Independent sources of condition dependency and multiple pathways determine a composite trait: lessons from carotenoid-based plumage colouration.

Many colour ornaments are composite traits consisting of at least four components, which themselves may be more complex, determined by independent evolutionary pathways, and potentially being under different environmental control. To date, little evidence exists that several different components of colour elaboration are condition dependent and no direct evidence exists that different ornamental components are affected by different sources of variation. For example, in carotenoid-based plumage colouration, one of the best-known condition-dependent ornaments, colour elaboration stems from both condition-dependent pigment concentration and structural components. Some environmental flexibility of these components has been suggested, but specifically which and how they are affected remains unknown. Here, we tested whether multiple colour components may be condition dependent, by using a comprehensive 3 × 2 experimental design, in which we carotenoid supplemented and immune challenged great tit nestlings (Parus major) and quantified effects on different components of colouration. Plumage colouration was affected by an interaction between carotenoid availability and immune challenge. Path analyses showed that carotenoid supplementation increased plumage saturation via feather carotenoid concentration and via mechanisms unrelated to carotenoid deposition, while immune challenge affected feather length, but not carotenoid concentration. Thus, independent condition-dependent pathways, affected by different sources of variation, determine colour elaboration. This provides opportunities for the evolution of multiple signals within components of ornamental traits. This finding indicates that the selective forces shaping the evolution of different components of a composite trait and the trait's signal content may be more complex than believed so far, and that holistic approaches are required for drawing comprehensive evolutionary conclusions.

Ranking-Dominance Relation for (Evolutionary) Multi-Objective Optimization

An alternative relation to Pareto-dominance relation is proposed. The new relation is based on ranking a set of solutions according to each separate objective and an aggregation function to calculate a scalar fitness value for each solution. The relation is called as ranking-dominance and it tries to tackle the curse of dimensionality commonly observedin evolutionary multi-objective optimization. Ranking-dominance can beused to sort a set of solutions even for a large number of objectives when Pareto-dominance relation cannot distinguish solutions from one another anymore. This permits search to advance even with a large number of objectives. It is also shown that ranking-dominance does not violate Pareto-dominance. Results indicate that selection based on ranking-dominance is able to advance search towards the Pareto-front in some cases, where selection based on Pareto-dominance stagnates. However, in some cases it is also possible that search does not proceed into direction of Pareto-front because the ranking-dominance relation permits deterioration of individual objectives. Results also show that when the number of objectives increases, selection based on just Pareto-dominance without diversity maintenance is able to advance search better than with diversity maintenance. Therefore, diversity maintenance is connive at the curse of dimensionality.

Database Rights in Safe European Home: The Path to More Rigorous Protection of Information

