Statistical Analysis of Species Level Phylogenetic Trees

Statistical Analysis of Species Level Phylogenetic Trees

Bibliographic Details
Main Author: Ferguson, Meg Elizabeth
Language:English
Published: Bowling Green State University / OhioLINK 2017
Subjects:
Statistics
statistics
phylogenetics
squid
missing data
Online Access:http://rave.ohiolink.edu/etdc/view?acc_num=bgsu1503051433382274
id ndltd-OhioLink-oai-etd.ohiolink.edu-bgsu1503051433382274
record_format oai_dc
spelling ndltd-OhioLink-oai-etd.ohiolink.edu-bgsu15030514333822742021-08-03T07:03:57Z Statistical Analysis of Species Level Phylogenetic Trees Ferguson, Meg Elizabeth Statistics statistics phylogenetics squid missing data 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. 2017-11-14 English text Bowling Green State University / OhioLINK http://rave.ohiolink.edu/etdc/view?acc_num=bgsu1503051433382274 http://rave.ohiolink.edu/etdc/view?acc_num=bgsu1503051433382274 unrestricted This thesis or dissertation is protected by copyright: all rights reserved. It may not be copied or redistributed beyond the terms of applicable copyright laws.
collection NDLTD
language English
sources NDLTD
topic Statistics
statistics
phylogenetics
squid
missing data
spellingShingle Statistics
statistics
phylogenetics
squid
missing data
Ferguson, Meg Elizabeth
Statistical Analysis of Species Level Phylogenetic Trees
author Ferguson, Meg Elizabeth
author_facet Ferguson, Meg Elizabeth
author_sort Ferguson, Meg Elizabeth
title Statistical Analysis of Species Level Phylogenetic Trees
title_short Statistical Analysis of Species Level Phylogenetic Trees
title_full Statistical Analysis of Species Level Phylogenetic Trees
title_fullStr Statistical Analysis of Species Level Phylogenetic Trees
title_full_unstemmed Statistical Analysis of Species Level Phylogenetic Trees
title_sort statistical analysis of species level phylogenetic trees
publisher Bowling Green State University / OhioLINK
publishDate 2017
url http://rave.ohiolink.edu/etdc/view?acc_num=bgsu1503051433382274
work_keys_str_mv AT fergusonmegelizabeth statisticalanalysisofspecieslevelphylogenetictrees
_version_ 1719452656164929536

Similar Items