Isomorphic chain graphs for modeling spatial dependence in ecological data

Graphical models (alternatively, Bayesian belief networks, path analysis models) are increasingly used for modeling complex ecological systems (e.g., Lee, In: Ferson S, Burgman M(eds) Quantative methods for conservation biology. Springer, Berlin Heilin Heideslperk New York, pp.127–147, 2000; Borsuk et al., J Water Res Plann Manage 129:271–282, 2003). Their implementation in this context leverages their utility in modeling interrelationships in multivariate systems, and in a Bayesian implementation, their intuitive appeal of yielding easily interpretable posterior probability estimates. However, methods for incorporating correlational structure to account for observations collected through time and/or space—features of most ecological data—have not been widely studied; Haas et al. (AI Appl 8:15–27, 1994) is one exception. In this paper, an “isomorphic” chain graph (ICG) model is introduced to account for correlation between samples by linking site-specific Bayes network models. Several results show that the ICG preserves many of the Markov properties (conditional and marginal dependencies) of the site-specific models. The ICG model is compared with a model that does not account for spatial correlation. Data from several stream networks in the Willamette River valley, Oregon (USA) are used. Significant correlation between sites within the same stream network is shown with an ICG model.     

Hierarchical space-time models for fire ignition and percentage of land burned by wildfires

Policy responses for local and global fire management as well as international green-gas inventories depend heavily on the proper understanding of the annual fire extend as well as its spatial variation across any given study area. Proper statistical models are important tools in quantifying these fire risks. We propose Bayesian methods to model jointly the probability of ignition and fire sizes in Australia and New Zeland. The data set on which we base our model and results consists of annual observations of several meteorological and topographical explanatory variables, together with the percentage of land burned over a grid with resolution of 1° across Austalia and New Zealand. Our model and conclusions bring improvements on the results reported by Russell-Smith et al. in Int J Wildland Fire, 16:361–377 (2007) based on a similar data set.     

Turbulence and turbulent flux events in a small estuary

Relatively little systematic research has been conducted on the turbulence characteristics of small estuaries. In the present study, detailed measurements were conducted in a small subtropical estuary with a focus on turbulent flux events. Acoustic Doppler velocimeters were installed in the mid-estuary at fixed locations and sampled simultaneously and continuously for 50 h. A turbulent flux event analysis was performed for the entire data sets extending the technique of Narasimha et al. (Phil Trans R Soc Ser A 365:841–858, 2007) to the unsteady open channel flow motion and to turbulent sub-events. Turbulent bursting events were defined in terms of the instantaneous turbulent flux. The data showed close results for all ADV units. The very-large majority of turbulent events lasted between 0.04 and 0.3 s with an average of 1 to 4 turbulent events observed per second. A number of turbulent bursting events consisted of consecutive turbulent sub-events, with between 1 and 3 sub-events per main event on average. For all ADV systems, the number of events, event duration and event amplitude showed some tidal trends, with basic differences between high- and low-water periods. A comparison between the present estuary data and the atmospheric boundary layer results of Narasimha et al. (Phil Trans R Soc Ser A 365:841–858, 2007) showed a number of similarities and demonstrated the significance of turbulent events in environmental flows. A burstiness index of 0.85 was found for the present data.     

The potential of spatial information in human biomonitoring by example of two German environmental epidemiology studies

This study aimed at statistically investigating the association between the internal exposure of children and young adults to uranium (U) and epidemiologically relevant external determinants of exposure. The investigation was performed with data from two studies within the framework of the German health-related environmental monitoring program: The German Environmental Survey for Children (GerES IV) conducted by the Federal Environment Agency (Umweltbundesamt) with data on 1,780 children 3–14 years of age and their home environment and the German Environmental Specimen Bank (ESB, section: human specimens) with data on 2,253 students 20–29 years of age. Both studies provided data on the U levels in human urine for all probands. GerES IV furthermore provided an extensive environmental and demographic database on, e.g., U levels in drinking water. The data from GerES IV and ESB were linked by GIS to spatially relevant exposure information, including background values of U in stream sediments and in upper and lower soils, U levels in mosses and particulate matter in the lower atmosphere, precipitation and elevation as well as forest density. Bivariate correlation analysis and two decision tree models showed moderate but significant associations between U in human urine and U levels in drinking water, stream sediments and upper and lower soils. Future investigations considering additional epidemiologically relevant data sets may differentiate the results. Furthermore, the sample design of future environmental epidemiology studies should take the spatial evaluation of the data into greater account.     

