Matching Items (69)
Description
The pattern and strength of genetic covariation is shaped by selection so that it is strong among functionally related characters and weak among functionally unrelated characters. Genetic covariation is expressed as phenotypic covariation within species and acts as a constraint on evolution by limiting the ability of linked characters to evolve independently of one another. Such linked characters are "constrained" and are expected to express covariation both within and among species. In this study, the pattern and magnitude of covariation among aspects of dental size and shape are investigated in anthropoid primates. Pleiotropy has been hypothesized to play a significant role in derivation of derived hominin morphologies. This study tests a series of hypotheses; including 1) that negative within- and among-species covariation exists between the anterior (incisors and canines) and postcanine teeth, 2) that covariation is strong and positive between the canines and incisors, 3) that there is a dimorphic pattern of within-species covariation and coevolution for characters of the canine honing complex, 4) that patterns of covariation are stable among anthropoids, and 5) that genetic constraints have been a strong bias on the diversification of anthropoid dental morphology. The study finds that patterns of variance-covariance are conserved among species. Despite these shared patterns of variance-covariance, dental diversification has frequently occurred along dimensions not aligned with the vector of genetic constraint. As regards the canine honing complex, there is no evidence for a difference in the pleiotropic organization or the coevolution of characters of the complex in males and females, which undermines arguments that the complex is selectively important only in males. Finally, there is no evidence for strong or negative pleiotropy between any dental characters, which falsifies hypotheses that predict such relationships between incisors and postcanine teeth or between the canines and the postcanine teeth.
ContributorsDelezene, Lucas (Author) / Kimbel, William H. (Thesis advisor) / Schwartz, Gary T (Committee member) / Spencer, Mark (Committee member) / Verrelli, Brian C (Committee member) / Arizona State University (Publisher)
Created2011
Description
Hispanic youth have the highest risk for obesity, making this population a key priority for early childhood interventions to prevent the development of adult obesity and its consequences. Involving parents in these interventions is essential to support positive long-term physical activity and nutrition habits. Interventions in the past have engaged parents by providing information about nutrition and fruit and vegetable intake through written materials or text such as newsletters and text messages. The Sustainability via Active Garden Education (SAGE) intervention used gardening and interactive activities to teach preschool children ages 3-5 about healthy eating and physical activity. It aimed to increase physical activity and fruit and vegetable intake in preschool children as well as improve related parenting practices. The intervention utilized newsletters to engage parents by promoting opportunities to increase physical activity and fruit and vegetable intake for their children at home. The newsletters also encouraged parents to discuss what was learned during the SAGE lessons with their children. The purpose of this paper is to describe the content of the newsletters and determine the parent perception of the newsletters through parent survey responses. This can help inform future childhood obesity interventions and parent engagement.
ContributorsVi, Vinny (Author) / Lee, Rebecca (Thesis director) / Martinelli, Sarah (Committee member) / Edson College of Nursing and Health Innovation (Contributor) / Barrett, The Honors College (Contributor)
Created2021-05
Description
The Cape Floral Region (CFR) in southwestern South Africa is one of the most diverse in the world, with >9,000 plant species, 70% of which are endemic, in an area of only ~90,000 km2. Many have suggested that the CFR's heterogeneous environment, with respect to landscape gradients, vegetation, rainfall, elevation, and soil fertility, is responsible for the origin and maintenance of this biodiversity. While studies have struggled to link species diversity with these features, no study has attempted to associate patterns of gene flow with environmental data to determine how CFR biodiversity evolves on different scales. Here, a molecular population genetic data is presented for a widespread CFR plant, Leucadendron salignum, across 51 locations with 5-kb of chloroplast (cpDNA) and 6-kb of unlinked nuclear (nuDNA) DNA sequences in a dataset of 305 individuals. In the cpDNA dataset, significant genetic structure was found to vary on temporal and spatial scales, separating Western and Eastern Capes - the latter of which appears to be recently derived from the former - with the highest diversity in the heart of the CFR in a central region. A second study applied a statistical model using vegetation and soil composition and found fine-scale genetic divergence is better explained by this landscape resistance model than a geographic distance model. Finally, a third analysis contrasted cpDNA and nuDNA datasets, and revealed very little geographic structure in the latter, suggesting that seed and pollen dispersal can have different evolutionary genetic histories of gene flow on even small CFR scales. These three studies together caution that different genomic markers need to be considered when modeling the geographic and temporal origin of CFR groups. From a greater perspective, the results here are consistent with the hypothesis that landscape heterogeneity is one driving influence in limiting gene flow across the CFR that can lead to species diversity on fine-scales. Nonetheless, while this pattern may be true of the widespread L. salignum, the extension of this approach is now warranted for other CFR species with varying ranges and dispersal mechanisms to determine how universal these patterns of landscape genetic diversity are.
