Validation of ecological state space models using the Laplace approximation

Many statistical models in ecology follow the state space paradigm. For such models, the important step of model validation rarely receives as much attention as estimation or hypothesis testing, perhaps due to lack of available algorithms and software. Model validation is often based on a naive adaptation of Pearson residuals, i.e. the difference between observations and posterior means, even if this approach is flawed. Here, we consider validation of state space models through one-step prediction errors, and discuss principles and practicalities arising when the model has been fitted with a tool for estimation in general mixed effects models. Implementing one-step predictions in the R package Template Model Builder, we demonstrate that it is possible to perform model validation with little effort, even if the ecological model is multivariate, has non-linear dynamics, and whether observations are continuous or discrete. With both simulated data, and a real data set related to geolocation of seals, we demonstrate both the potential and the limitations of the techniques. Our results fill a need for convenient methods for validating a state space model, or alternatively, rejecting it while indicating useful directions in which the model could be improved.     

Large variation in breast milk levels of organohalogenated compounds is dependent on mother's age, changes in body composition and exposures early in life

We identified factors that are important determinants of body burdens (breast milk levels) of polychlorinated biphenyls (PCBs), dioxins (polychlorinated dibenzo-p-dioxins (PCDDs) and polychlorinated dibenzofurans (PCDFs)) and polybrominated diphenyl ethers (PBDEs). PCBs, PCDD/Fs and PBDEs were analysed in breast milk from up to 325 first-time mothers in Uppsala, Sweden, who delivered between 1996 and 2006. Hierarchical clustering was used as a method for identification of groups of compounds with common sources of exposure and similar toxicokinetics. Based on correlations between levels of single compounds/congeners in breast milk, distinctly separated clusters were formed, strongly dependent on structural similarities of the organohalogen molecules. In a multiple regression model, levels of PCBs (except PCB 28), PCDD/Fs and BDE-153 were positively associated with age of the mother and weight loss after delivery and inversely associated with pre-pregnancy BMI (body mass index) and weight gain during pregnancy. Higher levels of mono-ortho PCB TEQ, non-ortho PCB TEQ and BDE-153 in milk were found among women with high physical activity. Women who were breastfed during infancy and grew up on the Baltic coast of Sweden, with high availability of contaminated fish from the Baltic sea, had higher levels of PCBs and PCDD/Fs in breast milk indicating that exposure early in life from breast milk and contaminated fish may still affect body burdens at the time of pregnancy. The importance of current consumption of fatty Baltic fish as a source of exposure was supported by the positive association with breast milk levels of mono-ortho PCB TEQ, PCDF TEQ and BDE-153. The results show that, in contrast to the lower brominated PBDE congeners, the hexa-brominated BDE-153 resembles the chlorinated compounds with regards to determinants in breast milk. This suggests that some of the PBDEs may have toxicokinetic properties and that are similar to the PCBs and PCDD/Fs. Our results show that a few simple advices to women regarding weight changes in connection with pregnancy and consumption of contaminated fatty fish during the whole lifetime may lower the levels of dioxins in breast milk by up to 60%.     

Content, distribution and fate of 33 elements in sediments of rivers receiving wastewater in Hanoi, Vietnam

Untreated industrial and domestic wastewater from Hanoi city is discharged into rivers that supply water for various agricultural and aqua-cultural food production systems. The aim of this study was to assess the content, distribution and fate of 33 elements in the sediment and pore water of the main wastewater receiving rivers. The sediment was polluted with potentially toxic elements (PTEs) with maximum concentrations of 73 As, 427 Cd, 281 Cr, 240 Cu, 218 Ni, 363 Pb, 12.5 Sb and 1240 Zn mg kg(-1) d.w. Observed distribution coefficients (log(10) K(d,obs)) were calculated as the ratio between sediment (mg kg(-1) d.w.) and pore water (mg L(-1)) concentrations. Maxima log(10) K(d,obs) were >4.26 Cd, >6.60 Cu, 4.78 Ni, 7.01 Pb and 6.62 Zn. The high values show a strong PTE retention and indicate the importance of both sorption and precipitation as retention mechanisms. Sulphide precipitation was a likely mechanism due to highly reduced conditions.     

