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- All Subjects: Genetics
Description
In most bird species, females disperse prior to their first breeding attempt, while males remain close to the place they were hatched for their entire lives (Greenwood and Harvey (1982)). Explanations for such female bias in natal dispersal have focused on the potential benefits that males derive from knowing the local environment to establish territories, while females search for suitable mates (Greenwood (1980)). However, the variables shaping dispersal decisions appear more complex (Mabry et al. (2013), Végvári et al. (2018)). There are a number of different variables that could act as a driving force behind dispersal including the social mating system, food competition, inbreeding avoidance, predation, and others. Here, we investigate whether females are the dispersing sex in great-tailed grackles, which have a mating system where the males hold territories and the females choose which territory to place their nest in (Johnson et al. (2000)). We used genetic approaches to identify sex biases in the propensity to disperse. In the experiment, we found that the male grackles were less related to each other while the female grackles were more related to each other. Building on that, the average distance between closely related individuals of the male group was longer than the average distance of closely related females. But, the mantel correlograms for the males and females both lack a consistent trend. Overall, the results indicated suggest that the males are the dispersing sex while the females are potentially philopatric and that the average dispersal distance for the grackle is greater than 2000 meters, the size of the sampling range used in the experiment. These results will inform our long-term study on the relationship between behavioral flexibility and rapid geographic range expansion by elucidating which individuals are likely to experience similar conditions across their lives, and which are likely to face new conditions when they become breeders.
ContributorsSevchik, August L (Author) / Langergraber, Kevin (Thesis director) / Logan, Corina (Committee member) / College of Integrative Sciences and Arts (Contributor) / School of Molecular Sciences (Contributor) / School of Life Sciences (Contributor) / Barrett, The Honors College (Contributor)
Created2020-05
Description
Abstract
Purpose—Use a framework of genetic knowledge to investigate the association between the genotypes of various genes with phenotypes, specifically the traits of elite athletes, in order to establish a personal opinion on their relevance to athletic performance.
Methods—Assemble and analyze selected published scientific studies on genotype and athletic performance and lastly to formulate a personal opinion on the value of genetic testing of athletes. ACTN3, ACE, MSTN, and apoE were the genes selected for analyses.
Results—Two genes, ACTN3 and ACE, showed a significant relationship of genotype to phenotypic traits related to athletic performance. ApoE did not demonstrate a phenotypic association with athletic performance, however it showed a correlation with injury susceptibility leading to traumatic brain injury (TBI). MSTN did not show a phenotypic association with athletic performance.
Conclusion—When considering the multifactorial nature of athletics, each sport must be investigated individually due to the different individual requirements. ACTN3 and ACE are the most widely studied genes, therefore, considerable data on their relevance to athletic performance was easily obtained and supported a relationship between genotype and athletic performance.
Purpose—Use a framework of genetic knowledge to investigate the association between the genotypes of various genes with phenotypes, specifically the traits of elite athletes, in order to establish a personal opinion on their relevance to athletic performance.
Methods—Assemble and analyze selected published scientific studies on genotype and athletic performance and lastly to formulate a personal opinion on the value of genetic testing of athletes. ACTN3, ACE, MSTN, and apoE were the genes selected for analyses.
Results—Two genes, ACTN3 and ACE, showed a significant relationship of genotype to phenotypic traits related to athletic performance. ApoE did not demonstrate a phenotypic association with athletic performance, however it showed a correlation with injury susceptibility leading to traumatic brain injury (TBI). MSTN did not show a phenotypic association with athletic performance.
Conclusion—When considering the multifactorial nature of athletics, each sport must be investigated individually due to the different individual requirements. ACTN3 and ACE are the most widely studied genes, therefore, considerable data on their relevance to athletic performance was easily obtained and supported a relationship between genotype and athletic performance.
ContributorsMinto, Jordan Taylor- Lloyd (Author) / Steele, Kelly (Thesis director) / Penton, C. Ryan (Committee member) / College of Integrative Sciences and Arts (Contributor) / Barrett, The Honors College (Contributor)
Created2017-05
Description
With the rising data output and falling costs of Next Generation Sequencing technologies, research into data compression is crucial to maintaining storage efficiency and costs. High throughput sequencers such as the HiSeqX Ten can produce up to 1.8 terabases of data per run, and such large storage demands are even more important to consider for institutions that rely on their own servers rather than large data centers (cloud storage)1. Compression algorithms aim to reduce the amount of space taken up by large genomic datasets by encoding the most frequently occurring symbols with the shortest bit codewords and by changing the order of the data to make it easier to encode. Depending on the probability distribution of the symbols in the dataset or the structure of the data, choosing the wrong algorithm could result in a compressed file larger than the original or a poorly compressed file that results in a waste of time and space2. To test efficiency among compression algorithms for each file type, 37 open-source compression algorithms were used to compress six types of genomic datasets (FASTA, VCF, BCF, GFF, GTF, and SAM) and evaluated on compression speed, decompression speed, compression ratio, and file size using the benchmark test lzbench. Compressors that outpreformed the popular bioinformatics compressor Gzip (zlib -6) were evaluated against one another by ratio and speed for each file type and across the geometric means of all file types. Compressors that exhibited fast compression and decompression speeds were also evaluated by transmission time through variable speed internet pipes in scenarios where the file was compressed only once or compressed multiple times.
