{"id":{"repo_id":"uiuc","oai_identifier":"oai:www.ideals.illinois.edu:2142/108428"},"canonical_url":"https://search.dev.ndltd.org/etd/uiuc/oai:www.ideals.illinois.edu:2142/108428","repository":{"repo_id":"uiuc","name":"University of Illinois - Urbana-Champaign","base_url":"https://www.ideals.illinois.edu/oai-pmh"},"display":{"title":"Supertree-like methods for genome-scale species tree estimation","abstract":"A critical step in many biological studies is the estimation of evolutionary trees (phylogenies) from genomic data. Of particular interest is the species tree, which illustrates how a set of species evolved from a common ancestor. While species trees were previously estimated from a few regions of the genome (genes), it is now widely recognized that biological processes can cause the evolutionary histories of individual genes to differ from each other and from the species tree. This heterogeneity across the genome is phylogenetic signal that can be leveraged to estimate species evolution with greater accuracy. Hence, species tree estimation is expected to be greatly aided by current large-scale sequencing efforts, including the 5000 Insect Genomes Project, the 10000 Plant Genomes Project, the (~60000) Vertebrate Genomes Project, and the Earth BioGenome Project, which aims to assemble genomes (or at least genome-scale data) for 1.5 million eukaryotic species in the next ten years. To analyze these forthcoming datasets, species tree estimation methods must scale to thousands of species and tens of thousands of genes; however, many of the current leading methods, which are heuristics for NP-hard optimization problems, can be prohibitively expensive on datasets of this size. In this dissertation, we argue that new methods are needed to enable scalable and statistically rigorous species tree estimation pipelines; we then seek to address this challenge through the introduction of three supertree-like methods: NJMerge, TreeMerge, and FastMulRFS. For these methods, we present theoretical results (worst-case running time analyses and proofs of statistical consistency) as well as empirical results on simulated datasets (and a fungal dataset for FastMulRFS). Overall, these methods enable statistically consistent species tree estimation pipelines that achieve comparable accuracy to the dominant optimization-based approaches while dramatically reducing running time.","abstract_html":"A critical step in many biological studies is the estimation of evolutionary trees (phylogenies) from genomic data. Of particular interest is the species tree, which illustrates how a set of species evolved from a common ancestor. While species trees were previously estimated from a few regions of the genome (genes), it is now widely recognized that biological processes can cause the evolutionary histories of individual genes to differ from each other and from the species tree. This heterogeneity across the genome is phylogenetic signal that can be leveraged to estimate species evolution with greater accuracy. Hence, species tree estimation is expected to be greatly aided by current large-scale sequencing efforts, including the 5000 Insect Genomes Project, the 10000 Plant Genomes Project, the (~60000) Vertebrate Genomes Project, and the Earth BioGenome Project, which aims to assemble genomes (or at least genome-scale data) for 1.5 million eukaryotic species in the next ten years. To analyze these forthcoming datasets, species tree estimation methods must scale to thousands of species and tens of thousands of genes; however, many of the current leading methods, which are heuristics for NP-hard optimization problems, can be prohibitively expensive on datasets of this size. In this dissertation, we argue that new methods are needed to enable scalable and statistically rigorous species tree estimation pipelines; we then seek to address this challenge through the introduction of three supertree-like methods: NJMerge, TreeMerge, and FastMulRFS. For these methods, we present theoretical results (worst-case running time analyses and proofs of statistical consistency) as well as empirical results on simulated datasets (and a fungal dataset for FastMulRFS). Overall, these methods enable statistically consistent species tree estimation pipelines that achieve comparable accuracy to the dominant optimization-based approaches while dramatically reducing running time.","abstract_has_math":false,"creators":["Molloy, Erin Katherine"],"institution":"University of Illinois at Urbana-Champaign","degree_name":"Ph.D.","degree_level":"Dissertation","degree_discipline":"Computer Science","degree_department":null,"school":null,"contributors":["Warnow, Tandy","Gropp, William","Snir, Marc","Nakhleh, Luay"],"advisors":[],"committee_chairs":[],"committee_members":[],"year":2020,"date_issued":"2020-10-07T20:59:24Z","date_published":"2020-10-07T20:59:24Z","updated_at":"2026-07-22T22:24:48Z","subjects":["phylogenetics","phylogenomics","species tree estimation","Multi-Species Coalescent model","gene duplication and loss"],"languages":["en"],"rights":["Copyright 2020 Erin Molloy"],"rights_urls":[],"identifier_entries":[]},"links":{"outbound_url":"http://hdl.handle.net/2142/108428","outbound_label":"Handle","outbound_source":"dc:identifier"},"metadata_groups":[{"id":"people","label":"People","entries":[{"key":"dc:contributor","label":"Contributor","values":["Warnow, Tandy","Gropp, William","Snir, Marc","Nakhleh, Luay"]},{"key":"dc:creator","label":"Author","values":["Molloy, Erin Katherine"]}]},{"id":"academic_context","label":"Academic Context","entries":[{"key":"dc:date","label":"Dc Date","values":["2020-10-07T20:59:24Z","2020-06-29","2020-08"]},{"key":"dc:type","label":"Dc Type","values":["text","Thesis"]},{"key":"thesis:degree_discipline","label":"Discipline","values":["Computer Science"]},{"key":"thesis:degree_level","label":"Degree Level","values":["Dissertation"]},{"key":"thesis:degree_name","label":"Degree Name","values":["Ph.D."]