Region‐wide temporal and spatial variation in Caribbean reef architecture: is coral cover the whole story?

The architectural complexity of coral reefs is largely generated by reef‐building corals, yet the effects of current regional‐scale declines in coral cover on reef complexity are poorly understood. In particular, both the extent to which declines in coral cover lead to declines in complexity and the length of time it takes for reefs to collapse following coral mortality are unknown. Here we assess the extent of temporal and spatial covariation between coral cover and reef architectural complexity using a Caribbean‐wide dataset of temporally replicated estimates spanning four decades. Both coral cover and architectural complexity have declined rapidly over time, with little evidence of a time‐lag. However, annual rates of change in coral cover and complexity do not covary, and levels of complexity vary greatly among reefs with similar coral cover. These findings suggest that the stressors influencing Caribbean reefs are sufficiently severe and widespread to produce similar regional‐scale declines in coral cover and reef complexity, even though reef architectural complexity is not a direct function of coral cover at local scales. Given that architectural complexity is not a simple function of coral cover, it is important that conservation monitoring and restoration give due consideration to both architecture and coral cover. This will help ensure that the ecosystem services supported by architectural complexity, such as nutrient recycling, dissipation of wave energy, fish production and diversity, are maintained and enhanced.     

When is stream invertebrate drift catastrophic? The role of hydraulics and sediment transport in initiating drift during flood events

1. The term ‘catastrophic drift’ is used to describe the large‐scale displacement of invertebrates that occurs during periods of increased river discharge. However, the physical processes that lead to animals entering the water column at such times remain poorly understood. Specifically, the hypothesis that the movement of bed sediments during floods triggers a large increase in drift has lacked a rigorous field test. 2. Using a portable flume, the hydraulic conditions and rates of bedload transport associated with small, frequent floods were created in situ within a reach of a gravel bed river. Experiments focussed on the patches of fine sediment which are the dominant source of bed material transported during small floods. The flume produced near bed velocities of up to 2 m s^?1 over the patches, increasing shear stress, initiating sediment transport and causing invertebrates to enter the drift. 3. The total number of individuals lost from the bed, as well as the taxonomic composition of the drift, were influenced strongly by shear stress and bedload. The rate of loss from the bed was low at shear stresses <9 dynes cm^?2 (0–4 individuals min^?1 from the 0.5 m² flume bed area). Once shear stress exceeded 9 dynes cm^?2, the threshold that resulted in consistent bedload transport from the patches, the rate of loss of animals increased to a maximum of 56 individuals min^?1. When bedload transport rates were at their highest, the taxonomic composition of the drift was more similar to the benthos than it was to the drift observed when bed material was stable. 4. Absolute rates of bedload transport created by the manipulations were extremely low (<7 g m^?1 s^?1) and typical of those measured during small, frequent floods. Events of this magnitude do not break up the armour layer across the reach as a whole and so exposed patches of fine sediment are the principal source of bedload material. Consequently, discharge events not considered as disturbances in geomorphic terms may initiate frequent episodes of so‐called ‘catastrophic drift’ from patches of stream bed.     

Scaling up: how do exogenous fluctuations in individual-based resource competition models re-emerge in aggregated stochastic population models?

In applied population dynamics the choice of stochastic per capita growth function has implications for population viability analyses, management recommendations, and pest control. This model choice is often based on statistical criteria, mathematical tractability or personal preferences, and general ecological guidelines are either too vague or entirely missing. To identify such guidelines, it is important to understand how exogenous and endogenous factors interact at the individual level and re-emerge at the aggregated population level. We therefore study different types of resource competition (contest vs. scramble competition) and different types of exogenous fluctuations (food and weather fluctuations) at the individual level in a simple individual-based simulation model. We statistically fit the resulting time series to find out (1) which functional form of the growth function (‘hyperbolic’ or ‘exponential’) better describes contest and scramble competition and (2) whether the pattern of population fluctuations resulting from the simulations can be assigned to vertical, lateral or nonlinear perturbations in the stochastic growth function (a classification scheme suggested by Royama 1992, Analytical Population Dynamics, Chapman and Hall, London). We found that the same type of competition can result in ‘hyperbolic’ or ‘exponential’ functional forms, depending on the type of exogenous fluctuations. So it is the interplay between exogenous variability and endogenous resource competition that affects model performance. In contrast to the widespread assumption of vertical (additive) perturbations, our findings highlight the importance of (non-additive) lateral and nonlinear perturbations and their combinations with vertical perturbations. The choice of the stochastic growth function should therefore consider not only statistical criteria but also ecological guidelines. We derive such ecological guidelines from our analysis.     

