Uma análise comparativa dos tempos de divergência dos eventos de cladogênese dentro dos gêneros Proechimys, Thrychomys e Trinomys de equimiídeos, baseada em seqüências do gene mitocondrial citocromo b, revelou distintos padrões de diversificação para esses três gêneros. Em geral houve pouca sobreposição entre os eventos de diversificação dos três gêneros comparados. Tanto Proechimys quanto Trinomys comportam diversas linhagens antigas, que vêm se diferenciando desde o Mioceno Médio. Thrichomys apresentou indício de uma perda de linhagens entre o final do Mioceno e o início do Plioceno, que pode estar associada ao Grande Intercâmbio Biótico Americano. Esses dados sugerem que as oscilações climáticas podem ter afetado de maneira diversa, com distintas respostas, os diferentes biomas ocupados por esses três gêneros. Nossos dados sugerem que apenas um modelo de diversificação não pode explicar a diversidade neotropical, enfatizando a necessidade de abordagens com modelos mais complexos. Este estudo demonstra a importância de associar uma estrutura temporal às análises filogenéticas. Associar tempo a eventos de cladogênese permite inferir modelos de especiação e extinção, comparar taxas de evolução entre táxons e correlacionar esses eventos com processos geológicos, paleoclimáticos e biogeográficos. / Comparative analysis of divergence times for cladogenic events within the echimyid genera Proechimys, Thrychomys, and Trinomys, based on sequences of the mitochondrial cytochrome-b gene, revealed distinct patterns of diversification for these three genera. In general there was little overlap between the events of diversification of the three genera, when compared. Both Proechimys and Trinomys consist of several lineages which have become differentiated since the Middle Miocene. Thrichomys seems to have undergone a severe bottleneck, with the survival of a single lineage, which may be associated with the Great American Biotic Interchange. These data suggest that fluctuations in past climate may have affected differently, the different biomes occupied by these three genera. Our data suggest that a single speciation mode fails to explain Neotropical biodiversity, emphasizing the need for approaches using complex models. This study demonstrates the importance of associating a temporal framework to phylogenetic analyses. Relating cladogenesis and time allows testing of hypotheses about the mode of speciation and extinction, comparison of rates of evolution across taxa, and correlation of such events with important geological, paleoclimatic, and biogeographic processes.

by Leung Man-sing. / Thesis (M.Phil.)--Chinese University of Hong Kong, 1981. / Bibliography: leaves 145-166.

From the 1920s until present day, the technological evolution of the office building, or more specifically, the office building skyscraper has been eminent. From past to present, the functions of this building have changed dramatically and with this change, a component cost shift has occurred. An investigation of different technologies that have transformed over the years has been performed on three notable skyscrapers: the Empire State Building (1931 completion), the World Trade Center (1971 completion), and One World Trade Center (late 2013 projected completion). All buildings are located in New York City, New York and were constructed at relatively equal intervals throughout time, from each other. A building can be broken down into different elements and for this analysis; five specific components were investigated. They were the podium, also known as the foundation and floors, the load-bearing members of the structure, or frame, the veneer or curtain wall system, the interior finishes of the building and any machinery involved with the buildings functional usage. All three buildings incorporate all five of these components in their design, but there are distinctions as to how the percentages of importance of each changed as the evolution and knowledge of technology progressed throughout time. This study has addressed the different methods each building used to achieve a technological cutting edge of their respective periods of time of construction, within the scope of the five main building components.

