Fragmentation of contaminant and endogenous DNA in ancient samples determined by shotgun sequencing; prospects for human palaeogenomics

Despite the successful retrieval of genomes from past remains, the prospects for human palaeogenomics remain unclear because of the difficulty of distinguishing contaminant from endogenous DNA sequences. Previous sequence data generated on high-throughput sequencing platforms indicate that fragmentation of ancient DNA sequences is a characteristic trait primarily arising due to depurination processes that create abasic sites leading to DNA breaks.

Evolution: the end of an ancient asexual scandal.

Bdelloid rotifers were believed to have persisted and diversified in the absence of sex. Two papers now show they exchange genes with each other, via horizontal gene transfers as known in bacteria and/or via other forms of non-canonical sex.

GENETIC ARCHITECTURE, EVOLUTION AND MAINTENANCE OF A COLOR CLINE AT A CONTINENTAL SCALE

On a geological time scale the conditions on earth are very variable and biological patterns (for example the distributions of species) are very dynamic. Understanding large scale patterns of variation observed today thus requires a deep understanding of the historical factors that drove their evolution. In this thesis, we reevaluated the evolution and maintenance of a continental color cline observed in the European barn owl (Tyto alba) using population genetic tools. The colour cline spans from south-est Europe where most individual have pure white underparts to north and east Europe where most individuals have rufous-brown underparts. Our results globally showed that the old scenario, stipulating that the color cline evolved by secondary contact of two color morphs (white and rufous) that evolved in allopatry during the last ice age has to be revised. We collected samples of about 700 barn owls from the Western Palearctic to establish the first population genetic data set for this species. Individuals were genotyped at 22 microsatellites markers, at one mitochondrial gene, and at a candidate color gene. The color of each individuals was assessed and their sex determined by molecular methods. We first showed that the genetic variation in Western Europe is very limited compared to the heritable color variation. We found no evidences of different glacial lineages, and showed that selection must be involved in the maintenance of the color cline (chapter 1). Using computer simulations, we demonstrated that the post-glacial colonization of Europe occurred from the Iberian Peninsula and that the color cline could not have evolved by neutral demographic processes during this colonization (chapter 2). Finally we reevaluated the whole history of the establishment of the Western Palearctic variation of the barn owl (chapter 3): This study showed that all Western European barn owls descend from white barn owls phenotypes from the Middle East that colonized the Iberian Peninsula via North-Africa. Following the end of the last ice age (20'000 years ago), these white barn owls colonized Western Europe and under selection a novel rufous phenotype evolved (during or after the colonization). An important part of the color variation could be explained by a single mutation in the melanocortin-1-receptor (MC1R) gene that appeared during or after the colonization. The colonization of Europe reached until Greece, where the rufous birds encountered white ones (which reached Greece from the Middle East over the Bosporus) in a secondary contact zone. Our analyses show that white and rufous barn owls in Greece interbreed only to a limited extent. This suggests that barn owls are at the verge of becoming two species in Greece and demonstrates that European barn owls represent an incipient ring species around the Mediterranean. The revisited history of the establishment of the European barn owl color cline makes this model system remarkable for several aspects. It is a very clear example of strong local adaptation that can be achieved despite high gene flow (strong color and MC1R differentiation despite almost no neutral genetic differentiation). It also offers a wonderful model system to study the interactions between colonization processes and selection processes which have, for now, been remarkably understudied despite their potentially ubiquitous importance. Finally it represents a very interesting case in the speciation continuum and appeals for further studying the amount of gene flow that occurs between the color morphs in Greece. -- Sur l'échelle des temps géologiques, les conditions sur terre sont très variables et les patrons biologiques (telle que la distribution des espèces) sont très dynamiques. Si l'on veut comprendre des patrons que l'on peut observer à large échelle aujourd'hui, il est nécessaire de d'abord comprendre les facteurs historiques qui ont gouverné leur établissement. Dans cette thèse, nous allons réévaluer, grâce à des outils modernes de génétique des populations, l'évolution et la maintenance d'un cline de couleur continental observé chez l'effraie des clochers européenne (Tyto alba). Globalement, nos résultats montrent que le scenario accepté jusqu'à maintenant, qui stipule que le cline de couleur a évolué à partir du contact secondaire de deux morphes de couleur (blanches et rousses) ayant évolué en allopatrie durant les dernières glaciations, est à revoir. Afin de constituer le premier jeu de données de génétique des populations pour cette espèce, nous avons récolté des échantillons d'environ 700 effraies de l'ouest Paléarctique. Nous avons génotypé tous les individus à 22 loci microsatellites, sur un gène mitochondrial et sur un autre gène participant au déterminisme de la couleur. Nous avons aussi mesuré la couleur de tous les individus et déterminé leur sexe génétiquement. Nous avons tout d'abord pu montrer que la variation génétique neutre est négligeable en comparaison avec la variation héritable de couleur, qu'il n'existe qu'une seule lignée européenne et que de la sélection doit être impliquée dans le maintien du cline de couleur (chapitre 1). Grâce à des simulations informatiques, nous avons démontré que l'ensemble de l'Europe de l'ouest a été recolonisé depuis la Péninsule Ibérique après les dernières glaciations et que le cline de couleur ne peut pas avoir évolué par des processus neutre durant cette colonisation (chapitre 2). Finalement, nous avons réévalué l'ensemble de l'histoire postglaciaire de l'espèce dans l'ouest Paléarctique (chapitre 3): l'ensemble des effraies du Paléarctique descendent d'effraie claire du Moyen-Orient qui ont colonisé la péninsule ibérique en passant par l'Afrique du nord. Après la fin de la dernière glaciation (il y a 20'000 ans), ces effraies claires ont colonisé l'Europe de l'ouest et ont évolués par sélection le phénotype roux (durant ou après la colonisation). Une part importante de la variation de couleur peut être expliquée par une mutation sur le gène MC1R qui est apparue durant ou juste après la colonisation. Cette vague de colonisation s'est poursuivie jusqu'en Grèce où ces effraies rousses ont rencontré dans une zone de contact secondaire des effraies claires (qui sont remontées en Grèce depuis le Moyen-Orient via le Bosphore). Nos analyses montrent que le flux de gènes entre effraies blanches et rousses est limité en Grèce, ce qui suggère qu'elles sont en passe de former deux espèces et ce qui montre que les effraies constituent un exemple naissant de spéciation en anneaux autour de la Méditerranée. L'histoire revisitée des effraies des clochers de l'ouest Paléarctique en fait un système modèle remarquable pour plusieurs aspects. C'est un exemple très claire de forte adaptation locale maintenue malgré un fort flux de gènes (différenciation forte de couleur et sur le gène MC1R malgré presque aucune structure neutre). Il offre également un très bon système pour étudier l'interaction entre colonisation et sélection, un thème ayant été remarquablement peu étudié malgré son importance. Et il offre finalement un cas très intéressant dans le « continuum de spéciation » et il serait très intéressant d'étudier plus en détail l'importance du flux de gènes entre les morphes de couleur en Grèce.

