<p>Recombination is the process in which genetic material is exchanged between one's homologous chromosome pairs during egg or sperm development (meiosis). Recombination is necessary for proper segregation of chromosomes during meiosis, and also plays a role in purging deleterious mutations, accelerating adaptation, and influencing the distribution of genomic features over evolutionary time. While recombination is clearly an important process, recombination rate is known to vary within and between individuals, populations, and species. Furthermore, what causes this variation remains relatively unknown. Using empirical and sequenced based estimates of recombination rate for the closely related species <italic>Drosophila pseudoobscura</italic> and <italic>Drosophila miranda</italic>, I seek to understand where recombination happens across the genome, to what extent recombination changes between species, and what genomic features are responsible for these changes. These data will deepen our understanding of mechanisms determining the recombination landscape, and shed light on generalized patterns and exceptions of recombination rate variation across the tree of life.</p> / Dissertation

This dissertation critiques and rejects Elliott Sober's dismissal of intelligent design as a scientific hypothesis. Sober builds the case for this dismissal in chapter 2 of his 2008 book Evidence and Evolution. Sober's case against intelligent design as science is a philosophical one, emerging from a Bayesian likelihood approach. Sober claims that unlike neo-Darwinian processes, intelligent design cannot supply independent evidence to support the claim that it is a measurably likely cause responsible for the emergence of biological organisms and the structures or processes of which they are composed. Without an assessable likelihood, Sober asserts that intelligent design (again, unlike neo-Darwinian mechanisms) is not testable, and since it is not testable, it does not qualify as a scientific hypothesis. This dissertation argues however, that according to Sober's own standards in Evidence, because intelligent design and the neo-Darwinian hypothesis both address unrepeated, major biological changes in the unobservable past, and because they both depend upon crucial analogies in order to support either inductive arguments or likelihood assessments, the two hypotheses stand on equivalent evidential and logical grounds. Either Sober must reject both neo-Darwinism and intelligent design, or he must allow them both as equivalent, rival hypotheses based upon a fair application of his argumentation requirements. In addition, after explaining important basics of analogy theory, and its crucial, even unavoidable role in the historical (or "origins") sciences, the dissertation goes on to show how intelligent design's empirical support, based upon analogy with humanly designed artifacts, machines and increasingly cell-like creations in the laboratory, is continuing to grow stronger by the year in both likelihood and in explanatory power. The dissertation thus concludes that intelligent design should be treated as a viable scientific explanation for the dramatic examples of specified complexity being discovered in biology, and indeed should be regarded as an increasingly vigorous rival to the neo-Darwinian explanation of such complexity.

