As a software project ages, its source code is improved by refining existing features, adding new ones, and fixing bugs. Software developers can attest that such changes often require accompanying changes to the infrastructure that converts source code into executable software packages, i.e., the build system. Intuition suggests that these build system changes slow down development progress by diverting developer focus away from making improvements to the source code. While source code evolution and maintenance is studied extensively, there is little work that focuses on the build system. In this thesis, we empirically study the static and dynamic evolution of build system complexity in proprietary and open source projects. To help counter potential bias of the study, 13 projects with different sizes, domains, build technologies, and release strategies were selected for examination, including Eclipse, Linux, Mozilla, and JBoss. We find that: (1) similar to Lehman's first law of software evolution, Java build system specifications tend to grow unless explicit effort is invested into restructuring them, (2) the build system accounts for up to 31\% of the code files in a project, and (3) up to 27\% of source code related development tasks require build maintenance. Project managers should include build maintenance effort of this magnitude in their project planning and budgeting estimations. / Thesis (Master, Computing) -- Queen's University, 2011-01-31 12:46:06.082

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Proterogyrinus scheelei Romer, from the Upper Mississippian of Greer, West Virginia is one of the earliest known members of the amphibian infraorder Embolomeri. The primitive, eogyrinid-like skull conforms to Panchen's allometric plot of the British eogyrinids. The only distinct autapomorphy is a raised pineal foramen rim and an acuminate median ridge on the skull table posteriorly, flanked by deep bilateral pockets. The kinetic junction extends from the otic notch anteriorly to the posterodorsal corner of the orbit. The braincase, bearing no ossified roof, is composed of separate otic-occipital and sphenethmoid units, the latter being undivided. The vertebrae are similar to those of embolomeres, except that the pleurocentrum retains a dorsal suture in adults, and the intercentrum, unossified dorsally in adults, is a ventral crescent. The presacral count is 32. The atlas-axis is reptiliomorph. Zygapophysis structure indicates that the column must have undergone axial rotation during lateral flexion. The limbs and girdles are similar to those of Archeria, except that they are slightly stouter. Humerus structure is primitive. Range of limb movement, at least in the pectoral limb, is very restricted. An almost total lack of autapomorphies indicates that Proterogyrinus is a primitive member of the stem family (Proterogyrinidae) of the infraorder Embolomeri. Although most of the supposed autapomorphies of anthracosaurs that were formerly thought to preclude them from reptile ancestry are not considered to be valid, there are no identifiable synapomorphies with reptiles either, making it impossible to support close relationship between the two groups.

The primitive New Zealand frog Leiopelma hochstetteri shows exceptional karyotypic variation. On the North Island, females carry univalent W chromosome and both sexes have 0 to 15 supernumerary chromosomes. Frogs from Great Barrier Island have a conventional 2n = 22 karyotype, with no sex chromosome differentiation in C-banded mitotic chromosomes. However, the lampbrush chromosomes of a Great Barrier Island female show evidence of heterogamety. This suggests that presumed ancestral female heterogamety has persisted on Great Barrier Island and given rise to a WZZ-female/ZZ-male sex chromosome system on the North Island. / A repeated sequence, Lh1, varies greatly within populations in copy number and distribution on genomic EcoRI fragments. In situ hybridization revealed the variable presence of large Lh1 arrays on supernumerary chromosomes and two autosomes. The extensive Lh1 variability implies that, like the supernumeraries, it is more selfish than functional in the L. hochstetteri genome.

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<p> At its core human evolutionary biology seeks to answer the question of how the defining characteristics of modern humans evolved, such as large-brains, obligatory bipedal gait, extended juvenile period, and increased longevity. Traditional fossil-based research uses morphology to infer behavior and life history and only recently have researchers been able to make predictions regarding the effect of modifications to the DNA and proteins of our forbearers. Using these innovative methods we investigated the molecular evolution of a superfamily of transcription factors called the Nuclear Receptors. The patterns of sequence evolution observed in our bioinformatic analyses suggest a shift in the intensity of selection pressure occurred on <i>NR2C1</i>, a gene that plays a role early in embryonic stem cell proliferation and neuronal differentiation. Methods are now available to reconstruct ancestral DNA and its corresponding protein sequences and thus generate testable hypotheses about the functional evolution of genes on specific lineages. These methods allowed us to analyze how modifications to the modern human version of <i> NR2C1</i> affected the ability of an embryonic stem cell to remain in its proliferative state. We began by creating three different copies of our gene of interest: the human copy, the chimpanzee copy, and the ancestral copy of <i>NR2C1</i> for the inferred last common ancestor of chimpanzee and modern humans. Inserting these three different gene variants into mouse embryonic stem cells that have had NR2C1 knocked down allowed us to quantitatively analyze the transcriptional and regulatory functions of <i>NR2C1</i>. </p>

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