No description available.

<p> Flower shape, color and size are extensively studied to both identify and classify different angiosperm taxa. The availability of well-supported molecular phylogenies produced using complex models of sequence evolution, coupled with an understanding of the genes that regulate morphological form in model organisms, and new methods to infer gene expression patterns in diverse species now allow us to understand the genetic basis of morphological differences among closely related species. Studies in Plantaginaceae, Gesneriaceae, Fabaceae and Brassicaceae show the importance of <i>CYCLOIDEA (CYC), RADIALIS (RAD)</i> and <i>DIVARICATA (DIV)</i> in regulating flower shape, but also show divergence in gene function within flowering plants. Previous studies in the zygomorphic model species <i>Antirrhinum majus </i> (snapdragon) have shown that <i>AmCYC</i> is expressed in the adaxial (dorsal) petals of flowers where it activates <i>AmRAD </i>. This expression of <i>AmRAD</i> within adaxial petals represses <i>AmDIV</i> expression causing <i>AmDIV</i> to be restricted to abaxial (ventral) and lateral petals. Like <i>Antirrhinum </i>, traditional <i>Diplacus</i> flowers have distinct dorsal, ventral and lateral petal identities. However, within the clade actinomorphic flowers have evolved independently on two occasions: once in <i>D. pictus </i> and once in <i>D. mohaviensis</i>. mRNA reveal <i> DIV</i> expression to be conserved between <i>D. pictus</i> and snapdragon, whereas <i>CYC</i> and <i>RAD</i> expression, and presumably function, differ between the two species. <i>DpCYC</i> is expressed in a narrow portion on the upper lip of abaxial petals, whereas <i> DpRAD</i> is expressed within both lateral and abaxial petals. <i> D. pictus</i> flowers are characterized by a novel upturned abaxial petal which may be linked to localized <i>CYC</i> expression along the upper surface of the structure. This study sheds new light on the mechanisms regulating flower shape in an endemic Californian monkey flower and shows the importance of testing hypotheses from model species such as <i>Arabidopsis </i> and snapdragon in non-model taxa such as <i>D. pictus</i> to undercover the true variety of mechanisms driving morphological evolution.</p>

<p> Key to understanding the transition that vertebrates made from water to land is determining the developmental and genomic bases for the changes. New bioinformatic tools provide an opportunity to automate the discovery, broaden the number of, and provide an evidence-based ranking for potential candidate genes. I sought to explore this potential for the fin/limb transition, using the substantial genetic and phenotypic data available in model organism databases. Model organism data was used to hypothesize candidate genes for the fin/limb transition. In addition, 131 fin/limb candidate genes from the literature were extracted and used as a basis for comparison with candidates from the model organism databases. Additionally, seven genes specific to limb and 24 genes specific to fin were identified as future fin/limb transition candidates.</p>

<p> Lipid-producing microalgae are a feedstock for commercial products such as nutritional supplements, aquatic animal feed, and biofuels. Unlike most algal phyla, the diatoms (Bacillariophyta) characteristically produce storage lipids throughout their entire lifecycle. In this study, lipids were extracted via chloroform-methanol and quantified as percent dry weight, &mgr;g/mL, and pg/100 &mgr;m³ and then analyzed for a phylogenetic signal by comparing the variability between lineages to the variability within lineages for each metric. These ten taxa were then paired with data gathered from the literature and examined for a phylogenetic signal using previously described methods. In the first analysis, there was greater variability between than within lineages during stationary growth when using percent dry weight as a metric. In the second analysis, a statistically significant phylogenetic signal was detected for nutrient-deplete growth experiments when examining the genus-level phylogeny (P = 0.013).</p>

This project represents an initial examination of the evolutionary history of the genus Pilobolus, and provides a starting point for developing a method to accurately classify members of this genus using molecular genetics. The data analysis presented in this paper suggests a potential evolutionary path in which P. umbonatus and P. sphaerosporus diverged (along a common path) from an original generic ancestor early, but independently, from the evolutionary course taken by P. kleinii. Both Maximum Likelihood and parsimony analyses concur in the branch patterns. Additionally, formation of species-specific clades between samples of P. sphaerosporus, P. kleinii and P. umbonatus suggests that there may be markers present in the ITS sequence that can be used for the development of a molecular test for the classification of species within the genus Pilobolus.Ball State UniversityMuncie, IN 47306 / Department of Biology