1. Introduction "The one that has compiled ... a database, the collection, securing the validity or presentation of which has required an essential investment, has the sole right to control the content over the whole work or over either a qualitatively or quantitatively substantial part of the work both by means of reproduction and by making them available to the public", Finnish Copyright Act, section 49.1 These are the laconic words that implemented the much-awaited and hotly debated European Community Directive on the legal protection of databases,2 the EDD, into Finnish Copyright legislation in 1998. Now in the year 2005, after more than half a decade of the domestic implementation it is yet uncertain as to the proper meaning and construction of the convoluted qualitative criteria the current legislation employs as a prerequisite for the database protection both in Finland and within the European Union. Further, this opaque Pan-European instrument has the potential of bringing about a number of far-reaching economic and cultural ramifications, which have remained largely uncharted or unobserved. Thus the task of understanding this particular and currently peculiarly European new intellectual property regime is twofold: first, to understand the mechanics and functioning of the EDD and second, to realise the potential and risks inherent in the new legislation in economic, cultural and societal dimensions. 2. Subject-matter of the study: basic issues The first part of the task mentioned above is straightforward: questions such as what is meant by the key concepts triggering the functioning of the EDD such as presentation of independent information, what constitutes an essential investment in acquiring data and when the reproduction of a given database reaches either qualitatively or quantitatively the threshold of substantiality before the right-holder of a database can avail himself of the remedies provided by the statutory framework remain unclear and call for a careful analysis. As for second task, it is already obvious that the practical importance of the legal protection providedby the database right is in the rapid increase. The accelerating transformationof information into digital form is an existing fact, not merely a reflection of a shape of things to come in the future. To take a simple example, the digitisation of a map, traditionally in paper format and protected by copyright, can provide the consumer a markedly easier and faster access to the wanted material and the price can be, depending on the current state of the marketplace, cheaper than that of the traditional form or even free by means of public lending libraries providing access to the information online. This also renders it possible for authors and publishers to make available and sell their products to markedly larger, international markets while the production and distribution costs can be kept at minimum due to the new electronic production, marketing and distributionmechanisms to mention a few. The troublesome side is for authors and publishers the vastly enhanced potential for illegal copying by electronic means, producing numerous virtually identical copies at speed. The fear of illegal copying canlead to stark technical protection that in turn can dampen down the demand for information goods and services and furthermore, efficiently hamper the right of access to the materials available lawfully in electronic form and thus weaken the possibility of access to information, education and the cultural heritage of anation or nations, a condition precedent for a functioning democracy. 3. Particular issues in Digital Economy and Information Networks All what is said above applies a fortiori to the databases. As a result of the ubiquity of the Internet and the pending breakthrough of Mobile Internet, peer-to-peer Networks, Localand Wide Local Area Networks, a rapidly increasing amount of information not protected by traditional copyright, such as various lists, catalogues and tables,3previously protected partially by the old section 49 of the Finnish Copyright act are available free or for consideration in the Internet, and by the same token importantly, numerous databases are collected in order to enable the marketing, tendering and selling products and services in above mentioned networks. Databases and the information embedded therein constitutes a pivotal element in virtually any commercial operation including product and service development, scientific research and education. A poignant but not instantaneously an obvious example of this is a database consisting of physical coordinates of a certain selected group of customers for marketing purposes through cellular phones, laptops and several handheld or vehicle-based devices connected online. These practical needs call for answer to a plethora of questions already outlined above: Has thecollection and securing the validity of this information required an essential input? What qualifies as a quantitatively or qualitatively significant investment? According to the Directive, the database comprises works, information and other independent materials, which are arranged in systematic or methodical way andare individually accessible by electronic or other means. Under what circumstances then, are the materials regarded as arranged in systematic or methodical way? Only when the protected elements of a database are established, the question concerning the scope of protection becomes acute. In digital context, the traditional notions of reproduction and making available to the public of digital materials seem to fit ill or lead into interpretations that are at variance with analogous domain as regards the lawful and illegal uses of information. This may well interfere with or rework the way in which the commercial and other operators have to establish themselves and function in the existing value networks of information products and services. 4. International sphere After the expiry of the implementation period for the European Community Directive on legal protection of databases, the goals of the Directive must have been consolidated into the domestic legislations of the current twenty-five Member States within the European Union. On one hand, these fundamental questions readily imply that the problemsrelated to correct construction of the Directive underlying the domestic legislation transpire the national boundaries. On the other hand, the disputes arisingon account of the implementation and interpretation of the Directive on the European level attract significance domestically. Consequently, the guidelines on correct interpretation of the Directive importing the practical, business-oriented solutions may well have application on European level. This underlines the exigency for a thorough analysis on the implications of the meaning and potential scope of Database protection in Finland and the European Union. This position hasto be contrasted with the larger, international sphere, which in early 2005 does differ markedly from European Union stance, directly having a negative effect on international trade particularly in digital content. A particular case in point is the USA, a database producer primus inter pares, not at least yet having aSui Generis database regime or its kin, while both the political and academic discourse on the matter abounds. 5. The objectives of the study The above mentioned background with its several open issues calls for the detailed study of thefollowing questions: -What is a database-at-law and when is a database protected by intellectual property rights, particularly by the European database regime?What is the international situation? -How is a database protected and what is its relation with other intellectual property regimes, particularly in the Digital context? -The opportunities and threats provided by current protection to creators, users and the society as a whole, including the commercial and cultural implications? -The difficult question on relation of the Database protection and protection of factual information as such. 6. Dsiposition The Study, in purporting to analyse and cast light on the questions above, is divided into three mainparts. The first part has the purpose of introducing the political and rationalbackground and subsequent legislative evolution path of the European database protection, reflected against the international backdrop on the issue. An introduction to databases, originally a vehicle of modern computing and information andcommunication technology, is also incorporated. The second part sets out the chosen and existing two-tier model of the database protection, reviewing both itscopyright and Sui Generis right facets in detail together with the emergent application of the machinery in real-life societal and particularly commercial context. Furthermore, a general outline of copyright, relevant in context of copyright databases is provided. For purposes of further comparison, a chapter on the precursor of Sui Generi, database right, the Nordic catalogue rule also ensues. The third and final part analyses the positive and negative impact of the database protection system and attempts to scrutinize the implications further in the future with some caveats and tentative recommendations, in particular as regards the convoluted issue concerning the IPR protection of information per se, a new tenet in the domain of copyright and related rights.