Ecological sexual segregation in fallow deer (Dama dama): a multispatial and multitemporal approach

We questioned the different interpretations of ecological sexual segregation from a novel perspective, i.e., by carrying out diverse temporal and spatial scale analyses within a long-term study (1984–2003). Thus we combined spatial (small/large) and temporal (small/large) scale analyses to identify the factors generating sexual segregation in fallow deer in San Rossore, Italy. The study site was divided into an eastern sector characterized by human disturbance (DS) and a western undisturbed sector (US). According to census data, human presence increased in DS from 1984, and while females gradually abandoned it, males remained—thus supporting the predation risk hypothesis (large spatial and temporal scale)—and actually increased their presence in DS, where they seemingly benefited from a lower female density. This supported the indirect competition hypothesis. The analysis of data on a large temporal and small spatial scale confirmed that intersexual competition, in particular for grass, was higher in a crowded pasture in US. Observations by means of radio-telemetry of 23 adult females and 25 adult males (1997–2001, reduced temporal and large spatial scale) showed that large scale segregation was relevant during the day and disappeared at night, when disturbance was absent and also the females reached DS. This also supported the predation risk hypothesis. Moreover, sexes showed different habitat choices inside DS at night, thus supporting the forage selection hypothesis (small spatial and temporal scale). In conclusion, failure to address the whole set of combinations of spatial and temporal scale analyses would have led to monocausal explanations of ecological sexual segregation.     

On the behaviour of the residence time at the bottom of the mixed layer

To understand why the findings of Deleersnijder et al. [(2006), Environ Fluid Mech 6: 25–42]—the residence time in the mixed layer in not necessarily zero at the pycnocline—are consistent with those of Delhez and Deleersnijder [(2006), Ocean Dyn 56:139–150]—the residence time in a control domain vanishes at the open boundaries of this control domain—, it is necessary to consider a control domain that includes part of the pycnocline, in which the eddy diffusivity is assumed to be zero. Then, depending on the behaviour of the eddy diffusivity near the bottom of the mixed layer, the residence time may be seen to exhibit a discontinuity at the interface between the mixed layer and the pycnocline. If such a discontinuity exists, the residence time is non-zero in the former and zero in the latter. This is illustrated by analytical solutions obtained under the assumption that the eddy diffusivity is constant in the mixed layer.     

The behaviour of ant transporters at the old and new nests during successive colony emigrations

Colonies of the ant Temnothorax albipennis improve their collective performance over successive emigrations (Langridge et al. Behav Ecol Sociobiol 56:523–529, 2004, Behav Ecol Sociobiol 62:447–456, 2008). Here, by analysing the performance of individual transporters (workers that carry the brood, queen and a proportion of adults), we investigate whether they spend less time at the old and new nests during repeated emigrations. Transporters expedited choosing and picking up brood items at the old nest and depositing them in the new nest. Such improvements were not associated with adult transport. Generally, when carrying brood items, but not when carrying adults, transporters visited several locations in the new nest before depositing them. Transporters did not interact with other adults when depositing brood items. Consequently, reductions in depositing times are the sum of time savings made by individual transporters. By contrast, transporters spent most time interacting with other adults before picking up brood items at the old nest. As the frequency of these interactions did not decline, we suggest the behaviours of interacting adults were modified in a way that hastened their completion. Thus, reductions in picking-up times probably occur because of time saved during interactions.     