The circadian cycle: is the whole greater than the sum of its parts?

The term 'circadian rhythm' describes an oscillatory behavior in the absence of exogenous environmental cues, with a period of about a day. As yet, we don't fully understand which biological mechanisms join together to supply a stable and self-sustained oscillation with such a long period. By chipping away at the molecular mechanism with genetic approaches, some common features are emerging. In combining molecular analyses and physiological experiments, those features that are crucial for structuring a circadian day could be uncovered.     

Alloparental feeding in Adélie penguins: why is it uncommon?

We investigated alloparental interactions and conditions which could facilitate or prevent the expression of alloparental behaviours in Adélie penguins (Pygoscelis adeliae), a long-lived seabird which nests in high-density colonies around Antarctica. Observation sessions were carried out during the crèche stage on 48 identified pairs and 50 identified chicks in a 217-nest subcolony. As the season progressed, young were fed less often by their own parents because these were increasingly absent from the breeding site and less responsive to their offspring’s solicitations. As a consequence, young and particularly those with a low body mass, coming from a two-chick brood, opted for gradually soliciting more from other adults to obtain food, preferentially those nesting in their direct vicinity. Unsuccessful breeders represented a low and constant part of the adult population and were not specifically solicited by unrelated young. Despite the increasing chick demand, only 4.1% (3 out of 73) of alloparental solicitations resulted in feeding, which is negligible compared to parental feeding. To investigate factors that could trigger the appearance of alloparental care, we carried out comparisons with king (Aptenodytes patagonicus) and emperor penguins (Aptenodytes forsteri) which represent the closest species for which data on alloparental behaviour were available. Our results show different trends to those observed in these species and three factors may explain the low occurrence of alloparental behaviour in Adélie penguins: (1) the low and constant proportion of unsuccessful breeders, (2) the absence of chick selectivity towards unsuccessful breeders, and (3) the late period of chick accessibility for potential alloparents.     

Animal models of neurological deficits: how relevant is the rat?

Animal models of neurological deficits are essential for the assessment of new therapeutic options. It has been suggested that rats are not as appropriate as primates for the symptomatic modelling of disease, but a large body of data argues against this view. Comparative analyses of movements in rats and primates show homology of many motor patterns across species. Advances have been made in identifying rat equivalents of akinesia, tremor, postural deficits and dyskinesia, which are relevant to Parkinson's disease. Rat models of hemiplegia, neglect and tactile extinction are useful in assessing the outcome of ischaemic or traumatic brain injury, and in monitoring the effects of therapeutic interventions. Studies in rodents that emphasize careful behavioural analysis should continue to be developed as effective and inexpensive models that complement studies in primates.     

Biotransformations in microstructured reactors: more than flowing with the stream?

The state of the art in the application of microstructured flow reactors for biocatalytic process research is reviewed. A microstructured reactor that is fully automated and analytically equipped presents a powerful screening tool with which to perform biocatalyst selection and optimization of process conditions at intermediary stages of process development. Enhanced mass transfer provided by the microstructured reactor can be exploited for process intensification, particularly during multiphase biocatalytic processing where mass transfer across phase boundaries is often limiting. Reversible immobilization of enzymes in microchannels remains a challenge for flexible realization of biotransformations in microstructured reactors. Compartmentalization in microstructured reactors could be useful in performing multistep chemoenzymatic conversions.     

Linking reproductive and feeding strategies in the parasitoid Ibalia leucospoides: does feeding always imply profit?

Resource acquisition and allocation to different biological functions over the course of life have strong implications for animal reproductive success. Animals can experience different environmental conditions during their lifetime, and this may play an important role in shaping their life-history and resource allocation strategies. In this study we investigate larval and adult resource allocation to reproductive and survival functions in the parasitoid wasp Ibalia leucospoides (family Ibaliidae). The pattern of larval resource allocation was inferred from the relationship between adult body size and ovigeny index (OI; a relative measure of investment in early reproduction determined as the ratio between the initial egg load and the potential lifetime fecundity); and adult resource allocation was explored through the influence of adult feeding on reproduction, maintenance and metabolism, in laboratory experiments. Food acquisition by this parasitoid in the wild was also examined. The relationship between size and OI was constant, suggesting no differential resource allocation to initial egg load and potential lifetime fecundity with size. This finding is in line with that predicted by adaptive models for the proovigenic egg maturation strategy (OI = 1). Despite of this, I. leucospoides showed a high OI of 0.77, which places this species among the weakly synovigenic ones (OI < 1). Adult feeding had no effect on post-emergence egg maturation. However, wasps extended their lifespan through feeding albeit only when food was provided ad libitum. Although the information we obtained on the feeding behaviour of free-foraging wasps is limited, our results suggest that food intake in the wild, while possible, may not be frequent in this parasitoid. We discuss the results relative to the environmental factors, such as reproductive opportunities and food availability, which may have driven the evolution of larval and adult pattern of resource allocation in parasitoids.     

