Dissertations / Theses on the topic 'Evolution'

Species evolution can often be adequately described with a phylogenetic tree. Interestingly, this is the case also for the evolution of homologous genes; a gene in an ancestral species may – through gene duplication, gene loss, lateral gene transfer (LGT), and speciation events – give rise to a gene family distributed across contemporaneous species. However, molecular sequence evolution and genetic recombination make the history – the gene tree – non-trivial to reconstruct from present-day sequences. This history is of biological interest, e.g., for inferring potential functional equivalences of extant gene pairs. In this thesis, we present biologically sound probabilistic models for gene family evolution guided by species evolution – effectively yielding a gene-species tree reconciliation. Using Bayesian Markov-chain Monte Carlo (MCMC) inference techniques, we show that by taking advantage of the information provided by the species tree, our methods achieve more reliable gene tree estimates than traditional species tree-uninformed approaches. Specifically, we describe a comprehensive model that accounts for gene duplication, gene loss, a relaxed molecular clock, and sequence evolution, and we show that the method performs admirably on synthetic and biological data. Further-more, we present two expansions of the inference procedure, enabling it to pro-vide (i) refined gene tree estimates with timed duplications, and (ii) probabilistic orthology estimates – i.e., that the origin of a pair of extant genes is a speciation. Finally, we present a substantial development of the model to account also for LGT. A sophisticated algorithmic framework of dynamic programming and numerical methods for differential equations is used to resolve the computational hurdles that LGT brings about. We apply the method on two bacterial datasets where LGT is believed to be prominent, in order to estimate genome-wide LGT and duplication rates. We further show that traditional methods – in which gene trees are reconstructed and reconciled with the species tree in separate stages – are prone to yield inferior gene tree estimates that will overestimate the number of LGT events.
Arters evolution kan i många fall beskrivas med ett träd, vilket redan Darwins anteckningsböcker från HMS Beagle vittnar om. Detta gäller också homologa gener; en gen i en ancestral art kan – genom genduplikationer, genförluster, lateral gentransfer (LGT) och artbildningar – ge upphov till en genfamilj spridd över samtida arter. Att från sekvenser från nu levande arter rekonstruera genfamiljens framväxt – genträdet – är icke-trivialt på grund av genetisk rekombination och sekvensevolution. Genträdet är emellertid av biologiskt intresse, i synnerhet för att det möjliggör antaganden om funktionellt släktskap mellan nutida genpar. Denna avhandling behandlar biologiskt välgrundade sannolikhetsmodeller för genfamiljsevolution. Dessa modeller tar hjälp av artevolutionens starka inverkan på genfamiljens historia, och ger väsentligen upphov till en förlikning av genträd och artträd. Genom Bayesiansk inferens baserad på Markov-chain Monte Carlo (MCMC) visar vi att våra metoder presterar bättre genträdsskattningar än traditionella ansatser som inte tar artträdet i beaktning. Mer specifikt beskriver vi en modell som omfattar genduplikationer, genförluster, en relaxerad molekylär klocka, samt sekvensevolution, och visar att metoden ger högkvalitativa skattningar på både syntetiska och biologiska data. Vidare presenterar vi två utvidgningar av detta ramverk som möjliggör (i) genträdsskattningar med tidpunkter för duplikationer, samt (ii) probabilistiska ortologiskattningar – d.v.s. att två nutida gener härstammar från en artbildning. Slutligen presenterar vi en modell som inkluderar LGT utöver ovan nämnda mekanismer. De beräkningsmässiga svårigheter som LGT ger upphov till löses med ett intrikat ramverk av dynamisk programmering och numeriska metoder för differentialekvationer. Vi tillämpar metoden för att skatta LGT- och duplikationsraten hos två bakteriella dataset där LGT förmodas ha spelat en central roll. Vi visar också att traditionella metoder – där genträd skattas och förlikas med artträdet i separata steg – tenderar att ge sämre genträdsskattningar, och därmed överskatta antalet LGT-händelser.

At the time of the doctoral defense, the following papers were unpublished and had a status as follows: Paper 3: Manuscript. Paper 5: Manuscript.

Den primära frågan i projektet har varit: Hur relaterar en tillbyggnad till den historia som en huvudbyggnad bär på? Resultatet är att den mest lämpade delen har växt ut, men anpassats för att rymma de funktioner som saknas i huvudbyggnaden. Min ambition har varit att få tillbyggnaden att både kännas som en naturlig del av Nationalmuseum och dess historia, samtidigt som den är ett eget kapitel. Den är både kopierande och hänsynslös. Var byggnaden skulle växa ut kom primärt av vad omgivningen skulle må bäst av. Vilken typ av vägg skulle ge de bästa uterummen? Rummet mot vattnet kommer att bli fantastiskt och rummet på andra sidan blir en förlängning av den idag väl fungerande lilla parken, med samma förutsättningar som denna. En studie av nationalmuseums travéstruktur generarade tankar kring hur byggnaden skulle kunna växa om man följde samma system. Den nya fasaden är en avgjutning av ett sådant travéavstånd (4427 mm) som upprepas. I denna fasad görs nya håltagningar för fönster, samt en portal för att möjliggöra flöden in och ut ur parken.
The primary question of this project was: How does an add relate to what it´s added to?  The result is that the most suitable part has grown, but adapted to accommodate the functions lacking in the main building. My ambition has been to get the building to be felt as a natural part of the National Museum and its history, as well as being a separate chapter. It is both replicating and reckless. How the building would grow is based of what the environment would benefit from. What type of wall would provide the best outdoor rooms? The room facing the water will be amazing and the room on the other side becomes an extension of the well-functioning small park, with the same conditions as this. A study of the National Museum trot structure made me think about how the building could grow following the same system. The new facade is a concrete "replica" (4427 mm) that is repeated. In this facade new holes are made for windows, and a portal to allow flows in and out of the park.

