Bridging gaps in demographic analysis with phylogenetic imputation

Phylogenetically informed imputation methods have rarely been applied to estimate missing values in demographic data but may be a powerful tool for reconstructing vital rates of survival, maturation, and fecundity for species of conservation concern. Imputed vital rates could be used to parameterize demographic models to explore how populations respond when vital rates are perturbed. We used standardized vital rate estimates for 50 bird species to assess the use of phylogenetic imputation to fill gaps in demographic data. We calculated imputation accuracy for vital rates of focal species excluded from the data set either singly or in combination and with and without phylogeny, body mass, and life-history trait data. We used imputed vital rates to calculate demographic metrics, including generation time, to validate the use of imputation in demographic analyses. Covariance among vital rates and other trait data provided a strong basis to guide imputation of missing vital rates in birds, even in the absence of phylogenetic information. Mean NRMSE for null and phylogenetic models differed by <0.01 except when no vital rates were available or for vital rates with high phylogenetic signal (Pagel's λ > 0.8). In these cases, including body mass and life-history trait data compensated for lack of phylogenetic information: mean normalized root mean square error (NRMSE) for null and phylogenetic models differed by <0.01 for adult survival and <0.04 for maturation rate. Estimates of demographic metrics were sensitive to the accuracy of imputed vital rates. For example, mean error in generation time doubled in response to inaccurate estimates of maturation time. Accurate demographic data and metrics, such as generation time, are needed to inform conservation planning processes, for example through International Union for Conservation of Nature Red List assessments and population viability analysis. Imputed vital rates could be useful in this context but, as for any estimated model parameters, awareness of the sensitivities of demographic model outputs to the imputed vital rates is essential.     

Preliminary assessment of surface soil lead concentrations in Melbourne,Australia

Urban soils in many cities have been found to be contaminated with lead from past usage of leaded petrol, deteriorating lead-based exterior paints and industrial sources. Currently, the spatial distribution of soil lead concentrations in the Melbourne metropolitan area is unknown. The objective of this study was to perform a preliminary assessment of the spatial distributions of the surface soil lead (Pb) concentrations in the Melbourne metropolitan area, Australia. Fifty-eight surface soil samples were collected at a depth of 0–2 cm along three linear transects oriented across the Melbourne metropolitan area. Surface soil samples were also collected at a higher density in five Melbourne suburbs. Soil cores (0–50 cm) were collected in four locations, soil transects were collected at intervals with distance away from the roadway (0–50 m) in two inner city parks, and one control soil sample was collected in a rural setting. The median soil Pb concentration of the soil transect samples was 173 mg/kg (range 32–710 mg/kg), and the median soil Pb concentration of the five suburbs was 69 mg/kg (range 9–1750 mg/kg). The suburb of Footscray had the highest soil Pb concentration with a median soil Pb concentration of 192 mg/kg (range 40–1750 mg/kg). Soil Pb concentrations were generally higher nearest the centre of the Melbourne metropolitan area and in the west of Melbourne and lower in the outer suburbs to the east and north of the city centre. Soil Pb concentrations decreased with distance from roadways in the two transects taken from urban parks, and soil lead decreased with depth in the four soil cores. The soil Pb concentrations in the Melbourne metropolitan area appear to be lower than soil lead concentrations observed in inner city areas of Sydney New South Wales (NSW) and Newcastle NSW. The spatial extent of the soil Pb hazard remains undefined in portions of the Melbourne metropolitan area.     

Non-indigenous macroalga hosts different epiphytic assemblages to conspecific natives in southeast Australia

Codium fragile ssp. tomentosoides is one of the five most invasive macroalgae worldwide. We compared epiphytic assemblages between native (ssp. tasmanicum and ssp. novae-zelandiae combined) and non-indigenous (ssp. tomentosoides) subspecies of Codium fragile on three rocky intertidal shores in southeast Australia. Twelve species of epiphytes covered up to 20% of the surface of both native and non-indigenous Codium subspecies, but none were unique to either subspecies. For C. fragile subspecies, epiphytic cover declined from the lower (older) parts of the thallus to the branch tips. The abundance and species composition of epiphytes differed significantly between native and non-indigenous C. fragile, but differences varied among rocky shores. Results demonstrate that non-indigenous C. fragile does not play a functionally similar role to closely related native Codium subspecies. Spatial differences in epiphytic assemblages between Codium subspecies among rocky shores demonstrate that effects of non-indigenous species may be strongly location specific. Thus, our study emphasises the need to investigate variation in the effects of invaders across the regional landscape.     

Estimating dispersal potential for marine larvae: dynamic models applied to scleractinian corals

Dispersal influences ecological dynamics, evolution, biogeography, and biodiversity conservation, but models of larval dispersal in marine organisms make simplifying assumptions that are likely to approximate poorly the temporal dynamics of larval survival and capacity for settlement. In particular, larval mortality rates are typically assumed to be constant throughout larval life; and all larvae are frequently assumed to acquire and lose competence at the same time. To improve upon these assumptions, we here develop simple models of dispersal potential that incorporate rates of mortality, and acquisition and loss of settlement competence. We fit these models to empirical competence and survival data for five scleractinian coral species, to test the models' ability to characterize empirical survival and competence patterns, and to estimate the dispersal potential implied by those patterns. The models fit the data well, incorporating qualitative features of competence and survival that traditional approaches to modeling dispersal do not, with important implications for dispersal potential. Most notably, there was high within-cohort variation in the duration of the competent period in all species, and this variation increases both self-recruitment and long-distance dispersal compared with models assuming a fixed competent period. These findings help to explain the seeming paradox of high genetic population structure, coupled with large geographic range size, observed in many coral species. More broadly, our approach offers a way to parsimoniously account for variation in competence dynamics in dispersal models, a phenomenon that our results suggest has important effects on patterns of connectivity in marine metapopulations.     