Microscale genetic differentiation in a sessile invertebrate with cloned larvae: investigating the role of polyembryony

Microscale genetic differentiation of sessile organisms can arise from restricted dispersal of sexual propagules, leading to isolation by distance, or from localised cloning. Cyclostome bryozoans offer a possible combination of both: the localised transfer of spermatozoa between mates with limited dispersal of the resulting larvae, in association with the splitting of each sexually produced embryo into many clonal copies (polyembryony). We spatially sampled 157 colonies of Crisia denticulata from subtidal rock overhangs from one shore in Devon, England at a geographic scale of ca. 0.05 to 130 m plus a further 21 colonies from Pembrokeshire, Wales as an outgroup. Analysis of molecular variance (AMOVA) revealed that the majority (67%) of genetic variation was distributed among individuals within single rock overhangs, with only 16% of variation among different overhangs within each shore and 17% of variation between the ingroup and outgroup shores. Despite local genetic variation, pairwise genetic similarity analysed by spatial autocorrelation was greatest at the smallest inter-individual distance we tested (5 cm) and remained significant and positive across generally within-overhang comparisons (<4 m). Spatial autocorrelation and AMOVA analyses both indicated that patches of C. denticulata located on different rock overhangs tended to be genetically distinct, with the switch from positive to negative autocorrelation, which is often considered to be the distance within which individuals reproduce with their close relatives or the radius of a patch, occurring at the 4–8 m distance class. Rerunning analyses with twenty data sets that only included one individual of each multilocus genotype (n = 97) or the single data set that contained just the unique genotypes (n = 67) revealed that the presence of repeat genotypes had an impact on genetic structuring (PhiPT values were reduced when shared genotypes were removed from the dataset) but that it was not great and only statistically evident at distances between individuals of 1–2 m. Comparisons to a further 20 randomisations of the data set that were performed irrespective of genotype (n = 97) suggested that this conclusion is not an artefact of reduced sample size. A resampling procedure using kinship coefficients, implemented by the software package GENCLONE gave broadly similar results but the greater statistical power allowed small but significant impacts of repeat genotypes on genetic structure to be also detected at 0.125–0.5 and 4–16 m. Although we predict that a proportion of the repeat multilocus genotypes are shared by chance, such generally within-overhang distances may represent a common distance of cloned larval dispersal. These results suggests that closely situated potential mates include a significant proportion of the available genetic diversity within a population, making it unlikely that, as previously hypothesised, the potential disadvantage of producing clonal broods through polyembryony is offset by genetic uniformity within the mating neighbourhood. We also report an error in the published primer note of Craig et al. (Mol Ecol Notes 1:281–282, 2001): loci Cd5 and Cd6 appear to be the same microsatellite. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

The invasive venomous striped eel catfish <Emphasis Type="Italic">Plotosus</Emphasis><Emphasis Type="Italic">lineatus</Emphasis> in the Levant: possible mechanisms facilitating its rapid invasional success

The venomous striped eel catfish Plotosus lineatus was first recorded in the Mediterranean in 2002. Within 1–3 years, it has spread throughout the entire Israeli coast. We have studied its spatiotemporal distribution patterns via trawl surveys in order to determine the scale and extent of this invasion. Findings indicate that a population explosion has occurred, and the catfish now inhabits all sandy and muddy substrates up to ca 80 m. P. lineatus was found to recruit in autumn in the Mediterranean and displays similar or improved growth patterns and condition factor compared to those found in its native habitat. We discuss the possible ecological mechanisms responsible for its success: Benthic invaders are among its main prey items, suggesting an invasional meltdown process. We also point to the decline of indigenous species using its trophic and behavioral–ecological niche and hypothesize that they might be outcompeted and displaced by the catfish.     

Large eddy simulation of plume dispersion behind an aircraft in the take-off phase

The aim of this paper is to provide an investigation, using large eddy simulation, into plume dispersion behind an aircraft in co-flowing take-off conditions. Validation studies of the computational model were presented by Aloysius and Wrobel (Environ Model Softw 24:929–937, 2009) and a study of the flow and dispersion properties of a double-engine aircraft jet was presented by Aloysius et al. (EEC/SEE/2007/001, EUROCONTROL Experimental Centre, ), in which only the engine was modelled. In this paper, the complete geometry of a Boeing 737 is modelled and investigated. The current work represents a contribution towards a better understanding of the source dynamics behind an airplane jet engine during the take-off and landing phases. The information provided from these simulations will be useful for future improvements of existing dispersion models.     