"Model Driven Software Development" is a recent trend in development of software-intensive systems. In the Model Driven Software Development process, all knowledge pertaining to the software system to be built is represented in the form of models, in the right formalism(s) and at the right level of abstraction. At the highest level of abstraction, domain models, rather than generic models are used. Although the idea of developing the software system at a higher abstraction level is appealing, many fundamental questions remain unresolved. Many issues such as how to define the syntax and semantics of models, how to represent and store models and how to trace model evolution should be addressed properly. In this thesis, the focus is on model transformations and the open problems related to it. In particular, how to compare models, how to trace model evolution (with as a goal to undo and redo model changes), how to deal with meta-model evolution, and ultimately with semantics evolution are explored. For each issue, we analyze problems, and propose some solutions. We use small case studies to make issues more concrete. All case studies are developed in AToM3 (A Tool for Multi-formalism and Meta-Modeling), developed in the Modeling, Simulation and Design Lab (MSDL) in the School of Computer Science of McGill University.

This work is a revised edition of the former article "Evolution and Mutation Physics” by the same author. Some unclear formulations have been eliminated. New ideas and new calculations have been included, especially the important connection between successive entropy - changes and increasing DNA –length at slowly decreasing temperature-decrease of surroundings.

Terrestrial Evolution focuses on the destruction of the natural environment by manmade obstructions such as housing developments, strip malls, roads, telephone lines, and utility poles. Each of the paintings address one or more of these aspects of development and communicates ideas of detachment from this seemingly endless process of building. Color, surface texture, composition, and visual imagery were all carefully thought out and planned parts of a complicated process for the communication of ideas on this particular subject matter.My hometown of Carmel, Indiana has been experiencing massive environmental change over the past ten years. Large housing editions and strip malls have been built to accommodate the influx of people moving to this northern suburb of Indianapolis. Land is being sold, bought, zoned, and covered with quickly built homes and strip malls. Once this suburban sprawl has begun, will it stop? How much of the environmental damage it has contributed is reversible?Terrestrial Evolution represents a very personal and visual response to the contemporary state of Carmel's woodlands, wetlands, and wildlife, which are being sacrificed for manmade development.
Department of Art

In a process called 'base rivalry', irreparable mutations are provoked in the replication of monotonous sequences, which depend on the cell temperature, the cell viscosity and monotonous sequence length. This explains the very long monotonous sequences and very long DNAs that occur over long evolutionary epochs. Presumably, base rivalry (with tautomerism or too low cell viscosity) also provokes the formation of tumors and the emergence of dangerous viral mutations.

In a previous publication [1] the author described the base rivalry in monotonous DNA sequences and their effect on the DNA repair mechanism. As described in the article, during the monotonous sequence replication, energies appear theoretically to increase with a progressive replication fork up to the quantum mechanical energy level n=2 because of the base rivalry, and these rivalry energies affect the bond strength between the complementary bases. If there is a tautomeric base pair in the replication position where the rivalry energy is large enough, then in this position an irreparable mutation will occur, since the DNA repair mechanism cannot repair that error because too much binding energy. Thus a mutation (caused by base rivalry) can occur only on condition that a transition of a base pair into its tautomeric form is happened. It is remarkable that this transition likewise can occur by the effect of base rivalry energy. The base rivalry - energy which has an effect on a normal base pair provokes a tunnel process in its hydrogen bond, and produces the tautomeric form. After whose replication a different, irreparable base pair develops from the tautomeric base pair, when the rivalry - energy leads into a very strong hydrogen bond. This happens, however, by chance and in the following we will compute the probabilities of such accidental events. The result of these calculations is the equation (32) which could be useful for the theory of evolution and besides for clearing up of virus mutations. It is remarkable that follows from these calculations that the length of DNA increases itself in the course of evolution (section 7).

Current toxic interactions between the systems of man, nature and machine in the diamond mining town of Cullinan are volatile and cannot be sustained. When the mine and the main economic system regress, how can the remaining dependent cultural and biophysical systems be sustained and what can Cullinan become after the demise of the machine? Impending deindustrialisation could mean that Cullinan will be silenced and its associated meaning and memory lost. The architecture of the Age of the Machine represents contemporary interactions between the biotic and bionic where industrial buildings, and the introverted town, reflect the dominance of the machine over nature. The objective of this dissertation is to set a precedent for place-responsive regenerative architecture within a post-mining context that is inspired by local nature and culture. An architecture that expresses a new co-evolving mutualistic relationship between the existing town and landscape (cultural and natural systems) will be considered. Programme: A local food hub The intention of this dissertation is to address the future shift of human communities and economic activities back to the alignment and synergy with life processes. A bionic evolution from the Age of the Machine, to the Age of Life is explored.
Dissertation (MArch(Prof))--University of Pretoria, 2014.
Architecture
MArch(Prof)
Unrestricted

The emerging science of religious evolution (the evolution of traits that distinguish religious individuals from non-religious ones) and the emerging science of cultural evolution have recently entered into a reciprocal relationship, each having something to offer the other. The theory of cultural evolution offers the field of religious evolution a powerful set of models and concepts for explaining important traits and facts that are not explained by genetic evolution. But theories of cultural evolution face their own important challenges, and theorists within the field do not agree about how cultural evolution itself should be explained, and focusing on religion makes some abstract and difficult questions in this domain more concrete and tractable. Thus, the field of religious evolution also offers the theory of cultural evolution a way of clarifying its commitments, and of demonstrating its ability to respond to important challenges. This dissertation addresses both sides of this reciprocal relationship, taking advantage of the opportunity to develop at the same time both a better understanding of the nature of religion and a better understanding of the nature of cultural phenomena in general. One goal, then, is to address philosophical, foundational questions about what religion is from within the scientific worldview. I address this general goal in two independent articles, which comprise Chapters 2 and 3. In the fourth chapter, however, I pursue a different goal, extracting from the study of religion a methodological lesson that applies for the study of cultural phenomena in general. Twenty years ago adaptationist theories in psychology appealed almost exclusively to genetic selection at the individual level, but developments since then have caused a growing number of scientists to suspect that this is too narrow a view of human evolution. I argue that the study of religion confirms these suspicions. Thus, by examining religion from the evolutionary perspective, we learn not just about the nature of religion, but also about the nature of the evolutionary perspective itself.
Arts, Faculty of
Philosophy, Department of
Graduate

