Integrated Likelihood for Phylogenomics under a No-Common-Mechanism Model

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dc.contributor.advisorNakhleh, Luay Ken_US
dc.creatorTidwell, Hunteren_US
dc.date.accessioned2019-05-16T19:07:15Zen_US
dc.date.available2019-05-16T19:07:15Zen_US
dc.date.created2019-05en_US
dc.date.issued2019-04-18en_US
dc.date.submittedMay 2019en_US
dc.date.updated2019-05-16T19:07:16Zen_US
dc.description.abstractThe availability of genome-wide sequence data from many species and individuals within species has ushered in the era of phylogenomics. In this era, species phylogeny inference is based on models of sequence evolution on gene trees and models of gene tree evolution within species phylogenies. All existing inference methods, except parsimony, assume a common mechanism across loci as represented by unvarying branch lengths of the species phylogeny. In this thesis, we propose a ``no common mechanism" (NCM) model, in which the parameters of the species phylogeny may vary between loci. We derive an analytically integrated likelihood of species networks given gene trees from multiple loci under an NCM model. We demonstrate the performance of inference under this integrated likelihood on simulated and biological data. The model presented here will afford opportunities for exploring connections among various methods for estimating species phylogenies from multiple, independent loci.en_US
dc.format.mimetypeapplication/pdfen_US
dc.identifier.citationTidwell, Hunter. "Integrated Likelihood for Phylogenomics under a No-Common-Mechanism Model." (2019) Master’s Thesis, Rice University. <a href="https://hdl.handle.net/1911/105399">https://hdl.handle.net/1911/105399</a>.en_US
dc.identifier.urihttps://hdl.handle.net/1911/105399en_US
dc.language.isoengen_US
dc.rightsCopyright is held by the author, unless otherwise indicated. Permission to reuse, publish, or reproduce the work beyond the bounds of fair use or other exemptions to copyright law must be obtained from the copyright holder.en_US
dc.subjectphylogenomicsen_US
dc.subjectphylogeny inferenceen_US
dc.subjectno-common-mechanismen_US
dc.subjectmaximum likelihooden_US
dc.subjectmultispecies network coalescenten_US
dc.subjectintegrated likelihooden_US
dc.titleIntegrated Likelihood for Phylogenomics under a No-Common-Mechanism Modelen_US
dc.typeThesisen_US
dc.type.materialTexten_US
thesis.degree.departmentComputer Scienceen_US
thesis.degree.disciplineEngineeringen_US
thesis.degree.grantorRice Universityen_US
thesis.degree.levelMastersen_US
thesis.degree.majorComputational Evolutionary Biologyen_US
thesis.degree.nameMaster of Scienceen_US
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