Recent trends in population genetics: more data! More math! Simple models?

Recent developments in population genetics are reviewed and placed in a historical context. Current and future challenges, both in computational methodology and in analytical theory, are to develop models and techniques to extract the most information possible from multilocus DNA datasets. As an example of the theoretical issues, five limiting forms of the island model of population subdivision with migration are presented in a unified framework. These approximations illustrate the interplay between migration and drift in structuring gene genealogies, and some of them make connections between the fairly complicated island-model genealogical process and the much simpler, unstructured neutral coalescent process which underlies most inferential techniques in population genetics.     

Are the numbers adding up? Exploiting discrepancies among complementary population models

Large carnivores are difficult to monitor because they tend to be sparsely distributed, sensitive to human activity, and associated with complex life histories. Consequently, understanding population trend and viability requires conservationists to cope with uncertainty and bias in population data. Joint analysis of combined data sets using multiple models (i.e., integrated population model) can improve inference about mechanisms (e.g., habitat heterogeneity and food distribution) affecting population dynamics. However, unobserved or unobservable processes can also introduce bias and can be difficult to quantify. We developed a Bayesian hierarchical modeling approach for inference on an integrated population model that reconciles annual population counts with recruitment and survival data (i.e., demographic processes). Our modeling framework is flexible and enables a realistic form of population dynamics by fitting separate density-dependent responses for each demographic process. Discrepancies estimated from shared parameters among different model components represent unobserved additions (i.e., recruitment or immigration) or removals (i.e., death or emigration) when annual population counts are reliable. In a case study of gray wolves in Wisconsin (1980–2011), concordant with policy changes, we estimated that a discrepancy of 0% (1980–1995), −2% (1996–2002), and 4% (2003–2011) in the annual mortality rate was needed to explain annual growth rate. Additional mortality in 2003–2011 may reflect density-dependent mechanisms, changes in illegal killing with shifts in wolf management, and nonindependent censoring in survival data. Integrated population models provide insights into unobserved or unobservable processes by quantifying discrepancies among data sets. Our modeling approach is generalizable to many population analysis needs and allows for identifying dynamic differences due to external drivers, such as management or policy changes.     

Is sequential feeding of whole wheat more efficient than ground wheat in laying hens?

The impact of sequential feeding of whole or ground wheat on the performance of layer hen was investigated using ISABROWN hens from 19 to 42 weeks of age. In addition, the effect of reduced dietary energy content of a complete diet was also investigated. Four treatments were tested. Whole wheat was alternated with a protein-mineral concentrate (balancer diet) in a treatment (sequential whole wheat: SWW), while another treatment alternated ground wheat (sequential ground wheat: SGW) with the same balancer diet. The control (C) was fed a complete layer diet conventionally. Another treatment (low energy: LE) was fed a complete diet conventionally. The diet contained lower energy (10.7 v. 11.6 MJ/kg) compared to the C. Each treatment was allocated 16 cages and each cage contained five birds. Light was provided 16 h daily (0400 to 2000 h). Feed offered was controlled (121 g/bird per day) and distributed twice (2 × 60.5 g) at 4 and 11 h after lights on. In the sequential treatment, only wheat (whole or ground) was fed during the first distribution and the balancer diet during the second distribution. Left over feed was always removed before the next distribution. The total feed intake was not different between SWW and SGW, but the two were lower than C (P < 0.05). Wheat intake was however, lowered with SGW compared to SWW (P < 0.05). Egg production and egg mass (EM) were not different between treatments. Egg weight was lower with SGW than with SWW (P < 0.05), but the two were similar to C. Body weight (BW) was lowered (P < 0.01) with SGW relative to SWW and C, SWW BW being also lower than the C one. The efficiency of egg production was increased (P < 0.01) with the SWW and SGW relative to the control. Birds fed LE had higher feed intake (P < 0.05) but they had similar egg production and EM compared to the two sequential treatments. The efficiency of feed utilization was also reduced (P < 0.01) with LE compared to SWW and SGW. It was concluded that sequential feeding is more efficient than conventional feeding. In addition, whole wheat appeared more efficient than ground wheat in terms of egg and BW.     

