A note on the accuracy of PAC-likelihood inference with microsatellite data

Stephens and Donnelly have introduced a simple yet powerful importance sampling scheme for computing the likelihood in population genetic models. Fundamental to the method is an approximation to the conditional probability of the allelic type of an additional gene, given those currently in the sample. As noted by Li and Stephens, the product of these conditional probabilities for a sequence of draws that gives the frequency of allelic types in a sample is an approximation to the likelihood, and can be used directly in inference. The aim of this note is to demonstrate the high level of accuracy of "product of approximate conditionals" (PAC) likelihood when used with microsatellite data. Results obtained on simulated microsatellite data show that this strategy leads to a negligible bias over a wide range of the scaled mutation parameter theta. Furthermore, the sampling variance of likelihood estimates as well as the computation time are lower than that obtained with importance sampling on the whole range of theta. It follows that this approach represents an efficient substitute to IS algorithms in computer intensive (e.g. MCMC) inference methods in population genetics. (c) 2006 Elsevier Inc. All rights reserved.

Population genetic models can be used to study the evolution of the interacting behaviours of parents and their progeny

An example of the evolution of the interacting behaviours of parents and progeny is studied using iterative equations linking the frequencies of the gametes produced by the progeny to the frequencies of the gametes in the parental generation. This population genetics approach shows that a model in which both behaviours are determined by a single locus can lead to a stable equilibrium in which the two behaviours continue to segregate. A model in which the behaviours are determined by genes at two separate loci leads eventually to fixation of the alleles at both loci but this can take many generations of selection. Models of the type described in this paper will be needed to understand the evolution of complex behaviour when genomic or experimental information is available about the genetic determinants of behaviour and the selective values of different genomes. (c) 2007 Elsevier Inc. All rights reserved.

Inference on microsatellite mutation processes in the invasive mite, Varroa destructor, using reversible jump Markov chain Monte Carlo

Varroa destructor is a parasitic mite of the Eastern honeybee Apis cerana. Fifty years ago, two distinct evolutionary lineages (Korean and Japanese) invaded the Western honeybee Apis mellifera. This haplo-diploid parasite species reproduces mainly through brother sister matings, a system which largely favors the fixation of new mutations. In a worldwide sample of 225 individuals from 21 locations collected on Western honeybees and analyzed at 19 microsatellite loci, a series of de novo mutations was observed. Using historical data concerning the invasion, this original biological system has been exploited to compare three mutation models with allele size constraints for microsatellite markers: stepwise (SMM) and generalized (GSM) mutation models, and a model with mutation rate increasing exponentially with microsatellite length (ESM). Posterior probabilities of the three models have been estimated for each locus individually using reversible jump Markov Chain Monte Carlo. The relative support of each model varies widely among loci, but the GSM is the only model that always receives at least 9% support, whatever the locus. The analysis also provides robust estimates of mutation parameters for each locus and of the divergence time of the two invasive lineages (67,000 generations with a 90% credibility interval of 35,000-174,000). With an average of 10 generations per year, this divergence time fits with the last post-glacial Korea Japan land separation. (c) 2005 Elsevier Inc. All rights reserved.

Farm forestry in Pakistan: an application of Theory of Planned Behaviour by probing into the measurement issues

A research has been conducted over methodological issues concerning the Theory of Planned Behaviour (TPB) by determining an appropriate measurement (direct and indirect) of constructs and selection of a plausible scaling techniques (unipolar and bipolar) of constructs: attitude, subjective norm, perceived behavioural control and intention that are important in explaining farm level tree planting in Pakistan. Unipolar scoring of beliefs showed higher correlation among the constructs of TPB than bipolar scaling technique. Both direct and indirect methods yielded significant results in explaining intention to perform farm forestry except the belief based measure of perceived behavioural control, which were analysed as statistically non-significant. A need to examine more carefully the scoring of perceived behavioural control (PBC) has been expressed

A micro-level simulation for the prediction of intention and behaviour

In this contribution we aim at anchoring Agent-Based Modeling (ABM) simulations in actual models of human psychology. More specifically, we apply unidirectional ABM to social psychological models using low level agents (i.e., intra-individual) to examine whether they generate better predictions, in comparison to standard statistical approaches, concerning the intentions of performing a behavior and the behavior. Moreover, this contribution tests to what extent the predictive validity of models of attitude such as the Theory of Planned Behavior (TPB) or Model of Goal-directed Behavior (MGB) depends on the assumption that peoples’ decisions and actions are purely rational. Simulations were therefore run by considering different deviations from rationality of the agents with a trembling hand method. Two data sets concerning respectively the consumption of soft drinks and physical activity were used. Three key findings emerged from the simulations. First, compared to standard statistical approach the agent-based simulation generally improves the prediction of behavior from intention. Second, the improvement in prediction is inversely proportional to the complexity of the underlying theoretical model. Finally, the introduction of varying degrees of deviation from rationality in agents’ behavior can lead to an improvement in the goodness of fit of the simulations. By demonstrating the potential of ABM as a complementary perspective to evaluating social psychological models, this contribution underlines the necessity of better defining agents in terms of psychological processes before examining higher levels such as the interactions between individuals.

