Phylogenetic comparison measurements and their application towards the accurate inference of evolutionary histories

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dc.contributor.advisor Oliver Eulenstein
dc.contributor.author Markin, Alexey
dc.contributor.department Computer Science
dc.date 2020-09-23T19:13:15.000
dc.date.accessioned 2021-02-25T21:35:20Z
dc.date.available 2021-02-25T21:35:20Z
dc.date.copyright Sat Aug 01 00:00:00 UTC 2020
dc.date.embargo 2020-09-10
dc.date.issued 2020-01-01
dc.description.abstract <p>The inference of evolutionary histories of species is one of the core problems in biology. The supertree or, more formally, the median tree framework appears to be the most robust approach to the inference of species phylogenies known today. In fact, the majority of popular phylogenomic methods employ the median tree strategy; these include ASTRAL, DupTree, and iGTP. The concept of median trees suggests computing a species phylogeny that minimizes a distance (defined by a fixed phylogenetic measurement) towards a given collection of input trees. The power of the median tree approach and the abundance of different (and often conflicting) evolutionary trees available today, make the phylogenetic comparison measurements a crucial area of research in computational biology. Therefore, a large part of this thesis is dedicated to advancing the algorithmic and theoretical aspects of the phylogenetic comparison measurements. Next, I present our new results on the inference of median trees under the classic phylogenetic comparison measurements. Moreover, I demonstrate novel theoretical guarantees for one of the main median tree methods in the field, ASTRAL. This result ties complex statistical models of evolution to the distance-based species tree inference. Further, I discuss the crucial transition from the tree-paradigm to the network-paradigm that involves the formulation of median network problems. Note that, in contrast to trees, the phylogenetic networks enable modeling of complex evolutionary events, such as horizontal gene transfer, recombination, hybridization, and virus reassortment. I present our most recent advancements in this area that includes a practical study of Influenza viruses.</p>
dc.format.mimetype application/pdf
dc.identifier archive/lib.dr.iastate.edu/etd/18180/
dc.identifier.articleid 9187
dc.identifier.contextkey 19236751
dc.identifier.doi https://doi.org/10.31274/etd-20200902-99
dc.identifier.s3bucket isulib-bepress-aws-west
dc.identifier.submissionpath etd/18180
dc.identifier.uri https://dr.lib.iastate.edu/handle/20.500.12876/94332
dc.language.iso en
dc.source.bitstream archive/lib.dr.iastate.edu/etd/18180/Markin_iastate_0097E_19023.pdf|||Fri Jan 14 21:38:01 UTC 2022
dc.subject.keywords Computational Biology
dc.subject.keywords Epidemiology
dc.subject.keywords Evolutionary inference
dc.subject.keywords Genetics
dc.subject.keywords Phylogenetic networks
dc.subject.keywords Phylogenetics
dc.title Phylogenetic comparison measurements and their application towards the accurate inference of evolutionary histories
dc.type article
dc.type.genre dissertation
dspace.entity.type Publication
relation.isOrgUnitOfPublication f7be4eb9-d1d0-4081-859b-b15cee251456
thesis.degree.discipline Computer Science
thesis.degree.level dissertation
thesis.degree.name Doctor of Philosophy
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