Space-time Bayesian small area disease risk models: development and evaluation with a focus on cluster detection

This paper extends the spatial local-likelihood model and the spatial mixture model to the space-time (ST) domain. For comparison, a standard random effect space-time (SREST) model is examined to allow evaluation of each model’s ability in relation to cluster detection. To pursue this evaluation, we use the ST counterparts of spatial cluster detection diagnostics. The proposed criteria are based on posterior estimates (e.g., misclassification rate) and some are based on post-hoc analysis of posterior samples (e.g., exceedance probability). In addition, we examine more conventional model fit criteria including mean square error (MSE). We illustrate the methodology with a real ST dataset, Georgia throat cancer mortality data for the years 1994–2005, and a simulated dataset where different levels and shapes of clusters are embedded. Overall, it is found that conventional SREST models fair well in ST cluster detection and in goodness-of-fit, while for extreme risk detection the local likelihood ST model does best.     

Why do females have so few extra-pair offspring?

It is generally accepted that if a female can improve her offspring’s genetics via extra-pair copulations (EPC), it is by copulating with extra-pair males whose phenotypes are more superior or whose genes are more compatible to hers than those of her bonded male. Here, we present a model that puts together uncertainties about the male genetic quality, a postcopulatory sperm bias in favor of the better or the more compatible genes, and costs that females pay by being choosy about extra-pair male quality. The model’s conclusions challenge traditional views of good genes explanations of EPC. When phenotypes give incomplete information about genotypes, a female choosing a phenotypically superior extra-pair male, may nevertheless find herself trading good genes of a bonded male for poor genes of an extra-pair male. Such “unfortunate sperm replacements” can limit the female involvement in EPC even when EPC are otherwise cost-free. The model also shows that even a female bonded to a phenotypically superior male may benefit by EPC, provided that sperm competition is biased toward sperm with more fit or more compatible genes. Furthermore, if choosiness is sufficiently costly, a female may even do best by copulating with a random extra-pair male.     

On the integrated modelling of coastal changes

This paper introduces a possible approach to integrated modelling of coastal change, focusing on coastal land use and cover change. Some of the mostimportant open issues in the context of integrated modelling of coastal change are introduced. The paper focuses on methdological aspects. Specific reference is made to Physiographic Unit Modelling as an approach to better handle spatial variability and ‘morphogenesis’, and as a way to focus on coastal change mechanisms instead of absolute coastal dynamics for achieving an important simplification of the problem. The application is briefly discussed with reference to a ‘minimal model’. The methodological structure introduced is considered particularly suitable to represent, according to a variable degree of simplification, the integrative dynamics between resources and uses of the resources.     

On the use of nearest neighbor contingency tables for testing spatial segregation

For two or more classes (or types) of points, nearest neighbor contingency tables (NNCTs) are constructed using nearest neighbor (NN) frequencies and are used in testing spatial segregation of the classes. Pielou’s test of independence, Dixon’s cell-specific, class-specific, and overall tests are the tests based on NNCTs (i.e., they are NNCT-tests). These tests are designed and intended for use under the null pattern of random labeling (RL) of completely mapped data. However, it has been shown that Pielou’s test is not appropriate for testing segregation against the RL pattern while Dixon’s tests are. In this article, we compare Pielou’s and Dixon’s NNCT-tests; introduce the one-sided versions of Pielou’s test; extend the use of NNCT-tests for testing complete spatial randomness (CSR) of points from two or more classes (which is called CSR independence, henceforth). We assess the finite sample performance of the tests by an extensive Monte Carlo simulation study and demonstrate that Dixon’s tests are also appropriate for testing CSR independence; but Pielou’s test and the corresponding one-sided versions are liberal for testing CSR independence or RL. Furthermore, we show that Pielou’s tests are only appropriate when the NNCT is based on a random sample of (base, NN) pairs. We also prove the consistency of the tests under their appropriate null hypotheses. Moreover, we investigate the edge (or boundary) effects on the NNCT-tests and compare the buffer zone and toroidal edge correction methods for these tests. We illustrate the tests on a real life and an artificial data set.     

