Matching Items (22)

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The evolution of addiction: a case study of nicotine dependence

Description

A variety of studies have shown that the tendency toward nicotine dependence has a genetic component. The work described in this thesis addresses three separate questions: i) are there unidentified SNPs in the nicotinic receptors or other genes that contribute

A variety of studies have shown that the tendency toward nicotine dependence has a genetic component. The work described in this thesis addresses three separate questions: i) are there unidentified SNPs in the nicotinic receptors or other genes that contribute to the risk for nicotine dependence; ii) is there evidence of ongoing selection at nicotinic receptor loci; and, iii) since nicotine dependence is unlikely to be the phenotype undergoing selection, is a positive effect on memory or cognition the selected phenotype. I first undertook a genome –wide association scan of imputed data using samples from the Collaborative Study of the Genetics of Nicotine Dependence (COGEND). A novel association was found between nicotine dependence and SNPs at 13q31. The genes at this newly associated locus on chromosome 13 encode a group of micro-RNAs and a member of the glypican gene family. These are among the first findings to implicate a non-candidate gene in risk for nicotine dependence. I applied several complimentary methods to sequence data from the 1000 Genomes Project to test for evidence of selection at the nicotinic receptor loci. I found strong evidence for selection for alleles in the nicotinic receptor cluster on chromosome 8 that confer risk of nicotine dependence. I then used the dataset from the Collaborative Studies on the Genetics of Alcoholism (COGA) and looked for an association between neuropsychological phenotypes and SNPs conferring risk of nicotine dependence. One SNP passed multiple test correction for association with WAIS digit symbol score. This SNP is not itself associated with nicotine dependence but is in reasonable (r 2 = 0.75) LD with SNPs that are associated with nicotine dependence. These data suggest at best, a weak correlation between nicotine dependence and any of the tested cognitive phenotypes. Given the reproducible finding of an inverse relationship between SNPs associated with risk for nicotine dependence and cocaine dependence, I hypothesize that the apparently detrimental phenotype of nicotine dependence may confer decreased risk for cocaine dependence. As cocaine use impairs the positive rewards associated with social interactions, reducing the risk of cocaine addiction may be beneficial to both the individual and the group.

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2014

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Genomic diversity and abundance of LINE retrotransposons in 4 anole lizards

Description

Vertebrate genomes demonstrate a remarkable range of sizes from 0.3 to 133 gigabase pairs. The proliferation of repeat elements are a major genomic expansion. In particular, long interspersed nuclear elements (LINES) are autonomous retrotransposons that have the ability to "cut

Vertebrate genomes demonstrate a remarkable range of sizes from 0.3 to 133 gigabase pairs. The proliferation of repeat elements are a major genomic expansion. In particular, long interspersed nuclear elements (LINES) are autonomous retrotransposons that have the ability to "cut and paste" themselves into a host genome through a mechanism called target-primed reverse transcription. LINES have been called "junk DNA," "viral DNA," and "selfish" DNA, and were once thought to be parasitic elements. However, LINES, which diversified before the emergence of many early vertebrates, has strongly shaped the evolution of eukaryotic genomes. This thesis will evaluate LINE abundance, diversity and activity in four anole lizards. An intrageneric analysis will be conducted using comparative phylogenetics and bioinformatics. Comparisons within the Anolis genus, which derives from a single lineage of an adaptive radiation, will be conducted to explore the relationship between LINE retrotransposon activity and causal changes in genomic size and composition.

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2013

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Hybridization and speciation in common and black-tufted marmosets (Callithrix jacchus and C. penicillata)

Description

As an evolutionary force, hybridization outcomes include introgression, admixture, speciation, and reproductive isolation. While hybridization has been studied in several primates, the marmoset genus Callithrix is an important, but little studied example of Neotropical hybridization. Varying degrees of reproductive isolation

