Bayesian Small Area Models for Assessing Wildlife Conservation Risk in Patchy Populations

Abstract:  Species conservation risk assessments require accurate, probabilistic, and biologically meaningful maps of population distribution. In patchy populations, the reasons for discontinuities are not often well understood. We tested a novel approach to habitat modeling in which methods of small area estimation were used within a hierarchical Bayesian framework. Amphibian occurrence was modeled with logistic regression that included third-order drainages as hierarchical effects to account for patchy populations. Models including the random drainage effects adequately represented species occurrences in patchy populations of 4 amphibian species in the Oregon Coast Range (U.S.A.). Amphibian surveys from other locations within the same drainage were used to calibrate local drainage-scale effects. Cross-validation showed that prediction errors for calibrated models were 77% to 86% lower than comparable regionally constructed models, depending on species. When calibration data were unavailable, small area and regional models performed similarly, although poorly. Small area estimation models complement wildlife ecology and habitat studies, and can help managers develop a regional picture of the conservation status for relatively rare species.     

Using long-term data for a reintroduced population to empirically estimate future consequences of inbreeding

Inbreeding depression is an important long-term threat to reintroduced populations. However, the strength of inbreeding depression is difficult to estimate in wild populations because pedigree data are inevitably incomplete and because good data are needed on survival and reproduction. Predicting future population consequences is especially difficult because this also requires projecting future inbreeding levels and their impacts on long-term population dynamics, which are subject to many uncertainties. We illustrate how such projections can be derived through Bayesian state-space modeling methods based on a 26-year data set for North Island Robins (Petroica longipes) reintroduced to Tiritiri Matangi Island in 1992. We used pedigree data to model increases in the average inbreeding level (F ) over time based on kinship of possible breeding pairs and to estimate empirically N_e/N (effective/census population size). We used multiple imputation to model the unknown components of inbreeding coefficients, which allowed us to estimate effects of inbreeding on survival for all 1458 birds in the data set while modeling density dependence and environmental stochasticity. This modeling indicated that inbreeding reduced juvenile survival (1.83 lethal equivalents [SE 0.81]) and may have reduced subsequent adult survival (0.44 lethal equivalents [0.81]) but had no apparent effect on numbers of fledglings produced. Average inbreeding level increased to 0.10 (SE 0.001) as the population grew from 33 (0.3) to 160 (6) individuals over the 25 years, giving a ratio of 0.56 (0.01). Based on a model that also incorporated habitat regeneration, the population was projected to reach a maximum of 331–1144 birds (median 726) in 2130, then to begin a slow decline. Without inbreeding, the population would be expected stabilize at 887–1465 birds (median 1131). Such analysis, therefore, makes it possible to empirically derive the information needed for rational decisions about inbreeding management while accounting for multiple sources of uncertainty.     

The value of Seasonal Correction Factors in assessing the health risk from domestic radon: a case study in Northamptonshire, UK

Following an intensive survey of domestic radon levels in the United Kingdom (UK), the former National Radiological Protection Board (NRPB), now the Radiation Protection Division of the Health Protection Agency (HPA-RPD), established a measurement protocol and promulgated Seasonal Correction Factors applicable to the country as a whole. Radon levels in the domestic built environment are assumed to vary systematically and repeatably during the year, being generally higher in winter. The Seasonal Correction Factors therefore comprise a series of numerical multipliers, which convert a 1-month or 3-month radon concentration measurement, commencing in any month of the year, to an effective annual mean radon concentration. In a recent project undertaken to assess the utility of short-term exposures in quantifying domestic radon levels, a comparative assessment of a number of integrating detector types was undertaken, with radon levels in 34 houses on common geology monitored over a 12-month period using dose-integrating track-etch detectors exposed in pairs (one upstairs, one downstairs) at 1-month and 3-month resolution. Seasonal variability of radon concentrations departed significantly from that expected on the basis of the HPA-RPD Seasonal Correction Factor set, with year-end discontinuities at both 1-month and 3-month measurement resolutions. Following this study, monitoring with electrets was continued in four properties, with weekly radon concentration data now available for a total duration in excess of three and a half years. Analysis of this data has permitted the derivation of reliable local Seasonal Correction Factors. Overall, these are significantly lower than those recommended by HPA-RPD, but are comparable with other results from the UK and from abroad, particularly those that recognise geological diversity and are consequently prepared on a regional rather than a national basis. This finding calls into question the validity of using nationally aggregated Seasonal Correction Factors, especially for shorter exposures, and the universal applicability of these corrections is discussed in detail.     

Biogeochemical consequences of a changing Arctic shelf seafloor ecosystem

Unprecedented and dramatic transformations are occurring in the Arctic in response to climate change, but academic, public, and political discourse has disproportionately focussed on the most visible and direct aspects of change, including sea ice melt, permafrost thaw, the fate of charismatic megafauna, and the expansion of fisheries. Such narratives disregard the importance of less visible and indirect processes and, in particular, miss the substantive contribution of the shelf seafloor in regulating nutrients and sequestering carbon. Here, we summarise the biogeochemical functioning of the Arctic shelf seafloor before considering how climate change and regional adjustments to human activities may alter its biogeochemical and ecological dynamics, including ecosystem function, carbon burial, or nutrient recycling. We highlight the importance of the Arctic benthic system in mitigating climatic and anthropogenic change and, with a focus on the Barents Sea, offer some observations and our perspectives on future management and policy.     