Ancient DNA analysis of 8000 B.C. near eastern farmers supports an early neolithic pioneer maritime colonization of Mainland Europe through Cyprus and the Aegean Islands

The genetic impact associated to the Neolithic spread in Europe has been widely debated over the last 20 years. Within this context, ancient DNA studies have provided a more reliable picture by directly analyzing the protagonist populations at different regions in Europe. However, the lack of available data from the original Near Eastern farmers has limited the achieved conclusions, preventing the formulation of continental models of Neolithic expansion. Here we address this issue by presenting mitochondrial DNA data of the original Near-Eastern Neolithic communities with the aim of providing the adequate background for the interpretation of Neolithic genetic data from European samples. Sixty-three skeletons from the Pre Pottery Neolithic B (PPNB) sites of Tell Halula, Tell Ramad and Dja'de El Mughara dating between 8,700-6,600 cal. B.C. were analyzed, and 15 validated mitochondrial DNA profiles were recovered. In order to estimate the demographic contribution of the first farmers to both Central European and Western Mediterranean Neolithic cultures, haplotype and haplogroup diversities in the PPNB sample were compared using phylogeographic and population genetic analyses to available ancient DNA data from human remains belonging to the Linearbandkeramik-Alföldi Vonaldiszes Kerámia and Cardial/Epicardial cultures. We also searched for possible signatures of the original Neolithic expansion over the modern Near Eastern and South European genetic pools, and tried to infer possible routes of expansion by comparing the obtained results to a database of 60 modern populations from both regions. Comparisons performed among the 3 ancient datasets allowed us to identify K and N-derived mitochondrial DNA haplogroups as potential markers of the Neolithic expansion, whose genetic signature would have reached both the Iberian coasts and the Central European plain. Moreover, the observed genetic affinities between the PPNB samples and the modern populations of Cyprus and Crete seem to suggest that the Neolithic was first introduced into Europe through pioneer seafaring colonization.

An architecture for decentralized service deployment

Peer-reviewed

Tan cerca, tan lejos: Aldo Rossi y el Grupo 2C. Arquitectura, ideología y disidencias en la Barcelona de los 70 = So close, so far : Aldo Rossi and the 2C Group. Architecture, ideology and dissents in the Barcelona of the 70s

The Catalan reception of the 1966 manifestos by Robert Venturi and Aldo Rossi marks the scenario of a breakup: while North America debates about the architectural shape as a linguistic structure, Italy dips its roots in the Modern Movement tradition as an origin for a new temporal and ideological architectural dimension. The first contacts between Rossi and Spain verify this search and allow the Italian to construct common itineraries with some architects from Barcelona. From these exchanges the 2C group will be born, taking part on typical vanguardist mechanisms: they will publish the magazine, 2C. The construction of the city (1972-1985), they will attend the XV Triennale di Milano in 1973 with the Torres Clavé Plan (1971) and the Aldo Rossi + 21 Spanish architects exhibition (1975) while he will organize the three issues of the Seminarios Internacionales de Arquitectura Contemporánea (S.I.AC.) which took place in Santiago, Sevilla and Barcelona between 1976 and 1980. In front of the unfolding of the firsts, the American contacts of Federico Correa, Oriol Bohigas, Lluís Domènech and the PER studio or the teaching work of Rafael Moneo from Barcelona since 1971, allow to draw replica itineraries with the foundation of the magazine Arquitecturas Bis (1974-1985), the organization of the meetings between international publications such as Lotus and Oppositions in Cadaqués (1975) and New York (1977), while stablishing exchanges with members of the Five Architects. Replicas that in 1976 conduct the initial ideological affirmations between Rossi and the 2C group towards irreconcilable distancing. Verifying the itinerary of the journey that the Italian leads from the Italian resistance towards the American backing down is part of the aim of this article