Population connectivity in the temperate damselfish <Emphasis Type="Italic">Parma microlepis</Emphasis>: analyses of genetic structure across multiple spatial scales

This study investigated the utility of microsatellite markers for providing information on levels of population connectivity for a low dispersing reef fish in New South Wales (NSW), Australia, at scales ≤400 km. It was hypothesized that the temperate damselfish Parma microlepis, which produces benthic eggs and has limited post-settlement dispersal, would exhibit spatial genetic structure and a significant pattern of isolation-by-distance (IBD). A fully nested hierarchical sampling design incorporating three spatial scales (sites, location and regions, separated by 1–2, 10–50 and 70–80 km respectively) was used to determine genetic variability at seven microsatellite loci. Broad-scale genetic homogeneity and lack of IBD was well supported by single and multi-locus analyses. The proportion of the total genetic variation attributable to differences among regions, locations or sites was effectively zero (Φ/R-statistics ≤0.007). The geographic distribution of genetic diversity and levels of polymorphism (H _E 0.21–0.95) indicate high mutation rates, large effective population sizes, and high rates of gene flow. Significant gene flow may be driven by factors influencing pre-settlement dispersal, including the East Australian Current (EAC) and habitat continuity. Genetic connectivity may not reflect demographically important connectivity, but does imply that P. microlepis populations are well connected from an evolutionary perspective. Total observed genetic diversity was accounted for within 1–2 km of reef and could be represented within small Marine Protected Areas. Reef fishes in NSW which have life histories similar to P. microlepis (e.g. pre-settlement durations ≥2 weeks) are also likely to exhibit genetic homogeneity. Genetic markers are, therefore, most likely to provide information on demographically relevant connectivity for species with lower dispersal capabilities, small population sizes, short life spans, and whose habitats are rare, or patchily distributed along-shore. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

When does bearing magnets affect the size of deflection in clock-shifted homing pigeons?

Pigeons whose internal clock is shifted by 6 h show deflections from the direction of untreated controls, yet these deflections are often smaller than predicted. Magnets temporarily disabling the magnetic compass increased these the deflections significantly (R. Wiltschko and Wiltschko 2001), indicating a compromise between sun compass and magnetic compass. – Recently, Ioalé et al. (2006) claim that they could not replicate our findings. The reason lies in a difference in the behavior of the clock-shifted pigeons without magnets: in the study of Ioalè et al. (2006), their deflections was already almost as large as that of our pigeons carrying magnets. This difference is probably caused by the limited experience of the pigeons of Ioalè et al. (2006): Their birds, in contrast to ours, had not used their sun’ compass during extended homing flights at various times of the year and, not having been faced with the necessity to compensate the saisonal changes of the sun’s arc, gave the sun compass more weight than our birds did.A comment to the paper by Ioalè, Odetti and Gagliardo (2006) Behav Ecol Sociobiol 60: 516–521.     

Timing matters when assessing dominance and chemical signatures in the paper wasp Polistes dominulus

A recent study (Izzo et al., Behav Ecol Sociobiol 64: 857–864, 2010) reported that cuticular hydrocarbons (CHCs) correlate with fertility, not dominance, in the paper wasp Polistes dominulus thus contradicting the results of recent investigations which concluded that social dominance is the main determinant for CHC signatures in this species. We suggest here that different forms of dominance in the pre-nesting and post-nesting phases caused the apparently contradictory results. Thus the assumption that dominance behaviour in the pre-nesting stage is synonymous with dominance after colony foundation is incorrect. We provide standardised definitions for forms of “dominance” observed in the P. dominulus life cycle to avoid apparent discrepancies in the future among studies dealing with the same topics in different annual stages.     

