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Affordability of products and services is an economic benefit that should accrue to consumers, whether they are corporations, government agencies or individuals. This concept of affordability goes beyond conventional wisdom that considers affordability as the ability to pay the price of a product or service. This dissertation defines and explores a broader concept of affordability – one of fitness to perform at the level of quality required by the consumer, to perform at that level whenever the product or service is used, and to do so with minimum consumption of resources. This concept of affordability is applied to technological systems by using the complexity sciences concept of fitness as the metaphor for technological systems' fitness. During a system design evolution, the specific design outcome is determined by that set of design search paths followed – it is path dependent. Dynamic mechanisms create, dictate and maintain path dependence. Initial conditions define the start and direction of a path. During subsequent design steps, positive feedback influences the designer to continue on that path. This dissertation describes underlying mechanisms that create, dictate and maintain path dependence; discusses the effects of path dependence on system design and system affordability; models these effects using system dynamics modeling; and suggests actions to address its effects. This dissertation also addresses several types of fitness landscapes, and suggests that the Data Envelopment Analysis (DEA) solution space is a form of fitness landscape suitable for evaluating the efficiency, and thus the fitness, of research and development (R&D) projects. It describes the use of DEA to evaluate and select Department of Defense (D0D) R&D projects as a new application of DEA. / Ph. D.

Phylogenetic trees capture the relationships between species and can be investigated by morphological and/or molecular data. When focusing on macroevolution, one considers the large-scale history of life with evolutionary changes affecting a single species of the entire clade leading to the enormous diversity of species obtained today. One major problem of biology is the explanation of this biodiversity. Therefore, one may ask which kind of macroevolutionary processes have given rise to observable tree shapes or patterns of species distribution which refers to the appearance of branching orders and time periods. Thus, with an increasing number of known species in the context of phylogenetic studies, testing hypotheses about evolution by analyzing the tree shape of the resulting phylogenetic trees became matter of particular interest. The attention of using those reconstructed phylogenies for studying evolutionary processes increased during the last decades. Many paleontologists (Raup et al., 1973; Gould et al., 1977; Gilinsky and Good, 1989; Nee, 2004) tried to describe such patterns of macroevolution by using models for growing trees. Those models describe stochastic processes to generate phylogenetic trees. Yule (1925) was the first who introduced such a model, the Equal Rate Markov (ERM) model, in the context of biological branching based on a continuous-time, uneven branching process. In the last decades, further dynamical models were proposed (Yule, 1925; Aldous, 1996; Nee, 2006; Rosen, 1978; Ford, 2005; Hernández-García et al., 2010) to address the investigation of tree shapes and hence, capture the rules of macroevolutionary forces. A common model, is the Aldous\\\'' Branching (AB) model, which is known for generating trees with a similar structure of \\\"real\\\" trees. To infer those macroevolutionary forces structures, estimated trees are analyzed and compared to simulated trees generated by models. There are a few drawbacks on recent models such as a missing biological motivation or the generated tree shape does not fit well to one observed in empirical trees. The central aim of this thesis is the development and study of new biologically motivated approaches which might help to better understand or even discover biological forces which lead to the huge diversity of organisms. The first approach, called age model, can be defined as a stochastic procedure which describes the growth of binary trees by an iterative stochastic attachment of leaves, similar to the ERM model. At difference with the latter, the branching rate at each clade is no longer constant, but decreasing in time, i.e., with the age. Thus, species involved in recent speciation events have a tendency to speciate again. The second introduced model, is a branching process which mimics the evolution of species driven by innovations. The process involves a separation of time scales. Rare innovation events trigger rapid cascades of diversification where a feature combines with previously existing features. The model is called innovation model. Three data sets of estimated phylogenetic trees are used to analyze and compare the produced tree shape of the new growth models. A tree shape statistic considering a variety of imbalance measurements is performed. Results show that simulated trees of both growth models fit well to the tree shape observed in real trees. In a further study, a likelihood analysis is performed in order to rank models with respect to their ability to explain observed tree shapes. Results show that the likelihoods of the age model and the AB model are clearly correlated under the trees in the databases when considering small and medium-sized trees with up to 19 leaves. For a data set, representing of