Computational models to predict stenosis growth in carotid arteries: which is the role of boundary conditions?

This work addresses the problem of prescribing proper boundary conditions at the artificial boundaries that separate the vascular district from the remaining part of the circulatory system. A multiscale (MS) approach is used where the Navier-Stokes equations for the district of interest are coupled to a non-linear system of ordinary differential equations which describe the circulatory system. This technique is applied to three 3D models of a carotid bifurcation with increasing stenosis resembling three phases of a plaque growth. The results of the MS simulations are compared to those obtained by two stand-alone models. The MS shows a great flexibility in numerically predicting the haemodynamic changes due to the presence of a stenosis. Nonetheless, the results are not significantly different from a stand-alone approach where flows derived by the MS without stenosis are imposed. This is a consequence of the dominant role played by the outside districts with respect to the stenosis resistance.     

From elaborate to compact seasonal plant epidemic models and back: is competitive exclusion in the details?

Seasonality, or periodic host absence, is a central feature in plant epidemiology. In this respect, seasonal plant epidemic models take into account the way the parasite overwinters and generates new infections. These are termed primary infections. In the literature, one finds two classes of models: high-dimensional elaborate models and low-dimensional compact models, where primary infection dynamics are explicit and implicit, respectively. Investigating a compact model allowed previous authors to show the existence of a competitive exclusion principle. However, the way compact models derive from elaborate models has not been made explicit yet. This makes it unclear whether results such as competitive exclusion extend to elaborate models as well. Here, we show that assuming primary infection dynamics are fast in a standard elaborate model translates into a compact form. Yet, it is not that usually found in the literature. Moreover, we numerically show that coexistence is possible in this original compact form. Reversing the question, we show that the usual compact form approximates an alternate elaborate model, which differs from the earlier one in that primary infection dynamics are density dependent. We discuss to which extent these results shed light on coexistence within soil- and air-borne plant parasites, such as within the take-all disease of wheat and the grapevine powdery mildew cryptic species complexes, respectively.     

Masting,mixtures and modes: are two models better than one?

A key hypothesis in population ecology is that synchronous and intermittent seed production, known as mast seeding, is driven by the alternating allocation of carbohydrates and mineral nutrients between growth and reproduction in different years, i.e. ‘resource switching’. Such behaviour may ultimately generate bimodal distributions of long‐term flower and seed production, and evidence of these patterns has been taken to support the resource switching hypothesis. Here, we show how a widely‐used statistical test of bimodality applied by many studies in different ecological contexts may fail to reject the null hypothesis that focal probability distributions are unimodal. Using data from five tussock grass species in South Island, New Zealand, we find clear evidence of bimodality only when flowering patterns are analyzed with probabilistic mixture models. Mixture models provide a theory oriented framework for testing hypotheses of mast seeding patterns, enabling the different responses underlying medium‐ and high‐ versus non‐ and low‐flowering years to be modelled more realistically by associating these with distinct probability distributions. Coupling theoretical expectations with more rigorous statistical approaches will empower ecologists to reject null hypotheses more often.     

Globalisation or Westernisation? Ethical concerns in the whole bio-business

Increasing awareness of the importance of the biodiversity of the whole global biosphere has led to further awareness that the problems which arise in connection with preservation and exploitation of our planet's biodiversity are best tackled from a global perspective. The 'Biodiversity Convention' and the 'Human Genome Project' are some of the concrete attempts at such globalisation. But, while these efforts are certainly very good at the intentional level and on paper, there is, at the practical level of implementation, the danger that globalisation may simply translate into westernisation, given the Western world's dominance and will to dominate the rest of the globe. How is 'global bioethics' to be possible in a world inhabited by different cultural groups whose material situation, powers, ideas, experiences and attitudes differ rather markedly and who are not, in any case, equally represented in globalisation efforts and fora? One index of the pertinence of this question is that talk about biodiversity, biotechnology, biotrade etc. is being increasingly matched by talk about biopiracy, biorade, biocolonialism etc. In this paper, I attempt to explore and develop these very general concerns.     

Stochastic or deterministic: what is the effective population size of HIV-1?

Various studies have attempted to estimate the effective population size of HIV-1 to determine the strength of stochastic effects in within-host evolution. The largely discrepant estimates, the complexity of the concept of the effective population size and the resulting uncertainty about the underlying assumptions make the interpretation of these estimates difficult. Here, we explain the concept and critically assess the current estimates. We discuss the biologically relevant factors that affect the estimate and use of the effective population size. We argue that these factors lead to an underestimation of the effective population size and, thus, to an overestimation of the strength of stochastic effects in HIV-1 evolution.