Harvard psychologist Steven Pinker recently examined a problem with understanding human cognition, particularly how the processes of biological evolution could explain the human ability to think abstractly, including the higher cognitive abilities for logic and math (hereafter, HCAs). Pinker credits the formulation of the problem of understanding human cognition and the evolutionary development of HCAs to the co-discoverer of evolution by natural selection, Alfred Russell Wallace. Pinker states the following response to the question raised by Wallace: "…Nonetheless it is appropriate to engage the profound puzzle [Wallace] raised; namely, why do humans have the ability to pursue abstract intellectual feats such as science, mathematics, philosophy, and law, given that opportunities to exercise these talents did not exist in the foraging lifestyle in which humans evolved and would not have parlayed themselves into advantages in survival and reproduction even if they did?" Wallace claimed that while ancestral cognitive operations, such as those operations for perception and motor control, were the product of evolution, he disagreed with Charles Darwin’s view that HCAs are the product of evolution by natural selection. Wallace is not the only one to doubt that HCAs are the product of evolution. Contemporary philosopher Thomas Nagel also rejects the view that HCAs are the product of evolution. Comparable to Wallace, although Nagel accepts that older operations of the brain, such as perception and motor control, are the product of evolution, Nagel denies that higher types of cognitive operations are the product of evolution. The aim of this dissertation is to argue that HCAs are the product of evolutionary processes, both natural selection and other mechanisms of change. The reason HCAs are the product of evolution is because HCAs are carried out by the neural reuse of older evolved brain regions. Neural reuse is the view that brain regions can be recruited for multiple cognitive uses. Ancestral brain regions, such as regions for perceptual and motor functions, can be reused for carrying out HCAs, such as language, logic, and math.

Understanding how environmental forces, genetic variation, and developmental process combine to mold adaptations remains a core challenge in evolutionary biology. Our research is answering this challenge. More specifically we focused on how these three drivers of adaptation have shaped the evolution of body morphology in poeciliid fish. The body morphology of poeciliid fish has been shown to be under strong ecological selection and sexual selection. In the poecilid fish Poecilia reticulata, body morphology can evolve rapidly, over a span of four to five years. These attributes makes it an ideal system to study the processes leading to adaptive evolution. Here we studied this adaptive evolution in poeciliid fish at two scales: among populations of a single species and within populations of a single species. At the broadest scale, we investigated local adaptation among populations of a single poeciliid species, Heterandria formosa. We quantified patterns in morphological variation among populations and tested for associations between this variation and ecological data, which are derived from long term population censuses. Results from this study illustrate the complicated construction of multivariate phenotypic variation and suggest that different agents of selection have acted on different components of body morphology. These patterns in inter-population phenotypic variation can be evidence of local adaptation; however, they can also be reflective of patterns in phenotypic plasticity induced by environmental or maternal effects. The role of maternal effects are especially relevant in H. formosa as females are live bearing and provide nutrients to developing embryos via a placenta. We used a common garden experiment and a large factorial breeding experiment to explicitly test for genetically based differences among populations in their responses to environmental variation (norms of reaction). This laboratory work allowed a definitive diagnosis of which features actually represented local adaptations among populations of Heterandria formosa. Results showed that male body morphology has a significant genetic component and signs of population specific response to both the environment during post-parturition development and in response to the maternal environment during embyronic development. The narrowest scope of our work focuses on the evolution of body morphology within an experimental population of the Trinidadian guppy. Interestingly, the strength and direction of selection on phenotypic variation is not the same among all individuals within a population. In particular, genetic correlations between the sexes can produce intralocus sexual conflicts (ISC) when selection favors different trait values in the genders. This form of sexual conflict can inhibit the evolution of males and females so that neither sex can reach its optimal trait value. Theory suggests that ISC will have a minimal effect in populations off there adaptive peak such as those in a novel or variable environment. However, ISC is likely to have an inhibitory effect in populations in a stable environment near their adaptive, thereby limiting adaptive evolution. Here we used an experimental population of Trinidadian guppies in a novel environment to unravel the emergence of sexual conflict as populations adapt to novel environments. Guppies from a high predation environment were translocated to a drainage with minimal predation. The phenotypic evolution of the population was tracked monthly. This work incorporates mark-recapture methods, complete pedigree reconstruction using high throughput sequencing, and geometric morphometric shape analysis. Results indicate that there are fitness differences among individuals and different optimal values in males and females but the role of sexual conflict within this population is currently negligible. To conclude, our work investigated the environmental and genetic factors influencing the evolution of body morphology in poeciliid fish. We demonstrate the complicated nature of selection with different selective agents acting on different aspects of body morphology. We found that populations of fish have unique environmental maternal effects which may ultimately be adaptive. We also conclude that while there are optimal trait value differences in males and female guppies but being off the adaptive peak limits the influence of ISC on morphological evolution. / A Dissertation submitted to the Department of Biological Science in partial fulfillment of the requirements for the degree of Doctor of Philosophy. / Summer Semester 2018. / July 13, 2018. / Local Adaptation, Morphometric, Poeciliid, Sexual Conflict / Includes bibliographical references. / Joseph Travis, Professor Directing Dissertation; Dennis Slice, University Representative; Emily DuVal, Committee Member; Gregory Erickson, Committee Member; Kimberly Hughes, Committee Member.