ContributorsHowell, Abigail (Author) / Cartwright, Reed (Thesis director) / Wilson Sayres, Melissa (Committee member) / Taylor, Jay (Committee member) / Barrett, The Honors College (Contributor)
Created2017-05
Description
Mammary gland development in humans during puberty involves the enlargement of breast tissue, but this is not true in non-human primates. To identify potential causes of this difference, I examined variation in substitution rates across genes related to mammary development. Genes undergoing purifying selection show slower-than-average substitution rates, while genes undergoing positive selection show faster rates. These may be related to the difference between humans and other primates. Three genes were found to be accelerated were FOXF1, IGFBP5, and ATP2B2, but only the latter one was found in humans and it seems unlikely that it would be related to the differences between mammary gland development at puberty between humans and non-human primates.
ContributorsArroyo, Diana (Author) / Cartwright, Reed (Thesis director) / Wilson Sayres, Melissa (Committee member) / Schwartz, Rachel (Committee member) / School of Life Sciences (Contributor) / Barrett, The Honors College (Contributor)
Created2016-05
Description
The use of genetic management in conservation has sparked much debate around the ethical and environmental impacts of the plans. A case study on the conservation of leopard frogs in Arizona was analyzed to better understand the benefits and issues surrounding genetic management plans. The first part of the case focuses on the recent management plan for Chiricahua Leopard Frogs implemented by the Arizona Game and Fish Department. The goal of the plan is to better understand the genetic dynamics of the established Chiricahua Leopard Frog populations to develop a more effective management plan. The second part of the case focuses on the Arizona Game and Fish Department’s management of the Northern Leopard Frog. There was little success with the initial breed and release program of the native species, however a nonnative subspecies of Northern Leopard Frog was able to establish a thriving population. This case study exemplifies the many complications with genetic management plans and the importance of careful assessment of options when deciding on a genetic management plan. Despite the complexity of genetic management plans, it is an important method to consider when discussing the conservation of a species.
ContributorsTurpen, Alexa (Author) / Murphree, Julie (Thesis director) / Collins, James (Thesis director) / Owens, Audrey (Committee member) / Barrett, The Honors College (Contributor) / School of Life Sciences (Contributor) / College of Integrative Sciences and Arts (Contributor) / School of Mathematical and Natural Sciences (Contributor)
Created2024-05
Pathways of Distinction Analysis of Liver Cancer Data: Genetic Differences Between Males and Females
Description
The Pathways of Distinction Analysis (PoDA) program calculates relationships between a given group of genes contained within a pathway, and a disease state. It was used here to investigate liver cancer, and to explore how genetic variability may contribute to the different rates of development of the disease in males and females. The goal of the study was to identify germline variation that differs by sex in hepatocellular carcinoma. Using the program, multiple pathways and genes were identified to have significant differences in their relationship to liver cancer in males and females. In animal studies, the genes which were identified using the PoDA analysis have been shown to impact liver cancer, often with different results for males and females. While these genes are often the focus in animal models, they are absent from current Genome Wide Association Studies (GWAS) catalogs for humans. By working to bridge the results of animal studies and human studies, the results help to identify the causes of liver cancer, and more specifically, the reason the disease affects males at much higher rates. The differences in pathways identified to be significant for the two sexes indicate the germline variance may play sex-specific roles in the development of hepatocellular carcinoma. Additionally, these results reinforce the capacity of the PoDA analysis to identify genes that may be missed by more traditional GWAS methods. This study lays the groundwork for further investigations into the identified genes and pathways, and how they behave differently within males and females.
ContributorsOlson, Erik Jon (Author) / Buetow, Kenneth (Thesis advisor) / Wilson, Melissa (Committee member) / Cartwright, Reed (Committee member) / Arizona State University (Publisher)
Created2021
Description
Background: Dyslexia is a neurodevelopmental impacting reading and writing ability present in around 5 to 9 percent of the population. The etiology of the condition is not currently well understood.
Purpose: To identify new genes of interest regarding the etiology of dyslexia, describe the interaction of those genes within known gene networks, and discuss potential relationships between their expression in the early developing brain and phenotypic outcomes.
Method: With informed consent, participants’ phenotypic and exome data were collected. Phenotypic data were collected using assessments measuring reading and spelling ability. Exome data were collected via saliva samples and processed at the UW-CRDR. Exome data were then filtering using Seqr and compared across participant families. Certain genes with identical variations were visually validated using the Integrated Genome Viewer, and then investigated using STRING Network Analysis and the Human Brain Transcriptome.
Results: Three genes were identified: BCL6, DNAH1, and DNAH12. Protein-protein interactions were confirmed between DNAH1 and DNAH12 via STRING Network Analysis. BLC6 and DNAH1 experience higher postnatal expression in the cerebellar cortex. DNAH12 experiences higher prenatal expression in the hippocampus.
Discussion: The findings appear to be consistent with a heterogenous and polygenic model of dyslexia. The correlation between the participants’ genotypes and phenotypes is not strong enough to draw significant conclusions regarding genotype/phenotype connections. A larger participant sample size and analysis of a large pool of shared genes may reveal a clearer relationship.
ContributorsBanta, Claire (Author) / Peter, Beate (Thesis director) / Liu, Li (Committee member) / Barrett, The Honors College (Contributor) / School of Life Sciences (Contributor) / Sanford School of Social and Family Dynamics (Contributor) / College of Integrative Sciences and Arts (Contributor)
Created2024-05