In den Lebenswissenschaften haben sich Ontologien in den letzten Jahren auf breiter Front durchgesetzt und sind in vielen Anwendungs- und Analyseszenarien kaum mehr wegzudenken. So etablierten sich nach und nach immer mehr domänenspezifische Ontologien, z.B. Anatomie-Ontologien oder Ontologien zur Beschreibung der Funktionen von Genen oder Proteinen. Da das Wissen in den Lebenswissenschaften sich rapide ändert und weiterentwickelt, müssen die entsprechenden Ontologien ständig angepasst und verändert werden, um einen möglichst aktuellen Wissensstand zu repräsentieren. Nutzer von Ontologien müssen mit dieser Evolution umgehen können, d.h. um \\\\\\\"Up-to-Date\\\\\\\" zu sein, sollten die aktuellsten Versionen einer Ontologie verwendet werden. Dies ist häufig nur schwer umsetzbar, da die Evolution weitreichende Einflüsse auf existierende Datenbestände, Analyseergebnisse oder Anwendungen haben kann. Innerhalb dieser Dissertation stehen Werkzeuge und Algorithmen zum Umgang mit sich ständig ändernden Ontologien im Bereich der Lebenswissenschaften im Mittelpunkt. Zunächst wird ein generelles Framework für quantitative Evolutionsanalysen eingeführt. Das Framework wird für eine umfassende Analyse der Evolution zahlreicher Ontologien der Lebenswissenschaften verwendet. Die Analysen zeigen, dass alle untersuchten Ontologien stetig verändert (angepasst) werden und ein signifikantes Wachstum aufweisen. Auch für auf Ontologien basierte Mappings, d.h. Verknüpfungen zwischen Datenquellen und Ontologien (Annotation-Mapping) sowie zwischen Ontologien selbst (Ontologie-Mapping), liegen starke und häufige Veränderungen vor. Es besteht somit ein Bedarf, die Evolution von Ontologien in den Lebenswissenschaften und deren Konsequenzen zu unterstützen, d.h. Nutzern von sich ständig ändernden Ontologien angemessene Algorithmen/Werkzeuge bereitzustellen. Die Erkenntnisse aus den durchgeführten Analysen bilden die Basis für die nachfolgenden Arbeiten. Eine immer wiederkehrende Aufgabe im Rahmen der Ontologieevolution besteht in der Bestimmung von Änderungen zwischen zwei Versionen einer Ontologie, d.h. worin besteht der Unterschied und wie hat sich die neuere Version aus der alten Version heraus entwickelt. Das Ergebnis, d.h. der Diff (die Differenz) zwischen den beiden Ontologieversionen, bildet die Basis für weitere Aufgaben wie beispielsweise die Anpassung abhängiger Daten. Innerhalb der Arbeit wird ein neuartiger auf Regeln basierter Algorithmus vorgestellt, welcher den Diff zwischen zwei Ontologieversionen bestimmt. Es werden sowohl einfache wie auch komplexe Änderungen erkannt, was eine kompakte, intuitive und verständliche Diff-Repräsentation garantiert. Es wird theoretisch wie praktisch gezeigt, dass ein vollständiger Diff bestimmt wird, was eine korrekte Migration von Ontologieversionen ermöglicht. Ein weiterer Schwerpunkt der Arbeit liegt in der Bestimmung änderungsintensiver bzw. stabiler Regionen in einer Ontologie. Dazu wird die Notation von Ontologieregionen und zugehörige Metrikern zur Beurteilung ihrer Änderungsintensität (Stabilität) eingeführt. Ein neuartiger automatisierter Algorithmus erlaubt die Bestimmung (in)stabiler Ontologieregionen auf Basis veröffentlichter Ontologieversionen in einem vorgegebenen Zeitraum. Durch erkannte Änderungen zwischen Ontologieversionen und mit Hilfe der Ontologiestruktur werden änderungsintensive bzw. stabile Ontologieregionen erkannt. Die Evaluierung anhand großer Ontologien der Lebenswissenschaften zeigt, dass der Algorithmus in der Lage ist (in)stabile Ontologieregionen automatisiert zu bestimmen. Abschließend wird das webbasierte System OnEX und dessen Versionierungsansatz präsentiert. OnEX ermöglicht einen benutzerfreundlichen und interaktiven Zugang zu Informationen über die Evolution und Änderungen in Ontologien der Lebenswissenschaften. Nutzer können Ontologien aus ihrem Interessengebiet bzgl. Evolution untersuchen, indem sie beispielsweise Änderungen an einer Ontologieversion einsehen, welche in einer Analyse oder Anwendung genutzt werden soll. Der OnEX zugrunde liegende Versionierungsansatz ermöglicht eine skalierbare und speichereffiziente Versionierung großer Ontologien durch die Nutzung von Zeitstempeln. Mit Hilfe des Ansatzes konnten 16 Ontologien mit ca. 700 Versionen seit 2002 versioniert und Nutzern über OnEX für Evolutionsanalysen zugänglich gemacht werden.