The Andes, along with the Amazon and Atlantic forests, harbor the richest avifauna in the world with roughly one third of all the world's species of birds. Many biogeographical studies have sought to explain the origin and diversification of Andean taxa. However, because of the Andes' extensive latitudinal span and complexity, there is no one single cause of origin or of diversification that can explain the diversity found in them. Along the Andes, multiple biogeographic patterns of disjunction between highland and lowland sister-groups have been linked to Andean uplift. For example, Ribas et al. (2007) provided evidence that the spatio-temporal diversification in the monophyletic parrot genus Pionus is causally linked to Andean tectonic and palaeoclimate change through vicariance. Thus, if the Andes uplift is responsible for some of the patterns of montane-lowland disjunctions, it may be one of the mechanisms underlying the taxonomic assembly of the Andean montane avifauna. In this dissertation I explored whether the origin and diversification of three groups of Andean birds--the exclusively Andean parrot genera Hapalopsittaca, the subclade of mangoes containing Doryfera, Schistes, and Colibri, and the ovenbirds of the tribe Thripophagini--can be linked to Earth history. The results show that the origin of these Andean taxa can be explained through vicariance from their lowland sister-groups, mediated by the uplift of the Andes. Thus, this thesis proposes that geological events are directly responsible for originating diversity throughout montane environments. Once in the Andes, the diversification of these montane taxa can be explained by events such as the tectonic evolution of the Andes--which created canyons and valleys that may have caused the vicariance of continuous populations--as well as by the climatic oscillation of the Pleistocene, which caused altitudinal shifts, expansion, and contraction of the montane vegetation belts during the climatic oscillations of the Pleistocene. In summary a significant part of the temporal patterns of origins and diversification of the three groups of birds included in this study can be linked to Earth history, both in terms of the tectonic history of the Andes and of the climatic events of the Pleistocene.

Adolescence is the time when humans begin utilizing mating strategies (e.g., flirting, fighting or rumor spreading about competitors) to attract and keep mates. Consistent empirical evidence shows that some adolescent boys are on a developmental pathway in which they utilize aggression and risky behaviors in their mating strategies, but there is little research on adolescent girls' use of aggression and risk-taking in mating. This study hypothesized that ethnically diverse, young adolescent girls nominated consistently as flirters were also more likely to be nominated as aggressive and report higher levels of risk taking behaviors (e.g., drug use, delinquency) than girls not nominated as flirters. This study assessed mating effort via a new approach: peer-report of flirting behavior, which is dissimilar to previous studies that asked participants to report on their mating effort behaviors or report on peers who were not participants in the study. It is proposed that flirting behavior will increase yearly from 6th to 8th grade, coinciding with the start of puberty. It is also predicted that consistent flirters will endorse dating more frequently, as mating behavior and mate success are strongly linked in the literature. This study also investigated the relationship between attractiveness, which is an aspect of mate value, and mating effort. Researchers have found that mating effort and mate value increase one's mating success and they are positively correlated. Also, this study analyzed the relationship between adolescents' familial adversity and their mating effort as previous research found that familial adversity has a causal influence on teenage sexual risk taking behaviors, earlier start of puberty, and earlier sexual debut. Sixth graders in two large middle schools in a low income, ethnically diverse, northeastern school district were followed for three years for a larger longitudinal study. This study uses data from a subsample of 190 adolescent girls with complete data for 7th and 8th grades. Measures were administered in language arts or social studies classes during the fall of each year. Measures included a peer-report of flirtatiousness and aggressive behavior via the Revised Class Play (Masten, Morrison, & Pelligrini, 1985), self-report of dating frequency, and self-report of risk taking behaviors including substance and alcohol use (Winters, 1992) and delinquency (Elliot, Huizinga, & Ageton, 1985). Attractiveness was assessed via peer-report ratings of yearbook photos and self-reports of body image and appearance satisfaction (Cash, 2000). Adverse familial background was measured as self-report of psychological aggression from parents (Straus, Hamby, Finkelhor, Moore, & Runyan, 1998) and living arrangements in 6th grade.

