Engineering tools

The aim of this report is to give an overview of the results of Work Package 5 “Engineering Tools”. In this workpackage numerical tools have been developed for all relevant CHCP systems in the PolySMART demonstration projects (WP3). First, existing simulation platforms have been described and specific characteristics have been identified. Several different simulation platforms are in principle appropriate for the needs in the PolySMART project. The result is an evaluation of available simulation and engineering tools for CHCP simulation, and an agreement upon a common simulation environment within the PolySMART project. Next, numerical models for components in the demonstration projects have been developed. These models are available to the PolySMART consortium. Of all modeled components an overall and detailed working principle is formulated, including a parameter list and (in some cases) a control strategy. Finally, for four CHCP systems in the PolySMART project, a system simulation model has been developed. For each system simulation a separate deliverable is available (D5.5b to D5.5e) These deliverables replace deliverable 5.4 ‘system models’. The numerical models for components and systems developed in the Polysmart project form a valuable basis for the component development and optimisation and for the system optimisation, both within and outside the project. Developers and researchers interested in more information about specific models can refer to the institutes and contact persons involved in the model development. 

Increasing the power of genome wide association studies in natural populations using repeated measures : evaluation and implementation

1. Genomewide association studies (GWAS) enable detailed dissections of the genetic basis for organisms' ability to adapt to a changing environment. In long-term studies of natural populations, individuals are often marked at one point in their life and then repeatedly recaptured. It is therefore essential that a method for GWAS includes the process of repeated sampling. In a GWAS, the effects of thousands of single-nucleotide polymorphisms (SNPs) need to be fitted and any model development is constrained by the computational requirements. A method is therefore required that can fit a highly hierarchical model and at the same time is computationally fast enough to be useful. 2. Our method fits fixed SNP effects in a linear mixed model that can include both random polygenic effects and permanent environmental effects. In this way, the model can correct for population structure and model repeated measures. The covariance structure of the linear mixed model is first estimated and subsequently used in a generalized least squares setting to fit the SNP effects. The method was evaluated in a simulation study based on observed genotypes from a long-term study of collared flycatchers in Sweden. 3. The method we present here was successful in estimating permanent environmental effects from simulated repeated measures data. Additionally, we found that especially for variable phenotypes having large variation between years, the repeated measurements model has a substantial increase in power compared to a model using average phenotypes as a response. 4. The method is available in the R package RepeatABEL. It increases the power in GWAS having repeated measures, especially for long-term studies of natural populations, and the R implementation is expected to facilitate modelling of longitudinal data for studies of both animal and human populations.