Pup production and breeding distribution of the Caspian seal (Phoca caspica) in relation to human impacts

Aerial surveys of Caspian seals on the winter ice field in Kazakhstan territorial waters were carried out in February 2005 and 2006 to assess the annual pup production for the species and natural predation on newborn pups. Estimated pup production was 21063 in 2005 and 16905 in 2006 (including an estimated figure for pups born in Russian territory in each year). The breeding population size of approximately 20 000 females is much less than published estimates from the late 1980s. Eagles were the principal natural predators of pups. Commercial icebreaker routes passed through areas of dense pup concentrations in 2006, although not in 2005. Our findings have important implications for the development of conservation strategies for the species. Natural mortality, loss to predators, and, more important, the current hunting quota substantially exceed the recruitment of the Caspian seal population. Anthropogenic sources of mortality should be managed to avoid further declines in the species.     

Tardy females,impatient males: protandry and divergent selection on arrival date in the two sexes of the barn swallow

Protandry reflects the earlier arrival of males than females to the site of reproduction. Such protandry is hypothesised to arise from sex differences in costs and benefits of early arrival. I investigated temporal patterns of arrival date of male and female barn swallows Hirundo rustica and temporal patterns of selection to test the hypothesis that sex differences in selection account for sex differences in arrival date. Mean arrival date of male barn swallows but not of females advanced during the last 33 years, giving rise to an increasing sex difference in arrival date. Early arrival was favoured by increasingly better survival in males, while females showed an opposite pattern that did not reach significance, although the effect differed between sexes. Early arrival increased fecundity in both sexes equally.The sex difference in viability selection in relation to arrival date changed from positive to negative as the degree of protandry increased in recent years, although there was no similar significant relationship for fecundity selection. Furthermore, sex differences in viability selection in a given year affected the degree of protandry in the following year through differential survival of certain phenotypes over others. Finally, temporal changes in sex difference in viability selection and protandry were related to an increase in the interval between first and second clutches, as the duration of the breeding season increased because of climatic amelioration. These findings suggest that arrival date is under divergent selection in the two sexes, providing a mechanism for the evolution of protandry.     

Modeling the Effect of Liming on Calcium Concentration in Swedish Lakes

To abate the severe acidification of Swedish lakes are about 7% directly limed (AL-lakes). These are important to include when assessing acidification. Consequently, we need to estimate their chemical status as if they were not lime-affected. We hypothesize that there is a spatial dependence for calcium (Ca) and magnesium (Mg) concentrations. Spatial variation is determined using variograms. We study lakes within two 150 ∗ 150 km quadrates (EMEP150-grid) in the middle and southern parts of Sweden. We model Ca in AL-lakes using the Ca and Mg concentrations in nearby, unaffected lakes (UL-lakes). The mean Ca/Mg for the three or seven closest UL-lakes is used. We assume that Ca/Mg is constant for UL-lakes and that Mg unaltered by liming. For UL-lakes, Ca and Mg are spatially dependent. For AL-lakes, there is a spatial dependence for Mg, but, as anticipated, not for Ca. The modeled Ca for UL-lakes show a good correspondence with measured Ca; r ² > 0.6; slopes close to 1 and intercepts almost 0. Using three or seven nearby lakes when modeling Ca give similar results. Modeled Ca was higher than measured Ca for 36% (three closest lakes) and 38% (seven closest) of the modeled AL-lakes in the middle part of Sweden. The corresponding results for the southern part were 10% and 9%, respectively. This model is an acceptable estimator of Ca in limed lakes and for estimating critical loads and acidification status on an EMEP-scale.     

