A framework for evolutionary systems biology

<p>Abstract</p> <p>Background</p> <p>Many difficult problems in evolutionary genomics are related to mutations that have weak effects on fitness, as the consequences of mutations with large effects are often simple to predict. Current systems biology has accumulated much data on mutations with large effects and can predict the properties of knockout mutants in some systems. However experimental methods are too insensitive to observe small effects.</p> <p>Results</p> <p>Here I propose a novel framework that brings together evolutionary theory and current systems biology approaches in order to quantify small effects of mutations and their epistatic interactions <it>in silico</it>. Central to this approach is the definition of fitness correlates that can be computed in some current systems biology models employing the rigorous algorithms that are at the core of much work in computational systems biology. The framework exploits synergies between the realism of such models and the need to understand real systems in evolutionary theory. This framework can address many longstanding topics in evolutionary biology by defining various 'levels' of the adaptive landscape. Addressed topics include the distribution of mutational effects on fitness, as well as the nature of advantageous mutations, epistasis and robustness. Combining corresponding parameter estimates with population genetics models raises the possibility of testing evolutionary hypotheses at a new level of realism.</p> <p>Conclusion</p> <p>EvoSysBio is expected to lead to a more detailed understanding of the fundamental principles of life by combining knowledge about well-known biological systems from several disciplines. This will benefit both evolutionary theory and current systems biology. Understanding robustness by analysing distributions of mutational effects and epistasis is pivotal for drug design, cancer research, responsible genetic engineering in synthetic biology and many other practical applications.</p

Taking the initiative on Maltese trawl industry management. Industry and science collaboration on identifying nursery and spawning areas for trawl fisheries target species

Malta has managed a Fisheries Management Zone (FMZ), which extends to 25 NM from the baseline of the Maltese Islands, since 1971. The key aim of the Malta FMZ is to protect the fisheries resources of Malta’s marine area and the ecosystems on which they depend. While bottom trawling is limited in terms of the number of vessels, it is one of the major contributors to landings. As of the start of the GAP project (April 2011), 12 bottom trawlers were licensed to trawl within the FMZ. The study was originally the initiative of fishers, motivated by the need to have data that could be used as a basis to advise on the management of the trawling fleet working within the FMZ. Throughout the sampling design stage, the methodology was discussed between fishers and scientists with the aim of using fishers’ knowledge to determine sampling locations while at the same time obtaining sound results. A 13-month study was conducted, using modified versions of “mazara” type nets traditionally used by Maltese bottom trawlers. The nets had two square mesh cod-ends with mesh sizes of 40 mm and 20 mm. Data were collected on seven target species and three non-target species which will be used to address data gaps with respect to nursery and spawning areas of local populations of targeted stocks. This chapter provides an initial discussion on the potential contribution of the information collected to provide management advice for Malta’s trawl fisheries management plan, the main focus of which is the control of fishing effort