Fertilization in a suite of coastal marine invertebrates from SE Australia is robust to near-future ocean warming and acidification

Climate change driven ocean acidification and hypercapnia may have a negative impact on fertilization in marine organisms because of the narcotic effect these stressors exert on sperm. In contrast, warmer, less viscous water may have a positive influence on sperm swimming speed and so ocean warming may enhance fertilization. To address questions on future vulnerabilities we examined the interactive effects of near-future ocean warming and ocean acidification/hypercapnia on fertilization in intertidal and shallow subtidal echinoids (Heliocidaris erythrogramma, H. tuberculata, Tripneustes gratilla, Centrostephanus rodgersii), an asteroid (Patiriella regularis) and an abalone (Haliotis coccoradiata). Batches of eggs from multiple females were fertilized by sperm from multiple males in all combinations of three temperature and three \textpH/P_\textCO2 {\text{pH}}/P_{{{\text{CO}}_{2} }} treatments. Experiments were placed in the setting of projected near-future conditions for southeast Australia, an ocean change hot spot. There was no significant effect of warming and acidification on the percentage of fertilization. These results indicate that fertilization in these species is robust to temperature and \textpH/P_\textCO2 {\text{pH}}/P_{{{\text{CO}}_{2} }} fluctuation. This may reflect adaptation to the marked fluctuation in temperature and pH that characterises their shallow water coastal habitats. Efforts to identify potential impacts of ocean change to the life histories of coastal marine invertebrates are best to focus on more vulnerable embryonic and larval stages because of their long time in the water column where seawater chemistry and temperature have a major impact on development.     

Nitrogen turnover in the leaf litter and fine roots of sugar maple

In order to better understand the nitrogen (N) cycle, a pulse of 15NO3- was applied in 1998 to a sugar maple (Acer saccharum) dominated northern hardwood forest receiving long-term (1994-2008) simulated atmospheric N deposition. Sugar maple leaf litter and live fine-root 15N were quantified for four years prior to labeling and for 11 subsequent years. Continuous sampling of 15N following addition of the tracer enabled calculation of leaf litter and fine-root N pool turnover utilizing an exponential decay function. Fine-root 15N recovery peaked at 3.7% +/- 1.7% the year the tracer was applied, while leaf litter 15N recovery peaked in the two years following tracer application at approximately 8%. These results suggest shoots are primarily constructed from N taken up in previous years, while fine roots are constructed from new N. The residence time of N was 6.5 years in leaf litter and 3.1 years in fine roots. The longer residence time and higher recovery rate are evidence that leaves were a stronger sink for labeled N than fine roots, but the relatively short residence time of tracer N in both pools suggests that there is not tight intra-ecosystem cycling of N in this mature forest.     

Power evaluation of focused cluster tests

Many statistical tests have been developed to assess the significance of clusters of disease located around known sources of environmental contaminants, also known as focused disease clusters. The majority of focused-cluster tests were designed to detect a particular spatial pattern of clustering, one in which the disease cluster centers around the pollution source and declines in a radial fashion with distance. However, other spatial patterns of environmentally related disease clusters are likely given that the spatial dispersion patterns of environmental contaminants, and thus human exposure, depend on a number of factors (i.e., meteorology and topography). For this study, data were simulated with five different spatial patterns of disease clusters, reflecting potential pollutant dispersion scenarios: (1) a radial effect decreasing with increasing distance, (2) a radial effect with a defined peak and decreasing with distance, (3) a simple angular effect, (4) an angular effect decreasing with increasing distance and (5) an angular effect with a defined peak and decreasing with distance. The power to detect each type of spatially distributed disease cluster was evaluated using Stone’s Maximum Likelihood Ratio Test, Tango’s Focused Test, Bithell’s Linear Risk Score Test, and variations of the Lawson–Waller Score Test. Study findings underscore the importance of considering environmental contaminant dispersion patterns, particularly directional effects, with respect to focused-cluster test selection in cluster investigations. The effect of extra variation in risk also is considered, although its effect is not substantial in terms of the power of tests.     

Soil microbial and faunal community responses to bt maize and insecticide in two soils

The effects of maize (Zea mays L.), genetically modified to express the Cry1Ab protein (Bt), and an insecticide on soil microbial and faunal communities were assessed in a glasshouse experiment. Soil for the experiment was taken from field sites where the same maize cultivars were grown to allow comparison between results under glasshouse conditions with those from field trials. Plants were grown in contrasting sandy loam and clay loam soils, half were sprayed with a pyrethroid insecticide (deltamethrin) and soil samples taken at the five-leaf stage, flowering, and maturity. The main effect on all measured parameters was that of soil type and there were no effects of Bt trait or insecticide on plant growth. The Bt trait resulted in more soil nematodes and protozoa (amoebae), whereas insecticide application increased plant Bt concentration and altered nematode community structure. The only significant effects on soil microbial community structure, microarthropods, and larvae of a nontarget root-feeding Dipteran, were due to soil type and plant growth stage. The results indicate that, although there were statistically significant effects of the Bt trait on soil populations, they were small. The relative magnitude of the effect could best be judged by comparison with the insecticide treatment, which was representative of current best practice. The Bt trait had no greater effect than the insecticide treatment. Results from this glasshouse experiment were in broad agreement with conclusions from field experiments using the same plant material grown in the same soils.