DAI-DEPUR: an integrated and distributed architecture for wastewater treatment plants supervision

The activated sludge process - the main biological technology usually applied towastewater treatment plants (WWTP) - directly depends on live beings (microorganisms), and therefore on unforeseen changes produced by them. It could be possible to get a good plant operation if the supervisory control system is able to react to the changes and deviations in the system and can take thenecessary actions to restore the system’s performance. These decisions are oftenbased both on physical, chemical, microbiological principles (suitable to bemodelled by conventional control algorithms) and on some knowledge (suitable to be modelled by knowledge-based systems). But one of the key problems in knowledge-based control systems design is the development of an architecture able to manage efficiently the different elements of the process (integrated architecture), to learn from previous cases (spec@c experimental knowledge) and to acquire the domain knowledge (general expert knowledge). These problems increase when the process belongs to an ill-structured domain and is composed of several complex operational units. Therefore, an integrated and distributed AIarchitecture seems to be a good choice. This paper proposes an integrated and distributed supervisory multi-level architecture for the supervision of WWTP, that overcomes some of the main troubles of classical control techniques and those of knowledge-based systems applied to real world systems

Architecture as a landscape

Postprint (published version)

IT architecture for category driven corporate procurement measurement

The purpose of this thesis was to investigate creating and improving category purchasing visibility for corporate procurement by utilizing financial information. This thesis was a part of the global category driven spend analysis project of Konecranes Plc. While creating general understanding for building category driven corporate spend visibility, the IT architecture and needed purchasing parameters for spend analysis were described. In the case part of the study three manufacturing plants of Konecranes Standard Lifting, Heavy Lifting and Services business areas were examined. This included investigating the operative IT system architecture and needed processes for building corporate spend visibility. The key findings of this study were the identification of the needed processes for gathering purchasing data elements while creating corporate spend visibility in fragmented source system environment. As an outcome of the study, roadmap presenting further development areas was introduced for Konecranes.

Truths ancient and modern

The paper presents a comparison of the theories of truth, and the solutions of the liar paradox, proposed by Thomas Bradwardine (c. 1290-1349), Jean Buridan (c. 1295-1358), and Alfred Tarski (1901-1983).

Enterprise architecture – the foundation for a strategy

This artcle describes work done with enterprise architecture of the National Digital Library. The National Digital Library is an initiative of the Finnish Ministry of Education and Culture. Its purpose is to promote the availability of the digital information resources of archives, libraries and museums, and to develope the long-term preservation of digital cultural heritage materials. Enterprise architectures are a tool for strategic management and planning. An enterprise architecture also functions as an aid at a more practical level. It shows, for example, what kind of changes and improvements may be made in one system without overlap or conflict with other systems.

Design and development of the architecture of an agricultural mobile robot

Parameters such as tolerance, scale and agility utilized in data sampling for using in Precision Agriculture required an expressive number of researches and development of techniques and instruments for automation. It is highlighted the employment of methodologies in remote sensing used in coupled to a Geographic Information System (GIS), adapted or developed for agricultural use. Aiming this, the application of Agricultural Mobile Robots is a strong tendency, mainly in the European Union, the USA and Japan. In Brazil, researches are necessary for the development of robotics platforms, serving as a basis for semi-autonomous and autonomous navigation systems. The aim of this work is to describe the project of an experimental platform for data acquisition in field for the study of the spatial variability and development of agricultural robotics technologies to operate in agricultural environments. The proposal is based on a systematization of scientific work to choose the design parameters utilized for the construction of the model. The kinematic study of the mechanical structure was made by the virtual prototyping process, based on modeling and simulating of the tension applied in frame, using the.

The Application of Enterprise Architecture Approach to Military Concept Development–Case Study

Abstract—Concept development and experimentation (CD&E) plays an important role in driving strategic transformation in the military community. Defence architecture frameworks, such as the NATO architecture framework, are considered excellent means to support CD&E. There is not much empirical evidence, however, to indicate how enterprise architectures (EA) are applied in the military community or particularly in military CD&E. Consequently, this paper describes and discusses empirical application of the EA approach in CD&E. The research method in the paper is a case study. Situational method engineering (SiME) is used as a framework to adapt the EA approach to the case project of the paper. The findings of the paper suggest that the EA is applicable to CD&E work, although all aspects of the original concept could not be expressed in the EA model of the case project. The results also show that the SiME method can support in applying the EA framework to the CD&E in the case project.