Threshold selection, mitosis and dual mutation in cooperative co-evolution: application to medical 3d tomography

International audienceWe present and analyse the behaviour of specialised operators designed for cooperative coevolution strategy in the framework of 3D tomographic PET reconstruction. The basis is a simple cooperative co-evolution scheme (the "fly algorithm"), which embeds the searched solution in the whole population, letting each individual be only a part of the solution. An individual, or fly, is a 3D point that emits positrons. Using a cooperative co-evolution scheme to optimize the position of positrons, the population of flies evolves so that the data estimated from flies matches measured data. The final population approximates the radioactivity concentration. In this paper, three operators are proposed, threshold selection, mitosis and dual mutation, and their impact on the algorithm efficiency is experimentally analysed on a controlled test-case. Their extension to other cooperative co-evolution schemes is discussed

Coevolved mutations reveal distinct architectures for two core proteins in the bacterial flagellar motor

Switching of bacterial flagellar rotation is caused by large domain movements of the FliG protein triggered by binding of the signal protein CheY to FliM. FliG and FliM form adjacent multi-subunit arrays within the basal body C-ring. The movements alter the interaction of the FliG C-terminal (FliGC) "torque" helix with the stator complexes. Atomic models based on the Salmonella entrovar C-ring electron microscopy reconstruction have implications for switching, but lack consensus on the relative locations of the FliG armadillo (ARM) domains (amino-terminal (FliGN), middle (FliGM) and FliGC) as well as changes during chemotaxis. The generality of the Salmonella model is challenged by the variation in motor morphology and response between species. We studied coevolved residue mutations to determine the unifying elements of switch architecture. Residue interactions, measured by their coevolution, were formalized as a network, guided by structural data. Our measurements reveal a common design with dedicated switch and motor modules. The FliM middle domain (FliMM) has extensive connectivity most simply explained by conserved intra and inter-subunit contacts. In contrast, FliG has patchy, complex architecture. Conserved structural motifs form interacting nodes in the coevolution network that wire FliMM to the FliGC C-terminal, four-helix motor module (C3-6). FliG C3-6 coevolution is organized around the torque helix, differently from other ARM domains. The nodes form separated, surface-proximal patches that are targeted by deleterious mutations as in other allosteric systems. The dominant node is formed by the EHPQ motif at the FliMMFliGM contact interface and adjacent helix residues at a central location within FliGM. The node interacts with nodes in the N-terminal FliGc α-helix triad (ARM-C) and FliGN. ARM-C, separated from C3-6 by the MFVF motif, has poor intra-network connectivity consistent with its variable orientation revealed by structural data. ARM-C could be the convertor element that provides mechanistic and species diversity.JK was supported by Medical Research Council grant U117581331. SK was supported by seed funds from Lahore University of Managment Sciences (LUMS) and the Molecular Biology Consortium

Does coevolution promote species richness in parasitic cuckoos?

Why some lineages have diversified into larger numbers of species than others is a fundamental but still relatively poorly understood aspect of the evolutionary process. Coevolution has been recognized as a potentially important engine of speciation, but has rarely been tested in a comparative framework. We use a comparative approach based on a complete phylogeny of all living cuckoos to test whether parasite–host coevolution is associated with patterns of cuckoo species richness. There are no clear differences between parental and parasitic cuckoos in the number of species per genus. However, a cladogenesis test shows that brood parasitism is associated with both significantly higher speciation and extinction rates. Furthermore, subspecies diversification rate estimates were over twice as high in parasitic cuckoos as in parental cuckoos. Among parasitic cuckoos, there is marked variation in the severity of the detrimental effects on host fitness; chicks of some cuckoo species are raised alongside the young of the host and others are more virulent, with the cuckoo chick ejecting or killing the eggs/young of the host. We show that cuckoos with a more virulent parasitic strategy have more recognized subspecies. In addition, cuckoo species with more recognized subspecies have more hosts. These results hold after controlling for confounding geographical effects such as range size and isolation in archipelagos. Although the power of our analyses is limited by the fact that brood parasitism evolved independently only three times in cuckoos, our results suggest that coevolutionary arms races with hosts have contributed to higher speciation and extinction rates in parasitic cuckoos

Modeling an agrifood industrial process using cooperative coevolution Algorithms

This report presents two experiments related to the modeling of an industrial agrifood process using evolutionary techniques. Experiments have been focussed on a specific problem which is the modeling of a Camembert-cheese ripening process. Two elated complex optimisation problems have been considered: -- a deterministic modeling problem, the phase prediction roblem, for which a search for a closed form tree expression has been performed using genetic programming (GP), -- a Bayesian network structure estimation problem, considered as a two-stage problem, i.e. searching first for an approximation of an independence model using EA, and then deducing, via a deterministic algorithm, a Bayesian network which represents the equivalence class of the independence model found at the first stage. In both of these problems, cooperative-coevolution techniques (also called ``Parisian'' approaches) have been proved successful. These approaches actually allow to represent the searched solution as an aggregation of several individuals (or even as a whole population), as each individual only bears a part of the searched solution. This scheme allows to use the artificial Darwinism principles in a more economic way, and the gain in terms of robustness and efficiency is important

Potential Heritable Aphid Tolerance and Resistance in Phaseolus vulgaris

The common bean, or Phaseolus vulgaris, is used often in both agriculture and scientific research, but the plant is frequently found infested with the insect pest Aphis fabae, the black bean aphid. The current project is the beginning of an endeavor to research the evolutionary relationship between the parasite and host. We hypothesize that tolerance to infestation by the black bean aphid in the common bean is a genetically heritable trait, allowing the plant to reproduce successfully

Local Networks to Compete in the Global Era. The Italian SMEs Experience

This study is concerned with the factors that influence the cooperation among cluster-based firms. Theorists have consistently demonstrated the role and importance of economic externalities, such as knowledge spillovers, within industrial clusters. Less attention has been paid to the investigation of social based externalities, though it has been suggested that these may also accrue from geographical agglomeration. This study explores the development of cooperation between firms operating in a single industry sector and in close proximity. The results suggest that social networking has a greater influence than geographic proximity in facilitating inter-firm co-operation. A semi-structured questionnaire has been developed and the answers were analysed with a stepwise regression model.Networks, Inter-Firm Cooperation, SMEs

Advances in the Social Evolution and Ecology of Bacterial Public Goods

The altruistic production of public goods is one of most popular puzzles in evolutionary biology, and is most commonly explained by the indirect fitness benefit accrued by producers. I develop our understanding of the ecology and evolution of public good production by considering how inter- and intraspecific interactions can affect indirect fitness benefits, and ultimately, the evolutionary trajectory of public good cooperation in a bacterial public good system: 1) I demonstrate the ability of public good cooperators to adapt to the presence of cheats by reducing their own cooperative output, constraining cheat fitness as a consequence. 2) I examine the relative contributions of inter- (bacteriophage) and intraspecific (social cheats) parasites on shaping bacterial mutation rates, and demonstrate that social cheats can gain a fitness advantage in the presence compared with the absence of interspecific parasites. 3) I formally show for the first time, that siderophore-mediated detoxification can be an altruistic trait, rapidly selecting for the evolution of de novo cheats, and discuss the implications this process may have for community structure and function. 4) I extend (3) to assess the impact the natural microbial community has on the fitness consequences of siderophore-mediated detoxification in a natural soil environment. 5) I discuss the interplay between rapid microbial evolution and community context, and propose the impacts such interplay may have for biotechnological applications.University of Exete