While an interest in the origin of human beings may be a cultural universal, there are various views and beliefs about how this event took place. In Canada, a recent (2010) Angus Reid survey revealed that only 61% of Canadians accepted that humans evolved over millions of years; 39% of the population either believed in creationism or did not accept evolution as a scientific fact. These statistics suggest that human evolution education is a topic that needs to be addressed.This thesis investigates the role of museums in public education about human evolution. Prior to this study, the number of Canadian museums with exhibits about this topic was unknown. Sixteen Canadian museums participated in this study, and the results demonstrated that only two had permanent exhibits on human evolution, and one creationist museum presented a biblically-based account of human origins. Here, it is argued that more of Canada's museums should consider incorporating human evolution education into their mandates.
Bien que l'intérêt envers les origines de l'Homme soit un universel culturel, plusieurs points de vue et croyances divergent au sujet du commencement de l'humanité. Au Canada, un récent sondage (2010) de la firme Angus Reid a révélé que seulement 61% des Canadiens acceptent le fait que l'humain ait évolué sur une période de millions d'années, et 39% croient plutôt au créationnisme ou ne considèrent pas l'évolution comme un fait scientifique. Ces statistiques suggèrent que l'évolution de l'homme soit un sujet qui doit être abordé. Cette thèse étudiera le rôle que jouent les musées dans l'éducation de la population à propos de l'évolution de l'homme. Le nombre de musées canadiens présentant une exposition sur le sujet n'était pas encore connu avant la réalisation de cette étude. Selon les résultats de celle-ci, seuls deux des seize musées canadiens qui y ont pris part consacraient une exposition permanente à l'évolution de l'homme, et un autre musée, créationniste, proposait une version biblique des origines de l'homme. Cette thèse démontre que davantage de musées canadiens devraient envisager d'avoir pour objectif l'éducation de la population sur l'évolution humaine.

Internationella studier visar att elever i alla stadier har stora brister i evolutionskunskap ochhar svårigheter att lära sig evolution. Denna uppsats ger en översikt överevolutionsundervisningen i den svenska skolan och försöker klarlägga varför evolution är såsvårt att förstå och lära ut.Styrdokumenten för den svenska skolan betonar inte övergripande evolutionskunskaper,och i de flesta läroböcker har evolution litet utrymme. Svenska elevers kunskaper i evolutionär svaga, och även många svenska biologilärare verkar ha bristande förståelse.Evolutionsprocessen är svår att förstå, den kräver ett helt annat tänkande änvardagstänkandet. De flesta elever tillämpar vardagstänkande i sina förklaringar av evolution,och har därmed ingen verklig förståelse av processen. Denna insikt måste finnas med iutformningen av evolutionsundervisningen, och läraren måste få eleverna att tänka på ett nyttsätt för att de verkligen skall förstå evolution.

Evolution of Piperales – matK gene and trnK intron sequence data reveal lineage specific resolution contrast. Piperales are one of the largest basal angiosperm orders with a nearly worldwide distribution. The order includes three species rich genera, Piper (ca. 1,000 species), Peperomia (ca. 1,500-1,700 species), and Aristolochia s. l. (ca. 500 species). Sequences of the matK gene and the non-coding trnK group II intron are analysed for a dense set of 105 taxa representing all families (except Hydnoraceae) and all generic segregates (except Euglypha within Aristolochiaceae) of Piperales. A large number of highly informative indels are found in the Piperales trnK/matK dataset. Within a narrow region approximately 500 nt downstream in the matK coding region (CDS), a length variable simple sequence repeat (SSR) expansion segment occurs, in which insertions and deletions have led to short frame-shifts. These are corrected shortly afterwards, resulting in a maximum of 6 amino acids being affected. Furthermore, additional non-functional matK copies were found in Zippelia begoniifolia, which can easily be discriminated from the functional open reading frame (ORF). The trnK/matK sequence data fully resolve relationships within Peperomia, whereas they are not effective within Piper. The resolution contrast is correlated with the rate heterogenity between those lineages. Parsimony, Bayesian and likelihood analyses result in virtually the same topology, and converge on the monophyly of Piperaceae and Saururaceae. Lactoris gains high support as sister to Aristolochiaceae subf. Aristolochioideae, but the different tree inference methods yield conflicting results with respect to the relationships of subfam. Asaroideae. In Piperaceae, a clade formed by the monotypic genus Zippelia and the small genus Manekia (=Sarcorhachis) is sister to the two large genera Piper and Peperomia. Systematics of pipevines – Combining morphological and fast-evolving molecular characters to investigate the relationships within subfamily Aristolochioideae (Aristolochiaceae) A combined phylogenetic analysis of the Aristolochioideae was conducted based on 72 morphological characters and molecular datasets (matK gene, trnK intron, trnL intron, trnL-trnF spacer). The analysis sampled 33 species as the ingroup, including two species of Thottea and 30 species of Aristolochia and the monotypic genus Euglypha, which represent all the infrageneric taxa formally described; Saruma henryi and Asarum caudatum were used as the outgroup. The results corroborate a sister-group relationship between Thottea and Aristolochia, and the paraphyly of Aristolochia with respect to Euglypha that consequently should be included into Aristolochia. Two of the three subgenera within Aristolochia (Isotrema and Pararistolochia) are shown to be monophyletic, whereas the signal obtained from the different datasets about the relationships within subg. Aristolochia is low and conflicting, resulting in collapsed or unsupported branches. The relationship between the New World and the Old World species of subgenus Aristolochia is conflictive because morphological data support these two groups as monophyletic, whereas molecular data show the monophyletic Old World species of Aristolochia nested within the New World species. A sister group relationship is proposed between A. lindneri and pentandrous species, which suggests that a group of five species from central and southern South America (including A. lindneri) could be monophyletic and sister to Aristolochia subsection Pentandrae, a monophyletic taxon consisting of about 35 species from southern USA, Mesoamerica, and the West Indies. Colonisation, phylogeography and evolution of endemism in Mediterranean Aristolochia (Aristolochiaceae). This study provides evidence for a multiple colonisation of the western Old World from Asian ancestors within Aristolochia section Diplolobus (subsection Aristolochia and Podanthemum). Within subsection Podanthemum it is assumed, that the colonisation of the African continent happened at least two times independently. In contrast, for subsection Aristolochia, a rapid morphological radiation in the Near East (or close to this area) with subsequent star like colonisation of the different current distribution areas, which is not paralleled on the molecular level, appears to be more likely. Phylogenetic tree reconstruction is unsupported for these clades, but most clades are highly supported as monophyletic. Interestingly the Mediterranean and temperate Eurasian species, which are morphologically distinct (A. pistolochia, A. clematitis) are not clustering within the main clades, but are independent lineages. Analogue, A. rigida a species from Somalia is well-supported sister to the subsection Aristolochia. Within subsection Podanthemum the colonisation event from an Asian ancestor is clearly traceable, whereas in subsection Aristolochia the path is not traceable, since the ancestors are extinct or not present in the connecting areas. Within the Mediterranean, Near East and Caucasian species of subsection Aristolochia two morphologically and biogeographically well supported groups can be identified: the Near East/Caucasian species and the West Mediterranean species. The previous groupings for the latter, based on morphological characters, could be substantiated only partly by our results. This study provides the first phylogeny of all West Mediterranean species. In addition an independent complex is established including some micro endemic species. The phylogenetic results are discussed with respect to biogeography, and morphology, to give a first insight into the radiation and colonisation of the genus Aristolochia in the Mediterranean region. Universal primers for a large cryptically simple cpDNA microsatellite region in Aristolochia. We provide a new and valuable marker to study species relationships and population genetics in order to trace evolutionary, ecological, and conservational aspects in the genus Aristolochia. Universal primers for amplification and subsequent sequencing of a chloroplast microsatellite locus inside the trnK intron are presented. Utility of the primers has been tested in 32 species representing all clades of Aristolochia, including population studies within the A. pallida complex, A. clusii and A. rotunda. The microsatellite region is characterized as a (AnTm)k repeat of 22–438 bp containing a combination of different repeats arranged as ‘cryptically simple’. Trapped! Pollination of Aristolochia pallida Willd. in the Mediterranean A first study of the pollination biology of a Mediterranean Aristolochia species in its natural habitat is presented. 183 flowers of Aristolochia pallida were investigated, which in total contained 73 arthropods, dominated by two groups of Diptera, Sciaridae (37%) and Phoridae (19%). However, only Phoridae are regarded as potential pollinators, since pollen has been found exclusively on the body surfaces of these insects. All Phoridae belong to the genus Megaselia and are recognised as four undescribed species. The measurements of flower and insect dimensions suggest that size is an important constrain for successful pollination: 1) the insects must have a definitive size for being able to enter the flower and 2) must be able to get in touch with the pollen. Only very few insect groups found in Aristolochia pallida fulfil these size requirements. However, size alone is not a sufficient constrain as too many fly species of the same size might be trapped but not function as pollinators. Instead, specific attraction is required as otherwise pollen is lost. Since all trapped Phoridae are males, a chemical attraction (pheromones) is proposed as an additional constrain. Since A. pallida flowers are protogynous, the record of Megaselia loaded with pollen found in a flower during its female stage proves that this insect must have been visited at least one different flower during its male stage before. Further on, this observation provides strong evidence that the flowers are cross-pollinated. All these factors indicate a highly specialised pollination of Aristolochia pallida by Megaselia species.