Theropod dinosaurs are an iconic and familiar group of extinct species that include predators such as Tyrannosaurus and Velociraptor, as well as an array of other Mesozoic taxa. Carnivorous theropods are the evolutionary ancestors of birds, and the evolutionary transition between theropods and birds is a textbook example of a major evolutionary transformation in the history of life. Despite a flurry of research on early birds and their dinosaurian relatives, however, several questions still remain. First, the anatomy of some major theropod groups has yet to be described in detail. Second, there is little consensus on the phylogenetic relationships of the basal members of a theropod subgroup called Coelurosauria: the clade of birds and their closest relatives (defined as all taxa closer to birds than to Allosaurus). Third, there has been little synthetic work on large-scale macroevolutionary patterns during theropod evolution. This dissertation includes three chapters that touches on these three major issues. Chapter 1 is a detailed description of the Late Cretaceous tyrannosaurid theropod Alioramus altai, based on its holotype specimen from the Tsaagan Khuushu locality in the Maastrichtian Nemegt Formation of Mongolia. This monographic description provides further evidence that Alioramus is an unusual long-snouted, gracile, and slender-limbed taxon with an unpredecented degree of cranial ornamentation among tyrannosaurids and an extremely pneumatized skeleton. Anatomical comparisons indicate that the long skull of Alioramus is an autapomorphic feature that is proportionally longer (relative to femur length) than in any other known tyrannosaurid specimen, including juveniles, and that Alioramus is morphologically distinctive relative to similarly-sized individuals of the contemporary and sympatric Tarbosaurus. The coexistence of the long-snouted Alioramus and robust and deep-snouted Tarbosaurus, which are found together at the Tsaagan Khuushu locality, demonstrate that multiple large tyrannosaurids were able to live in sympatry, likely because of niche partitioning due to differences in craniofacial morphology and functional behavior. Chapter 2 presents a comprehensive new phylogenetic analysis of coelurosaurian theropods, which is an updated version (and thus the latest iteration) of the long-standing Theropod Working Group (TWiG) analysis. The new analysis incoroporates a wealth of new taxa and character data into the TWiG matrix for the first time, most of which is relevant to basal (non-maniraptoran) coelurosaurs such as tyrannosauroids and ornithomimosaurs, which had previously been the subject of only cursory character and taxon sampling in TWiG studies. The full dataset was analyzed under parsimony, and the resulting phylogeny includes several well supported relationships and agrees with previous analyses in many aspects. As a result, it is argued that a consensus view of basal coelurosaurian relationships has emerged, including: 1) the monophyly of major subclades such as Tyrannosauroidea, Compsognathidae, and Ornithomimosauria; 2) the position of the singleton genera Bicentenaria, Zuolong, and Tugulusaurus near the base of Coelurosauria; 3) the placement of Tyrannosauroidea as the most basal major coelurosaurian subclade; 4) the inclusion of Guanlong, Dilong, and Proceratosaurus within Tyrannosauroidea; 5) the existence of a derived maniraptoran clade that includes alvarezsauroids, therizinosauroids, oviraptorosaurs, and paravians to the exclusion of ornithomimosaurs and tyrannosauroids. Remaining areas of uncertainty include the phylogenetic position of Compsognathidae and the singleton genus Ornitholestes, and relationships at the base of the Ornithomimosauria + Maniraptora clade and Maniraptora itself. The phylogeny indicates that much of the early history of Coelurosauria has yet to be sampled in the fossil record, that coelurosaurs originated at small body size, and that the evolution of the iconic Tyrannosaurus-like bauplan occurred only towards the end of the Cretaceous. Chapter 3 presents a geometric morphometric analysis that is used to study broad patterns in theropod skull shape variation and compare the distribution of taxa in cranial morphospace (form) to both phylogeny and quantitative metrics of biting behaviour (function). The analysis finds that theropod skulls primarily differ in relative anteroposterior length and snout depth and to a lesser extent in orbit size and depth of the cheek region, and that oviraptorosaurs deviate most strongly from the "typical" and ancestral theropod morphologies. Noncarnivorous taxa generally fall out in distinct regions of morphospace and exhibit greater overall disparity than carnivorous taxa, whereas large-bodied carnivores independently converge on the same region of morphospace. The distribution of taxa in morphospace is strongly correlated with phylogeny but only weakly correlated with functional biting behaviour. These results imply that phylogeny, not biting function, was the major determinant of theropod skull shape.

