Using data augmentation via the Gibbs Sampler to incorporate missing covariate structure in linear models for ecological assessments

Missing covariate values in linear regression models can be an important problem facing environmental researchers. Existing missing value treatment methods such as Multiple Imputation (MI), the EM algorithm and Data Augmentation (DA) have the assumption that both observed and unobserved data come from the same distribution, most commonly a multivariate normal or a conditionally multivariate normal family. These methods do try to incorporate the missing data mechanism and rely on the assumption of Missing At Random (MAR). We present a DA method which does not rely on the MAR assumption and can model missing data mechanisms and covariate structure. This method utilizes the Gibbs Sampler as a tool for incorporating these structures and mechanisms. We apply this method to an ecological data set that relates fish condition to environmental variables. Notice that the presented DA method detects relationships that are not detected when other missing data methods are employed.

Contribution of leaf life span and nutrient resorption to mean residence time: elasticity analysis

We tested the relative contribution of leaf life span (LLS) and nutrient resorption efficiency (RE) to nutrient mean residence time (MRT) in plants. To do so, we introduced the use of elasticity analysis, which aims to measure the impact on MRT of a small change in one component, relative to the impact of equal changes in the other element. We also quantified the joint effect of LLS and RE on MRT, which required the calculation of the second derivatives of MRT with respect to LLS and RE. The estimation of the first derivatives showed that, although MRT increases linearly with LLS for a given value of RE, the relative effect of RE on MRT elasticity varies according to RE values; when RE > 0.5, the MRT's elasticity increases exponentially. The calculation of the second derivatives confirmed the importance of RE on MRT's variation. We used the results of the elasticity analysis to analyze how MRT responded to variation in LLS and nitrogen RE on MRT at the intra- and interspecific levels. For this, we used 18 plant species from three stages of a Mediterranean old-field succession, grown in a common garden experiment at two levels of nitrogen supply.     

Food webs and intraguild predation: community interactions of a native mesocarnivore

Trophic level interactions between predators create complex relationships such as intraguild predation. Theoretical research has predicted two possible paths to stability in intraguild systems: intermediate predators either outcompete higher-order predators for shared resources or select habitat based on security. The effects of intraguild predation on intermediate mammalian predators such as swift foxes (Vulpes velox) are not well understood. We examined the relationships between swift foxes and both their predators and prey, as well the effect of vegetation structure on swift fox-coyote (Canis latrans) interactions, between August 2001 and August 2004. In a natural experiment created by the Pinon Canyon Maneuver Site in southeastern Colorado, USA, we documented swift fox survival and density in a variety of landscapes and compared these parameters in relation to prey availability, coyote abundance, and vegetation structure. Swift fox density varied significantly between study sites, while survival did not. Coyote abundance was positively related to the basal prey species and vegetation structure, while swift fox density was negatively related to coyote abundance, basal prey species, and vegetation structure. Our results support the prediction that, under intraguild predation in terrestrial systems, top predator distribution matches resource availability (resource match), while intermediate predator distribution inversely matches predation risk (safety match). While predation by coyotes may be the specific cause of swift fox mortality in this system, the more general mechanism appears to be exposure to predation moderated by shrub density.     

Plant-soil microorganism interactions: heritable relationship between plant genotype and associated soil microorganisms

Although soil microbial communities are known to play crucial roles in the cycling of nutrients in forest ecosystems and can vary by plant species, how microorganisms respond to the subtle gradients of plant genetic variation is just beginning to be appreciated. Using a model Populus system in a common garden with replicated clones of known genotypes, we evaluated microbial biomass and community composition as quantitative traits. Two main patterns emerged. (1) Plant genotype influenced microbial biomass nitrogen in soils under replicated genotypes of Populus angustifolia, F1, and backcross hybrids, but not P. fremontii. Genotype explained up to 78% of the variation in microbial biomass as indicated by broad-sense heritability estimates (i.e., clonal repeatability). A second estimate of microbial biomass (total phospholipid fatty acid) was more conservative and showed significant genotype effects in P. angustifolia and backcross hybrids. (2) Plant genotype significantly influenced microbial community composition, explaining up to 70% of the variation in community composition within P. angustifolia genotypes alone. These findings suggest that variation in above- and belowground traits of individual plant genotypes can alter soil microbial dynamics, and suggests that further investigations of the evolutionary implications of genetic feedbacks are warranted.     

