VictorJuiz/thesis huggingface dataset:
Global and Fine Scale Molecular Studies of Polyploid Evolution in Crataegus L. (Rosaceae)
Keywords: Polyploidy
Molecular evolution
Crataegus
Phylogeny
Population structure
Apomixis

As many as 70% of angiosperm species are known to contain polyploids, but many aspects of polyploid evolution are unclear in woody plants. Crataegus is a woody genus of Rosaceae comprising 140-200 species that are widely distributed in the Northern Hemisphere. Several species, particularly those in North America, are shown to contain polyploids. The overall goal of the thesis is to provide a better understanding of polyploid evolution by resolving problems from intergeneric to intraspecific levels in Crataegus using phylogenetic and population genetic approaches. Three major aspects were investigated: (1) Phylogeography of the Old and New World Crataegus; (2) Reproductive system and distribution of cytotypes of the black-fruited series Douglasianae in Pacific Northwest and; (3) Origins, population structure, and genetic diversity of diploid and polyploid species. Phylogenetic analyses of molecular data provide evidences of historical events such as trans-Beringian migrations and North Atlantic vicariance that contributed to modern distribution of Crataegus. Poor resolution and short internal branches in eastern North American species suggest genetic bottlenecks and/or rapid divergence following glaciations. In the Pacific Northwest, polyploids of series Douglasianae show a wider distribution and ecological amplitude than diploids. Parsimony tree and network analyses indicate that autotriploids and allotriploids occur in C. suksdorfii, while tetraploid C. suksdorfii are formed via the triploid bridge followed by introgression of sympatric C. douglasii. At the regional level, microsatellite data indicate a separation of the Pacific coastal diploids and triploids from the Columbia Plateau and Rocky Mountain triploids and tetraploids. High genetic differentiation among C. suksdorfii populations suggests that gene flow is limited by ploidy level differences as well as geographical distance. Within-population multilocus genotypic variation is greatest in sexual diploids, and least in apomictic triploids. Frequent gene flow via seed dispersal contributes to an appreciable level of intrapopulation diversity in apomictic tetraploids, and counterbalances the effects of apomixis and/or self-fertilization, which diminish genetic variation within and between seed families. These findings collectively clarify taxonomy and historical biogeography, provide an explicit reticulation model for polyploid formation, and shed light on evolution of natural populations in woody plants that show heterogeneous ploidy levels and reproductive systems.
Survival, Song and Sexual Selection
Keywords: Gryllus pennsylvanicus
Gryllus
Gryllidae
Orthoptera
life history
lifespan
condition dependence
calling effort
bioacoustics
selection analysis
mating preferences
male-male competition
field cricket
cricket fighting

Darwinian sexual selection predicts that males with the most extravagant secondary sexual traits suffer elevated mortality. Although correlative evidence has generally not borne this idea out, recent research, including a field cricket study, showed that investment in sexually selected traits is costly to survival. I investigated male survival, ornamentation (song) and mating success in a North American grylline, Gryllus pennsylvanicus, to test the generality of previous work and highlight the importance of ecology differences to resource allocation. As the calling songs of older male G. pennsylvanicus are highly attractive to females, in Chapter 2 I tested whether male age correlated with calling song and found a weak but statistically significant correlation, thus leaving open the possibility that choosy females use an age-based indicator mechanism. In Chapter 3, I tested the condition dependence of male survival and calling effort. In contrast to previous work, I found that high condition males both called more and lived longer than low condition males, although there was no trade-off between survival and calling effort. The substantial condition dependence of calling effort suggests that calling effort is under strong directional selection. In Chapter 4 I tested whether female mating preferences resulted in strong selection on male calling effort. I also tested for the condition dependence of female mating preferences. I found that female choosiness was condition-dependent, but the rank of preferred male songs (preference function) was not. Both low and high condition females preferred high calling effort over low calling effort song. In Chapter 5 I tested for evidence of nonlinear selection on male survival that might explain the nonlinear pattern of male investment in survival seen in Chapter 3 (i.e. male survival leveled-off with increasing condition). I found that socially experienced females, but not virgin and naive females, exerted linear selection on male age. I discuss these and the other results of my thesis in the context of previous work on field crickets and condition-dependent ornamentation. Finally, Appendix A reports results that confirm ancient Chinese cultural knowledge that large headed male crickets are more successful in male-male combat.
Evolutionary History and Biogeography of Papionin Monkeys
Keywords: primate
phylogenetic systematics
Pliocene
Pleistocene
Africa
fossil