Identifying the Role of Final Consumption in Structural Path Analysis: An Application to Water Uses

The complexity of the connexions within an economic system can only be reliably reflected in academic research if powerful methods are used. Researchers have used Structural Path Analysis (SPA) to capture not only the linkages within the production system but also the propagation of the effects into different channels of impacts. However, the SPA literature has restricted itself to showing the relations among sectors of production, while the connections between these sectors and final consumption have attracted little attention. In order to consider the complete set of channels involved, in this paper we propose a structural path method that endogenously incorporates not only sectors of production but also the final consumption of the economy. The empirical application comprises water usages, and analyses the dissemination of exogenous impacts into various channels of water consumption. The results show that the responsibility for water stress is imputed to different sectors and depends on the hypothesis used for the role played by final consumption in the model. This highlights the importance of consumers’ decisions in the determination of ecological impacts. Keywords: Input-Output Analysis, Structural Path Analysis, Final Consumption, Water uses.

Evolutionary perspective on the interplay between family life, and parent and offspring personality

Consistent inter-individual variation in behaviour over time and across contexts has been reported for a wide variety of animals, a phenomenon commonly referred to as personality. As behavioural patterns develop inside families, rearing conditions could have lasting effects on the expression of adult personality. In species with parental care, conflicts among family members impose selection on parental and offspring behaviour through co-adaptation. Here, we argue that the interplay between the evolution of personality traits (i.e. boldness, exploration, activity, aggressiveness and sociability) expressed outside the family context and the specialized behaviours expressed inside families (i.e. offspring begging behaviour and parental response to offspring solicitations) can have important evolutionary consequences. Personality differences among parents may relate to the typically observed variation in the way they respond to offspring demand, and dependent offspring may already express personality differences which may relate to the way they communicate with their parents and siblings. However, there has been little research on how personality relates to parental and offspring behaviours. Future research should thus focus on how and why personality may be related to the specialized parent and offspring behaviour that evolved as adaptations to family life.

Dendrochronological study of the avalanche path Canal del Roc Roig: first results of the ALUDEX Project in the Pyrenees

Historical data about ancient avalanches are scarce in the Pyrenees. Dendrochronology can provide new data about past avalanches and their return period, but up to now little research has been carried out with this purpose. The Aludex project aims to obtain information about the frequency and extent of extreme avalanches, using a dendrochronological and a nivo-meteorological approach. In this paper, we present the results of a dendrochronological study of the Canal del Roc Roig avalanche path which was affected by two extreme avalanches in February 1996. This first dendrochronological study has permitted us to assess the tree-ring signals due to avalanche events in 53 out of 132 dated trees. The trees presented a variety of responses to the 1996 avalanche events. It is shown that the type of tree-ring signal depends on tree age. The methodology has proved successful in detecting the 1996 and 1972 documented avalanche events, and provided outstanding evidence of undocumented past events such as one in 1930.