Urban soil-lead (Pb) footprint: retrospective comparison of public and private properties in New Orleans

Lead (Pb) is a toxin that after childhood exposure poses a lifetime of health risks. One route of exposure is soil-Pb as a result of ∼12 million metric tons of Pb residue in paint and gasoline sold in the US during the 20th Century. Pb accumulated in soil of the community is a good predictor for blood Pb of children living there. This retrospective study compares the soil-Pb on Housing Authority of New Orleans (HANO) properties with adjacent private residential (RES) properties within a 0.8 km (0.5 mile) radius. The sample subset (n = 951) is from two soil-Pb surveys (total n = 9,493) conducted between 1989 and 2000. The properties were in both the inner city (CORE) and outlying (OUTER) communities. The data were analyzed using multi-response permutation procedures (MRPP). The soil-Pb results differ significantly (P-value < 0.001) on same-aged HANO properties at different locations; thus, year of construction does not give adequate explanation for the soil-Pb differences. HANO and RES soils are significantly more Pb contaminated in the CORE than in OUTER communities (P-value < 0.001). The CORE has many more years of traffic congestion than OUTER communities; therefore, the lead additives to gasoline, and not lead-based paint, best elucidate the differences of the soil-Pb footprint at HANO and RES properties in the CORE and OUTER communites. Currently HANO properties are being redeveloped with cleaner soil, but soil on RES properties in the CORE of New Orleans remains a large source of Pb (median = 707 mg/kg in this study) for human exposure, especially children.     

Familiarity with adults,but not relatedness,affects the growth of juvenile red-backed salamanders (<Emphasis Type="Italic">Plethodon cinereus</Emphasis>)

The relative roles of kinship and familiarity in affecting an individual’s growth and fitness are not easy to disentangle. Not only is an individual more likely to have prior behavioral interactions with conspecifics in close proximity, it may also be related (in terms of kinship) to those nearby conspecifics. While some studies have inferred that kin discrimination affects fitness correlates, other studies found that familiarity alone can reduce aggressive interactions, thus increasing fitness. These studies have all focused on intra-age class pairs or groups. However, many animals interact with conspecifics from different cohorts. In many populations, adults of Plethodon cinereus territorially defend rocks and logs that retain moisture and food resources. We investigated whether juveniles of P. cinereus grew more in the presence of adults that were relatives or familiar. We collected pairs of juveniles and adults found under the same cover objects in the forest (familiar) and pairs of juveniles and adults found under different cover objects, approximately 10 m apart (unfamiliar). We determined parentage and relatedness of the adult–juvenile pairs and then placed these pairs in semi-natural mesocosms for 17 days. We found that juveniles housed with familiar adults had significantly greater increases in mass and snout–vent length than juveniles housed with unfamiliar adults in 2006 but not in 2007. Relatedness had no effect on growth. In addition, juveniles cohabitating with adults were not more likely to be their offspring. At least under certain environmental conditions, familiarity with adults, independent of relatedness or parentage, increased the growth of juvenile salamanders.     

Bald eagles and sea otters in the Aleutian Archipelago: indirect effects of trophic cascades

Because sea otters (Enhydra lutris) exert a wide array of direct and indirect effects on coastal marine ecosystems throughout their geographic range, we investigated the potential influence of sea otters on the ecology of Bald Eagles (Haliaeetus leucocephalus) in the Aleutian Islands, Alaska, USA. We studied the diets, productivity, and density of breeding Bald Eagles on four islands during 1993-1994 and 2000-2002, when sea otters were abundant and scarce, respectively. Bald Eagles depend on nearshore marine communities for most of their prey in this ecosystem, so we predicted that the recent decline in otter populations would have an indirect negative effect on diets and demography of Bald Eagles. Contrary to our predictions, we found no effects on density of breeding pairs on four islands from 1993-1994 to 2000-2002. In contrast, diets and diet diversity of Bald Eagles changed considerably between the two time periods, likely reflecting a change in prey availability resulting from the increase and subsequent decline in sea otter populations. The frequency of sea otter pups, rock greenling (Hexagammus lagocephalus), and smooth lumpsuckers (Aptocyclus ventricosus) in the eagle's diet declined with corresponding increases in Rock Ptarmigan (Lagopus mutus), Glaucous-winged Gulls (Larus glaucescens), Atka mackerel (Pleurogrammus monopterygius), and various species of seabirds during the period of the recent otter population decline. Breeding success and productivity of Bald Eagles also increased during this time period, which may be due to the higher nutritional quality of avian prey consumed in later years. Our results provide further evidence of the wide-ranging indirect effects of sea otter predation on nearshore marine communities and another apex predator, the Bald Eagle. Although the indirect effects of sea otters are widely known, this example is unique because the food-web pathway transcended five species and several trophic levels in linking one apex predator to another.     

Functional response of sport divers to lobsters with application to fisheries management.

