Advances in Sequence Analysis: Theory, Methods, Applications

This book gives a general view of sequence analysis, the statistical study of successions of states or events. It includes innovative contributions on life course studies, transitions into and out of employment, contemporaneous and historical careers, and political trajectories. The approach presented in this book is now central to the life-course perspective and the study of social processes more generally. This volume promotes the dialogue between approaches to sequence analysis that developed separately, within traditions contrasted in space and disciplines. It includes the latest developments in sequential concepts, coding, atypical datasets and time patterns, optimal matching and alternative algorithms, survey optimization, and visualization. Field studies include original sequential material related to parenting in 19th-century Belgium, higher education and work in Finland and Italy, family formation before and after German reunification, French Jews persecuted in occupied France, long-term trends in electoral participation, and regime democratization. Overall the book reassesses the classical uses of sequences and it promotes new ways of collecting, formatting, representing and processing them. The introduction provides basic sequential concepts and tools, as well as a history of the method. Chapters are presented in a way that is both accessible to the beginner and informative to the expert.

War Signals: A Theory of Trade, Trust and Conflict

We construct a dynamic theory of civil conflict hinging on inter-ethnic trust and trade. The model economy is inhabitated by two ethnic groups. Inter-ethnic trade requires imperfectly observed bilateral investments and one group has to form beliefs on the average propensity to trade of the other group. Since conflict disrupts trade, the onset of a conflict signals that the aggressor has a low propensity to trade. Agents observe the history of conflicts and update their beliefs over time, transmitting them to the next generation. The theory bears a set of testable predictions. First, war is a stochastic process whose frequency depends on the state of endogenous beliefs. Second, the probability of future conflicts increases after each conflict episode. Third, "accidental" conflicts that do not reflect economic fundamentals can lead to a permanent breakdown of trust, plunging a society into a vicious cycle of recurrent conflicts (a war trap). The incidence of conflict can be reduced by policies abating cultural barriers, fostering inter-ethnic trade and human capital, and shifting beliefs. Coercive peace policies such as peacekeeping forces or externally imposed regime changes have instead no persistent effects.

Fitness, inclusive fitness, and optimization

Individual-as-maximizing agent analogies result in a simple understanding of the functioning of the biological world. Identifying the conditions under which individuals can be regarded as fitness maximizing agents is thus of considerable interest to biologists. Here, we compare different concepts of fitness maximization, and discuss within a single framework the relationship between Hamilton's (J Theor Biol 7: 1-16, 1964) model of social interactions, Grafen's (J Evol Biol 20: 1243-1254, 2007a) formal Darwinism project, and the idea of evolutionary stable strategies. We distinguish cases where phenotypic effects are additive separable or not, the latter not being covered by Grafen's analysis. In both cases it is possible to define a maximand, in the form of an objective function phi(z), whose argument is the phenotype of an individual and whose derivative is proportional to Hamilton's inclusive fitness effect. However, this maximand can be identified with the expression for fecundity or fitness only in the case of additive separable phenotypic effects, making individual-as-maximizing agent analogies unattractive (although formally correct) under general situations of social interactions. We also feel that there is an inconsistency in Grafen's characterization of the solution of his maximization program by use of inclusive fitness arguments. His results are in conflict with those on evolutionary stable strategies obtained by applying inclusive fitness theory, and can be repaired only by changing the definition of the problem.

Evolutionary history of almond tree domestication in the Mediterranean basin.

Genetic diversity of contemporary domesticated species is shaped by both natural and human-driven processes. However, until now, little is known about how domestication has imprinted the variation of fruit tree species. In this study, we reconstruct the recent evolutionary history of the domesticated almond tree, Prunus dulcis, around the Mediterranean basin, using a combination of nuclear and chloroplast microsatellites [i.e. simple sequence repeat (SSRs)] to investigate patterns of genetic diversity. Whereas conservative chloroplast SSRs show a widespread haplotype and rare locally distributed variants, nuclear SSRs show a pattern of isolation by distance with clines of diversity from the East to the West of the Mediterranean basin, while Bayesian genetic clustering reveals a substantial longitudinal genetic structure. Both kinds of markers thus support a single domestication event, in the eastern side of the Mediterranean basin. In addition, model-based estimation of the timing of genetic divergence among those clusters is estimated sometime during the Holocene, a result that is compatible with human-mediated dispersal of almond tree out of its centre of origin. Still, the detection of region-specific alleles suggests that gene flow from relictual wild preglacial populations (in North Africa) or from wild counterparts (in the Near East) could account for a fraction of the diversity observed.

Evolutionary and Functional Analyses of the Interaction between the Myeloid Restriction Factor SAMHD1 and the Lentiviral Vpx Protein.