Stability of odorants from pig production in sampling bags for olfactometry

Odor from pig production facilities is typically measured with olfactometry, whereby odor samples are collected in sampling bags and assessed by human panelists within 30 h. In the present study, the storage stability of odorants in two types of sampling bags that are often used for olfactometry was investigated. The bags were made of Tedlar or Nalophan. In a field experiment, humid and dried air samples were collected from a pig production facility with growing-finishing pigs and analyzed with a gas chromatograph with an amperometric sulfur detector at 4, 8, 12, 28, 52, and 76 h after sampling. In a laboratory experiment, the bags were filled with a humid gas mixture containing carboxylic acids, phenols, indoles, and sulfur compounds and analyzed with proton-transfer-reaction mass spectrometry after 0, 4, 8, 12, and 24 h. The results demonstrated that the concentrations of carboxylic acids, phenols, and indoles decreased by 50 to >99% during the 24 h of storage in Tedlar and Nalophan bags. The concentration of hydrogen sulfide decreased by approximately 30% during the 24 h of storage in Nalophan bags, whereas in Tedlar bags the concentration of sulfur compounds decreased by <5%. In conclusion, the concentrations of odorants in air samples from pig production facilities significantly decrease during storage in Tedlar and Nalophan bags, and the composition changes toward a higher relative presence of sulfur compounds. This can result in underestimation of odor emissions from pig production facilities and of the effect of odor reduction technologies.     

Effects of boreal forest management practices on the climate impact of CO2 emissions from bioenergy

In Life Cycle Assessment (LCA), carbon dioxide (CO₂) emissions from biomass combustion are traditionally assumed climate neutral if the bioenergy system is CO₂ flux neutral, i.e. the quantity of CO₂ released approximately equals the amount of CO₂ sequestered in biomass. This convention is a plausible assumption for fast growing biomass species, but is inappropriate for slower growing biomass, like forests. In this case, the climate impact from biomass combustion can be potentially underestimated if CO₂ emissions are ignored, or overestimated, if biogenic CO₂ is considered equal to anthropogenic CO₂. The estimation of the effective climate impact should take into account how the CO₂ fluxes are distributed over time: the emission of CO₂ from bioenergy approximately occurs at a single point in time, while the absorption by the new trees is spread over several decades. Our research target is to include this dynamic time dimension in unit-based impact analysis, using a boreal forest stand as case study. The boreal forest growth is modelled with an appropriate function, and is investigated under different forestry regimes (affecting the growth rate and the year of harvest). Specific atmospheric decay functions for biomass-derived CO₂ are then elaborated for selected combinations of forest management options. The contribution to global warming is finally quantified using the GWP_bio index as climate metric. Results estimates the effects of these practices on the characterization factor used for the global warming potential of CO₂ from bioenergy, and point out the key role played by the selected time horizon.     

The influence of shade trees on coffee quality in small holder coffee agroforestry systems in Southern Colombia

Production of coffee, especially by small holders, is often associated with various forms of shade management. To analyse the effects of shade on physical coffee quality and on sensorial cup quality of Coffea arabica L. cv. Caturra KMC, a study was carried out with 94 plots on 16 farms in two municipalities, Timaná and Oporapa, located at elevations from 1272 to 1730 masl. in Huila, Colombia. The study was designed with emphasis on shade cover variation within each of the two study areas, while minimizing the variability of environment, agronomic management other than shade, and post-harvest processing. 46 samples of shade coffee and 46 samples of sun coffee were evaluated for physical and sensorial attributes using three professional coffee cuppers (assessors). A principal component analysis including all quality and environmental variables showed that sensory attributes were influenced negatively by shade, and that physical attributes were influenced positively by altitude. A mixed linear model, with coffee cupper and farm as random variables, revealed different shade effects on coffee quality in the two areas. In Oporapa, situated at high altitudes, shade had a negative effect on fragrance, acidity, body, sweetness and preference of the beverage, while no effect was found on the physical quality. In Timaná, situated at lower altitudes, shade did not have a significant effect on sensorial attributes, but significantly reduced the number of small beans. At high altitudes with low temperatures and no nutrient or water deficits, shade trees may thus have a partly adverse effect on C. arabica cv. Caturra resulting in reduced sensory quality. The occurrence of berry borer (Hypothenemus hampei) was lower at high altitudes and higher under shade. Future studies on shade and coffee quality should focus on the interaction between physical and chemical characteristics of beans.