<p> Historical biogeography has a diversity of methods for inferring ancestral geographic ranges on phylogenies, but many of the methods have conflicting assumptions, and there is no common statistical framework by which to judge which models are preferable. Probabilistic modeling of geographic range evolution, pioneered by Ree and Smith (2008, <i>Systematic Biology</i>) in their program LAGRANGE, could provide such a framework, but this potential has not been implemented until now. </p><p> I have created an R package, "BioGeoBEARS," described in chapter 1 of the dissertation, that implements in a likelihood framework several commonly used models, such as the LAGRANGE Dispersal-Extinction-Cladogenesis (DEC) model and the Dispersal-Vicariance Analysis (DIVA, Ronquist 1997, <i> Systematic Biology</i>) model. Standard DEC is a model with two free parameters specifying the rate of "dispersal" (range expansion) and "extinction" (range contraction). However, while dispersal and extinction rates are free parameters, the cladogenesis model is fixed, such that the geographic range of the ancestral lineage is inherited by the two daughter lineages through a variety of scenarios fixed to have equal probability. This fixed nature of the cladogenesis model means that it has been indiscriminately applied in all DEC analyses, and has not been subjected to any inference or formal model testing. </p><p> BioGeoBEARS also adds a number of features not previously available in most historical biogeography software, such as distance-based dispersal, a model of imperfect detection, and the ability to include fossils either as ancestors or tips on a time-calibrated tree. </p><p> Several important conclusions may be drawn from this research. First, formal model selection procedures can be applied in phylogenetic inferences of historical biogeography, and the relative importance of different processes can be measured. These techniques have great potential for strengthening quantitative inference in historical biogeography. No longer are biogeographers forced to simply assume, consciously or not, that some processes (such as vicariance or dispersal) are important and others are not; instead, this can be inferred from the data. Second, founder-event speciation appears to be a crucial explanatory process in most clades, the only exception being some intracontinental taxa showing a large degree of sympatry across widespread ranges. This is not the same thing as claiming that founder-event speciation is the <i>only</i> important process; founder event speciation as the only important process is inferred in only one case (<i>Microlophus</i> lava lizards from the Galapagos). The importance of founder-event speciation will not be surprising to most island biogeographers. However, the results are important nonetheless, as there are still some vocal advocates of vicariance-dominated approaches to biogeography, such as Heads (2012, <i>Molecular Panbiogeography of the Tropics</i>), who allows vicariance and range-expansion to play a role in his historical inferences, but explicitly excludes founder-event speciation <i> a priori.</i> The commonly-used LAGRANGE DEC and DIVA programs actually make assumptions very similar to those of Heads, even though many users of these programs likely consider themselves dispersalists or pluralists. Finally, the inclusion of fossils and imperfect detection within the same likelihood and model-choice framework clears the path for integrating paleobiogeography and neontological biogeography, strengthening inference in both. </p><p> Model choice is now standard practice in phylogenetic analysis of DNA sequences: a program such as ModelTest is used to compare models such as Jukes-Cantor, HKY, GTR+I+G, and to select the best model before inferring phylogenies or ancestral states. It is clear that the same should now happen in phylogenetic biogeography. BioGeoBEARS enables this procedure. Perhaps more importantly, however, is the potential for users to create and test new models. Probabilistic modeling of geographic range evolution on phylogenies is still in its infancy, and undoubtedly there are better models out there, waiting to be discovered. It is also undoubtedly true that different clades and different regions will favor different processes, and that further improvements will be had by linking the evolution of organismal traits (e.g., loss of flight) with the evolution of geographic range, within a common inference framework. In a world of rapid climate change and habitat loss, biogeographical methods must maximize both flexibility and statistical rigor if they are to play a role. This research takes several steps in that direction. </p><p> BioGeoBEARS is open-source and is freely available at the Comprehensive R Archive Network (http://cran.r-project.org/web/packages/BioGeoBEARS/index.html). A step-by-step tutorial, using the <i>Psychotria</i> dataset, is available at PhyloWiki (http://phylo.wikidot.com/biogeobears). </p><p> (Abstract shortened by UMI.)</p>