Geographical variation in metacercarial infection levels in marine invertebrate hosts: parasite species character versus local factors

Despite the important roles played by parasites in local population dynamics and community structure of marine ecosystems, there is a lack of information on the geographical variation in infection levels displayed by particular host–parasite species combinations. This study examines geographical variation in infection levels by the metacercarial stages of trematode parasites in crustacean and bivalve second intermediate hosts. Analyses were based on a dataset compiled from the literature, consisting of 164 local samples representing 49 host–parasite species pairs for crustaceans, and 338 entries representing 36 host–parasite species pairs for bivalves. The analyses indicate that for all measures of infection levels [prevalence (percentage of individuals infected), intensity (mean no. of metacercariae per infected individual), abundance (mean no. of metacercariae across all individuals in a sample)], there was statistically significant repeatability of infection values within host–parasite species pairs. However, it is only for values of intensity and abundance of infection in crustacean hosts that the repeatability was strong; this suggests that infection levels are specific properties of crustacean–trematode species pairs, showing significant consistency across localities despite spatial variation in abiotic and biotic conditions. Although the magnitude of variation in infection levels within parasite species pairs (measured as coefficients of variation) was independent of scale in crustacean hosts, infection levels in bivalves increased in variability at large (>100 km) spatial scales. These results suggest that there is a considerable geographical consistency in parasite load, especially in crustacean hosts, which should lead to consistent ecological and ecosystem effects of marine trematodes. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Temporal and spatial variation in protein,carbohydrate, and lipid levels in <Emphasis Type="Italic">Corallium rubrum</Emphasis> (Anthozoa,Octocorallia)

Red coral (Corallium rubrum) is an important component of the Mediterranean coralligenous habitat. The present study analyzes the relationship between energy storage molecule concentration (i.e. tissue balance of protein–carbohydrate–lipid levels) and the gonadal output in two populations located at different depths (16–18 m and 40–45 m depth) through a seasonal cycle (2002–2003). In June 2003, another six populations have been sampled to compare medium-scale geographical variation. The colonies sampled were less than 6 cm high, thus representing the majority of the population in the studied area. There was no clear relationship between energy storage (i.e. carbohydrate and lipid levels) and gonadal output, nor in the seasonal cycle or the spatial variation. A clear-cut seasonal trend of energy storage was detected only in the shallower population. The water temperature was warmer at 20 m depth and the water transparency (Secchi disk) was also higher (lower seston concentration) in 2003 when the same periods in 2002 and 2003 were compared (May–August). Carbohydrates seemed to be more sensitive to food constraints than lipids. The partial mortality detected in summer 2003 in the sampling area appeared to be recorded in the carbohydrate and lipid levels of this species, especially in the shallow population. The biochemical levels prove to be a useful tool to detect unusual environmental conditions that may cause partial or total mortality in benthic suspension feeders.     

Temporal and spatial changes in plant dune diversity in urban resorts

We investigated the temporal and spatial changes in the floristic composition and abundance in sand dunes along a coastal strip in the province of Buenos Aires (Argentina). Firstly, we analysed changes over a span of 70 years, comparing 41 of our own inventories carried out in 14 beach resorts in 2005–2006 with 18 inventories made in the first half of the XXth century (1930–1940) in the same study area. We grouped sampled plots into four categories for comparison, taking into account the time period (1930–1940 or 2005–2006) and location at each end of the surveyed coastal strip in the northern or southern ‘tourist’ sectors. Secondly, we analysed the effect of afforestation with exotic trees on extant sand dune vegetation for the period 2005–2006. A total of 74 plant inventories were carried out in afforested and natural dunes at the same resorts. In both comparisons we contrasted plant richness, percentage plant cover, similarity and diversity. A cluster analysis was used to classify categories taking into account plant abundance and composition. Significant differences in total diversity were observed between sampling years, suggesting an increase in diversity at the present time due to urbanization and recreation related activities. Nevertheless, no single exotic plant species was clearly dominant across the sampled sites, suggesting that these coastal areas are, up to now, resistant to alien invasion. Diversity indexes discriminated by plant groups indicating different habitat conditions and exotics were shown to be more sensitive to existing changes than to total richness and cover.     

