ONeSAMP: a program to estimate effective population size using approximate Bayesian computation

The estimation of effective population size from one sample of genotypes has been problematic because most estimators have been proven imprecise or biased. We developed a web-based program, ONeSAMP that uses approximate Bayesian computation to estimate effective population size from a sample of microsatellite genotypes. ONeSAMP requires an input file of sampled individuals' microsatellite genotypes along with information about several sampling and biological parameters. ONeSAMP provides an estimate of effective population size, along with 95% credible limits. We illustrate the use of ONeSAMP with an example data set from a re-introduced population of ibex Capra ibex.

The use of image analysis to estimate population growth rate in Daphnia magna

1. Population growth rate (PGR) is central to the theory of population ecology and is crucial for projecting population trends in conservation biology, pest management and wildlife harvesting. Furthermore, PGR is increasingly used to assess the effects of stressors. Image analysis that can automatically count and measure photographed individuals offers a potential methodology for estimating PGR. 2. This study evaluated two ways in which the PGR of Daphnia magna, exposed to different stressors, can be estimated using an image analysis system. The first method estimated PGR as the ratio of counts of individuals obtained at two different times, while the second method estimated PGR as the ratio of population sizes at two different times, where size is measured by the sum of the individuals' surface areas, i.e. total population surface area. This method is attractive if surface area is correlated with reproductive value (RV), as it is for D. magna, because of the theoretical result that PGR is the rate at which the population RV increases. 3. The image analysis system proved reliable and reproducible in counting populations of up to 440 individuals in 5 L of water. Image counts correlated well with manual counts but with a systematic underestimate of about 30%. This does not affect accuracy when estimating PGR as the ratio of two counts. Area estimates of PGR correlated well with count estimates, but were systematically higher, possibly reflecting their greater accuracy in the study situation. 4. Analysis of relevant scenarios suggested the correlation between RV and body size will generally be good for organisms in which fecundity correlates with body size. In these circumstances, area estimation of PGR is theoretically better than count estimation. 5. Synthesis and applications. There are both theoretical and practical advantages to area estimation of population growth rate when individuals' reproductive values are consistently well correlated with their surface areas. Because stressors may affect both the number and quality of individuals, area estimation of population growth rate should improve the accuracy of predicting stress impacts at the population level.

Revised QUICKI provides a strong surrogate estimate of insulin sensitivity when compared with the minimal model

OBJECTIVE: To compare insulin sensitivity (Si) from a frequently sampled intravenous glucose tolerance test (FSIGT) and subsequent minimal model analyses with surrogate measures of insulin sensitivity and resistance and to compare features of the metabolic syndrome between Caucasians and Indian Asians living in the UK. SUBJECTS: In all, 27 healthy male volunteers (14 UK Caucasians and 13 UK Indian Asians), with a mean age of 51.2 +/- 1.5 y, BMI of 25.8 +/- 0.6 kg/m(2) and Si of 2.85 +/- 0.37. MEASUREMENTS: Si was determined from an FSIGT with subsequent minimal model analysis. The concentrations of insulin, glucose and nonesterified fatty acids (NEFA) were analysed in fasting plasma and used to calculate surrogate measure of insulin sensitivity (quantitative insulin sensitivity check index (QUICKI), revised QUICKI) and resistance (homeostasis for insulin resistance (HOMA IR), fasting insulin resistance index (FIRI), Bennetts index, fasting insulin, insulin-to-glucose ratio). Plasma concentrations of triacylglycerol (TAG), total cholesterol, high density cholesterol, (HDL-C) and low density cholesterol, (LDL-C) were also measured in the fasted state. Anthropometric measurements were conducted to determine body-fat distribution. RESULTS: Correlation analysis identified the strongest relationship between Si and the revised QUICKI (r = 0.67; P = 0.000). Significant associations were also observed between Si and QUICKI (r = 0.51; P = 0.007), HOMA IR (r = -0.50; P = 0.009), FIRI and fasting insulin. The Indian Asian group had lower HDL-C (P = 0.001), a higher waist-hip ratio (P = 0.01) and were significantly less insulin sensitive (Si) than the Caucasian group (P = 0.02). CONCLUSION: The revised QUICKI demonstrated a statistically strong relationship with the minimal model. However, it was unable to differentiate between insulin-sensitive and -resistant groups in this study. Future larger studies in population groups with varying degrees of insulin sensitivity are recommended to investigate the general applicability of the revised QUICKI surrogate technique.

Can shells of freshwater mussels (Unionidae) be used to estimate low summer discharge of rivers and associated droughts?