Coastal directories and beyond: providing multidisciplinary coastal zone resource information for resource management

Baseline resource information in an easily accessible form is a vital starting point for developing coastal zone management. On behalf of a wide-ranging group of organizations involved in the management of the U.K. maritime zone, the Joint Nature Conservation Committee (JNCC) is compiling a series of 16 regional volumes. The volumes contain multi-disciplinary coastal zone resource information arranged in ten chapters under the general title ‘Coasts and Seas of the UK’. These volumes form part of a series of paper and electronic publications of coastal information being produced by JNCC’s Coastal Directories Project and are designed to meet the needs of planners and all others involved in decision-making and management of the coast.     

Embryonic,larval, and post-metamorphic development of the sea urchin <Emphasis Type="Italic">Cassidulus mitis</Emphasis> (Echinoidea; Cassiduloida): an endemic brooding species from Rio de Janeiro,Brazil

Cassiduloids are currently rare irregular echinoids with a highly conserved adult morphology. Aristotle’s lantern is present only during the post-metamorphic stage, and little is known about the early development of species in this group. Cassidulus mitis produces eggs of about 375 μm in diameter, lecithotrophic larvae with four reduced arms with skeletal fenestrated rods, cilia along the body surface, and a ciliated band on arms and lobes. Offspring is brooded among the female spines from embryo to settler’s stage. The echinopluteus larval stage is reached 6 days after fertilization, and the settler’s stage is formed at the age of 17 days. Aristotle’s lantern appears around the thirteenth day of development. The lantern is well developed and functional in settlers. It remains until at least 62 days after fertilization and can be used to acquire food from the environment. The early development of C. mitis is unusual concerning features of typical lecithotrophic larvae (such as reduced arms), but retains some features of planktotrophic larvae (such as skeletal rods and a ciliated band). Regarding egg size, early development in C. mitis seems to be transitioning from facultative lecithotrophic to typical obligate lecithotrophic pattern in echinoid larval evolution.     

Paternal care in the European starling,Sturnus vulgaris: nestling provisioning

The extent to which male birds in polygynous species with biparental care assist in nestling feeding often varies considerably between nests of different mating status. Both how much polygynous males assist and how they divide their effort between nests may have a profound effect on the evolution of mating systems. In this study we investigated how males in the facultatively polygynous European starling Sturnus vulgaris invested in their different nests. The amount of male assistance affected the quality of the offspring. Polygynous males invested as much as monogamous males, but divided their effort asymmetrically between nests, predominantly feeding nestlings of first-mated (primary) females. Although females partly compensated for loss of male assistance, total feeding frequency was lower at primary females’ nests than at monogamous females nests. Secondary females received even less assistance with nestling rearing, and the extent to which males assisted decreased with the length of the interval between the hatching of the primary and secondary clutches. These results are contrasted with those from a Belgian populations of starlings with a much more protracted breeding season and thus greater opportunities for males to attract additional mates during the nestling rearing period. The results show that both the “defence of male parental investment model” and the “asynchronous settlement model” have explanatory power, but that their validity depends on the potential length of the breeding season. Received: 21 July 1995/Accepted after revision: 13 July 1996     

Coastal protected area management and multi-tiered governance: the Cape Cod Model

Policy tools that allow for the coordination of various authorities at different levels of government are important for coastal protected areas. Frequently, multiple authorities manage these areas with varied and sometimes conflicting goals. This study examines a regulatory model implemented on the Cape Cod National Seashore in the US that uses federally-approved zoning to regulate private uses for protection of natural coastal resources. Local authorities implement the zoning which is designed to support national resource protection goals making this a prime model of cross-level governance for conservation. I use case study analysis to evaluate the program’s effectiveness by focusing on implementation and compliance in the context of multi-jurisdictional (i.e., national to local) relations. The analysis and subsequent discussion highlight the difficulties associated with implementation of intergovernmental mandates. Also, theoretical perspectives on compliance give insights about the implementation challenges of this model. The model’s limitations have implications for policymakers considering similar schemes implemented by split and hierarchical authorities with different, and possibly conflicting, coastal management goals.

