Species interactions restrict or promote population growth, structure communities, and contribute to evolution of diverse taxa. I seek to understand how multiple species interactions are maintained, how human altered species interactions influence evolution, and explore factors that contribute to variation in species interactions. In Chapter 1, I examine how plants interact with multiple guilds of mutualists, many of which are costly interactions. The evolution of traits used to attract different mutualist guilds may be constrained due to ecological or genetic mechanisms. I asked if two sets of plant traits that mediate interactions with two guilds of mutualists, pollinators and ant bodyguards, were positively or negatively correlated across 36 species of Gossypium (cotton). Traits to attract pollinators were positively correlated with traits to attract ant bodyguards. Rather than interaction with one mutualist guild limiting interactions with another mutualist guild, traits have evolved to increase attraction of multiple mutualist guilds simultaneously. In Chapters 2 and 3, motivated by the fact that agriculture covers nearly 50% of the global vegetated land surface, I explore the consequences of changes in plant mutualist and antagonist guilds in agriculture for selection on plant traits. I first explore how agriculture alters abundance and community structure of mutualist pollinators and antagonist seed predators of wild Helianthus annuus texanus. Mutualists were more abundant near crops, whereas antagonists were more abundant far from crops near natural habitat. In addition, mutualist pollinator communities were more diverse near sunflower crops. Plant mutualists and antagonists respond differently to agriculture. Next, I explore how these changes in abundance and community structure of mutualists and antagonists influenced natural selection on H. a. texanus floral traits. Natural selection on heritable floral traits differed near versus far from crop sunflowers, and overall selection was more heterogeneous near crop sunflowers. Furthermore, mutualist pollinators and antagonist seed predators mediated these differences in selection. Finally, in Chapter 4, I ask if variation in interaction outcomes differs across types of species interactions. Furthermore, I examined the relative importance of factors that create context-dependency in species interactions. Using meta-analysis of 353 papers, we found that mutualisms were more likely to change sign of the interaction outcome when compared across contexts than competition, and predation was the least likely to change sign. Overall, species identity caused the greatest variation in interaction outcomes: whom you interact with is more important for context-dependency than where or when the interaction occurs. Additionally, the most important factors driving context-dependency differed significantly among species interaction types. Altogether, my work makes progress in understanding how species maintain interactions with multiple guilds of mutualists, how agriculture alters species interactions and subsequent natural selection, and the variation in species interaction outcomes and their causes.

Governments have a choice whether to intervene in the transport infrastructure sector to manage, finance and own the assets of the sector, or to rely on markets and private sector actors for the provision of these systems. In this article the development of rail and road infrastructure in Sweden and the choice between government and market provision of these systems are analyzed from a co-evolutionary perspective. Technology, economics, and politics have influenced the government’s policy formation and decisions on organizational models over time, such as the nationalization of roads and railroads in the 1930s-40s. The aim for improved economic efficiency and reduction of cost differences between different parts of the country rather than political ideology explain why roads and railroads were nationalized. Through adjusting its ownership role and policy content the government has, over time, accommodated to the different influences from technology, economics and politics. The government’s ownership of transport infrastructure has not been challenged since the nationalization. This could be seen as a sign of a successful gradual policy adjustment from the government’s side, thereby avoiding private sector solutions. / <p>QC 20130614</p>

Vaccination against the Influenza A virus (IAV) is often an important and critical task for much of the population, as IAV causes yearly epidemics, and can cause even deadlier pandemics. Designing the vaccine requires an understanding of the current major circulating strains of Influenza, as well as an understanding of how those strains could change over time to become either less harmful or more deadly, or simply die out completely. An error in the prediction process can lead to a non-immunized population at risk of epidemics, or even a pandemic. Presented here is a posterior predictive approach to generate emerging influenza strains based on a realistic genomic model that incorporates natural features of viral evolution such as selection and recombination. Also introduced is a sequence sampling scheme to relieve the computational burden of the posterior predictive analysis by clustering sequences based on their pairwise similarity. Finally, the impact of “evolutionary accidents” that take the form of bursts of evolution and or of recombination on the predictive power of our procedure is tested. An analysis of the impact of these bursts is carried out in a retrospective study that focuses on the unexpected emergence of a new H3N2 strain in the 2007-08 influenza season. Measuring the R2 values of both pairwise and patristic distances, the model reaches a predictive power of ∼40%, but is not able to simulate the emergence of the target Brisbane/10/2007 sequence with a high probability. The inclusion of “evolutionary accidents” improved the algorithm’s ability to predict HA sequences, but the prediction power of the NA gene remained low.