SAMHD1 has recently been identified as an HIV-1 restriction factor operating in myeloid cells. As a countermeasure, the Vpx accessory protein from HIV-2 and certain lineages of SIV have evolved to antagonize SAMHD1 by inducing its ubiquitin-proteasome-dependent degradation. Here, we show that SAMHD1 experienced strong positive selection episodes during primate evolution that occurred in the Catarrhini ancestral branch prior to the separation between hominoids (gibbons and great apes) and Old World monkeys. The identification of SAMHD1 residues under positive selection led to mapping the Vpx-interaction domain of SAMHD1 to its C-terminal region. Importantly, we found that while SAMHD1 restriction activity toward HIV-1 is evolutionarily maintained, antagonism of SAMHD1 by Vpx is species-specific. The distinct evolutionary signature of SAMHD1 sheds light on the development of its antiviral specificity.

From MuSIASEM theory to practice: report and reflections from field research in Kampot province, Cambodia

This document contains a report and summary of the field research activities in a rural community of rice farmers in Kampot province, Cambodia in 2011, which I conducted within the context of my PhD research at ICTA-UAB (Institute of Environmental Science and Technology, Autonomous University of Barcelona, Spain). The purpose of the field research was to gather data for a MuSIASEM analysis (Multi-Scale Integrated Analysis of Societal and Ecosystem Metabolism) at the village and household level, in order to analyze the multidimensional challenges that small farmers may face nowadays within the context of global rural change and declining access to land. While the literature on MuSIASEM offers a great variety of theoretical explanations and practical applications, there is little information available for students regarding the practical steps required for doing a MuSIASEM analysis at the local level. Within this context, this report offers not only a documentation of the field research design and data collection methods, but further provides a general overview on some organizational and preparative aspects, including some personal reflections, that one may face when preparing and conducting field research for MuSIASEM analysis. In summary, this document thus serves three objectives: (i) to assure methodological transparency for the future work, based on the collected data during field research, (ii) to share my personal experience on the preparative and practical steps required for field research and data collection for a MuSIASEM analysis at the local level, and (iii) to make available for the further interested reader some more detailed background information on the case study village.

Molecular evolutionary patterns in the Glomeromycota;

Abstract Arbuscular mycorrhizal fungi (AMF) form symbiosis with roots of approximately 80% of known land plants. These fungi play a key role in the ecology and adaptation of plants to various ecosystems.by increasing the plant resources for various nutrients. Despite their important ecological role, we still have poor understanding of their genetic structure and their molecular evolution. The work presented in this thesis aims to isolate and analyse AMF genes with various molecular techniques, in order to obtain new insights about their genetics, phylogeny and molecular evolution. Some AMF genes were shown through phylogenetic analyses to be more related with plants or mycoparasites than with other fungal organisms. These results led to the prediction that lateral gene transfers (LGT) occurred between AMF and plants during their long-term co-évolution. By phylogenetic and molecular analyses, in the chapter 2 I demonstrate that the hypothesis of LGT is most likely a consequence of analyses carried out on contaminant non AMF-DNA. In addition, various features characteristic of AMF genes have been determined, allowing researchers to scan their own sequence databases for potential non-AMF contaminants. Phylogenetic relationships of AMF with other fungi has been mostly analysed using molecular markers of ribosomal origin. In chapter 2 I successfully isolated gene encoding α- and ß-tubulins from several AMF genera. Consequently, phylogenetic analyses showed that AMF possess an unexpected relationship with ancestral aquatic fungi (chytrids). These results are consistent with the prediction stating that AMF may have played an important role in the colonisation of land by green plants through the establishment of a symbiosis and after the divergence of AMF from aquatic ancestors. In Chapter 4 I tried to isolate the entire AMF gene family encoding P-Type II ATPases, in order to determine their molecular evolution with the fungal kingdom. These genes were further analysed to detect the level of sequence polymorphism that is present within an AMF population. The results obtained show that mutational events previously thought as occurring only among divergent evolutionary lineages (gene duplications, indel mutations in coding regions) can occur within a single population of AMF. These results have far reaching consequences for our understanding of the genetics and ecology of AMF. Résumé Les champignons endomycorrhiziens arbusculaires (CEA) forment une symbiose racinaire avec environ 80% des plantes vasculaires connues. Ces champignons possèdent un rôle important dans l'écologie et l'adaptation des plantes au sein de différents écosystèmes en .augmentant leurs ressources en nutriments. Le travail présenté dans cette thèse se propose d'isoler et d'analyser certains gènes de CEA avec différentes techniques moléculaires à fin d'obtenir de pÌus amples informations concernant l'évolution moléculaire, la phylogénie et leur diversité génétique à diverses échelles taxonomiques. Certaines analyses phylogénétiques des CEA ont conduit à l'hypothèse que des transferts horizontaux de gènes (THG) ont pu avoir lieu durant leur longue co-évolution avec les plantes vasculaires. Dans le chapitre 2 de cette thèse nous démontrons par analyses moléculaire et phylogénétique que l'hypothèse de THG est une conséquence de contaminations à partir d'ADN de plante ou d'autres micro-organismes. De plus, de nombreuses caractéristiques moléculaires de CEA ont pu être déterminées, permettant la mise en place d'un plan à suivre lors de l'analyse de gènes de CEA dans les études futures. Les relations évolutives des. CEA avec d'autres champignons ont été analysées majoritairement à l'aide de marqueurs moléculaires d'origine ribosomiale. Dans les chapitres 2 et 3 j'ai isolé des gènes codant pour l'a- et la ß-tubuline chez différents genres, de CEA. Les analyses phylogénétiques ont démontré une parenté entre les CEA et des champignons aquatiques ancestraux (chytrides). Ces résultats sont en accord avec l'hypothèse selon laquelle les CEA ont probablement joué un rôle primordial dans l'établissement des plantes sur terre à travers une symbiose et suite à leur évolution à partir d'ancêtres vivant dans des milieux aquatiques: Dans le chapitre 4 j'ai isolé une entière famille de gènes chez les CEA codant des ATPases de la membrane plasmique, et étudié leur évolution moléculaire dans le règne des champignons. Ces mêmes gènes ont été analysés ultérieurement à fin de déterminer le degré de polymorphisme de séquence qui peut être présent au sein d'une population de CEA. Les résultats obtenus montrent que des évènements mutationnels considérés comme apparaissant exclusivement dans des lignées évolutives très divergentes (duplication de gènes, insertions/délétions dans des régions transcrites du génome) ont lieu sein d'une même population de CEA. Cette découverte a un impact important sur nos connaissances concernant la génétique des populations des CEA et leur écologie.

