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Statistical Analysis of Species Level Phylogenetic Trees

Ferguson, Meg Elizabeth

Abstract Details

2017, Master of Science (MS), Bowling Green State University, Applied Statistics (Math).
In this thesis, statistical methods are used to analyze the generation of species-level phylogenies. Two software packages, one phylogenetic and one statistical, are used to investigate the difference in phylogeny topology across three methods. Maximum likelihood estimation, neighbor-joining, and UPGMA methodologies are applied in this comparison to study the accuracy of each software package in correctly placing taxa with the true phylogeny. Four genes are used to compare with variable length sequences and genes amongst forty-seven squid species. In addition, missing data techniques are employed to assess the impact missing data has on phylogeny generation. Two software platforms were used to generate phylogenies for genes 16S rRNA, 18s rRNA, 28S rRNA, and the mitochondrial gene cytochrome c oxidase I (COI). The phylogenetic software platform MEGA was utilized as well as the statistical software platform, R; within R, the packages ape, phangorn, and seqinr were used in tree generation. Results show discrepancies between phylogenies generated across the four single-gene trees and multiple-gene trees; only phylogenies generated using missing data in the form of partial sequences grouped all families correctly. Results from this study highlight the struggle in determining the best software package to use for phylogenetic analyses. It was discovered that in general, MEGA generated a more accurate single-gene phylogeny from gene 18S rRNA while R generated a more accurate single-gene phylogeny from gene 28S rRNA. Results also showed that sequences with 50% missing characters could be accurately placed within generated phylogenies.
John Chen, Dr. (Advisor)
Junfeng Shang, Dr. (Committee Member)
Craig Zirbel, Dr. (Committee Member)
113 p.

Recommended Citations

Citations

  • Ferguson, M. E. (2017). Statistical Analysis of Species Level Phylogenetic Trees [Master's thesis, Bowling Green State University]. OhioLINK Electronic Theses and Dissertations Center. http://rave.ohiolink.edu/etdc/view?acc_num=bgsu1503051433382274

    APA Style (7th edition)

  • Ferguson, Meg. Statistical Analysis of Species Level Phylogenetic Trees. 2017. Bowling Green State University, Master's thesis. OhioLINK Electronic Theses and Dissertations Center, http://rave.ohiolink.edu/etdc/view?acc_num=bgsu1503051433382274.

    MLA Style (8th edition)

  • Ferguson, Meg. "Statistical Analysis of Species Level Phylogenetic Trees." Master's thesis, Bowling Green State University, 2017. http://rave.ohiolink.edu/etdc/view?acc_num=bgsu1503051433382274

    Chicago Manual of Style (17th edition)