Evolution of Piperales – matK gene and trnK intron sequence data reveal lineage specific resolution contrast. Piperales are one of the largest basal angiosperm orders with a nearly worldwide distribution. The order includes three species rich genera, Piper (ca. 1,000 species), Peperomia (ca. 1,500-1,700 species), and Aristolochia s. l. (ca. 500 species). Sequences of the matK gene and the non-coding trnK group II intron are analysed for a dense set of 105 taxa representing all families (except Hydnoraceae) and all generic segregates (except Euglypha within Aristolochiaceae) of Piperales. A large number of highly informative indels are found in the Piperales trnK/matK dataset. Within a narrow region approximately 500 nt downstream in the matK coding region (CDS), a length variable simple sequence repeat (SSR) expansion segment occurs, in which insertions and deletions have led to short frame-shifts. These are corrected shortly afterwards, resulting in a maximum of 6 amino acids being affected. Furthermore, additional non-functional matK copies were found in Zippelia begoniifolia, which can easily be discriminated from the functional open reading frame (ORF). The trnK/matK sequence data fully resolve relationships within Peperomia, whereas they are not effective within Piper. The resolution contrast is correlated with the rate heterogenity between those lineages. Parsimony, Bayesian and likelihood analyses result in virtually the same topology, and converge on the monophyly of Piperaceae and Saururaceae. Lactoris gains high support as sister to Aristolochiaceae subf. Aristolochioideae, but the different tree inference methods yield conflicting results with respect to the relationships of subfam. Asaroideae. In Piperaceae, a clade formed by the monotypic genus Zippelia and the small genus Manekia (=Sarcorhachis) is sister to the two large genera Piper and Peperomia. Systematics of pipevines – Combining morphological and fast-evolving molecular characters to investigate the relationships within subfamily Aristolochioideae (Aristolochiaceae) A combined phylogenetic analysis of the Aristolochioideae was conducted based on 72 morphological characters and molecular datasets (matK gene, trnK intron, trnL intron, trnL-trnF spacer). The analysis sampled 33 species as the ingroup, including two species of Thottea and 30 species of Aristolochia and the monotypic genus Euglypha, which represent all the infrageneric taxa formally described; Saruma henryi and Asarum caudatum were used as the outgroup. The results corroborate a sister-group relationship between Thottea and Aristolochia, and the paraphyly of Aristolochia with respect to Euglypha that consequently should be included into Aristolochia. Two of the three subgenera within Aristolochia (Isotrema and Pararistolochia) are shown to be monophyletic, whereas the signal obtained from the different datasets about the relationships within subg. Aristolochia is low and conflicting, resulting in collapsed or unsupported branches. The relationship between the New World and the Old World species of subgenus Aristolochia is conflictive because morphological data support these two groups as monophyletic, whereas molecular data show the monophyletic Old World species of Aristolochia nested within the New World species. A sister group relationship is proposed between A. lindneri and pentandrous species, which suggests that a group of five species from central and southern South America (including A. lindneri) could be monophyletic and sister to Aristolochia subsection Pentandrae, a monophyletic taxon consisting of about 35 species from southern USA, Mesoamerica, and the West Indies. Colonisation, phylogeography and evolution of endemism in Mediterranean Aristolochia (Aristolochiaceae). This study provides evidence for a multiple colonisation of the western Old World from Asian ancestors within Aristolochia section Diplolobus (subsection Aristolochia and Podanthemum). Within subsection Podanthemum it is assumed, that the colonisation of the African continent happened at least two times independently. In contrast, for subsection Aristolochia, a rapid morphological radiation in the Near East (or close to this area) with subsequent star like colonisation of the different current distribution areas, which is not paralleled on the molecular level, appears to be more likely. Phylogenetic tree reconstruction is unsupported for these clades, but most clades are highly supported as monophyletic. Interestingly the Mediterranean and temperate Eurasian species, which are morphologically distinct (A. pistolochia, A. clematitis) are not clustering within the main clades, but are independent lineages. Analogue, A. rigida a species from Somalia is well-supported sister to the subsection Aristolochia. Within subsection Podanthemum the colonisation event from an Asian ancestor is clearly traceable, whereas in subsection Aristolochia the path is not traceable, since the ancestors are extinct or not present in the connecting areas. Within the Mediterranean, Near East and Caucasian species of subsection Aristolochia two morphologically and biogeographically well supported groups can be identified: the Near East/Caucasian species and the West Mediterranean species. The previous groupings for the latter, based on morphological characters, could be substantiated only partly by our results. This study provides the first phylogeny of all West Mediterranean species. In addition an independent complex is established including some micro endemic species. The phylogenetic results are discussed with respect to biogeography, and morphology, to give a first insight into the radiation and colonisation of the genus Aristolochia in the Mediterranean region. Universal primers for a large cryptically simple cpDNA microsatellite region in Aristolochia. We provide a new and valuable marker to study species relationships and population genetics in order to trace evolutionary, ecological, and conservational aspects in the genus Aristolochia. Universal primers for amplification and subsequent sequencing of a chloroplast microsatellite locus inside the trnK intron are presented. Utility of the primers has been tested in 32 species representing all clades of Aristolochia, including population studies within the A. pallida complex, A. clusii and A. rotunda. The microsatellite region is characterized as a (AnTm)k repeat of 22–438 bp containing a combination of different repeats arranged as ‘cryptically simple’. Trapped! Pollination of Aristolochia pallida Willd. in the Mediterranean A first study of the pollination biology of a Mediterranean Aristolochia species in its natural habitat is presented. 183 flowers of Aristolochia pallida were investigated, which in total contained 73 arthropods, dominated by two groups of Diptera, Sciaridae (37%) and Phoridae (19%). However, only Phoridae are regarded as potential pollinators, since pollen has been found exclusively on the body surfaces of these insects. All Phoridae belong to the genus Megaselia and are recognised as four undescribed species. The measurements of flower and insect dimensions suggest that size is an important constrain for successful pollination: 1) the insects must have a definitive size for being able to enter the flower and 2) must be able to get in touch with the pollen. Only very few insect groups found in Aristolochia pallida fulfil these size requirements. However, size alone is not a sufficient constrain as too many fly species of the same size might be trapped but not function as pollinators. Instead, specific attraction is required as otherwise pollen is lost. Since all trapped Phoridae are males, a chemical attraction (pheromones) is proposed as an additional constrain. Since A. pallida flowers are protogynous, the record of Megaselia loaded with pollen found in a flower during its female stage proves that this insect must have been visited at least one different flower during its male stage before. Further on, this observation provides strong evidence that the flowers are cross-pollinated. All these factors indicate a highly specialised pollination of Aristolochia pallida by Megaselia species.

