{"id":{"repo_id":"uiuc","oai_identifier":"oai:www.ideals.illinois.edu:2142/132481"},"canonical_url":"https://search.dev.ndltd.org/etd/uiuc/oai:www.ideals.illinois.edu:2142/132481","repository":{"repo_id":"uiuc","name":"University of Illinois - Urbana-Champaign","base_url":"https://www.ideals.illinois.edu/oai-pmh"},"display":{"title":"Novel computational methods for discordance-aware phylogenomic analysis","abstract":"Inferring the evolutionary history of a set of species is a key step in many biological and medical research projects, as species trees provide a context in which problems in comparative genomics, biodiversity, phylogeography and epidemiology can be addressed. Recent advances in sequencing technologies have led to an increasing availability of genome-scale data, and today phylogenomics projects construct species trees using hundreds to thousands of loci, potentially whole genomes. However, species tree estimation from multi-locus datasets presents several statistical and computational challenges, as most problems in this area are NP-hard. Also, due to a phenomenon known as “gene tree heterogeneity”, different locations within the genome of a species can evolve differently due to biological processes such as incomplete lineage sorting, gene duplication and loss and horizontal gene transfer, that further complicate species tree estimation. Despite advances in developing methods that can estimate an unrooted and non-parameterized topology of a species tree in the presence of gene tree discordance, less attention has been paid to estimating the root location, quantifying branch lengths in units that are usable for downstream analysis, and estimating divergence times. All of these are necessary for many applications of phylogenomics, such as constructing the tree of life and analyzing the origins of diseases, such as HIV and COVID-19. In this dissertation, we introduce new computational methods developed for these tasks, collectively referred to as \"post-species tree analysis\", that address different sources of gene tree discordance. For these methods, we present rigorous theoretical results including proofs of statistical consistency, sample complexity, and running time analyses, as well as extensive empirical results on simulated and biological datasets ranging from the root of the tree of life to recent speciations. Overall, these methods provide high accuracy and scalability for estimating the root, branch lengths and divergence times in the presence of gene tree discordance, and some are accompanied with strong theoretical guarantees.","abstract_html":"Inferring the evolutionary history of a set of species is a key step in many biological and medical research projects, as species trees provide a context in which problems in comparative genomics, biodiversity, phylogeography and epidemiology can be addressed. Recent advances in sequencing technologies have led to an increasing availability of genome-scale data, and today phylogenomics projects construct species trees using hundreds to thousands of loci, potentially whole genomes. However, species tree estimation from multi-locus datasets presents several statistical and computational challenges, as most problems in this area are NP-hard. Also, due to a phenomenon known as “gene tree heterogeneity”, different locations within the genome of a species can evolve differently due to biological processes such as incomplete lineage sorting, gene duplication and loss and horizontal gene transfer, that further complicate species tree estimation. Despite advances in developing methods that can estimate an unrooted and non-parameterized topology of a species tree in the presence of gene tree discordance, less attention has been paid to estimating the root location, quantifying branch lengths in units that are usable for downstream analysis, and estimating divergence times. All of these are necessary for many applications of phylogenomics, such as constructing the tree of life and analyzing the origins of diseases, such as HIV and COVID-19. In this dissertation, we introduce new computational methods developed for these tasks, collectively referred to as "post-species tree analysis", that address different sources of gene tree discordance. For these methods, we present rigorous theoretical results including proofs of statistical consistency, sample complexity, and running time analyses, as well as extensive empirical results on simulated and biological datasets ranging from the root of the tree of life to recent speciations. Overall, these methods provide high accuracy and scalability for estimating the root, branch lengths and divergence times in the presence of gene tree discordance, and some are accompanied with strong theoretical guarantees.","abstract_has_math":false,"creators":["Tabatabaee, Seyedeh Yasamin"],"institution":"University of Illinois Urbana-Champaign","degree_name":"Ph.D.","degree_level":"Dissertation","degree_discipline":"Computer Science","degree_department":null,"school":null,"contributors":["Warnow, Tandy","El-Kebir, Mohammed","Gropp, William","Liu, Ge","Mirarab, Siavash"],"advisors":[],"committee_chairs":[],"committee_members":[],"year":2025,"date_issued":"2025-12","date_published":"2025-12","updated_at":"2026-07-22T22:25:07Z","subjects":["phylogenetics","phylogenomics","gene tree discordance","species tree estimation","multi-species coalescent"],"languages":["en"],"rights":["Copyright 2025 Seyedeh Yasamin Tabatabaee"],"rights_urls":[],"identifier_entries":[]},"links":{"outbound_url":"https://hdl.handle.net/2142/132481","outbound_label":"Handle","outbound_source":"dc:identifier"},"metadata_groups":[{"id":"people","label":"People","entries":[{"key":"dc:contributor","label":"Contributor","values":["Warnow, Tandy","El-Kebir, Mohammed","Gropp, William","Liu, Ge","Mirarab, Siavash"]},{"key":"dc:creator","label":"Author","values":["Tabatabaee, Seyedeh Yasamin"]}]},{"id":"academic_context","label":"Academic Context","entries":[{"key":"dc:date","label":"Dc Date","values":["2025-12","2025-11-11"]},{"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 Urbana-Champaign"]}]},{"id":"subjects_keywords","label":"Subjects and Keywords","entries":[{"key":"dc:subject","label":"Dc Subject","values":["phylogenetics","phylogenomics","gene tree discordance","species tree estimation","multi-species coalescent"]}]},{"id":"language_rights","label":"Language and Rights","entries":[{"key":"dc:language","label":"Dc Language","values":["en"]},{"key":"dc:rights","label":"Dc Rights","values":["Copyright 2025 Seyedeh Yasamin