“Cooperation” has distinct meanings in biological and moral contexts. In nature, “cooperation” is commonly equated with “altruism,” and involves an apparent fitness cost to the actor. In the moral context, it is often employed to describe the behaviour required by a particular subset of morality, namely that of distributive justice. The existence of cooperation in nature poses a difficulty for those who seek explain it in evolutionary terms. There is an analogous problem in normative moral theory of reconciling cooperative behaviour with rationality. The constraints imposed by natural selection in the former context and by rationality in the latter make explaining or justifying cooperation difficult. Insofar as the social contract tradition is concerned with articulating or justifying the terms of social cooperation, these two problems are united through the contract metaphor. I examine these two structurally similar problems through the lens of the social contract tradition. In the descriptive arena, I argue that cultural group selection provides the most plausible explanation of the emergence of altruistic behaviours in nature. In the normative context, I argue that David Gauthier’s argument for the rationality of adopting the disposition of constrained maximization provides a defensible route to reconciling morality with rationality. I draw two conclusions with respect to how these two enterprises are connected. First, I argue, contrary to many critics of an empirically informed ethics, that the descriptive and normative projects are very much dependent upon one another. Insofar as culture is required for a descriptive account of the emergence of cooperation, and to the extent that reasoning about which norms ought to govern our interactions plays a role in their transmission, our descriptive account not only leaves room for normative considerations, but in fact requires them. Second, I argue that there is a convergence in the outcomes of both the descriptive and normative projects. I show that the explanation of the existence of cooperation that I favor also provides us with an explanation of the emergence of dispositions that structurally resemble those that Gauthier defends as rational. And thus we arrive at an account that brings together rationality, evolution, and morality.

This thesis examines the issue of software evolution from a Requirements Engineering perspective. This perspective is founded on the premise that software evolution is best managed with reference to the requirements of a given software system. In particular, I follow the Requirements Problem approach to software development: the problem of developing software can be characterized as finding a specification that satisfies user requirements, subject to domain constraints. To enable this, I propose a shift from treating requirements as artifacts to treating requirements as design knowledge, embedded in knowledge bases. Most requirements today, when they exist in tangible form at all, are static objects. Such artifacts are quickly out of date and difficult to update. Instead, I propose that requirements be maintained in a knowledge base which supports knowledge-level operations for asserting new knowledge and updating existing knowledge. Consistency checks and entailment of new specifications is done automatically by answering simple queries. Maintaining a requirements knowledge base in parallel with running code means that changes precipitated by evolution are always addressed relative to the ultimate purpose of the system. This thesis begins with empirical studies which establish the nature of the requirements evolution problem. I use an extended case study of payment cards to motivate the following discussion. I begin at an abstract level, by introducing a requirements engineering knowledge base (REKB) using a functional specification. Since it is functional, the specifics of the implementation are left open. I then describe one implementation, using a reason-maintenance system, and show how this implementation can a) solve static requirements problems; b) help stakeholders bring requirements and implementation following a change in the requirements problem; c) propose paraconsistent reasoning to support inconsistency tolerance in the REKB. The end result of my work on the REKB is a tool and approach which can guide software developers and software maintainers in design and decision-making in the context of software evolution.