phylogenetic trees of protein families, the age model outperforms the AB model. But for another data set, representing phylogenetic trees of species, the AB model performs slightly better. To support this observation a further analysis using larger trees is necessary. But an exact computation of likelihoods for large trees implies a huge computational effort. Therefore, an efficient method for likelihood estimation is proposed and compared to the estimation using a naive sampling strategy. Nevertheless, both models describe the tree generation process in a way which is easy to interpret biologically. Another interesting field of research in biology is the coevolution between species. This is the interaction of species across groups such that the evolution of a species from one group can be triggered by a species from another group. Most prominent examples are systems of host species and their associated parasites. One problem is the reconciliation of the common history of both groups of species and to predict the associations between ancestral hosts and their parasites. To solve this problem some algorithmic methods have been developed in recent years. But only a few host parasite systems have been analyzed in sufficient detail which makes an evaluation of these methods complex. Within the scope of coevolution, the proposed age model is applied to the generation of cophylogenies to evaluate such host parasite reconciliation methods. The presented age model as well as the innovation model produce tree shapes which are similar to obtained tree structures of estimated trees. Both models describe an evolutionary dynamics and might provide a further opportunity to infer macroevolutionary processes which lead to the biodiversity which can be obtained today. Furthermore with the application of the age model in the context of coevolution by generating a useful benchmark set of cophylogenies is a first step towards systematic studies on evaluating reconciliation methods.

Les gènes codant pour des protéines peuvent souvent être regroupés et intégrés en modules fonctionnels par rapport à un organelle. Ces modules peuvent avoir des composantes qui suivent une évolution corrélée pouvant être conditionnelle à un phénotype donné. Les gènes liés à la motilité possèdent cette caractéristique, car ils se suivent en cascade en réponse à des stimuli extérieurs. L’hyperthermophilie, d’autre part, est interreliée à la reverse gyrase, cependant aucun autre élément qui pourrait y être associé avec certitude n’est connu. Ceci peut être dû à un déplacement de gènes non orthologues encore non résolu. En utilisant une approche bio-informatique, une modélisation mathématique d’évolution conditionnelle corrélée pour trois gènes a été développée et appliquée sur des profils phylétiques d’archaea. Ceci a permis d’établir des théories quant à la fonction potentielle du gène du flagelle FlaD/E ainsi que l’histoire évolutive des gènes lui étant liés et ayant contribué à sa formation. De plus, une histoire évolutive théorique a été établie pour une ligase liée à l’hyperthermophilie. / Protein coding gene may often be grouped and integrated in functional modules with respect to an organelle. These modules may have constituents that follow a conditional correlated evolution to a given phenotype. Genes linked to motility posses this characteristic as they follow a cascade in response to external stimuli. Similarly, hyperthermophily is related to reverse gyrase, however no other element that could be associated with certainty is known. This may be caused by an unresolved case of non-orthologous gene displacement. Using a bioinformatic approach, a mathematical model for conditional correlated evolution for three genes has been developed and applied to the phyletic profiles of archaea. This has helped to develop theories about the potential functions of the flagellar gene FlaD/E and the evolutionary history of the genes that are linked to it and that may have contributed to its formation. In addition, a theoretical evolutionary history has been established for a ligase associated with hyperthermophily.

Many bacteria, viruses and other parasites cause severe morbidity or mortality in their host populations, creating strong selection for physiological or behavioural mechanisms to avoid disease. Likewise, changes in host susceptibility and contact patterns can dramatically influence the spread of infectious diseases, and hence selection for traits such as virulence and infectivity range in parasites. Understanding how ecological and evolutionary changes in one population affect selection in another represents a key challenge for theoreticians and empiricists alike, and is essential for gaining further insights into host-parasite relationships. This thesis contains theoretical models that explore how genetic and environmental factors shape the evolutionary and coevolutionary dynamics of hosts and parasites. In particular, the roles of genetic specificity (i.e. genotype-by-genotype interactions) and population mixing patterns are investigated, using both mathematical models and computer simulations. A broad range of scenarios are covered, including the coevolution of broad resistance and infectivity ranges (generalism), the persistence of coevolutionary cycling and the maintenance of sex, the effects of mating behaviour on disease prevalence and evolution, and the evolution of sexual and social behaviour. The models presented herein develop our understanding of host-parasite relationships and highlight the importance of genetic interactions and ecological feedbacks.

