival of the larvae. The simulations showed that the most significant factors for larval survival were nodule density and the sensitivity of the larvae to the signal. The dependence of larval survival rate on nodule density was well fitted by the Michealis-Menten kinetics. (c) 2005 Elsevier B.V All rights reserved.

Glacier shrinkage and climatic change in the Russian Altai from the mid-20th century: An assessment using remote sensing and PRECIS regional climate model

This paper examines changes in the surface area of glaciers in the North and South Chuya Ridges, Altai Mountains in 1952-2004 and their links with regional climatic variations. The glacier surface areas for 2004 were derived from the Advanced Spaceborne Thermal Emission and Reflection Radiometer (ASTER) imagery. Data from the World Glacier Inventory (WGI)dating to 1952 and aerial photographs from 1952 were used to estimate the changes. 256 glaciers with a combined area of 253±5.1 km2 have been identified in the region in 2004. Estimation of changes in extent of 126 glaciers with the individual areas not less than 0.5 km2 in 1952 revealed a 19.7±5.8% reduction. The observed glacier retreat is primarily driven by an increase in summer temperatures since the 1980s when air temperatures were increasing at a rate of 0.10 - 0.13oC a-1 at the glacier tongue elevation. The regional climate projections for A2 and B2 CO2 emission scenarios developed using PRECIS regional climate model indicate that summer temperatures will increase in the Altai in 2071-2100 by 6-7oC and 3-5oC respectively in comparison with 1961-1990 while annual precipitation will increase by 15% and 5%. The length of the ablation season will extend from June-August to the late April – early October. The projected increases in precipitation will not compensate for the projected warming and glaciers will continue to retreat in the 21st century under both B2 and A2 scenarios.