University of Pennsylvania ScholarlyCommons Publicly Accessible Penn Dissertations 2015 Detecting Selection on Noncoding Nucleotide Variation: Methods and Applications Yang Ding University of Pennsylvania,
[email protected] Follow this and additional works at: https://repository.upenn.edu/edissertations Part of the Bioinformatics Commons, Biology Commons, and the Evolution Commons Recommended Citation Ding, Yang, "Detecting Selection on Noncoding Nucleotide Variation: Methods and Applications" (2015). Publicly Accessible Penn Dissertations. 1687. https://repository.upenn.edu/edissertations/1687 This paper is posted at ScholarlyCommons. https://repository.upenn.edu/edissertations/1687 For more information, please contact
[email protected]. Detecting Selection on Noncoding Nucleotide Variation: Methods and Applications Abstract There has been a long tradition in molecular evolution to study selective pressures operating at the amino-acid level. But protein-coding variation is not the only level on which molecular adaptations occur, and it is not clear what roles non-coding variation has played in evolutionary history, since they have not yet been systematically explored. In this dissertation I systematically explore several aspects of selective pressures of noncoding nucleotide variation: The first project (Chapter 2) describes research on the determinants of eukaryotic translation dynamics, which include selection on non-coding aspects of DNA variation. Deep sequencing of ribosome-protected mRNA fragments and polysome gradients in various eukaryotic organisms have revealed an intriguing pattern: shorter mRNAs tend to have a greater overall density of ribosomes than longer mRNAs. There is debate about the cause of this trend. To resolve this open question, I systematically analysed 5’ mRNA structure and codon usage patterns in short versus long genes across 100 sequenced eukaryotic genomes.