Fishery managers must understand the dynamics of fishers and their prey to successfully predict the outcome of management actions. We measured the impact of a two-day exclusively recreational fishery on Caribbean spiny lobster in the Florida Keys, USA, over large spatial scales (>100 km) and multiple years and used a theoretical, predator-prey functional response approach to identify whether or not sport diver catch rates were density-independent (type I) or density-dependent (type II or III functional response), and if catch rates were saturated (i.e., reached an asymptote) at relatively high lobster densities. We then describe how this predator-prey framework can be applied to fisheries management for spiny lobster and other species. In the lower Keys, divers exhibited a type-I functional response, whereby they removed a constant and relatively high proportion of lobsters (0.74-0.84) across all pre-fishing-season lobster densities. Diver fishing effort increased in a linear manner with lobster prey densities, as would be expected with a type-I functional response, and was an order of magnitude lower in the upper Keys than lower Keys. There were numerous instances in the upper Keys where the density of lobsters actually increased from before to after the fishing season, suggesting some type of "spill-in effect" from surrounding diver-disturbed areas. With the exception of isolated reefs in the upper Keys, the proportion of lobsters removed by divers was density independent (type-I functional response) and never reached saturation at natural lobster densities. Thus, recreational divers have a relatively simple predatory response to spiny lobster, whereby catch rates increase linearly with lobster density such that catch is a reliable indicator of abundance. Although diver predation is extremely high (approximately 80%), diver predation pressure is not expected to increase proportionally with a decline in lobster density (i.e., a depensatory response), which could exacerbate local extinction. Furthermore, management actions that reduce diver effort should have a concomitant and desired reduction in catch. The recreational diver-lobster predator-prey construct in this study provides a useful predictive framework to apply to both recreational and commercial fisheries, and on which to build as management actions are implemented.     

Is Gray Water the Key to Unlocking Water for Resource-Poor Areas of the Middle East,North Africa,and Other Arid Regions of the World?

Support for the use of treated gray water as an alternative water resource in the Middle East and North Africa is high, especially given the lack of religious restrictions against its use, but several obstacles have kept application of treated gray water near 1 % in some areas. The largest of obstacles include the cost of treatment and the ambiguity surrounding the health safety of gray water and treated gray water. This paper aims to provide an overview of current gray water practices globally, with specific focus on household-level gray water practices in the Middle East and North Africa region, and highlight the need for cost reduction strategies and epidemiological evidence on the use of household-level gray water and treated gray water. Such actions are likely to increase the application of treated gray water in water-deprived areas of the Middle East and North Africa.     

Projected ozone trends and changes in the ozone-precursor relationship in the South Coast Air Basin in response to varying reductions of precursor emissions

This study examined the effects of varying future reductions in emissions of oxides of nitrogen (NO_x) and volatile organic compounds (VOC) on the location and magnitude of peak ozone levels within California’s South Coast Air Basin (SoCAB or Basin). As ozone formation is currently VOC-limited in the Basin, model simulations with 2030 baseline emissions (?61% for NO_x and ?32% for VOC from 2008) predict 10–20% higher peak ozone levels (i.e., NO_x disbenefit) in the western and central SoCAB compared with the 2008 base simulation. With additional NO_x reductions of 50% beyond the 2030 baseline emissions (?81% from 2008), the predicted ozone levels are reduced by about 15% in the eastern SoCAB but remain comparable to 2008 levels in the western and central Basin. The Basin maximum ozone site shifts westward to more populated areas of the Basin and will result potentially in greater population-weighted exposure to ozone with even a relatively small shortfall in the required NO_x reductions unless accompanied by additional VOC reductions beyond 2030 baseline levels. Once committed to a NO_x-focused control strategy, NO_x reductions exceeding 90% from 2008 levels will be necessary to attain the ozone National Ambient Air Quality Standards (NAAQS). The findings from this study and other recent work that the current VOC emission estimates are underestimated by about 50% suggest that greater future VOC reductions will be necessary to reach the projected 2030 baseline emissions. Increasing the base year VOC emissions by a factor of 1.5 result in higher 2008 baseline ozone predictions, lower relative response factors, and about 20% lower projected design values. If correct, these findings have important implications for the total and optimum mix of VOC and NO_x emission reductions that will be required to attain the ozone NAAQS in the SoCAB.

Implications: Results of this study indicate that ozone levels in the western and central SoCAB would remain the same or increase with even a relatively small shortfall in the projected NO_x reductions under planned NO_x-focused controls. This possibility, therefore, warrants a rigorous analysis of the costs and effects of varying reductions of VOC and NO_x on the formation and combined health impacts of ozone and secondary particles. Given the nonlinearity of ozone formation, such analyses should include the implications of gradually increasing global background ozone concentrations and the Basin’s topography and meteorology on the practical limits of alternative emission control strategies.