With the number of sequenced microbial species soon to be in the tens of thousands, we are in a unique position to investigate microbial function, ecology, and evolution on a large scale. In this dissertation I first describe the use of hundreds of in silico models of bacterial metabolic networks to study the long-term the evolution of growth and gene-essentiality phenotypes. The results show that, over billions of years of evolution, the conservation of bacterial phenotypic properties drops by a similar fraction per unit time following an exponential decay. The analysis provides a framework to generate and test hypotheses related to the phenotypic evolution of different microbial groups and for comparative analyses based on phenotypic properties of species. Mapping of genome sequences to phenotypic predictions -such as used in the analysis just described- critically relies on accurate functional annotations. In this context, I next describe GLOBUS, a probabilistic method for genome-wide biochemical annotations. GLOBUS uses Gibbs sampling to calculate probabilities for each possible assignment of genes to metabolic functions based on sequence information and both local and global genomic context data. Several important functional predictions made by GLOBUS were experimentally validated in Bacillus subtilis and hundreds more were obtained across other species. Complementary to the automated annotation method, I also describe the manual reconstruction and constraints-based analysis of the metabolic network of the malaria parasite Plasmodium falciparum. After careful reconciliation of the model with available biochemical and phenotypic data, the high-quality reconstruction allowed the prediction and in vivo validation of a novel potential antimalarial target. The model was also used to contextualize different types of genome-scale data such as gene expression and metabolomics measurements. Finally, I present two projects related to population genetics aspects of sequence and genome evolution. The first project addresses the question of why highly expressed proteins evolve slowly, showing that, at least for Escherichia coli, this is more likely to be a consequence of selection for translational efficiency than selection to avoid misfolded protein toxicity. The second project investigates genetic robustness mediated by gene duplicates in the context of large natural microbial populations. The analysis shows that, under these conditions, the ability of duplicated yeast genes to effectively compensate for the loss of their paralogs is not a monotonic function of their sequence divergence.

Evolution is a force that has molded human existence since its divergence from chimpanzees about 5.4 million years ago. In that same amount of time, an influenza virus, which replicates every six hours, would have undergone an equivalent number of generations over only a hundred years. The fast replication times of influenza, coupled with its high mutation rate, make the virus a perfect model to study real-time evolution at a mega-Darwin scale, more than a million times faster than human evolution. While recent developments in high-throughput sequencing provide an optimal opportunity to dissect their genetic evolution, a concurrent growth in computational tools is necessary to analyze the large influx of complex genomic data. In my thesis, I present novel computational methods to examine different aspects of influenza evolution. I first focus on seasonal influenza, particularly the problems that hamper public health initiatives to combat the virus. I introduce two new approaches: 1. The q2-coefficient, a method of quantifying pathogen surveillance, and 2. FluGraph, a technique that employs network topology to track the spread of seasonal influenza around the world. The second chapter of my thesis examines how mutations and reassortment combine to alter the course of influenza evolution towards pandemic formation. I highlight inherent deficiencies in the current phylogenetic paradigm for analyzing evolution and offer a novel methodology based on algebraic topology that comprehensively reconstructs both vertical and horizontal evolutionary events. I apply this method to viruses, with emphasis on influenza, but foresee broader application to cancer cells, bacteria, eukaryotes, and other taxa.