Time-Delayed Theory of the Neolithic Transition in Europe

The classical wave-of-advance model of the neolithic transition (i.e., the shift from hunter-gatherer to agricultural economies) is based on Fisher's reaction-diffusion equation. Here we present an extension of Einstein's approach to Fickian diffusion, incorporating reaction terms. On this basis we show that second-order terms in the reaction-diffusion equation, which have been neglected up to now, are not in fact negligible but can lead to important corrections. The resulting time-delayed model agrees quite well with observations

An Analysis of black-box optimization problems in reinsurance: evolutionary-based approaches

Black-box optimization problems (BBOP) are de ned as those optimization problems in which the objective function does not have an algebraic expression, but it is the output of a system (usually a computer program). This paper is focussed on BBOPs that arise in the eld of insurance, and more speci cally in reinsurance problems. In this area, the complexity of the models and assumptions considered to de ne the reinsurance rules and conditions produces hard black-box optimization problems, that must be solved in order to obtain the optimal output of the reinsurance. The application of traditional optimization approaches is not possible in BBOP, so new computational paradigms must be applied to solve these problems. In this paper we show the performance of two evolutionary-based techniques (Evolutionary Programming and Particle Swarm Optimization). We provide an analysis in three BBOP in reinsurance, where the evolutionary-based approaches exhibit an excellent behaviour, nding the optimal solution within a fraction of the computational cost used by inspection or enumeration methods.

Nuclear magnetic resonance chemical shifts with the statistical average of orbital-dependent model potentials in Kohn-Sham density functional theory

The performance of the SAOP potential for the calculation of NMR chemical shifts was evaluated. SAOP results show considerable improvement with respect to previous potentials, like VWN or BP86, at least for the carbon, nitrogen, oxygen, and fluorine chemical shifts. Furthermore, a few NMR calculations carried out on third period atoms (S, P, and Cl) improved when using the SAOP potential

Second-order Møller-Plesset perturbation theory without basis set superposition error : II : open-shell systems

The basis set superposition error-free second-order MØller-Plesset perturbation theory of intermolecular interactions was studied. The difficulties of the counterpoise (CP) correction in open-shell systems were also discussed. The calculations were performed by a program which was used for testing the new variants of the theory. It was shown that the CP correction for the diabatic surfaces should be preferred to the adiabatic ones

Exploring chromium (VI) dioxodihalides chemistry: is density functional theory the most suitable tool?

A comparative systematic study of the CrO2F2 compound has been performed using different conventional ab initio methodologies and density functional procedures. Two points have been analyzed: first, the accuracy of results yielded by each method under study, and second, the computational cost required to reach such results. Weighing up both aspects, density functional theory has been found to be more appropriate than the Hartree-Fock (HF) and the analyzed post-HF methods. Hence, the structural characterization and spectroscopic elucidation of the full CrO2X2 series (X=F,Cl,Br,I) has been done at this level of theory. Emphasis has been given to the unknown CrO2I2 species, and specially to the UV/visible spectra of all four compounds. Furthermore, a topological analysis in terms of charge density distributions has revealed why the valence shell electron pair repulsion model fails in predicting the molecular shape of such CrO2X2 complexes