Due to shared coevolutionary history of snakes and primates with snakes acting as their main predators, snakes elicit fear in most of the primates, humans included. Humans are able to notice a stimulus that elicits fear, e.g., a snake, much faster. Such ability might have surely positively affected their survival in the past. In the nature, aposematic coloration acts as a warning of a dangerous prey to its predators not to devour it. The highly poisonous American coral snakes have this coloration pattern. The harmless king snakes of the Central and North Americas gain an anti-predatory advantage by becoming the coral snakes 'Batesian mimics, copying their bright pattern. Such pattern elicits an innate fear reaction in various species of wild birds who avoid a mere contact with patterned plastic dummies. The question arises whether other taxa, including primates and humans, generally recognize such pattern as dangerous. The aim of this study was to find whether humans fear coral snakes, although they have not long coevolutionary history with them. Further it was analyze, which visual factors of the snakes affect this fear reaction (i.e., a warning coloration, pattern or shape of snake). The atractiveness of these snakes was tested. Another question was whether humans are able to intuitively recognize...

Recentemente, tornou-se acessível a análise filogenética com base em caracteres contínuos. Isso amplia a quantidade de caracteres que podem ser utilizados em análises filogenéticas baseadas em morfologia, mas não há ainda um consenso sobre como esse tipo de caráter deve ser codificado e analisado. Este trabalho analisa o uso de caracteres contínuos em filogenias com dois diferentes enfoques: simulações em computador e aplicação em uma análise com dados reais. As simulações realizadas indicam que de fato pode-se recuperar filogenias com base em caracteres contínuos, com alguns cuidados. O mais importante deles é o uso de pesagem implícita. Mesmo com esse cuidado, os ramos pouco suportados podem ser incorretos, provavelmente devido a um efeito de atração de ramos longos. Na análise do gênero Anchylorhynchus, utilizei caracteres discretos e contínuos, em separado e combinados. As árvores obtidas com as matrizes separadas são bastante diferentes, e a árvore da matriz combinada é semelhante àquela obtida somente com os caracteres discretos. O suporte dos ramos, contudo, cresce com a adição dos caracteres contínuos. Os caracteres contínuos, portanto, não devem ser vistos como uma alternativa, mas como um acréscimo às análises tradicionais. A revisão taxonômica de Anchylorhynchus resultou na descrição de nove espécies novas e reconhecimento de quatro sinônimos novos. O gênero resultou ser um grupo monofilético com um total de 24 espécies reconhecidas. Além disso, as informações sobre a biologia e a distribuição geográfica desses gorgulhos foi atualizada. Em conjunto com a filogenia obtida, essas informações basearam reconstruções biogeográficas e da associação histórica com as plantas hospedeiras. / Recently, phylogenetic analysis based on continuous characters was made accessible. This increases the pool of characters available for morphology-based phylogenetic analyses, but there is still no consensus on how this kind of characters should be coded and analyzed. In the present study, I assessed the use of continuous characters in phylogenies from two distinct perspectives: computer simulations and an application to real data. The simulations indicate that one can indeed recover phylogenies based on continuous characters, given some precautions. The most important of them is the use of implied weighting. Even when this is done, poorly supported branches may be incorrect, probably due to long-branch attraction. For the phylogenetic analysis of Anchylorhynchus, I used both continuous and discrete characters, separately or combined. Trees obtained with separate matrices were significantly different, and the combined matrix resulted in a tree very similar to the tree obtained with discrete characters alone. Branch supports, however, increased with the addition of continuous characters. Continuous characters, therefore, should not be considered an alternative to traditional analyses. Rather, they should be added to discrete-character matrices. The taxonomic revision of Anchylorhynchus resulted in nine new species described and four new synonyms recognized. The genus resulted to be a monophyletic group containing 24 recognized species. Moreover, the information on weevils\' biology and geographical distribution was updated. Together with the phylogeny this information embased reconstructions of host relationships and biogeography.