The chelation of metal ions by the acylpolyamine toxins from the web-spider Nephilengys cruentata: effects in the intoxication/detoxification of preys

Summary. Orb-web-spiders present a series of different strategies for prey capture, involving the use of different types of silk for web building, the use of adhesive traps in the webs, the secretion of toxic compounds to the spider’s preys in the adhesive coating of the capture web and the biosynthesis of a wide range of structurally related acylpolyamine toxins in their venoms. The polyamine toxins usually block neuromuscular junctions and/or the central nervous system (CNS) of Arthropods, targeting specially the ionotropic glutamate receptors; this way these toxins are used are as chemical weapons to kill / paralyze the spider’s prey. Polyamine toxins contain many azamethylene groups involved with the chelation of metal ions, which in turn can interact with the glutamate receptors, affecting the toxicity of these toxins. It was demonstrated that the chelation of Ni⁺², Fe⁺², Pb⁺², Ca⁺² and Mg⁺² ions by the desalted crude venom of Nephilengys cruentata and by the synthetic toxin JSTX-3, did not cause any significant change in the toxicity of the acylpolyamine toxins to the model-prey insect (honeybees). However, it was also reported that the chelation of Zn⁺² ions by the acylpolyamines potentiated the lethal / paralytic action of these toxins to the honeybees, while the chelation of Cu⁺² ions caused the inverse effect. Atomic absorption spectrometry and Plasma-ICP analysis both of N. cruentata venom and honeybee’s hemolymph revealed that the spider’s venom concentrates Zn⁺² ions, while the honeybee’s hemolymph concentrates Cu⁺² ions. These results are suggesting that the natural accumulation of Zn⁺² ions in N. cruentata venom favors the prey catching and/or its maintenance in the web, while the natural accumulation of Cu⁺² ions in prey’s hemolymph minimizes the efficiency of the acylpolyamine toxins as killing/paralyzing tool.     

Optimal patch time allocation for time-limited foragers

The Charnov Marginal Value Theorem (MVT) predicts the optimal foraging duration of animals exploiting patches of resources. The predictions of this model have been verified for various animal species. However, the model is based on several assumptions that are likely too simplistic. One of these assumptions is that animals are living forever (i.e., infinite horizon). Using a simple dynamic programming model, we tested the importance of this assumption by analysing the optimal strategy for time-limited foragers. We found that, for time-limited foragers, optimal patch residence times should be greater than those predicted from the classic, static MVT, and the deviation should increase when foragers are approaching the end of their life. These predictions were verified for females of the parasitoid Anaphes victus (Hymenoptera: Mymaridae) exploiting egg patches of its host, the carrot weevil Listronotus oregonensis (Coleoptera: Curculionidae). As predicted by the model, females indeed remained for a longer time on host patches when they approached the end of their life. Experimental results were finally analysed with a Cox regression model to identify the patch-leaving decision rules females used to behave according to the model’s predictions.     

Freshwaters: which NOM matters?

One of the difficulties encountered in the study of natural organic matter (NOM) in aquatic environments concerns terminology: a large number of different names and acronyms are used. In fact, this diversity merely reflects the variety of approaches applied to the study of NOM, leading to the definition and measurement of different operationally-defined fractions. As a result, the choice of the ‘best’ method to use and of the ‘best’ fraction to work on in a particular case is far from straightforward. This has as a consequence that often very simple methods for NOM characterisation are used in applied environmental studies and surveys. This study includes, first, a review of the most widely applied terminology, as described in over 500 articles, and, second, a first attempt at assessing how the panoply of methods available is really used in applied environmental studies.     

Between introgression events and fragmentation, islands are the last refuge for the American crocodile in Caribbean Mexico

Habitat loss and degradation in the Mexican Caribbean, caused by the development of tourism, have decreased the potential nesting area for the American crocodile (Crocodylus acutus) and have fragmented the populations of the Yucatan peninsula. Our study investigated five populations (three continental: North, South, Sian Ka’an, and two insular: Cozumel, Banco Chinchorro) of C. acutus in the Mexican Caribbean using seven different inter simple sequence repeat (ISSR) markers as tools for genetic variability and population differentiation. Three classification methods were tested and compared: distance analysis, self-organizing map, and Bayesian methods, to evaluate the resolution of each method with ISSR markers. The 77 loci selected revealed a high variability between populations (polymorphism from 17% for Sian Ka’an to 75% for Banco Chinchorro) with a total polymorphism of 84% and a global coefficient of gene differentiation (G _ST ) of 0.296, but low values of Nei’s Gene diversity (from 0.065 for Sian Ka’an to 0.233 for Banco Chinchorro). Our results suggest elevated inbreeding in all local populations with higher indices for Banco Chinchorro and lower indices for Sian Ka’an. Three independent classification methods gave similar results, and suggested that most continental individuals are admixtures, with different levels of introgression, with the sympatric species Crocodylus moreletii. We propose that the islands/atolls remain the sole areas with genetically “pure” American crocodiles and we discuss these results for future conservation of this endangered crocodile species.     