Due to improved computing power, connectivity and interaction capability of mobile devices, their popularity and general acceptance in mass population has increased in recent years. Mobile applications are software systems running on mobile hand-held devices such as smart phones and tablets. Due to obvious differences in mobile applications, the evolution studies on them is of high importance. The primary objective is to study and compare the mobile applications evolution with the Lehman's laws of software evolution. Next is to identify and report how the software development team size influences mobile applications evolution. The study is conducted on 9 different open source mobile applications among which 5 were developed by single core developer and 4 were developed by multiple core developers. The selected projects' code repository is cloned into local copy and a number of tools are used on those repositories for extraction of relevant metrics from the artifacts. The Lehman laws are tested graphically, analytically and in some cases statistically. Six of the Lehman's laws are tested for validation in sample mobile applications. Among the six laws, I-Continuing Change is found supportive, III-Self Regulation and VI-Continuing Growth are found partial supportive in mobile applications. The II-Increasing complexity and V-Conservation of Familiarity are inconclusive. The IV-Conservation of Organizational Stability is not supportive in our sample mobile applications. Moreover, mobile applications are developed by a single or a few developers. Small team mobile projects have less time between releases compared to large team projects. The growth pattern of mobile applications is different than that predicted by Lehman laws.

Grammatical Evolution (GE) is a method of utilising a general purpose evolutionary algorithm to ???evolve??? programs written in an arbitrary BNF grammar. This thesis extends GE as follows: GE as an extension of Genetic Programming (GP) A novel method of automatically extracting information from the grammar is introduced. This additional information allows the use of GP style crossover which in turn allows GE to perform identically to a strongly typed GP system as well as a non-typed (or canonical) GP system. Two test problems are presented one which is more easily solved by the GP style crossover and one which favours the tradition GE ???Ripple Crossover???. With this new crossover operator GE can now emulate GP (as well as retaining its own unique features) and can therefore now be seen as an extension of GP. Dynamically Defined Functions An extension to the BNF grammar is presented which allows the use of dynamically defined functions (DDFs). DDFs provide an alternative to the traditional approach of Automatically Defined Functions (ADFs) but have the advantage that the number of functions and their parameters do not need to be specified by the user in advance. In addition DDFs allow the architecture of individuals to change dynamically throughout the course of the run without requiring the introduction of any new form of operator. Experimental results are presented confirming the effectiveness of DDFs. Self-Selecting (or variable) crossover. A self-selecting operator is introduced which allows the system to determine, during the course of the run, which crossover operator to apply; this is tested over several problem domains and (especially where small populations are used) is shown to be effective in aiding the system to overcome local optima. Spatial Co-Evolution in Age Layered Planes (SCALP) A method of combining Hornby???s ALPS metaheuristic and a spatial co-evolution system used by Mitchell is presented; the new SCALP system is tested over three problem domains of increasing difficulty and performs extremely well in each of them.