As an evolutionary force, hybridization outcomes include introgression, admixture, speciation, and reproductive isolation. While hybridization has been studied in several primates, the marmoset genus Callithrix is an important, but little studied example of Neotropical hybridization. Varying degrees of reproductive isolation exist between Callithrix species, and hybridization occurs at species borders or regions containing introduced and native species. Interbreeding between Callithrix species carries important implications for biodiversity and genetic integrity within the genus. However, species origins and levels of genetic admixture in marmoset hybrid zones are generally unknown, and few population genetic studies of individual Callithrix species exist. Using the mitochondrial control region and 44 microsatellite markers, this work explored the genetic diversity and species origins of two C. penicillata and C. jacchus hybrid zones, as well as genetic diversity and divergence in the parental species. Both marker types showed that C. penicillata is more genetically diverse than C. jacchus. Based on mtDNA, C. jacchus seems to have experienced a past population expansion and C. penicillata evolved under constant population size. The data revealed the existence of a previously undocumented natural hybrid zone along the São Francisco River in NE Brazil and confirmed species origins of an anthropogenic zone in Rio de Janeiro state. The data also showed much lower levels of admixture and genetic diversity within the natural hybrid zone than in the anthropogenic zone. Further, the data suggested that the São Francisco River is an important geographic barrier to gene flow in the natural hybrid zone. On the other hand, admixture patterns within the anthropogenic hybrid zone suggested collapse of reproductive barriers, and the formation of a hybrid marmoset swarm. Thus, this work suggested different evolutionary dynamics in anthropogenic vs. natural animal hybrid zones. Restriction Associated DNA sequencing (RADseq) identified a large number of single nucleotide polymorphisms within C. jacchus and C. penicillata genomes. These preliminary data were used to measure intraspecific genomic diversity and interspecific divergence. In the future, RADseq will be used to study genus-wide diversity of Callithrix species, examine past and present marmoset demographic history, and applied to the evolutionary study of marmoset hybridization.

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2013

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Locomotor function and the evolution of the primate pelvis

Description

The bony pelvis is a pivotal component of the locomotor system, as it links the hindlimb with the trunk and serves as anchorage for the primary propulsive musculature. Its shape is therefore expected to be adapted to the biomechanical demands

The bony pelvis is a pivotal component of the locomotor system, as it links the hindlimb with the trunk and serves as anchorage for the primary propulsive musculature. Its shape is therefore expected to be adapted to the biomechanical demands of habitual locomotor behavior. However, because the relationship between locomotor mechanics and pelvic morphology is not well understood, the adaptive significance of particular pelvic traits and overall pelvic shape remains unclear. This study used an integrative, dual approach to elucidate the relationship between form and function in the primate pelvis. A biomechanical cylinder model of pelvic stress resistance was tested using in vitro strain analysis of monkey and ape cadaver specimens. These results were used to refine adaptive hypotheses relating pelvic form to locomotor mechanics. Hypotheses of adaptation were then tested via univariate and geometric morphometric methods using a taxonomically broad, comparative sample of 67 primate taxa. These results suggest that the pelvis exhibits some iliac and ischial adaptations to stress resistance that are associated with the biomechanical demands of habitual locomotor loading and of body size. The ilium and ischium exhibit relatively low levels of strain during experimental loading as well as adaptations that increase strength. The pubis exhibits relatively high strains during loading and does not vary as predicted with locomotion. This integrated study clarifies the relationship between strain and adaptation; these results support the hypothesis that bones adapted to stress resistance exhibit low strains during typical loading. In general, the cylinder model of pelvic biomechanics is unsupported. While the predictions of loading regimes were generally rejected, the inability of these methods to test the possible occurrence of overlapping loading regimes precludes outright rejection of the cylinder model. However, the lack of support for predicted global responses to applied loading regimes suggests that pelvic stress resistance may be better explained by a model that accounts for local, functional subunits of pelvic structure. The coalescence of a localized model of pelvic biomechanics and comparative morphometrics has great potential to shed light on the evolution of the complex, multi-functional structure of the pelvis.

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2010

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From fertilization to birth: representing development in high school biology textbooks

Description

Biology textbooks are everybody's business. In accepting the view that texts are created with specific social goals in mind, I examined 127 twentieth-century high school biology textbooks for representations of animal development. Paragraphs and visual representations were coded and placed

Biology textbooks are everybody's business. In accepting the view that texts are created with specific social goals in mind, I examined 127 twentieth-century high school biology textbooks for representations of animal development. Paragraphs and visual representations were coded and placed in one of four scientific literacy categories: descriptive, investigative, nature of science, and human embryos, technology, and society (HETS). I then interpreted how embryos and fetuses have been socially constructed for students. I also examined the use of Haeckel's embryo drawings to support recapitulation and evolutionary theory. Textbooks revealed that publication of Haeckel's drawings was influenced by evolutionists and anti-evolutionists in the 1930s, 1960s, and the 1990s. Haeckel's embryos continue to persist in textbooks because they "safely" illustrate similarities between embryos and are rarely discussed in enough detail to understand comparative embryology's role in the support of evolution. Certain events coincided with changes in how embryos were presented: (a) the growth of the American Medical Association (AMA) and an increase in birth rates (1950s); (b) the Biological Sciences Curriculum Study (BSCS) and public acceptance of birth control methods (1960s); (c) Roe vs. Wade (1973); (d) in vitro fertilization and Lennart Nilsson's photographs (1970s); (e) prenatal technology and fetocentrism (1980s); and (f) genetic engineering and Science-Technology-Society (STS) curriculum (1980s and 1990s). By the end of the twentieth century, changing conceptions, research practices, and technologies all combined to transform the nature of biological development. Human embryos went from a highly descriptive, static, and private object to that of sometimes contentious public figure. I contend that an ignored source for helping move embryos into the public realm is schoolbooks. Throughout the 1900s, authors and publishers accomplished this by placing biology textbook embryos and fetuses in several different contexts--biological, technological, experimental, moral, social, and legal.