Tabatabaee"]}]},{"id":"identifiers","label":"Identifiers","entries":[{"key":"dc:identifier","label":"Identifier","values":["https://hdl.handle.net/2142/132481"]}]},{"id":"additional","label":"Additional Metadata","entries":[{"key":"dc:description","label":"Description","values":["Inferring the evolutionary history of a set of species is a key step in many biological and medical research projects, as species trees provide a context in which problems in comparative genomics, biodiversity, phylogeography and epidemiology can be addressed. Recent advances in sequencing technologies have led to an increasing availability of genome-scale data, and today phylogenomics projects construct species trees using hundreds to thousands of loci, potentially whole genomes. However, species tree estimation from multi-locus datasets presents several statistical and computational challenges, as most problems in this area are NP-hard. Also, due to a phenomenon known as “gene tree heterogeneity”, different locations within the genome of a species can evolve differently due to biological processes such as incomplete lineage sorting, gene duplication and loss and horizontal gene transfer, that further complicate species tree estimation. Despite advances in developing methods that can estimate an unrooted and non-parameterized topology of a species tree in the presence of gene tree discordance, less attention has been paid to estimating the root location, quantifying branch lengths in units that are usable for downstream analysis, and estimating divergence times. All of these are necessary for many applications of phylogenomics, such as constructing the tree of life and analyzing the origins of diseases, such as HIV and COVID-19. In this dissertation, we introduce new computational methods developed for these tasks, collectively referred to as \"post-species tree analysis\", that address different sources of gene tree discordance. For these methods, we present rigorous theoretical results including proofs of statistical consistency, sample complexity, and running time analyses, as well as extensive empirical results on simulated and biological datasets ranging from the root of the tree of life to recent speciations. Overall, these methods provide high accuracy and scalability for estimating the root, branch lengths and divergence times in the presence of gene tree discordance, and some are accompanied with strong theoretical guarantees.","Submission original under an indefinite embargo labeled 'Open Access'. The submission was exported from vireo on 2026-02-19 without embargo terms","The student, Seyedeh Yasamin Tabatabaee, accepted the attached license on 2025-11-10 at 11:19.","The student, Seyedeh Yasamin Tabatabaee, submitted this Dissertation for approval on 2025-11-10 at 11:34.","This Dissertation was approved for publication on 2025-11-11 at 10:09.","DSpace SAF Submission Ingestion Package generated from Vireo submission #22854 on 2026-02-19 at 18:24:30"]},{"key":"dc:format","label":"Dc Format","values":["application/pdf"]},{"key":"dc:title","label":"Title","values":["Novel computational methods for discordance-aware phylogenomic analysis"]}]}],"canonical_facts":{"dc:contributor":["Warnow, Tandy","El-Kebir, Mohammed","Gropp, William","Liu, Ge","Mirarab, Siavash"],"dc:creator":["Tabatabaee, Seyedeh Yasamin"],"dc:date":["2025-12","2025-11-11"],"dc:description":["Inferring the evolutionary history of a set of species is a key step in many biological and medical research projects, as species trees provide a context in which problems in comparative genomics, biodiversity, phylogeography and epidemiology can be addressed. Recent advances in sequencing technologies have led to an increasing availability of genome-scale data, and today phylogenomics projects construct species trees using hundreds to thousands of loci, potentially whole genomes. However, species tree estimation from multi-locus datasets presents several statistical and computational challenges, as most problems in this area are NP-hard. Also, due to a phenomenon known as “gene tree heterogeneity”, different locations within the genome of a species can evolve differently due to biological processes such as incomplete lineage sorting, gene duplication and loss and horizontal gene transfer, that further complicate species tree estimation. Despite advances in developing methods that can estimate an unrooted and non-parameterized topology of a species tree in the presence of gene tree discordance, less attention has been paid to estimating the root location, quantifying branch lengths in units that are usable for downstream analysis, and estimating divergence times. All of these are necessary for many applications of phylogenomics, such as constructing the tree of life and analyzing the origins of diseases, such as HIV and COVID-19. In this dissertation, we introduce new computational methods developed for these tasks, collectively referred to as \"post-species tree analysis\", that address different sources of gene tree discordance. For these methods, we present rigorous theoretical results including proofs of statistical consistency, sample complexity, and running time analyses, as well as extensive empirical results on simulated and biological datasets ranging from the root of the tree of life to recent speciations. Overall, these methods provide high accuracy and scalability for estimating the root, branch lengths and divergence times in the presence of gene tree discordance, and some are accompanied with strong theoretical guarantees.","Submission original under an indefinite embargo labeled 'Open Access'. The submission was exported from vireo on 2026-02-19 without embargo terms","The student, Seyedeh Yasamin Tabatabaee, accepted the attached license on 2025-11-10 at 11:19.","The student, Seyedeh Yasamin Tabatabaee, submitted this Dissertation for approval on 2025-11-10 at 11:34.","This Dissertation was approved for publication on 2025-11-11 at 10:09.","DSpace SAF Submission Ingestion Package generated from Vireo submission #22854 on 2026-02-19 at 18:24:30"],"dc:format":["application/pdf"],"dc:identifier":["https://hdl.handle.net/2142/132481"],"dc:language":["en"],"dc:rights":["Copyright 2025 Seyedeh Yasamin Tabatabaee"],"dc:subject":["phylogenetics","phylogenomics","gene tree discordance","species tree estimation","multi-species coalescent"],"dc:title":["Novel computational methods for discordance-aware phylogenomic analysis"],"dc:type":["text","Thesis"],"thesis:degree_discipline":["Computer Science"],"thesis:degree_level":["Dissertation"],"thesis:degree_name":["Ph.D."],"thesis:institution_name":["University of Illinois Urbana-Champaign"]},"updated_at":"2026-07-22T22:25:07Z"}