Climate change has been invoked to explain patterns of speciation, extinction and biogeographic change over time, however it can be a difficult hypothesis to test empirically. One area of particular interest is climate change in the African Neogene, linked with the origin of hominins. A perfect model clade to test these hypotheses is the papionin monkeys, a diverse group (both extinct and extant), represented by an excellent fossil record. I describe new fossil papionin specimens from Coopers Cave, South Africa, and redescribe and discuss some previously known fossil material. This rich data set provides a necessary deep-time perspective, and, in conjunction with independently generated data, can be used to test hypotheses related to climatic and geological events (such as increasing late Pleistocene aridity and persistence of forest refugia) that may be directly linked to patterns of speciation and biogeographic distribution in the fossil record and in living species. Testing these hypotheses requires a robust phylogenetic hypothesis. I collected morphological character data for a species-level phylogenetic analysis of the papionin clade in order to reconstruct the phylogeny of the group. My analysis found that the living species Theropithecus gelada is nested within extinct theropiths, and is primitive relative to the Pleistocene taxa Theropithecus darti, T. oswaldi and T. leakeyi. Also falling within the theropith lineage are the early Pliocene taxon Pliopapio, the South African taxa Dinopithecus and Gorgopithecus, and two species whose relationships were uncertain until my analysis. “Papio” quadratirostris and “Papio” baringensis are nested within the theropiths, and should be referred to the genus Theropithecus. Biogeographic analysis demonstrates that papionin monkeys share a similar pattern with other Neogene African mammals; they first disperse out of Africa during the mid-Miocene, return to Africa by the late Miocene and undergo a series of vicariant speciation events and range restriction to central Africa, but disperse out into eastern and southern Africa by the Pleistocene. These speciation and dispersal events are tightly correlated with global climatic and tectonic changes.
Taxonomic, Phylogenetic, and Morphological Diversity of Anomodonts (Tetrapoda, Therapsida)
Keywords: paleontology
extinction
diversity
richness

Anomodonts are a group of non-mammalian synapsids (“mammal-like reptiles”) that represents the dominant herbivores of their time. Their great taxonomic and morphological diversity, unparalleled by any other clade of Permian-Triassic terrestrial tetrapods, is well documented by a cosmopolitan fossil record. In addition, anomodonts survived the most severe extinction event in Earth’s history at the end of the Permian and experienced a second diversification in the Triassic. Thus, they are an ideal clade to investigate macroevolutionary patterns and play an important role in evaluating the impact of the end-Permian extinction on the terrestrial realm. This work combines descriptive, phylogenetic, and quantitative approaches to study evolutionary patterns of anomodonts with special focus on diversity patterns through time. A taxonomic revision of the Late Permian dicynodont genus Emydops reflects the necessity for a solid taxonomic basis for diversity studies. The description of a new species of this genus is combined with a discussion of dental variability and pathology in dicynodont anomodonts. A detailed description of the postcranial anatomy of the basal anomodont Suminia reveals new insights into the early evolution of anomodonts and therapsids in general. Several derived features, in particular in the autopodium, are unique to Suminia and together with a comparative morphometric analysis indicate grasping abilities of this taxon and the earliest evidence for arboreality in the vertebrate fossil record. The cranial anatomy of the Triassic dicynodont Kombuisia is restudied and a phylogenetic evaluation of the survivorship of anomodonts across the Permian-Triassic boundary reveals more surviving lineages than previously recognized. A review of anomodont-bearing tetrapod faunas forms the basis for a faunal similarity analysis that reveals stratigraphic as well as geographic patterns in faunal groupings. The taxonomic diversity of anomodonts reflects three diversifications and subsequent extinctions in the early Middle Permian, the Early Triassic and the mid-late Triassic.
Information, Central Bank Communication, and Aggregate Fluctuations
Keywords: Macroeconomics
Imperfect Information
Central Bank Communication
Monetary Policy

This thesis examines two closely related issues: (1) the ability of imperfect information models to explain some aspects of business cycle dynamics, and (2) the interaction between central bank communications and monetary policy. These issues are related because central bank communications can only be studied in models with imperfect information. In chapter 1, I investigate the ability of a noisy rational expectations model to generate plausible macroeconomic dynamics. The model allows for imperfect, heterogeneous information, and signal extraction from endogenous variables. I find that imperfect information significantly improves the model's ability to generate persistent, hump-shaped responses to a transitory monetary policy shock. This is achieved without the need for mechanical frictions. In addition, the model generates realistic inflation forecast errors. Chapter 2 explores the relationship between central bank statements about future policy and the degree of commitment. I allow the central bank to make (possibly vague) statements about its expected future policy. I begin by assuming that the central bank adopts a loss function which internalizes the bygone costs of deviating from such a pre-announced policy action. The resulting policy is a convex combination of pure discretion and full commitment. As the precision of central bank statements increases, this policy converges to the full commitment policy. I then show that this type of commitment to internalize bygone costs is sustainable only for moderate degrees of precision. Chapter 3 studies the impact of central bank communications about the state of the economy. In particular, I examine the extent to which increased central bank transparency creates a meaningful trade-off between beneficially conveying fundamental information and adversely contaminating observed data with the central bank's opinion. This question is addressed in a variant of the model from chapter 1. In this environment, both the central bank and private agents learn about the state of the economy from observations of endogenous variables. By making the central bank learn from endogenous variables, I am able to study the impact of communications precision on the bank's signal extraction problem.
Essays on Monetary Coordination, Exchange Rate Volatility and Interfirm Networks
Keywords: Monetary Coordination
Exchange Rate Volatility
Interfirm Networks