},{"key":"thesis:institution_name","label":"Thesis Institution Name","values":["University of Illinois at Urbana-Champaign"]}]},{"id":"subjects_keywords","label":"Subjects and Keywords","entries":[{"key":"dc:subject","label":"Dc Subject","values":["phylogenetics","phylogenomics","species tree estimation","Multi-Species Coalescent model","gene duplication and loss"]}]},{"id":"language_rights","label":"Language and Rights","entries":[{"key":"dc:language","label":"Dc Language","values":["en"]},{"key":"dc:rights","label":"Dc Rights","values":["Copyright 2020 Erin Molloy"]}]},{"id":"identifiers","label":"Identifiers","entries":[{"key":"dc:identifier","label":"Identifier","values":["http://hdl.handle.net/2142/108428"]}]},{"id":"additional","label":"Additional Metadata","entries":[{"key":"dc:description","label":"Description","values":["A critical step in many biological studies is the estimation of evolutionary trees (phylogenies) from genomic data. Of particular interest is the species tree, which illustrates how a set of species evolved from a common ancestor. While species trees were previously estimated from a few regions of the genome (genes), it is now widely recognized that biological processes can cause the evolutionary histories of individual genes to differ from each other and from the species tree. This heterogeneity across the genome is phylogenetic signal that can be leveraged to estimate species evolution with greater accuracy. Hence, species tree estimation is expected to be greatly aided by current large-scale sequencing efforts, including the 5000 Insect Genomes Project, the 10000 Plant Genomes Project, the (~60000) Vertebrate Genomes Project, and the Earth BioGenome Project, which aims to assemble genomes (or at least genome-scale data) for 1.5 million eukaryotic species in the next ten years. To analyze these forthcoming datasets, species tree estimation methods must scale to thousands of species and tens of thousands of genes; however, many of the current leading methods, which are heuristics for NP-hard optimization problems, can be prohibitively expensive on datasets of this size. In this dissertation, we argue that new methods are needed to enable scalable and statistically rigorous species tree estimation pipelines; we then seek to address this challenge through the introduction of three supertree-like methods: NJMerge, TreeMerge, and FastMulRFS. For these methods, we present theoretical results (worst-case running time analyses and proofs of statistical consistency) as well as empirical results on simulated datasets (and a fungal dataset for FastMulRFS). Overall, these methods enable statistically consistent species tree estimation pipelines that achieve comparable accuracy to the dominant optimization-based approaches while dramatically reducing running time.","Submission original under an indefinite embargo labeled 'Open Access'. The submission was exported from vireo on 2020-10-02 without embargo terms","The student, Erin Molloy, accepted the attached license on 2020-06-18 at 11:34.","The student, Erin Molloy, submitted this Dissertation for approval on 2020-06-18 at 11:54.","This Dissertation was approved for publication on 2020-06-29 at 13:22.","DSpace SAF Submission Ingestion Package generated from Vireo submission #15454 on 2020-10-02 at 15:10:35","Made available in DSpace on 2020-10-07T20:59:24Z (GMT). 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Of particular interest is the species tree, which illustrates how a set of species evolved from a common ancestor. While species trees were previously estimated from a few regions of the genome (genes), it is now widely recognized that biological processes can cause the evolutionary histories of individual genes to differ from each other and from the species tree. This heterogeneity across the genome is phylogenetic signal that can be leveraged to estimate species evolution with greater accuracy. Hence, species tree estimation is expected to be greatly aided by current large-scale sequencing efforts, including the 5000 Insect Genomes Project, the 10000 Plant Genomes Project, the (~60000) Vertebrate Genomes Project, and the Earth BioGenome Project, which aims to assemble genomes (or at least genome-scale data) for 1.5 million eukaryotic species in the next ten years. To analyze these forthcoming datasets, species tree estimation methods must scale to thousands of species and tens of thousands of genes; however, many of the current leading methods, which are heuristics for NP-hard optimization problems, can be prohibitively expensive on datasets of this size. In this dissertation, we argue that new methods are needed to enable scalable and statistically rigorous species tree estimation pipelines; we then seek to address this challenge through the introduction of three supertree-like methods: NJMerge, TreeMerge, and FastMulRFS. For these methods, we present theoretical results (worst-case running time analyses and proofs of statistical consistency) as well as empirical results on simulated datasets (and a fungal dataset for FastMulRFS). Overall, these methods enable statistically consistent species tree estimation pipelines that achieve comparable accuracy to the dominant optimization-based approaches while dramatically reducing running time.","Submission original under an indefinite embargo labeled 'Open Access'. The submission was exported from vireo on 2020-10-02 without embargo terms","The student, Erin Molloy, accepted the attached license on 2020-06-18 at 11:34.","The student, Erin Molloy, submitted this Dissertation for approval on 2020-06-18 at 11:54.","This Dissertation was approved for publication on 2020-06-29 at 13:22.","DSpace SAF Submission Ingestion Package generated from Vireo submission #15454 on 2020-10-02 at 15:10:35","Made available in DSpace on 2020-10-07T20:59:24Z (GMT). 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