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University of Houston

1. Price, Nicholas 1979-. Bioinformatic Studies on Selection in Protein-Coding- and RNA-Specifying Genes.

Degree: Biology and Biochemistry, Department of, 2014, University of Houston

During my dissertation I used a combination of comparative and phylogenetic approaches to test for selection on genic regions. Specifically, I tested for mutational and environmental robustness in Drosophila pre-miRNAs, as well as selection on synonymomous and nonsynonymous sites in mammalian protein coding genes. Contrary to previous claims of selection for mutational robustness in mammalian pre-miRNAs, I demonstrate that mutational robustness evolved neutrally in Drosophila pre-miRNas. Furthermore, I show that mutational robustness did not evolve as a byproduct of selection for environmental robustness. In Chapter 3, I identify orthologous processed pseudogenes and use them to test for selection on synonymous sites. By estimating the rate of substitution at synonymous sites in genes (d_S), and corresponding sites in pseudogenes (d_ψ), I demonstrate that only about ~8% of synonymous changes could possibly be under selection. This is in stark contrast to the ~30% previously claimed. However, I show that both deviations from neutrality can be caused by an increase in divergence between the sequences examined, in combination, with a difference in nucleotide composition between genes and pseudogenes. In the last part of my dissertation, I estimate selection on nonsynonymous sites in mammals (d_N/d_S), and examine the previously claimed positive correlation between generation time and selection. To ensure the correct estimation of selection, I examine the effects of sequencing errors and alignment quality. After accounting for phylogenetic independence, I find no correlation between generation time and selection. Furthermore, I find a significant decrease in the efficiency of selection in monkeys, after the simian and prosimian split.   Advisors/Committee Members: Graur, Dan (advisor), Azevedo, Ricardo B. R. (committee member), Cooper, Timothy F. (committee member), Josić, Krešimir (committee member), Kohn, Michael H. (committee member).

Subjects/Keywords: Selection; genic regions

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APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6th Edition):

Price, N. 1. (2014). Bioinformatic Studies on Selection in Protein-Coding- and RNA-Specifying Genes. (Thesis). University of Houston. Retrieved from http://hdl.handle.net/10657/1823

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Chicago Manual of Style (16th Edition):

Price, Nicholas 1979-. “Bioinformatic Studies on Selection in Protein-Coding- and RNA-Specifying Genes.” 2014. Thesis, University of Houston. Accessed October 24, 2019. http://hdl.handle.net/10657/1823.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

MLA Handbook (7th Edition):

Price, Nicholas 1979-. “Bioinformatic Studies on Selection in Protein-Coding- and RNA-Specifying Genes.” 2014. Web. 24 Oct 2019.

Vancouver:

Price N1. Bioinformatic Studies on Selection in Protein-Coding- and RNA-Specifying Genes. [Internet] [Thesis]. University of Houston; 2014. [cited 2019 Oct 24]. Available from: http://hdl.handle.net/10657/1823.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Council of Science Editors:

Price N1. Bioinformatic Studies on Selection in Protein-Coding- and RNA-Specifying Genes. [Thesis]. University of Houston; 2014. Available from: http://hdl.handle.net/10657/1823

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

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