This dissertation consists of three independent essays in Macroeconomics. The first essay analyzes monetary coordination between currency areas. It is shown that search frictions can generate the deviations from the law of one price and that each country is tempted to exploit these deviations by inflation. Monetary coordination eliminates the inefficiency caused by inflation. The welfare gains from coordination increase when the two economies become more integrated. In contrast to traditional models, the need for coordination exists even after each country is allowed to directly tax foreign holdings of its currency. The second essay studies the behavior of exchange rates in an environment with search frictions. In contrast to traditional models, even without any nominal rigidity, the model can generate enough volatility of exchange rates found in the data. The changes in the behavior of exchange rates under different regimes are also examined in this essay. The model shows a sharp increase in the volatility of exchange rates when moving from a pegged to a floating exchange regime, while there is no such systematic change in fluctuations of output or consumption. Moreover, the co-movements of output and consumption across countries are higher under a fixed rate regime than under a flexible rate regime. These results are consistent with empirical findings. The final essay focuses on the competition between groups of allied firms. In the essay we propose a model of group fitness and develop an approach to evaluate the fitness of groups and the utility of their member firms. A group has high fitness if member firms have four features: (i) high capacity, (ii) being embedded in dense relationships, (iii) holding complementary resources and (iv) having limited competition and conflict. We illustrate the effectiveness of our model and methodology by applying it to the airline groups between 1997 and 2002. By examining what really happened to the airline groups afterwards, we found that the predictions based on the comparison between the fitness scores of actual groups formed and those of the corresponding population constructed are reasonably accurate, and that the implications based on the ranking of individual firm utility within each group are generally supported.
Essays on the Political Economy of the Centralized Provision of Local Public Goods
Keywords: local public goods
political economy
fiscal federalism
distributive politics
school finance
accountability
No Child Left Behind
infrastructure spending
Quebec
California

This thesis explores the political economy aspects of the provision of local public goods by higher levels of government. Chapter 1 focuses on local public goods as instruments for special interest politics at the supra-local level, with an emphasis on public infrastructure. To capture the implications of long-run relationships between political parties and their loyal supporters, I set out a dynamic probabilistic voting model which predicts that the geographic pattern of spending depends on the way the government balances long-run `machine politics' considerations with the more immediate concern to win over swing voters. To assess the empirical relevance of both forces, I analyse rich data on road spending from a panel of electoral districts in Québec. Empirical results exploiting the province's linguistic fragmentation provide robust evidence that partisan loyalty is a key driver of the geographic allocation of spending. Chapter 2 proposes a theoretical framework to analyse the coexistence of multiple tiers of government in local public good provision. I study the effects of such partial decentralization on accountability using a two-period political agency model, in which two levels of government are involved in public good provision and voters are imperfectly informed about each government's contribution to the public good. The model predicts that the net effect of a departure from complete centralization (or decentralization) balances the benefits of vertical complementarity against the loss of accountability following from imperfect information and detrimental vertical interactions. Chapter 3 investigates the impact of partial decentralization on local electoral accountability in the context of California's school finance system. I exploit the peculiarities California's school finance system and the federal No Child Left Behind Act of 2001 to estimate the extent to which politicians are punished or rewarded for observed policy outcomes, and how this channel is affected by the degree of centralization. Results show that voters are responsive to differences in dropout rates and pupil-teacher ratios, and that incumbents are less likely to be reelected when a district's degree of centralization is high. Increased federal involvement after 2001 is associated with sharper local electoral accountability.
Multilinear Subspace Learning for Face and Gait Recognition
Keywords: Subspace Learning
Multilinear
Tensor
Face Recognition
Gait Recognition
Biometrics
Dimensionality Reduction
Embedding
Feature Extraction