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2010

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Developing alternative genetic systems for structural DNA nanotechnology and Darwinian evolution

Description

A major goal of synthetic biology is to recapitulate emergent properties of life. Despite a significant body of work, a longstanding question that remains to be answered is how such a complex system arose? In this dissertation, synthetic nucleic acid

A major goal of synthetic biology is to recapitulate emergent properties of life. Despite a significant body of work, a longstanding question that remains to be answered is how such a complex system arose? In this dissertation, synthetic nucleic acid molecules with alternative sugar-phosphate backbones were investigated as potential ancestors of DNA and RNA. Threose nucleic acid (TNA) is capable of forming stable helical structures with complementary strands of itself and RNA. This provides a plausible mechanism for genetic information transfer between TNA and RNA. Therefore TNA has been proposed as a potential RNA progenitor. Using molecular evolution, functional sequences were isolated from a pool of random TNA molecules. This implicates a possible chemical framework capable of crosstalk between TNA and RNA. Further, this shows that heredity and evolution are not limited to the natural genetic system based on ribofuranosyl nucleic acids. Another alternative genetic system, glycerol nucleic acid (GNA) undergoes intrasystem pairing with superior thermalstability compared to that of DNA. Inspired by this property, I demonstrated a minimal nanostructure composed of both left- and right-handed mirro image GNA. This work suggested that GNA could be useful as promising orthogonal material in structural DNA nanotechnology.

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2011

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Definitely directed evolution (1890-1926): the importance of variation in major evolutionary works by Theodor Eimer, Edward Drinker Cope, and Leo Berg

Description

This dissertation shows that the central conceptual feature and explanatory motivation of theories of evolutionary directionality between 1890 and 1926 was as follows: morphological variation in the developing organism limits the possible outcomes of evolution in definite directions. Put broadly,

This dissertation shows that the central conceptual feature and explanatory motivation of theories of evolutionary directionality between 1890 and 1926 was as follows: morphological variation in the developing organism limits the possible outcomes of evolution in definite directions. Put broadly, these theories maintained a conceptual connection between development and evolution as inextricably associated phenomena. This project develops three case studies. The first addresses the Swiss-German zoologist Theodor Eimer's book Organic Evolution (1890), which sought to undermine the work of noted evolutionist August Weismann. Second, the American paleontologist Edward Drinker Cope's Primary Factors (1896) developed a sophisticated system of inheritance that included the material of heredity and the energy needed to induce and modify ontogenetic phenomena. Third, the Russian biogeographer Leo Berg's Nomogenesis (1926) argued that the biological world is deeply structured in a way that prevents changes to morphology taking place in more than one or a few directions. These authors based their ideas on extensive empirical evidence of long-term evolutionary trajectories. They also sought to synthesize knowledge from a wide range of studies and proposed causes of evolution and development within a unified causal framework based on laws of evolution. While being mindful of the variation between these three theories, this project advances "Definitely Directed Evolution" as a term to designate these shared features. The conceptual coherence and reception of these theories shows that Definitely Directed Evolution from 1890 to 1926 is an important piece in reconstructing the wider history of theories of evolutionary directionality.

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2014

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Three perspectives on multilevel selection: an experimental, historical, and synthetic analysis of group-level selection

Description

During the 1960s, the long-standing idea that traits or behaviors could be

explained by natural selection acting on traits that persisted "for the good of the group" prompted a series of debates about group-level selection and the effectiveness with which natural

During the 1960s, the long-standing idea that traits or behaviors could be

explained by natural selection acting on traits that persisted "for the good of the group" prompted a series of debates about group-level selection and the effectiveness with which natural selection could act at or across multiple levels of biological organization. For some this topic remains contentious, while others consider the debate settled, even while disagreeing about when and how resolution occurred, raising the question: "Why have these debates continued?"

Here I explore the biology, history, and philosophy of the possibility of natural selection operating at levels of biological organization other than the organism by focusing on debates about group-level selection that have occurred since the 1960s. In particular, I use experimental, historical, and synthetic methods to review how the debates have changed, and whether different uses of the same words and concepts can lead to different interpretations of the same experimental data.