Interacting galaxies are thought to be the essential building blocks of elliptical galaxies under the hierarchical galaxy formation scenario. The goal of my dissertation is to broaden our understanding of galaxy merger evolution through both observational studies and instrument developments. Observationally, I approach the goal photometrically and spectroscopically. The photometric studies better constrain the number density evolution of wet and dry mergers through five CFHTLS broad band photometry up to z~1. Meanwhile, by comparing the merger and elliptical galaxy mass density function, I discovered that the most massive mergers are not all formed via merging processes, unless the merging timescale is much longer than the expected value. Spectroscopically, the kinematic properties of close pair galaxies were studied to understand how star formation were quenched at z~0.5. I discovered that the number of red-red pairs are rare, which does not support the gravitational quenching mechanism suggested by the hot halo model. In instrumentation, one efficient way to study galaxy mergers is to use the integral field spectroscopic technique, capitalizing its intrinsic capability of obtaining 2-D spectra effectively. However, the currently available integral field spectrographs are inadequate to provide the required combination of integral field size and spectral resolution for merger studies. I, therefore, have developed two optical designs of a wide integral field infrared spectrograph (WIFIS), which I call WIFIS1 and WIFIS2, to satisfy the requirements of merger studies. Both the designs provide an integral field of 12" x 5" on 10-m telescopes (or equivalently 52" x 20" on 2.3-m telescopes). WIFIS1 delivers spectral resolving powers of 5,500 covering each of JHK bands in a single exposure; WIFIS2 does a lower power of 3,000 focusing on a shorter wavebands of zJ and H bands. All the WIFIS2 optical components have either been or being fabricated, and some of the components have been characterized in the laboratory, including its integral field unit, gratings, and mirrors. The expected completion of WIFIS based on WIFIS2 is 2013 summer, which will be followed by WIFIS1-based spectrograph in a few years.

“Cooperation” has distinct meanings in biological and moral contexts. In nature, “cooperation” is commonly equated with “altruism,” and involves an apparent fitness cost to the actor. In the moral context, it is often employed to describe the behaviour required by a particular subset of morality, namely that of distributive justice. The existence of cooperation in nature poses a difficulty for those who seek explain it in evolutionary terms. There is an analogous problem in normative moral theory of reconciling cooperative behaviour with rationality. The constraints imposed by natural selection in the former context and by rationality in the latter make explaining or justifying cooperation difficult. Insofar as the social contract tradition is concerned with articulating or justifying the terms of social cooperation, these two problems are united through the contract metaphor. I examine these two structurally similar problems through the lens of the social contract tradition. In the descriptive arena, I argue that cultural group selection provides the most plausible explanation of the emergence of altruistic behaviours in nature. In the normative context, I argue that David Gauthier’s argument for the rationality of adopting the disposition of constrained maximization provides a defensible route to reconciling morality with rationality. I draw two conclusions with respect to how these two enterprises are connected. First, I argue, contrary to many critics of an empirically informed ethics, that the descriptive and normative projects are very much dependent upon one another. Insofar as culture is required for a descriptive account of the emergence of cooperation, and to the extent that reasoning about which norms ought to govern our interactions plays a role in their transmission, our descriptive account not only leaves room for normative considerations, but in fact requires them. Second, I argue that there is a convergence in the outcomes of both the descriptive and normative projects. I show that the explanation of the existence of cooperation that I favor also provides us with an explanation of the emergence of dispositions that structurally resemble those that Gauthier defends as rational. And thus we arrive at an account that brings together rationality, evolution, and morality.

This thesis examines the issue of software evolution from a Requirements Engineering perspective. This perspective is founded on the premise that software evolution is best managed with reference to the requirements of a given software system. In particular, I follow the Requirements Problem approach to software development: the problem of developing software can be characterized as finding a specification that satisfies user requirements, subject to domain constraints. To enable this, I propose a shift from treating requirements as artifacts to treating requirements as design knowledge, embedded in knowledge bases. Most requirements today, when they exist in tangible form at all, are static objects. Such artifacts are quickly out of date and difficult to update. Instead, I propose that requirements be maintained in a knowledge base which supports knowledge-level operations for asserting new knowledge and updating existing knowledge. Consistency checks and entailment of new specifications is done automatically by answering simple queries. Maintaining a requirements knowledge base in parallel with running code means that changes precipitated by evolution are always addressed relative to the ultimate purpose of the system. This thesis begins with empirical studies which establish the nature of the requirements evolution problem. I use an extended case study of payment cards to motivate the following discussion. I begin at an abstract level, by introducing a requirements engineering knowledge base (REKB) using a functional specification. Since it is functional, the specifics of the implementation are left open. I then describe one implementation, using a reason-maintenance system, and show how this implementation can a) solve static requirements problems; b) help stakeholders bring requirements and implementation following a change in the requirements problem; c) propose paraconsistent reasoning to support inconsistency tolerance in the REKB. The end result of my work on the REKB is a tool and approach which can guide software developers and software maintainers in design and decision-making in the context of software evolution.