Gene flow and gene flux shape evolutionary patterns of variation in Drosophila subobscura

Gene flow (defined as allele exchange between populations) and gene flux (defined as allele exchange during meiosis in heterokaryotypic females) are important factors decreasing genetic differentiation between populations and inversions. Many chromosomal inversions are under strong selection and their role in recombination reduction enhances the maintenance of their genetic distinctness. Here we analyze levels and patterns of nucleotide diversity, selection and demographic history, using 37 individuals of Drosophila subobscura from Mount Parnes (Greece) and Barcelona (Spain). Our sampling focused on two frequent O-chromosome arrangements that differ by two overlapping inversions (OST and O3+4), which are differentially adapted to the environment as observed by their opposing latitudinal clines in inversion frequencies. The six analyzed genes (Pif1A, Abi, Sqd, Yrt, Atpa and Fmr1) were selected for their location across the O-chromosome and their implication in thermal adaptation. Despite the extensive gene flux detected outside the inverted region, significant genetic differentiation between both arrangements was found inside it. However, high levels of gene flow were detected for all six genes when comparing the same arrangement among populations. These results suggest that the adaptive value of inversions is maintained, regardless of the lack of genetic differentiation within arrangements from different populations, and thus favors the Local Adaptation hypothesis over the Coadapted Genome hypothesis as the basis of the selection acting on inversions in these populations.

Evolutionary Games in Networked Populations: Models and Experiments

Cooperation and coordination are desirable behaviors that are fundamental for the harmonious development of society. People need to rely on cooperation with other individuals in many aspects of everyday life, such as teamwork and economic exchange in anonymous markets. However, cooperation may easily fall prey to exploitation by selfish individuals who only care about short- term gain. For cooperation to evolve, specific conditions and mechanisms are required, such as kinship, direct and indirect reciprocity through repeated interactions, or external interventions such as punishment. In this dissertation we investigate the effect of the network structure of the population on the evolution of cooperation and coordination. We consider several kinds of static and dynamical network topologies, such as Baraba´si-Albert, social network models and spatial networks. We perform numerical simulations and laboratory experiments using the Prisoner's Dilemma and co- ordination games in order to contrast human behavior with theoretical results. We show by numerical simulations that even a moderate amount of random noise on the Baraba´si-Albert scale-free network links causes a significant loss of cooperation, to the point that cooperation almost vanishes altogether in the Prisoner's Dilemma when the noise rate is high enough. Moreover, when we consider fixed social-like networks we find that current models of social networks may allow cooperation to emerge and to be robust at least as much as in scale-free networks. In the framework of spatial networks, we investigate whether cooperation can evolve and be stable when agents move randomly or performing Le´vy flights in a continuous space. We also consider discrete space adopting purposeful mobility and binary birth-death process to dis- cover emergent cooperative patterns. The fundamental result is that cooperation may be enhanced when this migration is opportunistic or even when agents follow very simple heuristics. In the experimental laboratory, we investigate the issue of social coordination between indi- viduals located on networks of contacts. In contrast to simulations, we find that human players dynamics do not converge to the efficient outcome more often in a social-like network than in a random network. In another experiment, we study the behavior of people who play a pure co- ordination game in a spatial environment in which they can move around and when changing convention is costly. We find that each convention forms homogeneous clusters and is adopted by approximately half of the individuals. When we provide them with global information, i.e., the number of subjects currently adopting one of the conventions, global consensus is reached in most, but not all, cases. Our results allow us to extract the heuristics used by the participants and to build a numerical simulation model that agrees very well with the experiments. Our findings have important implications for policymakers intending to promote specific, desired behaviors in a mobile population. Furthermore, we carry out an experiment with human subjects playing the Prisoner's Dilemma game in a diluted grid where people are able to move around. In contrast to previous results on purposeful rewiring in relational networks, we find no noticeable effect of mobility in space on the level of cooperation. Clusters of cooperators form momentarily but in a few rounds they dissolve as cooperators at the boundaries stop tolerating being cheated upon. Our results highlight the difficulties that mobile agents have to establish a cooperative environment in a spatial setting without a device such as reputation or the possibility of retaliation. i.e. punishment. Finally, we test experimentally the evolution of cooperation in social networks taking into ac- count a setting where we allow people to make or break links at their will. In this work we give particular attention to whether information on an individual's actions is freely available to poten- tial partners or not. Studying the role of information is relevant as information on other people's actions is often not available for free: a recruiting firm may need to call a job candidate's refer- ences, a bank may need to find out about the credit history of a new client, etc. We find that people cooperate almost fully when information on their actions is freely available to their potential part- ners. Cooperation is less likely, however, if people have to pay about half of what they gain from cooperating with a cooperator. Cooperation declines even further if people have to pay a cost that is almost equivalent to the gain from cooperating with a cooperator. Thus, costly information on potential neighbors' actions can undermine the incentive to cooperate in dynamical networks.