ContributorsTassone, Erica (Author) / Verrelli, Brian C (Thesis advisor) / Dowling, Thomas (Committee member) / Cartwright, Reed (Committee member) / Rosenberg, Michael S. (Committee member) / Wojciechowski, Martin (Committee member) / Arizona State University (Publisher)
Created2013
Description
Triops (Branchiopoda: Notostraca) and Streptocephalus (Branchiopoda: Anostraca) are two crustaceans which cohabitate in ephemeral freshwater pools. They both lay desiccation resistant eggs that disperse passively to new hydrologically isolated environments. The extent of genetic distance among regions and populations is of perennial interest in animals that live in such isolated habitats. Populations in six natural ephemeral pool habitats located in two different regions of the Sonoran Desert and a transition area between the Sonoran and Chihuahuan Deserts were sampled. Sequences from Genbank were used for reference points in the determination of species as well as to further identify regional genetic distance within species. This study estimated the amount of within and between genetic distance of individuals from each region and population through the use of a neutral marker, cytochrome oxidase I (COI). We concluded that, although the method of passive dispersal may differ between the two genera, the differences do not results in different patterns of genetic distances between regions and populations. Furthermore, we only found the putative species, Triops longicaudatus "short", with enough distinct speciation. Although Triops longicaudatus "long" and Triops newberryi may be in the early stages of speciation, this study does not find enough support to conclude that they have separated.
ContributorsMurphy Jr., Patrick Joseph (Author) / Rutowski, Ronald (Thesis director) / Cartwright, Reed (Committee member) / Lessios, Nikos (Committee member) / School of Life Sciences (Contributor) / School of Human Evolution and Social Change (Contributor) / Barrett, The Honors College (Contributor)
Created2016-05
Description
The evolution of blindness in cave animals has been heavily studied; however, little research has been done on the interaction of migration and drift on the development of blindness in these populations. In this study, a model is used to compare the effect that genetic drift has on the fixation of a blindness allele for varying amounts of migration and selection. For populations where the initial frequency is quite low, genetic drift plays a much larger role in the fixation of blindness than populations where the initial frequency is high. In populations where the initial frequency is high, genetic drift plays almost no role in fixation. Our results suggest that migration plays a greater role in the fate of the blindness allele than selection.
ContributorsMerry, Alexandra Leigh (Author) / Cartwright, Reed (Thesis director) / Rosenberg, Michael (Committee member) / Schwartz, Rachel (Committee member) / Barrett, The Honors College (Contributor) / School of Life Sciences (Contributor)
Created2014-05
Description
In the digital humanities, there is a constant need to turn images and PDF files into plain text to apply analyses such as topic modelling, named entity recognition, and other techniques. However, although there exist different solutions to extract text embedded in PDF files or run OCR on images, they typically require additional training (for example, scholars have to learn how to use the command line) or are difficult to automate without programming skills. The Giles Ecosystem is a distributed system based on Apache Kafka that allows users to upload documents for text and image extraction. The system components are implemented using Java and the Spring Framework and are available under an Open Source license on GitHub (https://github.com/diging/).