Vaccination against the Influenza A virus (IAV) is often an important and critical task for much of the population, as IAV causes yearly epidemics, and can cause even deadlier pandemics. Designing the vaccine requires an understanding of the current major circulating strains of Influenza, as well as an understanding of how those strains could change over time to become either less harmful or more deadly, or simply die out completely. An error in the prediction process can lead to a non-immunized population at risk of epidemics, or even a pandemic. Presented here is a posterior predictive approach to generate emerging influenza strains based on a realistic genomic model that incorporates natural features of viral evolution such as selection and recombination. Also introduced is a sequence sampling scheme to relieve the computational burden of the posterior predictive analysis by clustering sequences based on their pairwise similarity. Finally, the impact of “evolutionary accidents” that take the form of bursts of evolution and or of recombination on the predictive power of our procedure is tested. An analysis of the impact of these bursts is carried out in a retrospective study that focuses on the unexpected emergence of a new H3N2 strain in the 2007-08 influenza season. Measuring the R2 values of both pairwise and patristic distances, the model reaches a predictive power of ∼40%, but is not able to simulate the emergence of the target Brisbane/10/2007 sequence with a high probability. The inclusion of “evolutionary accidents” improved the algorithm’s ability to predict HA sequences, but the prediction power of the NA gene remained low.

This work presents detailed analysis from the GEEC2 spectroscopic survey of galaxy groups at 0.8<z<1. This deep survey, which has a magnitude limit of r_AB<24.75, had previously found a population of intermediate ('green') galaxies between the star-forming ('blue') and quiescent ('red') sequences. GMOS-S spectroscopy for the 11 X-ray selected galaxy groups was obtained and is highly complete ( > 66 per cent) for eight of the eleven groups. Using an optical-NIR colour-colour diagram, the galaxies in the sample are separated with a dust insensitive method into the three categories, star-forming, quiescent, and intermediate. The strongest environmental dependence is observed in the fraction of quiescent galaxies, which is higher inside groups than in the field for all stellar masses. While intermediate galaxies represent ~15-20 per cent of the star-forming population in both the group and field, the average specific star formation rates (sSFR) of the group population is lower by a factor of ~3. The intermediate population also does not show the strong Hδ absorption that is characteristic of starburst galaxies. Inside groups, only 4.4-6.7 per cent of star-forming galaxies are starbursts, which gives additional validity to the assumption that the quenching of star-formation is the primary process in the transition from the star-forming to the quiescent state. With the use of stellar synthesis models, two possible scenarios for the origins of the intermediate population are investigated, including the quenching of star-forming galaxies via environmental processes and the rejuvenation of star formation in early-type galaxies via mixed mergers. To model the quenching scenario, we have tested the use of different exponential quenching timescales (τ_2) and different types of delays between satellite accretion and the onset of quenching. We found that the fraction of intermediate galaxies depends most strongly on the value of τ_2. The relative fractions of galaxies rule out both the no-delay scenario, which would require a long τ_2 that over-produces intermediate galaxies, as well as the constant 3 Gyr delay model, which does not produce a sufficient number of quiescent galaxies. The observed fractions are best matched with a model that includes a dynamical delay time and a τ_2=0.25 Gyr, but this model also predicts intermediate galaxies Hδ strength higher than that observed. For the rejuvenation scenario, we found that the time visible in the intermediate region is directly related to the size of the second 'burst' of star-formation, which can then be further constrained by the Hδ strength for the intermediate population. The observations are best matched to a burst size of ~1 per cent, at a rate of ~3 times per Gyr. In order to properly distinguish between the two scenarios, we will need to both increase the signal-to-noise ratio for the Hδ measurements and conduct a deeper survey of satellite galaxies both inside groups and in the field.