Identification of potential HIV restriction factors by combining evolutionary genomic signatures with functional analyses.

BACKGROUND: Known antiretroviral restriction factors are encoded by genes that are under positive selection pressure, induced during HIV-1 infection, up-regulated by interferons, and/or interact with viral proteins. To identify potential novel restriction factors, we performed genome-wide scans for human genes sharing molecular and evolutionary signatures of known restriction factors and tested the anti-HIV-1 activity of the most promising candidates. RESULTS: Our analyses identified 30 human genes that share characteristics of known restriction factors. Functional analyses of 27 of these candidates showed that over-expression of a strikingly high proportion of them significantly inhibited HIV-1 without causing cytotoxic effects. Five factors (APOL1, APOL6, CD164, TNFRSF10A, TNFRSF10D) suppressed infectious HIV-1 production in transfected 293T cells by >90% and six additional candidates (FCGR3A, CD3E, OAS1, GBP5, SPN, IFI16) achieved this when the virus was lacking intact accessory vpr, vpu and nef genes. Unexpectedly, over-expression of two factors (IL1A, SP110) significantly increased infectious HIV-1 production. Mechanistic studies suggest that the newly identified potential restriction factors act at different steps of the viral replication cycle, including proviral transcription and production of viral proteins. Finally, we confirmed that mRNA expression of most of these candidate restriction factors in primary CD4+ T cells is significantly increased by type I interferons. CONCLUSIONS: A limited number of human genes share multiple characteristics of genes encoding for known restriction factors. Most of them display anti-retroviral activity in transient transfection assays and are expressed in primary CD4+ T cells.

Evolutionary computing in search-based software engineering

This master’s thesis aims to study and represent from literature how evolutionary algorithms are used to solve different search and optimisation problems in the area of software engineering. Evolutionary algorithms are methods, which imitate the natural evolution process. An artificial evolution process evaluates fitness of each individual, which are solution candidates. The next population of candidate solutions is formed by using the good properties of the current population by applying different mutation and crossover operations. Different kinds of evolutionary algorithm applications related to software engineering were searched in the literature. Applications were classified and represented. Also the necessary basics about evolutionary algorithms were presented. It was concluded, that majority of evolutionary algorithm applications related to software engineering were about software design or testing. For example, there were applications about classifying software production data, project scheduling, static task scheduling related to parallel computing, allocating modules to subsystems, N-version programming, test data generation and generating an integration test order. Many applications were experimental testing rather than ready for real production use. There were also some Computer Aided Software Engineering tools based on evolutionary algorithms.

Repeatability, correlation and path analysis of physical and chemical characteristics of peach fruits

This study aimed to determine the number of measurements necessary to evaluate physical and chemical characteristics of peach fruits, study the relationships between them and their direct and indirect effects on the content of ascorbic acid and total carotenoids. The characteristics skin and pulp color, fruit weight, suture, equatorial and polar diameters, firmness, soluble solids (SS), titratable acidity (TA), SS/TA ratio, ascorbic acid and total carotenoids were evaluated in 39 cultivars of peach and 3 cultivars of nectarine from the orchard of the Universidade Federal de Viçosa. The repeatability coefficient was estimated by ANOVA and CPCOR. Phenotypic correlation coefficients (rf) were estimated and, after the multicollinearity diagnostics, they were unfolded to direct and indirect effects of the explanatory variables on the response variable using path analysis. There was agreement on the magnitude of repeatability coefficients obtained by the two methods; however, they varied among the 14 characteristics. The highest correlations were found between FW, SD, ED and PD. Seven fruits are sufficient to evaluate the physical and chemical characteristics of peach with a correlation coefficient of 90%. The characteristics considered in the path diagrams (b* skin, hº skin, b* pulp, hº pulp, ED, PD, FIR, SS, SS/AT and TC) are not the main determinants of the ascorbic acid. The yellow hue of the pulp (hº pulp) has the potential to be used in indirect selection for total carotenoids.

