Rapid radiation in spiny lobsters (Palinurus spp) as revealed by classic and ABC methods using mtDNA and microsatellite data

Background: Molecular tools may help to uncover closely related and still diverging species from a wide variety of taxa and provide insight into the mechanisms, pace and geography of marine speciation. There is a certain controversy on the phylogeography and speciation modes of species-groups with an Eastern Atlantic-Western Indian Ocean distribution, with previous studies suggesting that older events (Miocene) and/or more recent (Pleistocene) oceanographic processes could have influenced the phylogeny of marine taxa. The spiny lobster genus Palinurus allows for testing among speciation hypotheses, since it has a particular distribution with two groups of three species each in the Northeastern Atlantic (P. elephas, P. mauritanicus and P. charlestoni) and Southeastern Atlantic and Southwestern Indian Oceans (P. gilchristi, P. delagoae and P. barbarae). In the present study, we obtain a more complete understanding of the phylogenetic relationships among these species through a combined dataset with both nuclear and mitochondrial markers, by testing alternative hypotheses on both the mutation rate and tree topology under the recently developed approximate Bayesian computation (ABC) methods. Results: Our analyses support a North-to-South speciation pattern in Palinurus with all the South-African species forming a monophyletic clade nested within the Northern Hemisphere species. Coalescent-based ABC methods allowed us to reject the previously proposed hypothesis of a Middle Miocene speciation event related with the closure of the Tethyan Seaway. Instead, divergence times obtained for Palinurus species using the combined mtDNA-microsatellite dataset and standard mutation rates for mtDNA agree with known glaciation-related processes occurring during the last 2 my. Conclusion: The Palinurus speciation pattern is a typical example of a series of rapid speciation events occurring within a group, with very short branches separating different species. Our results support the hypothesis that recent climate change-related oceanographic processes have influenced the phylogeny of marine taxa, with most Palinurus species originating during the last two million years. The present study highlights the value of new coalescent-based statistical methods such as ABC for testing different speciation hypotheses using molecular data.

Inferring population history with DIY ABC: a user-friendly approach to approximate Bayesian computation

Genetic data obtained on population samples convey information about their evolutionary history. Inference methods can extract part of this information but they require sophisticated statistical techniques that have been made available to the biologist community (through computer programs) only for simple and standard situations typically involving a small number of samples. We propose here a computer program (DIY ABC) for inference based on approximate Bayesian computation (ABC), in which scenarios can be customized by the user to fit many complex situations involving any number of populations and samples. Such scenarios involve any combination of population divergences, admixtures and population size changes. DIY ABC can be used to compare competing scenarios, estimate parameters for one or more scenarios and compute bias and precision measures for a given scenario and known values of parameters (the current version applies to unlinked microsatellite data). This article describes key methods used in the program and provides its main features. The analysis of one simulated and one real dataset, both with complex evolutionary scenarios, illustrates the main possibilities of DIY ABC.

Synthesis and characterization of biocompatible, thermoresponsive ABC and ABA triblock copolymer gelators

The synthesis of doubly thermoresponsive PPO-PMPC-PNIPAM triblock copolymer gelators by atom transfer radical polymerization using a PPO-based macroinitiator is described. Provided that the PPO block is sufficiently long, dynamic light scattering and differential scanning calorimetry studies confirm the presence of two separate thermal transitions corresponding to micellization and gelation, as expected. However, these ABC-type triblock copolymers proved to be rather inefficient gelators: free-standing gels at 37 degrees C required a triblock copolymer concentration of around 20 wt%. This gelator performance should be compared with copolymer concentrations of 6-7 wt% required for the PNIPAM-PMPC-PNIPAM triblock copolymers reported previously. Clearly, the separation of micellar self-assembly from gel network formation does not lead to enhanced gelator efficiencies, at least for this particular system. Nevertheless, there are some features of interest in the present study. In particular, close inspection of the viscosity vs temperature plot obtained for a PPO43-PMPC160-PNIPAM(81) triblock copolymer revealed a local minimum in viscosity. This is consistent with intramicelle collapse of the outer PNIPAM blocks prior to the development of the intermicelle hydrophobic interactions that are a prerequisite for macroscopic gelation.

An integrated dynamic whole life costing analysis for air distribution systems

Air distribution systems are one of the major electrical energy consumers in air-conditioned commercial buildings which maintain comfortable indoor thermal environment and air quality by supplying specified amounts of treated air into different zones. The sizes of air distribution lines affect energy efficiency of the distribution systems. Equal friction and static regain are two well-known approaches for sizing the air distribution lines. Concerns to life cycle cost of the air distribution systems, T and IPS methods have been developed. Hitherto, all these methods are based on static design conditions. Therefore, dynamic performance of the system has not been yet addressed; whereas, the air distribution systems are mostly performed in dynamic rather than static conditions. Besides, none of the existing methods consider any aspects of thermal comfort and environmental impacts. This study attempts to investigate the existing methods for sizing of the air distribution systems and proposes a dynamic approach for size optimisation of the air distribution lines by taking into account optimisation criteria such as economic aspects, environmental impacts and technical performance. These criteria have been respectively addressed through whole life costing analysis, life cycle assessment and deviation from set-point temperature of different zones. Integration of these criteria into the TRNSYS software produces a novel dynamic optimisation approach for duct sizing. Due to the integration of different criteria into a well- known performance evaluation software, this approach could be easily adopted by designers in busy nature of design. Comparison of this integrated approach with the existing methods reveals that under the defined criteria, system performance is improved up to 15% compared to the existing methods. This approach is interpreted as a significant step forward reaching to the net zero emission building in future.