The current dissertation looks at the molecular evolution of protein-coding genes in the flowering plant Arabidopsis thaliana and within two RNA viruses, humanimmunodeficiency virus (HIV) and Astroviridae. We analyzed members of the receptor-like kinase (RLK) gene family in Arabidopsis thaliana for positive selection. Likelihood analysis found evidence for positive selection in 12 of the 52 RLK family sequences groups. These 12 groups represent 97 of the 403 sequences analyzed. The majority of genes in groups subject to positive selection have not been functionally characterized, but sites under selection are predominantly located in the extracellular region. In HIV we use Akaike Information Criteria (AIC) based model averaging for models of nucleotide evolution to examine estimates of genetic distance and the ratio of transition/transversion (ts/tv). AIC weighted estimates of distance and ts/tv were shown to be robust relative to model assumptions. AIC weighted estimates of the ts/tv ratio in simulated HIV sequences generally had less variance than similar estimates made by selecting the single best scoring AIC model. Astroviruses are a leading cause of viral gastroenteritis in infants worldwide and little is known about the mechanisms of astrovirus-induced diarrhea or the virally encoded components responsible for disease. We report the genomic sequence of nine novel TAstV-2 isolates. Nucleotide and amino acid identities for the isolates were generally > 90% conserved. Phylogenies constructed using genomic RNA and the individual open reading frames (ORF) provide evidence for recombination and indicate differences in substitution rates between non-structural and structural genes. Analysis of the viral capsid genes using codon models of evolution indicate site-specific positive selection in both turkey and human astroviruses.

This work is concerned with an evolution inclusion of a form, in a triple of spaces \V -> H -> V*", where U is a continuous non-decreasing process, M is a locally square-integrable martingale and the operators A (multi-valued) and B satisfy some monotonicity condition, a coercivity condition and a condition on growth in u. An existence and uniqueness theorem is proved for the solutions, using semi-implicit time-discretization schemes. Examples include evolution equations and inclusions driven by square integrable Levy martingales.

Evolutionary algorithms are a competent nature-inspired approach for complex computational problem solving. One recent development is Grammatical Evolution, a grammar-based evolutionary algorithm which uses genotypes of variable length binary strings and a unique genotype-to-phenotype mapping process based on a BNF grammar definition describing the output language that is able to create valid individuals of an arbitrary structure or programming language. This study surveys Grammatical Evolution, identifies its most important issues, investigates the competence of the algorithm in a series of agent-oriented benchmark problems, provides experimental results which cast doubt about its effectiveness and efficiency on problems involving the evolution of the behaviour of an agent, and presents Constituent Grammatical Evolution (CGE), a new innovative evolutionary automatic programming algorithm. CGE extends Grammatical Evolution by incorporating the concepts of constituent genes and conditional behaviour-switching. It builds from elementary and more complex building blocks a control program which dictates the behaviour of an agent and it is applicable to the class of problems where the subject of search is the behaviour of an agent in a given environment. Experimental results show that the new algorithm significantly improves Grammatical Evolution in all problems it has been benchmarked. Additionally, the investigation undertaken in this work required the development of a series of tools which are presented and described in detail. These tools provide an extendable open source and publicly available framework for experimentation in the area of evolutionary algorithms and their application in agent-oriented environments and complex systems.

Background: A large number of life science ontologies has been developed to support different application scenarios such as gene annotation or functional analysis. The continuous accumulation of new insights and knowledge affects specific portions in ontologies and thus leads to their adaptation. Therefore, it is valuable to study which ontology parts have been extensively modified or remained unchanged. Users can monitor the evolution of an ontology to improve its further development or apply the knowledge in their applications.

Many software systems eventually undergo changes to their basic architectural structure. Such changes may be prompted by new feature requests, new quality attribute requirements, changing technology, or other reasons. Whatever the causes, architecture evolution is commonplace in real-world software projects. Today’s software architects, however, have few techniques to help them plan such evolution. In particular, they have little assistance in planning alternatives, making trade-offs among these different alternatives, or applying best practices for particular domains. To address this, we have developed an approach for assisting architects in planning and reasoning about software architecture evolution. Our approach is based on modeling and analyzing potential evolution paths that represent different ways of evolving the system. We represent an evolution path as a sequence of transitional architectural states leading from the initial architecture to the target architecture, along with evolution operators that characterize the transitions among these states. We support analysis of evolution paths through the definition and application of constraints that express rules governing the evolution of the systemand evaluation functions that assess path quality. Finally, a set of these modeling elements may be grouped together into an evolution style that encapsulates a body of knowledge relevant to a particular domain of architecture evolution. We evaluate this approach in three ways. First, we evaluate its applicability to real-world architecture evolution projects. This is accomplished through case studies of two very different software organizations. Second, we undertake a formal evaluation of the computational complexity of verifying evolution constraints. Finally, we evaluate the implementability of the approach based on our experiences developing prototype tools for software architecture evolution.

This thesis explores the mechanisms underlying motion vision in the praying mantis (Sphodromantis lineola) and how this visual predator perceives camouflaged prey. By recording the mantis optomotor response to wide-field motion I was able to define the mantis Dmax, the point where a pattern is displaced by such a distance that coherent motion is no longer perceived. This allowed me to investigate the spatial characteristics of the insect wide field motion processing pathway. The insect Dmax was found to be very similar to that observed in humans which suggests similar underlying motion processing mechanisms; whereby low spatial frequency local motion is being pooled over a larger visual area compared to higher spatial frequency motion. By recording the mantis tracking response to computer generated targets, I was able to investigate whether there are any benefits of background matching when prey are moving and whether pattern influences the predatory response of the mantis towards prey. I found that only prey with large pattern elements benefit from background matching during movement; and above all prey which remain un-patterned but match the mean luminance of the background receive the greatest survival advantage. Additionally, I examined the effects of background motion on the tracking response of the mantis towards moving prey. By using a computer generated target as prey, I investigated the benefits associated with matching background motion as a protective strategy to reduce the risk of detection by predators. I found the mantis was able to successfully track a moving target in the presence of background My results suggests that although there are no overall benefits for prey to match background motion, it is costly to move out of phase with the background motion. Finally, I examined the contrast sensitivity of the mantis wide-field and small target motion detection pathways. Using the mantis tracking response to small targets and the optomotor response to wide-field motion; I measured the distinct temporal and spatial signatures of each pathway. I found the mantis wide-field and small target movement detecting pathways are each tuned to a different set of spatial and temporal frequencies. The wide-field motion detecting pathway has a high sensitivity to a broad range of spatio-temporal frequencies making it sensitive to a broad range of velocities; whereas the small-target motion-detection pathway has a high sensitivity to a narrow set of spatio-temporal combinations with optimal sensitivity to targets with a low spatial frequencymotion.