Evolutionary steps in the reproductive biology of Annonaceae

Flowers of Annonaceae are characterized by fleshy petals, many stamens with hard connective shields and numerous carpels with sessile stigmas often covered by sticky secretions. The petals of many representatives during anthesis form a closed pollination chamber. Protogynous dichogamy with strong scent emissions especially during the pistillate stage is a character of nearly all species. Scent emissions can be enhanced by thermogenesis. The prevailing reproductive system in the family seems to be self-compatibility. The basal genus Anaxagorea besides exhibiting several ancestral morphological characters has also many characters which reappear in other genera. Strong fruit-like scents consisting of fruit-esters and alcohols mainly attract small fruit-beetles (genus Colopterus, Nitidulidae) as pollinators, as well as several other beetles (Curculionidae, Chrysomelidae) and fruit-flies (Drosophilidae), which themselves gnaw on the thick petals or their larvae are petal or ovule predators. The flowers and the thick petals are thus a floral brood substrate for the visitors and the thick petals of Anaxagorea have to be interpreted as an antipredator structure. Another function of the closed thick petals is the production of heat by accumulated starch, which enhances scent emission and provides a warm shelter for the attracted beetles. Insight into floral characters and floral ecology of Anaxagorea, the sister group of the rest of the Annonaceae, is particularly important for understanding functional evolution and diversification of the family as a whole. As beetle pollination (cantharophily) is plesiomorphic in Anaxagorea and in Annonaceae, characters associated with beetle pollination appear imprinted in members of the whole family. Pollination by beetles (cantharophily) is the predominant mode of the majority of species worldwide. Examples are given of diurnal representatives (e.g., Guatteria, Duguetia, Annona) which function on the basis of fruit-imitating flowers attracting mainly fruit-inhabiting nitidulid beetles, as well as nocturnal species (e.g., large-flowered Annona and Duguetia species), which additionally to most of the diurnal species exhibit strong flower warming and provide very thick petal tissues for the voracious dynastid scarab beetles (Dynastinae, Scarabaeidae). Further examples will show that a few Annonaceae have adapted in their pollination also to thrips, flies, cockroaches and even bees. Although this non-beetle pollinated species have adapted in flower structure and scent compounds to their respective insects, they still retain some of the specialized cantharophilous characters of their ancestors.

Evolutionary patchwork of an insecticidal toxin shared between plant-associated pseudomonads and the insect pathogens Photorhabdus and Xenorhabdus.

BACKGROUND: Root-colonizing fluorescent pseudomonads are known for their excellent abilities to protect plants against soil-borne fungal pathogens. Some of these bacteria produce an insecticidal toxin (Fit) suggesting that they may exploit insect hosts as a secondary niche. However, the ecological relevance of insect toxicity and the mechanisms driving the evolution of toxin production remain puzzling. RESULTS: Screening a large collection of plant-associated pseudomonads for insecticidal activity and presence of the Fit toxin revealed that Fit is highly indicative of insecticidal activity and predicts that Pseudomonas protegens and P. chlororaphis are exclusive Fit producers. A comparative evolutionary analysis of Fit toxin-producing Pseudomonas including the insect-pathogenic bacteria Photorhabdus and Xenorhadus, which produce the Fit related Mcf toxin, showed that fit genes are part of a dynamic genomic region with substantial presence/absence polymorphism and local variation in GC base composition. The patchy distribution and phylogenetic incongruence of fit genes indicate that the Fit cluster evolved via horizontal transfer, followed by functional integration of vertically transmitted genes, generating a unique Pseudomonas-specific insect toxin cluster. CONCLUSIONS: Our findings suggest that multiple independent evolutionary events led to formation of at least three versions of the Mcf/Fit toxin highlighting the dynamic nature of insect toxin evolution.