Knowledge-based design cost estimation through extending industry foundation classes

In order to overcome divergence of estimation with the same data, the proposed digital costing process adopts an integrated design of information system to design the process knowledge and costing system together. By employing and extending a widely used international standard, industry foundation classes, the system can provide an integrated process which can harvest information and knowledge of current quantity surveying practice of costing method and data. Knowledge of quantification is encoded from literatures, motivation case and standards. It can reduce the time consumption of current manual practice. The further development will represent the pricing process in a Bayesian Network based knowledge representation approach. The hybrid types of knowledge representation can produce a reliable estimation for construction project. In a practical term, the knowledge management of quantity surveying can improve the system of construction estimation. The theoretical significance of this study lies in the fact that its content and conclusion make it possible to develop an automatic estimation system based on hybrid knowledge representation approach.

Calibration and evaluation of individual-based models using Approximate Bayesian Computation

This paper investigates the feasibility of using approximate Bayesian computation (ABC) to calibrate and evaluate complex individual-based models (IBMs). As ABC evolves, various versions are emerging, but here we only explore the most accessible version, rejection-ABC. Rejection-ABC involves running models a large number of times, with parameters drawn randomly from their prior distributions, and then retaining the simulations closest to the observations. Although well-established in some fields, whether ABC will work with ecological IBMs is still uncertain. Rejection-ABC was applied to an existing 14-parameter earthworm energy budget IBM for which the available data consist of body mass growth and cocoon production in four experiments. ABC was able to narrow the posterior distributions of seven parameters, estimating credible intervals for each. ABC’s accepted values produced slightly better fits than literature values do. The accuracy of the analysis was assessed using cross-validation and coverage, currently the best available tests. Of the seven unnarrowed parameters, ABC revealed that three were correlated with other parameters, while the remaining four were found to be not estimable given the data available. It is often desirable to compare models to see whether all component modules are necessary. Here we used ABC model selection to compare the full model with a simplified version which removed the earthworm’s movement and much of the energy budget. We are able to show that inclusion of the energy budget is necessary for a good fit to the data. We show how our methodology can inform future modelling cycles, and briefly discuss how more advanced versions of ABC may be applicable to IBMs. We conclude that ABC has the potential to represent uncertainty in model structure, parameters and predictions, and to embed the often complex process of optimizing an IBM’s structure and parameters within an established statistical framework, thereby making the process more transparent and objective.

Predicting how many animals will be where: how to build, calibrate and evaluate individual-based models

Individual-based models (IBMs) can simulate the actions of individual animals as they interact with one another and the landscape in which they live. When used in spatially-explicit landscapes IBMs can show how populations change over time in response to management actions. For instance, IBMs are being used to design strategies of conservation and of the exploitation of fisheries, and for assessing the effects on populations of major construction projects and of novel agricultural chemicals. In such real world contexts, it becomes especially important to build IBMs in a principled fashion, and to approach calibration and evaluation systematically. We argue that insights from physiological and behavioural ecology offer a recipe for building realistic models, and that Approximate Bayesian Computation (ABC) is a promising technique for the calibration and evaluation of IBMs. IBMs are constructed primarily from knowledge about individuals. In ecological applications the relevant knowledge is found in physiological and behavioural ecology, and we approach these from an evolutionary perspective by taking into account how physiological and behavioural processes contribute to life histories, and how those life histories evolve. Evolutionary life history theory shows that, other things being equal, organisms should grow to sexual maturity as fast as possible, and then reproduce as fast as possible, while minimising per capita death rate. Physiological and behavioural ecology are largely built on these principles together with the laws of conservation of matter and energy. To complete construction of an IBM information is also needed on the effects of competitors, conspecifics and food scarcity; the maximum rates of ingestion, growth and reproduction, and life-history parameters. Using this knowledge about physiological and behavioural processes provides a principled way to build IBMs, but model parameters vary between species and are often difficult to measure. A common solution is to manually compare model outputs with observations from real landscapes and so to obtain parameters which produce acceptable fits of model to data. However, this procedure can be convoluted and lead to over-calibrated and thus inflexible models. Many formal statistical techniques are unsuitable for use with IBMs, but we argue that ABC offers a potential way forward. It can be used to calibrate and compare complex stochastic models and to assess the uncertainty in their predictions. We describe methods used to implement ABC in an accessible way and illustrate them with examples and discussion of recent studies. Although much progress has been made, theoretical issues remain, and some of these are outlined and discussed.