This thesis uses a range of different size spectra to compare contrasting benthic habitats in the aquatic realm. Temporal and spatial variation in benthic size spectra were investigated across a full salinity gradient (i.e. from freshwater, through estuarine to marine) in the River Yealm, south Devon, in order to gauge the influence of large differences in taxonomy and evolutionary history. Abundance and biomass size spectra showed a similar pattern among sites in all seasons but winter, suggesting that the size structure of benthic communities may be similar in sites with very different community compositions. A subsequent study comparing size spectra across salinity by employing artificial substrata suggested that substratum type also had little effect on the size structure of these benthic communities. A technique was developed for obtaining microbial size distributions for benthic communities and showed that microbial size structures were also similar between the marine and freshwater sites within the Yealm system. A final study demonstrated that the shape of size spectra was clearly affected by metal contamination. Size spectra across a salinity gradient -(i.e. from freshwater to lower estuary) in the highly contaminated Fal system were very different to those in the uncontaminated Yealm, due mostly to the low macrofaunal abundance in the former. This thesis is the first to assess patterns in benthic size spectra across a full salinity range in the same system. It is hoped that it will provide a base line for further studies in this exciting research area in macroecology and that biomass spectra might also prove useful as metrics for biomonitoring.

Hur läroböcker är utformade och vilket innehåll de har är inte en slump, utan ett resultat av åratal av forskning och ett samhälle i konstant förändring. Idag tar vi det som en självklarhet att ett stort kapitel i biologiundervisningen, såväl på högstadiet som i gymnasiet, tas upp av evolutionen, det vill säga läran om livets utveckling. Så har det inte alltid varit. Denna undersökning ämnar till att se om det finns ett samband mellan sekulariseringen av skolan och hur ämnet evolution har formats i biologiläroböckerna för högstadiet och gymnasiet. En textanalys har gjorts av 20 läroböcker från olika stadier och tidsperioder, resultaten har sammanställts och diskuterats. Sammanfattningsvis kan konstateras att biologiböckernas innehåll har förändrats i takt med dels sekulariseringen av den svenska skolan och dels olika skolreformer som gjorts under 1900-talet. Till detta kan vi addera de framsteg som naturvetenskapen gjort från andra halvan av 1800-talet fram till idag. Biologin i skolan har visat sig vara ett ämne som i allra högsta grad förändras med tiden, vilket tydligt avspeglas i de undersökta läromedlen. Skillnader mellan folkskolan och läroverken har funnits, resultat som kan tyda på att sekulariseringen av läroverken skedde snabbare än vad den gjorde i folkskolan.

No description available.

<p> Human development and health involves the complex and coordinated regulation of gene expression across diverse tissues. Gene regulation is therefore an essential process in human biology. In the field of human genetics, this has only become more apparent as genomic technologies have made genome-wide surveys of genetic variation underlying human traits possible. In my thesis work, I studied the impact of variation in gene regulation on human traits from three distinct perspectives of human genetics. I first examined the contribution of gene regulation to human disease susceptibility by combining gene expression data with a genome-wide association study to identify novel asthma susceptibility candidate genes. I then studied the effects of depleting specific transcription factors from the cell on downstream gene expression by incorporating gene expression data (following cellular depletion of those factors) with genomic transcription factor binding data. Finally, I considered the role of gene regulation in human evolution by integrating RNA-seq data collected in human, chimpanzee, and rhesus macaque lymphoblastoid cell lines with promoter reporter assays conducted in the same lines. Throughout this work, I have synthesized multiple genomic data sets and multiple distinct sub-disciplines of human genetics in order to arrive at a unified view of the role of gene regulation in determining human traits.</p>