Analysis of a two-layer cloud system with RAMS model and comparison to airborne observations

A three-dimensional numerical model (Regional Atmospheric Modeling System—-RAMS) was used to study the formation and evolution of water forms in a two-layer cloud structure observed during a field campaign over Brest (France). The model performance in regular operations, using conventional meteorological data as initial and lateral boundary conditions, was also examined. Remote sensing observations of the cloud system and in-situ aircraft data, selected during the campaign, were used to validate the model outputs. The model simulations showed that the lower cloud formation was characterized by high number concentration of pristine ice and snow, while the concentration of aggregates, graupel and hail were considerably lower. Hydrometeors in liquid phase appeared demonstrating high number concentration and water content on the top of this layer. The upper cloud layer consisted only of frozen water substances in lower amounts. The qualitative and quantitative comparison of the model-calculated meteorological and microphysical fields to the available observational data revealed that the model reflected fairly well the cloud structure (e.g., the spatio-temporal variability of the cloud parameters, the geometry of the cloud system). However, there were deviations as far as the model underestimating the ice water content (IWC) and number concentration (N_t) fields is concerned, especially at the atmospheric layer between 2.5 and 4 km of altitude. These deviations of the model simulated quantities from the measured ones may be attributed either to the performance of the model’s microphysics scheme, to instrument inaccuracies and to the local disturbance caused by the aircraft.     

Differential responses of honeybee (<Emphasis Type="BoldItalic">Apis mellifera</Emphasis>) patrilines to changes in stimuli for the generalist tasks of nursing and foraging

Which task a social insect worker engages in is influenced by the worker’s age, genotype and the colony’s needs. In the honeybee, Apis mellifera, genotype influences both the age a worker switches tasks and its propensity of engaging in specialist tasks, such as water collecting, which only some workers will perform. In this study, we used colonies with natural levels of genetic diversity and manipulated colony age demography to drastically increase the stimuli for the generalist tasks of foraging and nursing, which all workers are thought to engage in at some point in their lives. We examined the representation of worker patrilines engaged in nursing and foraging before and after the perturbation. The representation of patrilines among foragers and nurses differed from that of their overall colony’s population. In the case of foraging, over- and underrepresentation of some patrilines was not simply due to differences in rates of development among patrilines. We show that replacement foragers tend to be drawn from patrilines that were overrepresented among foragers before the perturbation, suggesting that there is a genetic component to the tendency to engage in foraging. In contrast, the representation of patrilines in replacement nurses differed from that in the unperturbed nursing population. Our results show that there is a genetic influence on even the generalist tasks of foraging and nursing, and that the way patrilines in genetically diverse colonies respond to increases in task stimuli depends upon the task. The possible significance of this genetic influence on task allocation is discussed. Electronic supplementary material Supplementary material is available in the online version of this article at doi: and is accessible to authorized users.     

Using digital cameras to investigate animal colouration: estimating sensor sensitivity functions

Spectrophotometers allow the objective measurement of colour and as a result are rapidly becoming a key piece of equipment in the study of animal colouration; however, they also have some major limitations. For example, they can only record point samples, making it difficult to reconstruct topographical information, and they generally require subjects to be inanimate during measurement. Recently, the use of digital cameras has been explored as an alternative to spectrophotometry. In particular, this allows whole scenes to be captured and objectively converted to animal colour space, providing spatial (and potentially temporal) data that would be unobtainable using spectrophotometry; however, mapping between camera and animal colour spaces requires knowledge of the spectral sensitivity functions of the camera’s sensors. This information is rarely available, and making direct measures of sensor sensitivity can be prohibitively expensive, technically demanding and time-consuming. As a result, various methods have been developed in the engineering and computing sciences that allow sensor sensitivity functions to be estimated using only readily collected data on the camera’s response to a limited number of colour patches of known surface reflectance. Here, I describe the practical application of one such method and demonstrate how it allows the recovery of sensor sensitivities (including in the ultraviolet) with a high enough degree of accuracy to reconstruct whole images in terms of the quantal catches of an animal’s photoreceptors, with calculated values that closely match those determined from spectrophotometric measurements. I discuss the potential for this method to advance our understanding of animal colouration.     