ContributorsLessios-Damerow, Julia (Contributor) / Peirson, Erick (Contributor) / Laubichler, Manfred (Contributor) / ASU-SFI Center for Biosocial Complex Systems (Contributor)
Created2017-09-28
Description
Skeletal diseases related to reduced bone strength, like osteoporosis, vary in frequency and severity among human populations due in part to underlying genetic differentiation. With >600 disease-associated mutations (DAMs), COL1a1, which encodes the primary subunit of type I collagen, the main structural protein in bone, is most commonly associated with this phenotypic variation. Although numerous studies have explored genotype-phenotype relationships with COL1a1, surprisingly, no study has undertaken an evolutionary approach to determine how changes in constraint over time can be modeled to help predict bone-related disease factors. Here, molecular population and comparative species genetic analyses were conducted to characterize the evolutionary history of COL1a1. First, nucleotide and protein sequences of COL1a1 in 14 taxa representing ~450 million years of vertebrate evolution were used to investigate constraint across gene regions. Protein residues of historically high conservation are significantly correlated with disease severity today, providing a highly accurate model for disease prediction, yet interestingly, intron composition also exhibits high conservation suggesting strong historical purifying selection. Second, a human population genetic analysis of 192 COL1a1 nucleotide sequences representing 10 ethnically and geographically diverse samples was conducted. This random sample of the population shows surprisingly high numbers of amino acid polymorphisms (albeit rare in frequency), suggesting that not all protein variants today are highly deleterious. Further, an unusual haplotype structure was identified across populations, but which is only associated with noncoding variation in the 5' region of COL1a1 where gene expression alteration is most likely. Finally, a population genetic analysis of 40 chimpanzee COL1a1 sequences shows no amino acid polymorphism, yet does reveal an unusual haplotype structure with significantly extended linkage disequilibrium >30 kilobases away, as well as a surprisingly common exon duplication that is generally highly deleterious in humans. Altogether, these analyses indicate a history of temporally and spatially varying purifying selection on not only coding, but noncoding COL1a1 regions that is also reflected in population differentiation. In contrast to clinical studies, this approach reveals potentially functional variation, which in future analyses could explain the observed bone strength variation not only seen within humans, but other closely related primates.
ContributorsStover, Daryn Amanda (Author) / Verrelli, Brian C (Thesis advisor) / Dowling, Thomas E (Committee member) / Rosenberg, Michael S. (Committee member) / Stone, Anne C (Committee member) / Schwartz, Gary T (Committee member) / Arizona State University (Publisher)
Created2010
Description
The modern web presents an opportunity for educators and researchers to create tools that are highly accessible. Because of the near-ubiquity of modern web browsers, developers who hope to create educational and analytical tools can reach a large au- dience by creating web applications. Using JavaScript, HTML, and other modern web development technologies, Genie was developed as a simulator to help educators in biology, genetics, and evolution classrooms teach their students about population genetics. Because Genie was designed for the modern web, it is highly accessible to both educators and students, who can access the web application using any modern web browser on virtually any device. Genie demonstrates the efficacy of web devel- opment technologies for demonstrating and simulating complex processes, and it will be a unique educational tool for educators who teach population genetics.
ContributorsRoos, Benjamin Hirsch (Author) / Cartwright, Reed (Thesis director) / Wilson Sayres, Melissa (Committee member) / Mayron, Liam (Committee member) / Barrett, The Honors College (Contributor) / Computer Science and Engineering Program (Contributor)
Created2015-05
Description
Background
Improvements in sequencing technology now allow easy acquisition of large datasets; however, analyzing these data for phylogenetics can be challenging. We have developed a novel method to rapidly obtain homologous genomic data for phylogenetics directly from next-generation sequencing reads without the use of a reference genome. This software, called SISRS, avoids the time consuming steps of de novo whole genome assembly, multiple genome alignment, and annotation.