This paper examines if shell oxygen isotope ratios (d18Oar) of Unio sp. can be used as a proxy of past discharge of the river Meuse. The proxy was developed from a modern dataset for the reference time interval 1997–2007, which showed a logarithmic relationship between discharge and measured water oxygen isotope ratios(d18Ow). To test this relationship for past time intervals,d18Oar values were measured in the aragonite of the growth increments of four Unio sp. shells; two from a relatively wet period and two from a very dry time interval (1910–1918 and 1969–1977, respectively). Shell d18Oar records were converted into d18Ow values using existing water temperature records. Summer d18Ow values, reconstructed from d18Oar of 1910–1918, showed a similar range as the summer d18Ow values for the reference time interval 1997–2007, whilst summer reconstructed d18Ow values for the time interval 1969–1977 were anomalously high. These high d18Ow values suggest that the river Meuse experienced severe summer droughts during the latter time interval. d18Ow values were then applied to calculate discharge values. It was attempted to estimate discharge from the reconstructed d18Ow values using the logarithmic relationship between d18Ow and discharge. A comparison of the calculated summer discharge results with observed discharge data showed that Meuse low-discharge events below a threshold value of 6 m3/s can be detected in the reconstructed d18Ow records, but true quantification remains problematic.

Combining satellite data and models to estimate cloud radiative effect at the surface and in the atmosphere

Satellite measurements and numerical forecast model reanalysis data are used to compute an updated estimate of the cloud radiative effect on the global multi-annual mean radiative energy budget of the atmosphere and surface. The cloud radiative cooling effect through reflection of shortwave radiation dominates over the longwave heating effect, resulting in a net cooling of the climate system of –21 Wm-2. The shortwave radiative effect of cloud is primarily manifest as a reduction in the solar radiation absorbed at the surface of -53 Wm-2. Clouds impact longwave radiation by heating the moist tropical atmosphere (up to around 40 Wm-2 for global annual means) while enhancing the radiative cooling of the atmosphere over other regions, in particular higher latitudes and sub-tropical marine stratocumulus regimes. While clouds act to cool the climate system during the daytime, the cloud greenhouse effect heats the climate system at night. The influence of cloud radiative effect on determining cloud feedbacks and changes in the water cycle are discussed.

Multimodel estimate of the global terrestrial water balance: setup and first results

Six land surface models and five global hydrological models participate in a model intercomparison project (WaterMIP), which for the first time compares simulation results of these different classes of models in a consistent way. In this paper the simulation setup is described and aspects of the multi-model global terrestrial water balance are presented. All models were run at 0.5 degree spatial resolution for the global land areas for a 15-year period (1985-1999) using a newly-developed global meteorological dataset. Simulated global terrestrial evapotranspiration, excluding Greenland and Antarctica, ranges from 415 to 586 mm year-1 (60,000 to 85,000 km3 year-1) and simulated runoff ranges from 290 to 457 mm year-1 (42,000 to 66,000 km3 year-1). Both the mean and median runoff fractions for the land surface models are lower than those of the global hydrological models, although the range is wider. Significant simulation differences between land surface and global hydrological models are found to be caused by the snow scheme employed. The physically-based energy balance approach used by land surface models generally results in lower snow water equivalent values than the conceptual degree-day approach used by global hydrological models. Some differences in simulated runoff and evapotranspiration are explained by model parameterizations, although the processes included and parameterizations used are not distinct to either land surface models or global hydrological models. The results show that differences between model are major sources of uncertainty. Climate change impact studies thus need to use not only multiple climate models, but also some other measure of uncertainty, (e.g. multiple impact models).

Attribution of climate change: a methodology to estimate the potential contribution to increases in potato yield in Scotland since 1960

Maincrop potato yields in Scotland have increased by 3035 similar to t similar to ha-1 since 1960 as a result of many changes, but has changing climate contributed anything to this? The purpose of this work was to answer this question. Daily weather data for the period 19602006 were analysed for five locations covering the zones of potato growing on the east coast of Scotland (between 55.213 and 57.646 similar to N) to determine trends in temperature, rainfall and solar radiation. A physiologically based potato yield model was validated using data obtained from a long-term field trial in eastern Scotland and then employed to simulate crop development and potential yield at each of the five sites. Over the 47 similar to years, there were significant increases in annual air and 30 similar to cm soil temperatures (0.27 and 0.30 similar to K similar to decade-1, respectively), but no significant changes in annual precipitation or in the timing of the last frost in spring and the first frost of autumn. There was no evidence of any north to south gradient of warming. Simulated emergence and canopy closure became earlier at all five sites over the period with the advance being greater in the north (3.7 and 3.6 similar to days similar to decade-1, respectively) than the south (0.5 and 0.8 similar to days similar to decade-1, respectively). Potential yield increased with time, generally reflecting the increased duration of the green canopy, at average rates of 2.8 similar to t similar to ha-1 decade-1 for chitted seed (sprouted prior to planting) and 2.5 similar to t similar to ha-1 decade-1 for unchitted seed. The measured warming could contribute potential yield increases of up to 13.2 similar to t similar to ha-1 for chitted potato (range 7.119.3 similar to t similar to ha-1) and 11.5 similar to t similar to ha-1 for unchitted potato (range 7.115.5 similar to t similar to ha-1) equivalent to 3439% of the increased potential yield over the period or 2326% of the increase in actual measured yields.