Factors influencing adoption of improved grassland management by small-scale dairy farmers in central Mexico and the implications for future research on smallholder adoption in developing countries

There have been limited recent advances in understanding of what influences uptake of innovations despite the current international focus on smallholder agriculture as a means of achieving food security and rural development. This paper provides a rigorous study of factors influencing adoption by smallholders in central Mexico and builds on findings to identify a broad approach to significantly improve research on and understanding of factors influencing adoption by smallholders in developing countries. Small-scale dairy systems play an important role in providing income, employment and nutrition in the highlands of central Mexico. A wide variety of practices and technologies have been promoted by the government public services to increase milk production and economic efficiency, but there have been very low levels of uptake of most innovations, with the exception of improving grassland through introduction of grass varieties together with management practices. A detailed study was conducted with 80 farmers who are already engaged with the use of this innovation to better understand the process of adoption and identify socioeconomic and farm variables, cognitive (beliefs), and social–psychological (social norms) factors associated with farmers' use of improved grassland. The Theory of Reasoned Action (TRA) was used as a theoretical framework and Spearman Rank Order correlation was conducted to analyse the data. Most farmers (92.5%) revealed strong intention to continue to use improved grassland (which requires active management and investment of resources) for the next 12 months; whereas 7.5% of farmers were undecided and showed weak intention, which was associated with farmers whose main income was from non-farm activities as well as with farmers who had only recently started using improved grassland. Despite farmers' experience of using improved grassland (mean of 18 years) farmers' intentions to continue to adopt it was influenced almost as much by salient referents (mainly male relatives) as by their own attitudes. The hitherto unnoticed longevity of the role social referents play in adoption decisions is an important finding and has implications for further research and for the design of extension approaches. The study demonstrates the value and importance of using TRA or TPB approaches to understand social cognitive (beliefs) and social–psychological (social norms) factors in the study of adoption. However, other factors influencing adoption processes need to be included to provide fuller understanding. An approach that would enable this, and the development of more generalisable findings than from location specific case studies, and contribute to broader conceptualisation, is proposed.

The coevolution of two phytoplankton species on a single resource: allelopathy as a pseudo-mixotrophy

Without the top-down effects and the external/physical forcing, a stable coexistence of two phytoplankton species under a single resource is impossible — a result well known from the principle of competitive exclusion. Here I demonstrate by analysis of a mathematical model that such a stable coexistence in a homogeneous media without any external factor would be possible, at least theoretically, provided (i) one of the two species is toxin producing thereby has an allelopathic effect on the other, and (ii) the allelopathic effect exceeds a critical level. The threshold level of allelopathy required for the coexistence has been derived analytically in terms of the parameters associated with the resource competition and the nutrient recycling. That the extra mortality of a competitor driven by allelopathy of a toxic species gives a positive feed back to the algal growth process through the recycling is explained. And that this positive feed back plays a pivotal role in reducing competition pressures and helping species succession in the two-species model is demonstrated. Based on these specific coexistence results, I introduce and explain theoretically the allelopathic effect of a toxic species as a ‘pseudo-mixotrophy’—a mechanism of ‘if you cannot beat them or eat them, just kill them by chemical weapons’. The impact of this mechanism of species succession by pseudo-mixotrophy in the form of alleopathy is discussed in the context of current understanding on straight mixotrophy and resource-species relationship among phytoplankton species.

Workaround motivation model (WAMM): an adaptation of the Theory of Interpersonal Behaviour

The study of workarounds (WA) has increased in importance due to their impact on patient safety and efficiency. However, there are no adequate theories to explain the motivation to create and use a workaround in a healthcare sitting. Although theories of technology acceptance help to understand the reasons to accept or reject technology, they fail to explain drivers for alternatives. Also workarounds involve creators and performers that have different motivations. Models such as Theory of Planned Behaviour (TPB) or Theory of Reasoned Action (TRA) can help to explain the role of workaround users, but lack explanation of workaround creators’ dynamics. Our aim is to develop a theoretical foundation to explain workaround motivation behaviour models with norms that relate to sanctions to provide an integrated Workaround Motivation Model; WAMM. The development of WAMM model is explained in this paper based on workaround cases as part of further research to establish the model.

Identifying behavioural predictors of small power electricity consumption in office buildings

It is widely accepted that there is a gap between design energy and real world operational energy consumption. The behaviour of occupants is often cited as an important factor influencing building energy performance. However, its consideration, both during design and operation, is overly simplistic, often assuming a direct link between attitudes and behaviour. Alternative models of decision making from psychology highlight a range of additional influential factors and emphasise that occupants do not always act in a rational manner. Developing a better understanding of occupant decision making could help inform office energy conservation campaigns as well as models of behaviour employed during the design process. This paper assesses the contribution of various behavioural constructs on small power consumption in offices. The method is based upon the Theory of Planned Behaviour (TPB) which assumes that intention is driven by three factors: attitude, subjective norms, and perceived behavioural control, but we also consider a fourth construct: habit measured through the Self- Report Habit Index (SRHI). A questionnaire was issued to 81 participants in two UK offices. Questionnaire results for each behavioural construct were correlated against each participant’s individual workstation electricity consumption. The intentional processes proposed by TPB could not account for the observed differences in occupants’ interactions with small power appliances. Instead, occupants were interacting with small power “automatically”, with habit accounting for 11% of the variation in workstation energy consumption. The implications for occupant behaviour models and employee engagement campaigns are discussed.