A framework for predicting personal exposures to environmental hazards

This paper presents a general framework for constructing a predictive distribution of the exposure to an environmental hazard sustained by a randomly selected member of a designated population. The individual’s exposure is assumed to arise from random movement through the environment, resulting in a distribution of exposure that can be used for environmental risk analysis. A specialization of the general framework is that of predicting human exposure to air pollution that can be used to develop models for such things as exposure to particulate matter; practical aspects of their construction are considered. These models can help answer questions such as what fraction of the population sustained ‘high’ levels of exposure for say 5 days in a row. The immediate implementation of the above framework takes the form of a computing platform referred to as pCNEM. This provides a facility for simulating exposures to airborne pollutants and is described in detail elsewhere. This paper considers some theoretical aspects underpinning probabilistic exposure models of this type, with the ideas illustrated in developing a model for predicting human exposure to PM ₁₀.     

Fine-scale observations of the predatory behaviour of the carnivorous copepod <Emphasis Type="Italic">Paraeuchaeta norvegica</Emphasis> and the escape responses of their ichthyoplankton prey,Atlantic cod (<Emphasis Type="Italic">Gadus morhua</Emphasis>)

Paraeuchaeta norvegica (8.5 mm total length) and yolk-sac stage Atlantic cod larvae (4 mm total length) (Gadus morhua) larvae were observed in aquaria (3 l of water) using silhouette video photography. This allowed direct observations (and quantitative measurement) of predator–prey interactions between these two species in 3-dimensions. Tail beats, used by cod larvae to propel themselves through the viscous fluid environment, also generate signals detectable by mechanoreceptive copepod predators. When the prey is close enough for detection and successful capture (approximately half a body-length), the copepod launches an extremely rapid high Reynolds number attack, grabbing the larva around its midsection. While capture itself takes place in milliseconds, minutes are required to subdue and completely ingest a cod larva. The behavioural observations are used to estimate the hydrodynamic signal strength of the cod larva’s tail beats and the copepod’s perceptive field for larval fish prey. Cod larvae are more sensitive to fluid velocity than P. norvegica and also appear capable of distinguishing between the signal generated by a swimming and an attacking copepod. However, the copepod can lunge at much faster velocities than a yolk-sac cod larva can escape, leading to the larva’s capture. These observations can serve as input to the predator–prey component of ecosystem models intended to assess the impact of P. norvegica on cod larvae.     

Vocal alliances in Chacma baboons (<Emphasis Type="Italic">Papio hamadryas ursinus</Emphasis>)

Theory predicts that females in species with matrilineal dominance hierarchies should use nepotistic support systems to maintain their family’s rank. Female Old World monkeys, however, form alliances against other females at surprisingly low rates. Nonetheless, in many species, females utter threat vocalizations when observing others’ disputes, suggesting that these vocalizations may function as ‘vocal alliances’. We describe a playback experiment testing the efficacy of vocal alliances in free-ranging female baboons. Subjects were played the same female’s threat-grunts under three separate conditions: after being threatened by the signaller’s close relative to mimic kin support, after being threatened by a female maternally unrelated to the signaller to mimic non-kin support, and after a friendly interaction with the signaller’s close relative as a control. Subjects responded more strongly to the playback and avoided the signaller and her matrilineal relatives for a longer period of time in kin support trials than in either non-kin support or no aggression trials. In contrast, there was no difference in subjects’ behaviour between non-kin support and no aggression trials. These results corroborate observational data showing that vocal support occurs at a higher rate than physical support in female baboons, and that kin are more likely to provide vocal support than non-kin. We conclude that vocal support plays a similar role as physical support in the alliances of female baboons.     

Offensive and defensive sperm competition roles in the dung beetle Onthophagus taurus (Coleoptera: Scarabaeidae)

Sperm competition is predicted to generate opposing selection pressures on males. On one hand, selection should favour ‘defensive’ adaptations that protect a male’s ejaculate from displacement, while, on the other hand, selection should favour ‘offensive’ adaptations that overcome paternity assurance mechanisms of rivals. Here, we use the sterile male technique to assess sperm precedence when a male dung beetle Onthophagus taurus mates in both a defensive (first male) and an offensive (second male) role. Significant variation in a male’s sperm precedence (both P ₁ and P ₂) was detected, and an individual’s defensive (P ₁) and offensive (P ₂) abilities were positively correlated. Thus, it appears that sexual selection simultaneously selects for ‘defensive’ and ‘offensive’ adaptations in O. taurus. We discuss a variety of male traits in O. taurus that potentially contribute to a male’s ability to be successful when mating in an ‘offensive’ and a ‘defensive’ role.