Thesis (Ph. D.)--University of Hawaii at Manoa, 1995. / Includes bibliographical references (leaves 202-237). / Microfiche. / xvi, 237 leaves, bound ill., photos. 29 cm

Thesis by publication. / Thesis (PhD) -- Macquarie University, School of Biological Sciences, 1990. / Bibliography: leaves 269-324. / Introduction -- Models of parental allocation -- Sex expression in homosporous pteridophytes -- The origin of heterospory -- Pollination and the origin of the seed habit -- Brood reduction in gymnosperms -- Pollination: costs and consequences -- Adaptive explanations for the rise of the angiosperms -- Parent-specific gene expression and the triploid endosperm -- New perspectives on the angiosperm female gametophyte -- Overview -- Glossary -- Kinship terms in plants -- Literature Cited. / Among vascular plants/ different life cycles are associated with characteristic ranges of propagule size. In the modern flora, isospores of homosporous pteridophytes are almost all smaller than 150 urn diameter, megaspores of heterosporous pteridophytes fall in the range 100-1000 urn diameter, gymnosperm seeds are possibly all larger than the largest megaspores, but the smallest angiosperm seeds are of comparable size to large isospores. -- Propagule size is one of the most important features of a sporophyte's reproductive strategy. Roughly speaking, larger propagules have larger food reserves, and a greater probability of successful establishment, than smaller propagules, but a sporophyte can produce more smaller propagules from the same quantity of resources. Different species have adopted very different size-versus-number compromises. The characteristic ranges of propagule size, in each of the major groups of vascular plants, suggest that some life cycles are incompatible with particular size-versus-number compromises. -- Sex expression in homosporous plants is a property of gametophytes (homosporous sporophytes are essentially asexual). Gametophytes should produce either eggs or sperm depending on which course of action gives the greatest chance of reproductive success. A maternal gametophyte must contribute much greater resources to a young sporophyte than the paternal gametophyte. Therefore, smaller gametophytes should tend to reproduce as males, and gametophytes with abundant resources should tend to reproduce as females. Consistent with these predictions, large female gametophytes release substances (antheridiogens) which induce smaller neighbouring ametophytes to produce sperm. -- The mechanism of sex determination in heterosporous species appears to be fundamentally different. Large megaspores develop into female gametophytes, and small icrospores develop into male gametophytes. Sex expression appears to be determined by the sporophyte generation. This is misleading. As argued above, the optimal sex expression of a homosporous gametophyte is influenced by its access to resources. This is determined by (1) the quantity of food reserves in its spore and (2) the quantity of resources accumulated by the gametophyte's own activities. If a sporophyte produced spores of two sizes, gametophytes developing from the larger spores' would be more likely to reproduce as females than gametophytes developing from the smaller spores, because the pre-existing mechanisms of sex determination would favor production of archegonia by larger gametophytes. Thus, the predicted mechanisms of sex determination in homosporous species could also explain the differences in sex expression of gametophytes developing from large and small spores in heterosporous species. / Megaspores of living heterosporous pteridophytes contain sufficient resources for female reproduction without photosynthesis by the gametophyte (Platyzoma excepted), whereas microspores only contain sufficient resources for male reproduction. Furthermore, many more microspores are produced than megaspores. A gametophyte's optimal sex expression is overwhelmingly determined by the amount of resources supplied in its spore by the sporophyte, and is little influenced by the particular environmental conditions where the spore lands. Gametophytes determine sex expression in heterosporous species, as well as homosporous species. A satisfactory model for the evolution of heterospory needs to explain under what circumstances sporophytes will benefit from producing spores of two distinct sizes. -- In Chapter 4, I present a model for the origin of heterospory that predicts the existence of a "heterospory threshold". For propagule sizes below the threshold, homosporous reproduction is evolutionarily stable because gametophytes must rely on their own activities to accumulate sufficient resources for successful female reproduction. Whether a gametophyte can accumulate sufficient resources before its competitors is strongly influenced by environmental conditions. Gametophytes benefit from being able to adjust their sex expression in response to these conditions. For propagule sizes above the threshold, homosporous reproduction is evolutionarily unstable, because the propagule's food reserves are more than sufficient for a "male" gametophyte to fertilize all eggs within its neighbourhood. A population of homosporous sporophytes can be invaded by sporophytes that produce a greater number of smaller spores which