Effects of the forced ventilation on composting of a solid olive-mill by-product ("alperujo") managed by mechanical turning

The evaluation of the most suitable aeration technology for olive-mill by-product "alperujo" (AL) composting was carried out by using two identical piles prepared by mixing AL with a bulking agent (fresh cow bedding) and a mature compost (as inoculant). Forced ventilation was employed in conjunction with mechanical turning in one of the piles, whereas only mechanical turning was used in the other pile. These two treatment methods were evaluated by assessing process efficiency and end-product quality. The results show that the composting process was completed in less time when forced ventilation was coupled with mechanical turning. A slight delay in the evolution of pH, C/N ratio, and biodegradation of fats and organic matter was observed when only turning was employed. However, the recommended method for composting AL was mechanical turning without forced ventilation since the composition of the end-product in this case was comparable to the composted AL using forced ventilation coupled with mechanical turning. Furthermore, there were substantial economic savings by selecting mechanical turning alone, which included capital costs for equipment.     

Estimating plant-available nitrogen release from manures, composts, and specialty products

Recent adoption of national rules for organic crop production have stimulated greater interest in meeting crop N needs using manures, composts, and other organic materials. This study was designed to provide data to support Extension recommendations for organic amendments. Specifically, our objectives were to (i) measure decomposition and N released from fresh and composted amendments and (ii) evaluate the performance of the model DECOMPOSITION, a relatively simple N mineralization/immobilization model, as a predictor of N availability. Amendment samples were aerobically incubated in moist soil in the laboratory at 22 degrees C for 70 d to determine decomposition and plant-available nitrogen (PAN) (n = 44), and they were applied preplant to a sweet corn crop to determine PAN via fertilizer N equivalency (n = 37). Well-composted materials (n = 14) had a single decomposition rate, averaging 0.003 d(-1). For uncomposted materials, decomposition was rapid (>0.01 d(-1)) for the first 10 to 30 d. The laboratory incubation and the full-season PAN determination in the field gave similar estimates of PAN across amendments. The linear regression equation for lab PAN vs. field PAN had a slope not different from one and a y-intercept not different than zero. Much of the PAN released from amendments was recovered in the first 30 d. Field and laboratory measurements of PAN were strongly related to PAN estimated by DECOMPOSITION (r(2) > 0.7). Modeled PAN values were typically higher than observed PAN, particularly for amendments exhibiting high initial NH(4)-N concentrations or rapid decomposition. Based on our findings, we recommend that guidance publications for manure and compost utilization include short-term (28-d) decomposition and PAN estimates that can be useful to both modelers and growers.     

micro-XANES and micro-XRF investigations of metal binding mechanisms in biosolids

Micro-X-ray fluorescence (micro-XRF) microprobe analysis and micro-X-ray absorption near-edge structure (micro-XANES) spectroscopy were employed to identify Fe and Mn phases and their association with selected metals in two biosolids (limed composted [LC] and Nu-Earth) before and after treatment to remove organic carbon (OC). Spatial correlations derived from elemental mapping of XRF images showed strong correlations between Fe and Cd, Cr, Pb, or Zn (r2= 0.65-0.92) before and after removal of most of the OC. The strong correlation between Fe and Cu that was present in intact samples disappeared after OC removal, suggesting that Cu was associated with OC coatings that may have been present on Fe compounds. Except for Fe and Cr, the spatial correlations of metals with Mn were improved after treatment to remove OC, indicating that the treatment may have altered more than the OC in the system. The Fe micro-XANES spectra of the intact biosolids sample showed that every point had varying mixtures of Fe(II and III) species and no two points were identical. The lack of uniformity in Fe species in the biosolids sample illustrates the complexity of the materials and the difficulty of studying biosolids using conventional analytical tools or chemical extraction techniques. Still, these microscopic observations provide independent information supporting the previous laboratory and field hypothesis that Fe compounds play a major role in retention of environmentally important trace elements in biosolids. This could be due to co-precipitation of the metals with Fe, adsorption of metals by Fe compounds, or a combination of both mechanisms.     

Nitrogen and phosphorus status of soils and trophic state of lakes associated with forage-based beef cattle operations in Florida

Forage-based livestock systems have been implicated as major contributors to deteriorating water quality, particularly for phosphorus (P) from commercial fertilizers and manures affecting surface and ground water quality. Little information exists regarding possible magnitudes of nutrient losses from pastures that are managed for both grazing and hay production and how these might impact adjacent bodies of water. We examined the changes that have occurred in soil fertility levels of rhizoma peanut (Arachis glabrata Benth.)-based beef cattle pastures (n = 4) in Florida from 1988 to 2002. These pastures were managed for grazing in spring followed by haying in late summer and were fertilized annually with P (39 kg P2O5 ha(-1)) and K (68 kg K2O ha(-1)). Additionally, we investigated trends in water quality parameters and trophic state index (TSI) of lakes (n = 3) associated with beef cattle operations from 1993 to 2002. Overall, there was no spatial or temporal buildup of soil P and other crop nutrients despite the annual application of fertilizers and daily in-field loading of animal waste. In fact, soil fertility levels showed a declining trend for crop nutrient levels, especially soil P (y = 146.57 - 8.14 x year; r2= 0.75), even though the fields had a history of P fertilization and the cattle were rotated into the legume fields. Our results indicate that when nutrients are not applied in excess, cow-calf systems are slight exporters of P, K, Ca, and Mg through removal of cut hay. Water quality in lakes associated with cattle production was "good" (30-46 TSI) based on the Florida Water Quality Standard. These findings indicate that properly managed livestock operations may not be major contributors to excess loads of nutrients (especially P) in surface water.