Evolución dirigida de proteínas: La evolución dirigida es una técnica que nos permite explorar funciones enzimáticas que no son requeridas en el ambiente natural. Esta técnica, simula procesos genéticos naturales y de selección. Esta estrategia se utiliza cuando un diseño racional es muy complicado. Consiste en una repetición de ciclos de diversificación y selección que llevan a la acumulación de mutaciones benéficas. Aquí se presenta dos ejemplos de evolución dirigida con los cuales se ha trabajado directamente: la ADN polimerasa del organismo  Thermus aquaticus usada comúnmente en PCR, y la proteína LacI que regula la expresión de genes usados para el metabolismo de lactosa en E. Coli.
Directed evolution allows us to explore protein functionalities not required in the natural environment. It mimics natural genetic processes and selective pressures. This approach is used when the molecular basis is not completely understood and rational design is a difficult task. This approach consists of serial cycles of consecutive diversification and selection which eventually lead to the accumulation of beneficial mutations. Here are presented two cases where directed evolution is used to modify two different proteins: Taq polymerase, enzyme used for DNA extension in PCR, and the LacI repressor protein which regulates gene expression on E.coli.

Mestrado em Sistemas de Informação
Com a ameaça imposta às operadoras por aplicações OTT como WhatsApp ou Skype, diversas iniciativas coordenadas pela GSMA foram criadas para tentar responder a este fenómeno. Paralelamente, com a evolução de tecnologias como HTML5 e WebRTC, novos serviços como o Twilio têm surgido, oferecendo APIs para o desenvolvimento de novas aplicações Web. No entanto, a integração destas tecnologias em tradicionais redes de telecomunicações não faz parte das actuais especificações. Sendo assim, o objectivo desta dissertação consiste na especificação e implementação de um protótipo baseado nestas tecnologias emergentes, integrado com uma rede IMS. Primeiramente, foi feito um estudo do estado de arte, definindo requisitos e casos de uso a serem explorados. De seguida, o desenho da solução foi feito e implementado, tendo sido criado uma plataforma que alia WebRTC e a OneAPI da GSMA (que define funcionalidades básicas para operadores), oferecendo interoperabilidade entre ambos os mundos. A solução é composta por um servidor aplicacional que expõe a API e gateway WebRTC, tendo sido testada e considerada adaptada às necessidades estabelecidas.
With the threat to operators by OTT applications such as Skype or WhatsApp, several initiatives coordinated by GSMA were created in an effort to respond to this phenomenon. In parallel, with the evolution of technologies such as HTML5 and WebRTC, new services such as Twilio are now available, offering APIs for web application development. However, the integration of these technologies and traditional telecommunication networks is not a part of the current standards. As such, the objective of this dissertation is the specification and implementation of a prototype based on these emerging technologies, integrated in an IMS network. First, a state-of-the-art analysis was made, defining requirements and use-cases to be explored. Secondly, the design and implementation of the solution was done, creating a platform that unites WebRTC and GSMA’s OneAPI (which exposes basic operator features), offering interoperability between both worlds. The solution is composed by an application server that exposes the API and a WebRTC gateway, having been successfully tested and adapted to the established needs.

Automated theorem proving is a method to establish or disprove logical theorems. While these can be theorems in the classical mathematical sense, we are more concerned with logical encodings of properties of algorithms, hardware and software. Especially in the area of hardware verification, propositional logic is used widely in industry. Satisfiability Module Theories (SMT) is a set of logics which extend propositional logic with theories relevant for specific application domains. In particular, software verification has received much attention, and efficient algorithms have been devised for reasoning over arithmetic and data types. Built-in support for theories by decision procedures is often significantly more efficient than reductions to propositional logic (SAT). Most efficient SAT solvers are based on the DPLL architecture, which is also the basis for most efficient SMT solvers. The main shortcoming of both kinds of logics is the weak support for non-ground reasoning, which noticeably limits the applicability to real world systems. The Model Evolution Calculus (ME) was devised as a lifting of the DPLL architecture from the propositional setting to full first-order logic. In previous work, we created the solver Darwin as an implementation of ME, and showed how to adapt improvements from the DPLL setting. The first half of this thesis is concerned with ME and Darwin. First, we lift a further crucial ingredient of SAT and SMT solvers, lemma-learning, to Darwin and evaluate its benefits. Then, we show how to use Darwin for finite model finding, and how this application benefits from lemma-learning. In the second half of the thesis we present Model Evolution with Linear Integer Arithmetic (MELIA), a calculus combining function-free first-order logic with linear integer arithmetic (LIA). MELIA is based on ME and supports similar inference rules and redundancy criteria. We prove the correctness of the calculus, and show how to obtain complete proof procedures and decision procedures for some interesting classes of MELIA's logic. Finally, we explain in detail how MELIA can be implemented efficiently based on the techniques employed in SMT solvers and Darwin.

An area of Artificial Intelligence, used for instance in optimization, is evolutionary algorithms. By using mechanisms similar to those that cause evolution, evolutionary algorithms can improve e.g. problem solving algorithms by artificial evolution.The purpose of this study was to show that it’s possible to simulate evolution by modelling it as an evolutionary algorithm. This was achieved by simulating the evolution of silverfish’ genes in two environments with the only difference of the presence of a threat. The results were considered to be successful as the majorityof the genes which were presumed to be important for survival changed in such away. The results could be repeated between simulations indicating that random change of the genes and deterministic factors in the environment shaped the genes of the silverfish and that after simulation the silverfish were optimally fit for the environment.
Ett område inom Artificiell Intelligens som bl a används för optimering är evolutionära algoritmer. Genom att använda mekanismer liknande de som orsakar evolution så kan t ex algoritmer förbättras genom artificiell evolution. Syftet med den här studien var att visa att det är möjligt att simulera evolutionen genom att modellera den som en evolutionär algoritm. Detta gjordes genom att simulera evolutionen av silverfiskars gener i två miljöer vars enda skillnad var en förekomst av ett hot. Resultaten ansågs vara lyckade då merparten av de gener som förmodades vara viktiga för överlevnad förändrades på ett sådant sätt. Resultaten kunde upprepas mellan simuleringar vilket indikerar att genom stokastisk förändring av gener och deterministiska faktorer i miljön så optimerades silverfiskarnas gener för att göra det möjligt att överleva i respektive miljö.