I begin with the results of a group-selection experiment I conducted using the parasitoid wasp Nasonia, and discuss how the interpretation depends on how one conceives of and defines a "group." Then I review the history of the group selection controversy and argue that this history is best interpreted as multiple, interrelated debates rather than a single continuous debate. Furthermore, I show how the aspects of these debates that have changed the most are related to theoretical content and empirical data, while disputes related to methods remain largely unchanged. Synthesizing this material, I distinguish four different "approaches" to the study of multilevel selection based on the questions and methods used by researchers, and I use the results of the Nasonia experiment to discuss how each approach can lead to different interpretations of the same experimental data. I argue that this realization can help to explain why debates about group and multilevel selection have persisted for nearly sixty years. Finally, the conclusions of this dissertation apply beyond evolutionary biology by providing an illustration of how key concepts can change over time, and how failing to appreciate this fact can lead to ongoing controversy within a scientific field.

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2014

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Development of an artificial genetic system capable of Darwinian evolution

Description

The principle of Darwinian evolution has been applied in the laboratory to nucleic acid molecules since 1990, and led to the emergence of in vitro evolution technique. The methodology of in vitro evolution surveys a large number of different molecules

The principle of Darwinian evolution has been applied in the laboratory to nucleic acid molecules since 1990, and led to the emergence of in vitro evolution technique. The methodology of in vitro evolution surveys a large number of different molecules simultaneously for a pre-defined chemical property, and enrich for molecules with the particular property. DNA and RNA sequences with versatile functions have been identified by in vitro selection experiments, but many basic questions remain to be answered about how these molecules achieve their functions. This dissertation first focuses on addressing a fundamental question regarding the molecular recognition properties of in vitro selected DNA sequences, namely whether negatively charged DNA sequences can be evolved to bind alkaline proteins with high specificity. We showed that DNA binders could be made, through carefully designed stringent in vitro selection, to discriminate different alkaline proteins. The focus of this dissertation is then shifted to in vitro evolution of an artificial genetic polymer called threose nucleic acid (TNA). TNA has been considered a potential RNA progenitor during early evolution of life on Earth. However, further experimental evidence to support TNA as a primordial genetic material is lacking. In this dissertation we demonstrated the capacity of TNA to form stable tertiary structure with specific ligand binding property, which suggests a possible role of TNA as a pre-RNA genetic polymer. Additionally, we discussed the challenges in in vitro evolution for TNA enzymes and developed the necessary methodology for future TNA enzyme evolution.

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2013

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Where did you come from? Where will you go?: human evolutionary biology education and American students' academic interests and achievements, professional goals, and socioscientific decision-making

Description

In the United States, there is a national agenda to increase the number of qualified science, technology, engineering, and maths (STEM) professionals and a movement to promote science literacy among the general public. This project explores the association between formal

In the United States, there is a national agenda to increase the number of qualified science, technology, engineering, and maths (STEM) professionals and a movement to promote science literacy among the general public. This project explores the association between formal human evolutionary biology education (HEB) and high school science class enrollment, academic achievement, interest in a STEM degree program, motivation to pursue a STEM career, and socioscientific decision–making for a sample of students enrolled full–time at Arizona State University. Given a lack of a priori knowledge of these relationships, the Grounded Theory Method was used and was the foundation for a mixed–methods analysis involving qualitative and quantitative data from one–on–one interviews, focus groups, questionnaires, and an online survey. Theory development and hypothesis generation were based on data from 44 students. The survey instrument, developed to test the hypotheses, was completed by 486 undergraduates, age 18–22, who graduated from U.S. public high schools. The results showed that higher exposure to HEB was correlated with greater high school science class enrollment, particularly for advanced biological science classes, and that, for some students, HEB exposure may have influenced their enrollment, because the students found the content interesting and relevant. The results also suggested that students with higher K–12 HEB exposure felt more prepared for undergraduate science coursework. There was a positive correlation between HEB exposure and interest in a STEM degree and an indirect relationship between higher HEB exposure and motivation to pursue a STEM career. Regarding a number of socioscientific issues, including but not limited to climate change, homosexuality, and stem cell research, students' behaviors and decision–making more closely reflected a scientific viewpoint—or less–closely aligned to a religion–based perspective—when students had greater HEB exposure, but this was sometimes contingent on students' lifetime exposure to religious doctrine and acceptance of general evolution or human evolution. This study has implications for K–12 and higher education and justifies a paradigm shift in evolution education research, such that more emphasis is placed on students' interests, perceived preparation for continued learning, professional goals and potential contributions to society rather than just their knowledge and acceptance.

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2014