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Transposon Ecology: The Power of Community Ecology Methods on Genomic Transposable Element Data

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Title: Transposon Ecology: The Power of Community Ecology Methods on Genomic Transposable Element Data
Author: Saylor, Brent
Department: Department of Integrative Biology
Program: Integrative Biology
Advisor: Cottenie, KarlGregory, T. Ryan
Abstract: More than half of the human genome is made up of self-replicating mobile sequences of DNA called transposable elements (TEs). Much of the research on TEs has focused on the molecular mechanisms by which they transpose, their mutagenic effects, and the influences of their activity on the evolution of the host genomes in which they reside. In the 1980s, the “selfish DNA” papers popularized the idea of TEs as parasites, an analogy that grew into the idea of the genome as an ecosystem in which TEs were equivalent to species. In this thesis, I put this idea to work by testing the effectiveness of community ecology methods at identifying community-level TE patterns and exploring the potential insights that this approach may provide. I used redundancy analysis, community phylogenetics, and the 4th corner analysis to analyze the relationship between the TE community, TE traits, and the genomic environment. Each of these methods was adaptable to genomic TE data. The redundancy analysis found that, on average, 50% of the differences between TE communities of 11 genomes were explained by where that community was positioned on the chromosome (spatial patterns). In the human genome, 60% of the differences between TE communities were explained by spatial patterns, of which 33% is explained by the chromatin state and the remaining 66% remained unexplained. I also showed that TE traits affected the differences in TE communities, with older TE families having more structure within genomes. Phylogenetic community ecology methods indicated that 17-30% of the TE communities in the Drosophila melanogaster genome were phylogenetically non-random. This pattern could indicate important community structuring assembly processes. Finally, the 4th corner analysis showed that the TE community spatial patterns are associated with TE-specific traits. This association with the traits of individual TEs, and not TE families, makes it possible to predict where new TEs may be found and which TEs might occur in new environments. Overall, this thesis represents the first systematic application of ecological methods per se to genomic TE data and assessment of their utility, and lays the groundwork for many future studies in transposon ecology.
URI: http://hdl.handle.net/10214/17468
Date: 2019-08
Rights: Attribution-NonCommercial-ShareAlike 4.0 International
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Attribution-NonCommercial-ShareAlike 4.0 International Except where otherwise noted, this item's license is described as Attribution-NonCommercial-ShareAlike 4.0 International