Which form of exchange governance performs better in a dynamic environment? This remains an unanswered question in the transaction cost analysis (TCA) and relational exchange literatures. Some researchers purport that transactional governance provides superior performance by providing firms the flexibility to change suppliers. Others suggest that relational governance leads to superior performance because of the willingness of both parties to adapt. Reviews of TCA have turned up ambivalent empirical findings with regard to the effects of uncertainty despite a track record of strong empirical support for other predictions. Because most of TCA and relational exchange theories' predictions enjoy strong support, this research builds upon these theories to propose a theoretical modeling framework for a dynamic environment in a supply chain network (SCN) setting. This dissertation extends TCA and relational exchange to a dynamic, network environment. It uses the approach of building a simulation in order to study in detail the relationship between key exchange factors and the selection of transactional and relational exchange governance over time. This research effort extended TCA theory with a complex adaptive model of supply chain network governance evolution that attempts to link environmental, network, production, firm and exchange factors in a continuously evolving loop. The proposed framework expands transaction cost analysis' explanatory power. Results partially support past scholarly proposal that uncertainty functions as an antecedent of asset specificity rather than as an independent construct affecting governance outcome dependent upon which form of uncertainty is being considered. The successful simulation of supply chain networks as complex adaptive systems shift the focus from deterministic, confirmatory models of exchange to an exploratory, positive model. Instead of exchange governance as an outcome, it is the catalyst of the evolutionary process.

The evolution of sexual reproduction has been dubbed "the queen of problems in evolutionary biology". While there is a large amount of theory about the evolution of sex, there is relatively little well controlled empirical data. This thesis is an attempt to use an experimental evolution based approach in order to provide empirical insights into two different areas in the evolution of sex: the relative effects of beneficial and detrimental mutations on sex, and the effect of migration and gene flow on adaptation to new environments. In order to undertake this, a system comprising [i.e. comprised] of two Saccharomyces cerevisiae strains isogenic except for the ability to undergo sex was used. Theories about the evolution of sex can be broadly grouped into those which provide advantages for accumulating beneficial and clearing detrimental mutations. An empirical determination of their relative effects is useful in determining which theories are likely to be important to the evolution and maintenance of sexual reproduction. The first experiment consisted of propagating the sexual and asexual S. cerevisiae lines, as well as lines with increased mutation rates under both directional and stabilising selection for approximately 300 generations. The sexual lines increased in fitness significantly more quickly than the asexual lines under directional selection, regardless of mutation rate. In contrast, no lines, regardless of sexual status or mutation rate decreased or increased in fitness over the course of the experiment under stabilising selection, indicating that standard asexual selection was adequate to remove the vast majority of detrimental mutations. Thus in this experiment, sex is of much greater importance in accumulating beneficial mutations than in clearing detrimental mutations. The second experiment attempted to understand the effects of sexual reproduction and gene flow on adaptation. Predictions state that sexual organisms will be at a disadvantage to asexuals when adapting to multiple niches with migration between them, as maladapted hybrids are formed when mating occurs outside niches. To test this, sexual and asexual S. cerevisiae were adapted for approximately 350 generations to two differing environments, with varying rates of migration between them. In contrast to predictions, sexual lines showed higher adaptation to the new environments than asexuals irrespective of migration rate. The cause of this was investigated, and found to be caused by a loss of the trade off between the two environments in those treatments with high migration rates. This is interpreted as selection for generalists occurring in those lines which experience both environments. In summary, this thesis uses a powerful S. cerevisiae system in order to gain empirical insights into the evolution of sexual reproduction. The experiments further previous work with the same system into more complex and realistic scenarios, and provide novel empirical insights into the understanding of the evolution and maintenance of sex

This thesis examines the evolution of feminist praxis within the riot grrrl movement, focusing on two specific riot grrrl demographics - founding riot grrrls in the early 1990s and currently active riot grrrls in southern California. This thesis argues that riot grrrl activism is still thriving but in diverse, strategically modified ways. Using José Muñoz’s concept of “disidentification,” it analyzes how contemporary riot grrrls have appropriated and adapted the original movement’s tenets to allow for greater accessibility and diversity.

Present-day patterns of species diversity and their ecological characteristics in the tropics result from more than 100 million years of evolution. The environmental conditions in which species evolved have left a fingerprint on their functional traits, so investigating this legacy may improve our understanding of current patterns of ecosystem function and potentially guide us in managing our resources more wisely as the climate changes. Amazonian forests are ideal for such a study as they play a major role in the global carbon cycle and harbour a remarkable diversity of angiosperm lineages and species with a broad range of ecologies. Here, I linked data from long-term forest inventory plots, environmental conditions, and a newly constructed phylogeny in order to investigate the legacy of evolution on modern-day patterns of ecosystem function and diversity. I show first that evolutionarily related taxa are more similar in their demography and carbon storage and processing ability (i.e. wood density, potential size, growth and mortality-rates) than expected by chance. Thus, the degree of evolutionary history shared between lineages is a good proxy for their carbon traits. Next, using the evolutionary relationships among lineages I find a legacy of evolutionary history on current patterns of whole ecosystem productivity across the Amazon, such that communities with more evolutionarily distinct lineages have greater wood productivity. Finally, I compare the role of heritability versus selection on shaping lineages preferences for certain environments (i.e. soils and climate). I show that there is a tendency for evolutionarily related taxa to have more similar environmental preferences than expected by chance, but that certain kinds of habitat specialisation have also occurred repeatedly and independently in many lineages. These findings are important for understanding the future of Amazonian forests under global change and support an evolutionary perspective as an important component of conservation strategies.