Using meteorological wind data to estimate turbine generation output: a sensitivity analysis

Various studies investigating the future impacts of integrating high levels of renewable energy make use of historical meteorological (met) station data to produce estimates of future generation. Hourly means of 10m horizontal wind are extrapolated to a standard turbine hub height using the wind profile power or log law and used to simulate the hypothetical power output of a turbine at that location; repeating this procedure using many viable locations can produce a picture of future electricity generation. However, the estimate of hub height wind speed is dependent on the choice of the wind shear exponent a or the roughness length z0, and requires a number of simplifying assumptions. This paper investigates the sensitivity of this estimation on generation output using a case study of a met station in West Freugh, Scotland. The results show that the choice of wind shear exponent is a particularly sensitive parameter which can lead to significant variation of estimated hub height wind speed and hence estimated future generation potential of a region.

A study into the accuracy of using meteorological wind data to estimate turbine generation output

Meteorological (met) station data is used as the basis for a number of influential studies into the impacts of the variability of renewable resources. Real turbine output data is not often easy to acquire, whereas meteorological wind data, supplied at a standardised height of 10 m, is widely available. This data can be extrapolated to a standard turbine height using the wind profile power law and used to simulate the hypothetical power output of a turbine. Utilising a number of met sites in such a manner can develop a model of future wind generation output. However, the accuracy of this extrapolation is strongly dependent on the choice of the wind shear exponent alpha. This paper investigates the accuracy of the simulated generation output compared to reality using a wind farm in North Rhins, Scotland and a nearby met station in West Freugh. The results show that while a single annual average value for alpha may be selected to accurately represent the long term energy generation from a simulated wind farm, there are significant differences between simulation and reality on an hourly power generation basis, with implications for understanding the impact of variability of renewables on short timescales, particularly system balancing and the way that conventional generation may be asked to respond to a high level of variable renewable generation on the grid in the future.

Updated estimate of aerosol direct radiative forcing from satellite observations and comparison against the Hadley Centre climate model

The fourth assessment report of the Intergovernmental Panel on Climate Change (IPCC) includes a comparison of observation-based and modeling-based estimates of the aerosol direct radiative forcing. In this comparison, satellite-based studies suggest a more negative aerosol direct radiative forcing than modeling studies. A previous satellite-based study, part of the IPCC comparison, uses aerosol optical depths and accumulation-mode fractions retrieved by the Moderate Resolution Imaging Spectroradiometer (MODIS) at collection 4. The latest version of MODIS products, named collection 5, improves aerosol retrievals. Using these products, the direct forcing in the shortwave spectrum defined with respect to present-day natural aerosols is now estimated at −1.30 and −0.65 Wm−2 on a global clear-sky and all-sky average, respectively, for 2002. These values are still significantly more negative than the numbers reported by modeling studies. By accounting for differences between present-day natural and preindustrial aerosol concentrations, sampling biases, and investigating the impact of differences in the zonal distribution of anthropogenic aerosols, good agreement is reached between the direct forcing derived from MODIS and the Hadley Centre climate model HadGEM2-A over clear-sky oceans. Results also suggest that satellite estimates of anthropogenic aerosol optical depth over land should be coupled with a robust validation strategy in order to refine the observation-based estimate of aerosol direct radiative forcing. In addition, the complex problem of deriving the aerosol direct radiative forcing when aerosols are located above cloud still needs to be addressed.

Assessment of the Wind Gust Estimate Method in mesoscale modelling of storm events over West Germany

A physically based gust parameterisation is added to the atmospheric mesoscale model FOOT3DK to estimate wind gusts associated with storms over West Germany. The gust parameterisation follows the Wind Gust Estimate (WGE) method and its functionality is verified in this study. The method assumes that gusts occurring at the surface are induced by turbulent eddies in the planetary boundary layer, deflecting air parcels from higher levels down to the surface under suitable conditions. Model simulations are performed with horizontal resolutions of 20 km and 5 km. Ten historical storm events of different characteristics and intensities are chosen in order to include a wide range of typical storms affecting Central Europe. All simulated storms occurred between 1990 and 1998. The accuracy of the method is assessed objectively by validating the simulated wind gusts against data from 16 synoptic stations by means of “quality parameters”. Concerning these parameters, the temporal and spatial evolution of the simulated gusts is well reproduced. Simulated values for low altitude stations agree particularly well with the measured gusts. For orographically exposed locations, the gust speeds are partly underestimated. The absolute maximum gusts lie in most cases within the bounding interval given by the WGE method. Focussing on individual storms, the performance of the method is better for intense and large storms than for weaker ones. Particularly for weaker storms, the gusts are typically overestimated. The results for the sample of ten storms document that the method is generally applicable with the mesoscale model FOOT3DK for mid-latitude winter storms, even in areas with complex orography.

An improved sum-product estimate for general finite fields

An improved sum-product estimate for subsets of a finite field whose order is not prime is provided. It is shown, under certain conditions, that max{∣∣∣A+A∣∣∣,∣∣∣A⋅A∣∣∣}≫∣∣A∣∣12/11(log2∣∣A∣∣)5/11. This new estimate matches, up to a logarithmic factor, the current best known bound obtained over prime fields by Rudnev