Face and gait recognition problems are challenging due to largely varying appearances, highly complex pattern distributions, and insufficient training samples. This dissertation focuses on multilinear subspace learning for face and gait recognition, where low-dimensional representations are learned directly from tensorial face or gait objects. This research introduces a unifying multilinear subspace learning framework for systematic treatment of the multilinear subspace learning problem. Three multilinear projections are categorized according to the input-output space mapping as: vector-to-vector projection, tensor-to-tensor projection, and tensor-to-vector projection. Techniques for subspace learning from tensorial data are then proposed and analyzed. Multilinear principal component analysis (MPCA) seeks a tensor-to-tensor projection that maximizes the variation captured in the projected space, and it is further combined with linear discriminant analysis and boosting for better recognition performance. Uncorrelated MPCA (UMPCA) solves for a tensor-to-vector projection that maximizes the captured variation in the projected space while enforcing the zero-correlation constraint. Uncorrelated multilinear discriminant analysis (UMLDA) aims to produce uncorrelated features through a tensor-to-vector projection that maximizes a ratio of the between-class scatter over the within-class scatter defined in the projected space. Regularization and aggregation are incorporated in the UMLDA solution for enhanced performance. Experimental studies and comparative evaluations are presented and analyzed on the PIE and FERET face databases, and the USF gait database. The results indicate that the MPCA-based solution has achieved the best overall performance in various learning scenarios, the UMLDA-based solution has produced the most stable and competitive results with the same parameter setting, and the UMPCA algorithm is effective in unsupervised learning in low-dimensional subspace. Besides advancing the state-of-the-art of multilinear subspace learning for face and gait recognition, this dissertation also has potential impact in both the development of new multilinear subspace learning algorithms and other applications involving tensor objects.
Sensitive Solution-processed Quantum Dot Photodetectors
Keywords: Photodetectors
Quantum Dots

Optical sensing for imaging applications has traditionally been enabled by single-crystalline photodetectors. This approach has dramatically curtailed monolithic integration of a variety of optically-sensitive materials onto silicon read-out circuits. The advent of solution-processed optoelectronic materials such as colloidal quantum dots offers the potential of a revolution in optoelectronics. Their solution-processibility enables low-cost monolithic integration with an arbitrary substrate. This dissertation presents the first high-sensitivity solution-processed photodetectors. It does so by leveraging the high degree of control offered by nanoscale materials engineering. Material processing routes are developed to achieve sufficient carrier mobility and sensitization that lead to high photoconductive gain up to 10^3 A/W, observed for the first time in soft materials. A method to remove charge-transport-inhibiting moieties from the nanocrystal surface is developed. Surface treatment procedures are then advanced to prolong the carrier lifetime and thus sensitize the material. The sequence of these processing stages is crucial for the noise performance of the device. Processing conditions that lead to high photoconductive gain and low noise current are then reported to achieve highly sensitive photodetectors with reported D* on the order 10^13 Jones. The spectral tunability offered by colloidal quantum dots enables monolithic multispectral photodetectors. The material challenges, imposed by the behaviour of matter in the nanoscale, are addressed to report sensitive photodetectors in the visible and infrared parts of spectrum. Carrier lifetime determines the temporal response of a photoconductor. The abundance of trap states on the nanocrystal surface and their associated carrier lifetimes mandate careful attention in order to preserve the trap states that yield temporal response acceptable for imaging applications. It is shown for the first time that the temporal response of a quantum dot photoconductor can be tailored by careful control over surface chemistry. Materials species were identified as responsible for particular photocurrent temporal components. These findings are then exploited to isolate and remove surface species responsible for undesirably long time constants. A solution-processed photoconductive detector is reported that exhibits high sensitivity (D* ~10^12 Jones) and temporal response of 25 ms, suitable for imaging applications.
Infrared Sensitive Solution-processed Quantum Dot Photovoltaics in a Nanoporous Architecture
Keywords: photovoltaic
quantum dot
infrared
PbS
nanoporous

If solar energy is to be a significant component of our energy supply, technologies are required which produce high efficiency solar cells using inexpensive materials and versatile manufacturing processes. Solution-processed materials have been used to create low cost, easily fabricated devices, but have suffered from low power conversion efficiencies. A lack of infrared energy capture limits their efficiency. In this work we develop solution-processed photovoltaic devices using lead sulphide quantum dots and high surface area porous oxide electrodes. The resultant devices have a spectral response from 400 to 1800 nm. In fabricating these devices we utilize crosslinking molecules. We explore the impact crosslinkers have on the mobility and morphology of quantum dot films using field effect transistors and transmission electron microscopy. We also explore a hybrid organic/inorganic route for controlling the net doping in quantum dot films. We investigate the chemical and compositional changes that lead sulphide quantum dots films undergo during crosslinker treatment and annealing. Using this information we optimize our charge separation efficiency and our open circuit voltage. The resulting devices have an infrared power conversion efficiency of 2%, four orders of magnitude higher than that in previously reported lead sulphide quantum dot devices.