could land in additional locations and fertilize additional eggs. Such'spores would be male-specialists on account of their size. Therefore, both spore types would be maintained in the population because of frequency-dependent selection. -- The earliest vascular plants were homosporous. Several homosporous groups gave rise to heterosporous lineages, at least one of which was the progeniture of the seed plants. The first heterosporous species appear in the Devonian. During the Devonian, there was a gradual increase in maximum spore size, possibly associated with the evolution of trees and the appearance of the first forests. As the heterospory threshold was approached, the optimal spore size for female reproduction diverged from the optimal spore size for male reproduction. Below the threshold, a compromise spore size gave the highest fitness returns to sporophytes, but above the threshold, sporophytes could attain higher fitness by producing two types of spores. -- The evolution of heterospory had profound consequences. Once a sporophyte produced two types of spores, microspores and megaspores could become specialized for male and female function respectively. The most successful heterosporous lineage (or lineages) is that of the seed plants. The feature that distinguishes seed plants from other heterosporous lineages is pollination, the capture of microspores before, rather than after, propagule dispersal. Traditionally, pollination has been considered to be a major adaptive advance because it frees sexual reproduction from dependence on external fertilization by freeswimming sperm, but pollination has a more important advantage. In heterosporous pteridophytes, a megaspore is provisioned whether or not it will be fertilized whereas seeds are only provisioned if they are pollinated. / The total cost per seed cannot be assessed solely from the seed's energy and nutrient content. Rather, each seed also has an associated supplementary cost of adaptations for pollen capture and of resources committed to ovules that remain unpollinated. The supplementary cost per seed has important consequences for understanding reproductive strategies. First, supplementary costs are expected to be proportionally greater for smaller seeds. Thus, the benefits of decreasing seed size (in order to produce more seeds) are reduced for species with small seeds. This effect may explain minimum seed sizes. Second, supplementary costs are greater for populations at lower density. Thus, there is a minimum density below which a species cannot maintain its numbers. -- By far the most successful group of seed plants in the modern flora are the angiosperms. Two types of evidence suggest that early angiosperms had a lower supplementary cost per seed than contemporary gymnosperms. First, the minimum size of angiosperm seeds was much smaller than the minimum size of gymnosperm seeds. This suggests that angiosperms could produce small seeds more cheaply than could gymnosperms. Second, angiosperm-dominated floras were more speciose than the gymnosperm-dominated floras they replaced. This suggests that the supplementary cost per seed of angiosperms does not increase as rapidly as that of gymnosperms, as population density decreases. In consequence, angiosperms were able to displace gymnosperms from many habitats, because the angiosperms had a lower cost of rarity. -- Angiosperm embryology has a number of distinctive features that may be related to the group's success. In gymnosperms, the nutrient storage tissue of the seed is the female gametophyte. In most angiosperms, this role is taken by the endosperm. Endosperm is initiated by the fertilization of two female gametophyte nuclei by a second sperm that is genetically identical to the sperm which fertilizes the egg. Endosperm has identical genes to its associated embryo, except that there are two copies of maternal genes for every copy of a paternal gene. -- Chapter 9 presents a hypothesis to explain the unusual genetic constitution of endosperm. Paternal genes benefit from their endosperm receiving more resources than the amount which maximizes the fitness of maternal genes, and this conflict is expressed as parent-specific gene expression in endosperm. The effect of the second maternal genome is to increase maternal control of nutrient acquisition. -- Female gametophytes of angiosperms are traditionally classified as monosporic, bisporic or tetrasporic. Bisporic and tetrasporic embryo sacs contain the derivatives of more than one megaspore nucleus. Therefore, there is potential for conflict between the different nuclear types within an embryo sac, but this possibility has not been recognized by plant embryologists. In Chapter 10, I show that many previously inexplicable observations can be understood in terms of genetic conflicts within the embryo sac. / Mode of access: World Wide Web. / 324 leaves ill

Univ., Diplomarbeit, 2006--Frankfurt (Main)

Literaturangaben

Diss. (sammanfattning) Uppsala : Uppsala universitet, 2009. / Härtill 5 uppsatser.

Thesis (M.S.)--Michigan State University. Interdepartmental Biological Sciences, 2008. / Title from PDF t.p. (viewed on Aug. 3, 2009) Includes bibliographical references (p.166-168). Also issued in print.

Thesis (Doctoral)--Ruprecht-Karls-Universität in Heidelberg, 1982.