O continente sul-americano é a única região biogeográfica onde podemos encontrar um grupo estenohalino de elasmobrânquios: as arraias da família Potamotrygonidae. Entre 19 e 21 espécies de potamotrigonídeos estão taxonomicamente organizadas em três gêneros, distribuídas pelas bacias dos rios Atrato, Magdalena, Maracaibo, Orinoco, Essequibo, Amazonas e do Prata, os quais desembocam no Oceano Atlântico e no Mar do Caribe. Diversos cenários biogeográficos postulados para explicar a presença de linhagens predominantemente marinhas nos sistemas fluviais da América do sul foram propostos. O mais aceito para a origem e diversificação de Potamotrygonidae é a de invasão de um ancestral caribenho no sistema fluvial sul-americano durante as ingressões marinhas do Mioceno inferior no noroeste do continente, seguido de isolamento por alteração dos padrões de drenagens do Orinoco e formação dos Andes. A fauna parasitária de Potamotrygonidae está representada predominantemente por membros de Cercomeromorpha, um clado composto por linhagens de platelmintos membros de Cestoda e Monogenoidea. Dois gêneros de monogenóideos parasitas branquiais podem ser encontrados em potamotrigonídeos: Potamotrygonocotyle (Monocotylidae), para o qual 12 espécies são conhecidas, e a monotípica Paraheteronchocotyle amazonense (Hexabothriidae). O objetivo desta tese é propor uma hipótese de relacionamento filogenético baseada em dados moleculares para as espécies de Potamotrygonocotyle, e discutir padrões de evolução da espécie P. aramasae e seu hospedeiro Paratrygon aiereba, distribuídos em diferentes rios amazônicos. Sequências nucleotídicas do gene mitocondrial cox1 e nuclear ITS1 foram utilizadas simultaneamente em uma busca de uma hipótese filogenética para todas as espécies conhecidas de Potamotrygonocotyle. Os resultados recuperaram o status monofilético de cinco espécies, sugeriram complexos de linhagens crípticas para três espécies nominais e revelaram relacionamentos de grupo-irmão não detectados na hipótese filogenética mais recente para o gênero, baseada em dados morfológicos. Adicionalmente, os resultados apresentados suportam decisões taxonômicas recentes envolvendo sinonímias entre espécie nominais de Potamotrygonocotyle. Finalmente, os relacionamentos filogenéticos de haplótipos de diferentes populações de P. aramasae e seu hospedeiro P. aiereba foram acessados pela análise cladística de múltiplos marcadores mitocondriais, com o objetivo de se detectar possíveis padrões filogeográficos e testá-los sob predições filogenéticas de três hipóteses de diversificação amazônica (Hidrogeológica, de Museu e Paleogeográfica). Sequências dos genes ribossomal 16S e citocromo oxidase 1 foram obtidas para espécimes de parasitas de seis sub-bacias amazônicas. Os hospedeiros foram amostrados em 10 sub-bacias amazônicas e na sub-bacia do rio Essequibo, para os quais foram obtidas sequências nucleotídicas dos genes mitocondriais citocromo oxidase 1, citocromo b e ATPase. Os resultados sugerem a ausência de padrões filogeográficos para o parasita, cujos resultados indicam um modelo de alta dispersão. Em contraste, P. aireba é caracterizada por populações bem estruturadas, de acordo com as sub-bacias amostradas. O padrão filogeográfico geral desta espécie é concordante com as predições da Hipótese de Museu (linhagens mais antigas em rios dos escudos pré-cambrianos; linhagens apicais na bacia sedimentar amazônica). / South America is the only biogeographical region in the world where is possible to find an exclusive stenohalin group of elasmobranchs: the Potamotrygonidae stingrays. Between 19 and 21 species of potamotrygonid stingrays are taxonomically organized in three genera, distributed in the Atrato, Magdalena, Maracaibo, Orinoco, Essequibo, Amazonas e la Plata river Basins, discharging in both Atlantic and Caribbean waters. Distinct biogeographical scenarios have been proposed to explain the presence of predominantly marine lineages in the south American fluvial systems. The most accepted theory for Potamotrygonidae is the invasion of a Caribbean ancestor in the south-American freshwater system during the marine ingression of the early Miocene in the northwest of the continent, followed by its isolation due alterations of Orinoco rivers drainage patterns, as well as formation of Andes. The parasitic fauna of potamotrygonids is predominantly represented by members of Cercomeromorpha, a clade composed by members of Cestoda and Monogenoidea. Two genera of gill parasites monogenoidean might be found in potamotrygonids: Potamotrygonocotyle (Monocotylidae), for which 12 species are currently recognized, and the monotypic Paraheteronchocotyle amazonense (Hexabothriidae). The goal of this study is to propose