Results
For simulations SISRS is able to identify large numbers of loci containing variable sites with phylogenetic signal. For genomic data from apes, SISRS identified thousands of variable sites, from which we produced an accurate phylogeny. Finally, we used SISRS to identify phylogenetic markers that we used to estimate the phylogeny of placental mammals. We recovered eight phylogenies that resolved the basal relationships among mammals using datasets with different levels of missing data. The three alternate resolutions of the basal relationships are consistent with the major hypotheses for the relationships among mammals, all of which have been supported previously by different molecular datasets.
Conclusions
SISRS has the potential to transform phylogenetic research. This method eliminates the need for expensive marker development in many studies by using whole genome shotgun sequence data directly. SISRS is open source and freely available at https://github.com/rachelss/SISRS/releases.
Improvements in sequencing technology now allow easy acquisition of large datasets; however, analyzing these data for phylogenetics can be challenging. We have developed a novel method to rapidly obtain homologous genomic data for phylogenetics directly from next-generation sequencing reads without the use of a reference genome. This software, called SISRS, avoids the time consuming steps of de novo whole genome assembly, multiple genome alignment, and annotation.
Results
For simulations SISRS is able to identify large numbers of loci containing variable sites with phylogenetic signal. For genomic data from apes, SISRS identified thousands of variable sites, from which we produced an accurate phylogeny. Finally, we used SISRS to identify phylogenetic markers that we used to estimate the phylogeny of placental mammals. We recovered eight phylogenies that resolved the basal relationships among mammals using datasets with different levels of missing data. The three alternate resolutions of the basal relationships are consistent with the major hypotheses for the relationships among mammals, all of which have been supported previously by different molecular datasets.
Conclusions
SISRS has the potential to transform phylogenetic research. This method eliminates the need for expensive marker development in many studies by using whole genome shotgun sequence data directly. SISRS is open source and freely available at https://github.com/rachelss/SISRS/releases.
ContributorsSchwartz, Rachel (Author) / Harkins, Kelly (Author) / Stone, Anne (Author) / Cartwright, Reed (Author) / Biodesign Institute (Contributor) / Center for Evolution and Medicine (Contributor) / College of Liberal Arts and Sciences (Contributor) / School of Human Evolution and Social Change (Contributor) / School of Life Sciences (Contributor)
Created2015-06-11
Description
Because collective cognition emerges from local signaling among group members, deciphering communication systems is crucial to understanding the underlying mechanisms. Alarm signals are widespread in the social insects and can elicit a variety of behavioral responses to danger, but the functional plasticity of these signals has not been well studied. Here we report an alarm pheromone in the ant Temnothorax rugatulus that elicits two different behaviors depending on context. When an ant was tethered inside an unfamiliar nest site and unable to move freely, she released a pheromone from her mandibular gland that signaled other ants to reject this nest as a potential new home, presumably to avoid potential danger. When the same pheromone was presented near the ants' home nest, they were instead attracted to it, presumably to respond to a threat to the colony. We used coupled gas chromatography/mass spectrometry to identify candidate compounds from the mandibular gland and tested each one in a nest choice bioassay. We found that 2,5-dimethylpyrazine was sufficient to induce rejection of a marked new nest and also to attract ants when released at the home nest. This is the first detailed investigation of chemical communication in the leptothoracine ants. We discuss the possibility that this pheromone's deterrent function can improve an emigrating colony's nest site selection performance.
ContributorsSasaki, Takao (Author) / Hoelldobler, Bert (Author) / Millar, Jocelyn G. (Author) / Pratt, Stephen (Author) / College of Liberal Arts and Sciences (Contributor) / School of Life Sciences (Contributor) / ASU-SFI Center for Biosocial Complex Systems (Contributor) / Center for Social Dynamics and Complexity (Contributor)
Created2014-09-01