An investigation into the occurrence and distribution of polycyclic aromatic hydrocarbons in two soil size fractions at a former industrial site in NE England,UK using in situ PFE–GC–MS

Polycyclic aromatic hydrocarbon (PAH) concentrations were determined in 16 topsoils (0–10 cm) collected across the site of a former tar works in NE England. The soils were prepared in the laboratory to two different particle size fractions: <250 μm (fraction A) and >250 μm to <2 mm (fraction B). Sixteen priority PAHs were analysed in the soils using in situ pressurised fluid extraction (PFE) followed by gas chromatography—mass spectrometry (GC–MS). The average total PAH concentration in the soils ranged from 9.0 to 1,404 mg/kg (soil fraction A) and from 6.6 to 872 mg/kg (soil fraction B). These concentrations are high compared with other industrially contaminated soils reported in the international literature, indicating that the tar works warrants further investigation/remediation. A predominance of higher-molecular-weight compounds was determined in the samples, suggesting that the PAHs were of pyrogenic (anthropogenic) origin. Statistical comparison (t-test) of the mean total PAH concentrations in soil fractions A and B indicated that there was a significant difference (95% confidence interval) between the fractions in all but two of the soil samples. Additionally, comparisons of the distributions of individual PAHs (i.e. 16 PAHs × 16 soil samples) in soil fractions A and B demonstrated generally higher PAH concentrations in fraction A (i.e. 65.8% of all individual PAH concentrations were higher in soil fraction A). This is important because fraction A corresponds to the particle size thought to be most important in terms of human contact with soils and potential threats to human health.     

Fourth-corner generation of plant functional response groups

Plant functional response groups (PFGs) are now widely established as a tool to investigate plant—environment relationships. Different statistical methods to form PFGs are used in the literature. One way is to derive emergent groups by classifying species based on correlation of biological attributes and subjecting these groups to tests of response to environmental variables. Another way is to search for associations of occurrence data, environmental variables and trait data simultaneously. The fourth-corner method is one way to assess the relationships between single traits and habitat factors. We extended this statistical method to a generally applicable procedure for the generation of plant functional response groups by developing new randomization procedures for presence/absence data of plant communities. Previous PFG groupings used either predefined groups or emergent groups i.e. classifications based on correlations of biological attributes (Lavorel et al Trends Ecol Evol 12:474–478, 1997), of the global species pool and assessed their functional response. However, since not all PFGs might form emergent groups or may be known by experts, we used a permutation procedure to optimise functional grouping. We tested the method using an artificial test data set of virtual plants occurring in different disturbance treatments. Direct trait-treatment relationships as well as more complex associations are incorporated in the test data. Trait combinations responding to environmental variables could be clearly distinguished from non-responding combinations. The results are compared with the method suggested by Pillar (J Veg Sci 10:631–640) for the identification of plant functional groups. After exploring the statistical properties using an artificial data set, the method is applied to experimental data of a greenhouse experiment on the assemblage of plant communities. Four plant functional response groups are formed with regard to differences in soil fertility on the basis of the traits canopy height and spacer length.     

Comments on “turbulent velocity profile in fully-developed open channel flows”

In a recent paper published in this journal, Bonakdari et al. (Environ Fluid Mech 8:1–17, 2008) presented a new formulation of the vertical velocity profile in the central portion of steady fully developed turbulent open-channel flows which is based on an analysis of the Navier–Stokes equations. The predicted mean streamwise velocity profiles presented by the authors represent dip phenomenon (maximum velocity below the free surface). The discusser would like to point out some contradictions and an error in the main demonstration. This error appears in the right-hand side term of the main Eq. 22 (Environ Fluid Mech 8:1–17, 2008) in the parameter α. Our corrected demonstration shows that α is equal to and not to as obtained by the authors (Environ Fluid Mech 8:1–17, 2008). The values of α used by the authors are under-estimated by 1, this difference has a significant effect on velocities and therefore will involve a difference between measured and predicted velocity profiles. Finally, the assumption of at the free surface is in contradiction with predicted velocity profiles.