a phylogenetic hypothesis based in molecular data for members of Potamotrygonocotyle, as well as to discuss evolutionary patterns of the species P. aramasae and its host Paratrygon aiereba, distributed through different amazon rivers. Nucleotide sequences of the mitochondrial gene cox1, and the nuclear gene ITS1 were simultaneously used to infer phylogenetic sister-group relationships among allrecognized species of Potamotrygonocotyle. The results recovered the monophyletic status of five species, suggested cryptic lineages for three species complexes, and revealed sister-groups relationships not detected previously by the phylogenetic analysis of morphological data. Additionally, the results supports recent taxonomic decisions involving synonyms among nominal species within the genus. The phylogenetic relationships of haplotypes from distinct populations of the parasite P. aramasae, as well as from its host Paratrygon aiereba, were accessed by the cladistic analysis of mitochondrial markers, in an attempt of detecting possible phylogeographic patterns, and to test them against phylogenetic predictions of three amazonian bio-diversification hypotheses (Hydrogeology, Museum, Paleogeography). Sequences of the ribosomal 16S gene and cytochrome oxidase 1 were obtained from parasite specimens collected in six amazon sub-basins. The hosts were sampled in 10 amazon sub-basins, as well as in the Essequibo sub-basin, for which cythocrome oxidase 1, cythocrome b, and ATPase sequences were obtained. No clear phylogeographic patterns were revealed for theparasite haplotypes, and the results suggest a high dispersion model. In contrast, P. aiereb is characterized by strongly structured populations, according to the sub-basin sampled. The general phylogeographic pattern recovered for this species is in agreement with the Museum Hypothesis predictions (older lineages in rivers of the pre-cambrian shields; apical lineages inhabiting the sedimentary amazon basin).

Les odeurs émises par les plantes sont souvent interprétées dans le cadre de leur interaction avec les insectes pollinisateurs, herbivores et ennemis naturels, en tant que signaux de communication dont la fonction est l'attraction ou la répulsion de ces insectes. Pourtant, la communication a une définition précise en biologie évolutive, et le terme « signal » ne doit s'appliquer qu'à des traits de l'émetteur qui ont été sélectionnés dans le cadre de l'interaction avec le récepteur par voie sensorielle. De plus, certaines études démontrent que les Composés organiques volatils (COV) émis par les feuilles participent à la défense des plantes contre divers stress abiotiques (notamment stress oxydant et thermique) et biotiques (pathogènes, induction des défenses). L'idée de cette thèse, c'est d'essayer de faire rentrer l'ensemble de ces contextes et fonctions potentielles dans un cadre commun. En utilisant comme modèle les figuiers, leurs pollinisateur et parasites spécialistes, j'ai choisi comme approche de comparer les variations des odeurs de figue à celles de odeurs de feuille, au cours du développement des figues et au cours d'une journée. Dans les deux cas, les feuilles constituent un témoin permettant de déterminer si les variations observées peuvent être adaptatives vis-à-vis de l'interaction avec les insectes, mais aussi de considérer explicitement les fonctions potentielles des odeurs émises en dehors de la réceptivité. Ainsi, les fonctions de protection contre les stress habituellement attribuées aux odeurs de feuilles sont également pertinentes pour les odeurs de figues. A partir de là, le constat que le concept de communication n'est pas pertinent pour décrire le rôle des odeurs dans les interactions figuier-parasite permet de développer une réflexion sur la manière dont les phytophages et leurs ennemis naturels sont susceptibles d'influer sur l'évolution des odeurs émises par les plantes. Enfin, dans le cas de la communication olfactive figuier-pollinisateur, l'étude du cas de Ficus septica, chez qui deux pollinisateurs écologiquement différenciés coexistent, permet d'imaginer un mécanisme potentiel de co-spéciation écologique dans lequel la divergence des modalités de communication olfactive participerait à la mise en place de l'isolement reproducteur. / The scents emitted by plants are often interpreted in the light of their interaction with pollinators, phytophagous insects and their natural ennemies, as communication signals whose function is to attract or repel those insects. However, according to the adaptive definition of communication, a trait can be called “signal” only if it has been selected for the sensory interaction with a receptor. In addition, it has been shown that the volatile organic compounds (VOC) emitted by leaves participate to the defense of the plant against abiotic (especially oxidative/heat stress) and biotic stresses (pathogens, induction of defenses). The idea underlying this thesis it to put all all the contexts of emission and functions together within a common framework. Using the fig-pollinator-parasite model, the approach I choose was to compare the variation of fig scent with that of leaf scent, along their development and daily. In both cases, leaf scent is a control trait that allows to determine if the variations observed in figs are possibly adaptive regarding the interaction with insects, and to explicitely consider the potential functions of the scents emitted out of receptivity. Stress-protective functions that are evidenced in leaf scents are thus also relevant in figs. Then, the fact that communication is not relevant to describe the role of scents in the fig-parasite interaction led me to develop a reflection on the way phytophagous insects and their natural enemies could influence the evolution of plant scents. Finally, in the case of fig-pollinator communication, studying the case of Ficus septica, that is associated to two co-occuring ecologically differenciated pollinators, allows to imagine a potential co-speciation mechanism, where the divergence of communication mode would contribute to the establishment of reproductive isolation.

The aim of this thesis project was to elucidate patterns and processes associated with the biotic interactions in a natural plant–herbivore–parasitoid food web characterized by spatial and temporal heterogeneity with regard to species composition. The system examined is based on island populations of the perennial herb Meadowsweet (Filipendula ulmaria, Rosaceae), located in the Skeppsvik Archipelago. The area is subject to isostatic rebound, amounting to 0.85 cm per year; this makes it possible to calculate the age of the rising islands. Meadowsweet colonizes new islands when they are about 100 years old. Meadowsweet is consumed by two major herbivores in the study area: Galerucella tenella and Altica engstroemi (Coleoptera: Chrysomelidae). Both herbivores overwinter in the topsoil and successful colonization occurs when the islands reach a height that prevents the beetles from being removed or killed as a result of wave wash during the winter. I found that both herbivores significantly reduced individual plant fitness and population growth rate. A “cafeteria experiment” with Galerucella showed that this beetle discriminated between plants from different islands, avoiding plants from old islands which contained high concentrations of putative defence compounds, while readily accepting plants from younger islands which contained lower concentrations of these chemicals. Further, the plant species exhibited a trade-off between growth and production of the putative defence compounds. Taken together, these results were interpreted as providing evidence of herbivore-driven evolution of resistance in Meadowsweet. Further, laboratory studies suggested that Galerucella gradually includes a less preferred host plant (Rubus arcticus, Rosaceae) in its diet as Meadowsweet resistance increases. This implies that Galerucella drives its own host-breadth enlargement by selectively inducing a ‘rent rise’ in the original host, Meadowsweet. In a number of field studies I showed that the oligophagous parasitoid Asecodes mento (Hymenoptera: Eulophidae) has a strong positive effect on Meadowsweet seed set by removing large numbers of G. tenella larvae. This top-down effect is, however, altered by the presence of a close relative of G. tenella, namely G. calmariensis, which is monophagous on Purple loosestrife (Lythrum salicaria, Lythraceae). G. tenella experiences associational susceptibility when coexisting with G. calmariensis since the latter supports a higher and more fit pool of shared parasitoids and because Meadowsweet attracts a higher proportion of the shared parasitoid females than Purple loosestrife. This implies that G. tenella densities are very low in coexisting populations and that Meadowsweet experiences associational resistance and produces more seeds when co-occurring with Purple loosestrife. Thus, selection for increased resistance in Meadowsweet is likely to be relaxed in populations mixed with Purple loosestrife. I conclude that the evolution of plant resistance is likely to depend on the length of time and intensity of selection. When Meadowsweet colonizes new islands it experiences a period of enemy-free space; followed by a midlife and ageing with selection by herbivores. The intensity of this selection does, however, depend on the presence of additional plant and herbivore species.