{"id":{"repo_id":"uiuc","oai_identifier":"oai:www.ideals.illinois.edu:2142/93068"},"canonical_url":"https://search.dev.ndltd.org/etd/uiuc/oai:www.ideals.illinois.edu:2142/93068","repository":{"repo_id":"uiuc","name":"University of Illinois - Urbana-Champaign","base_url":"https://www.ideals.illinois.edu/oai-pmh"},"display":{"title":"Population genomics of Sulfolobus islandicus: genome-wide recombination and antagonistic interactions","abstract":"Microbial speciation is a topic of great debate, given that bacteria and archaea are generally asexually reproducing organisms that occasionally engage in genetic transfer and recombination. With the onset of the era of genomic sequencing of natural populations of microorganisms, it has been revealed that genetic recombination is not just a useful laboratory tool for microbial geneticists, but instead a prominent feature of microbial population biology. Conceptual models of how microbial species may form, especially those that incorporate genetic recombination, are currently being tested using the rapidly accumulating wealth of sequence data from entire microbial populations and communities. Sulfolobus islandicus is a model organism for studying microbial population biology due to its island population structure that isolates endemic populations to specific regions. A single population from the Mutnovsky Volcano region of Kamchatka, Russia was studied in-depth to determine why diverging species showed large 'continents' of fixation between co-existing 'species'. The effects of mutation, selection, and recombination were analyzed genome-wide using a set of ten genomes from the two species that co-exist in this population. Although mutation rates had no correlation with patterns of genetic diversity, the interplay between recombination and selection were shown to define the non-uniform distribution of genetic diversity in the S. islandicus chromosome. The analysis also identified large genomic regions (>100Kb) of low recombination. To follow up on this result, strains were brought into the laboratory to investigate genome-wide inter-species recombination rates. A combination of high-throughput genome sequencing and novel computational tools determined that recombination rates do not vary significantly across the genome. This contrasts with the natural population study, implying that environmental selection acts against inter-species hybrids to reinforce species boundaries. Finally, antagonistic interactions among these ten genome strains, as well as an expanded set of strains isolated from multiple hot springs and time points were catalogued and shown to correlate with genetic distance. Characterization of the genetic underpinnings and mechanism of the antagonism have begun, but definitive conclusions will require further work and alternative approaches.","abstract_html":"Microbial speciation is a topic of great debate, given that bacteria and archaea are generally asexually reproducing organisms that occasionally engage in genetic transfer and recombination. With the onset of the era of genomic sequencing of natural populations of microorganisms, it has been revealed that genetic recombination is not just a useful laboratory tool for microbial geneticists, but instead a prominent feature of microbial population biology. Conceptual models of how microbial species may form, especially those that incorporate genetic recombination, are currently being tested using the rapidly accumulating wealth of sequence data from entire microbial populations and communities. Sulfolobus islandicus is a model organism for studying microbial population biology due to its island population structure that isolates endemic populations to specific regions. A single population from the Mutnovsky Volcano region of Kamchatka, Russia was studied in-depth to determine why diverging species showed large 'continents' of fixation between co-existing 'species'. The effects of mutation, selection, and recombination were analyzed genome-wide using a set of ten genomes from the two species that co-exist in this population. Although mutation rates had no correlation with patterns of genetic diversity, the interplay between recombination and selection were shown to define the non-uniform distribution of genetic diversity in the S. islandicus chromosome. The analysis also identified large genomic regions (>100Kb) of low recombination. To follow up on this result, strains were brought into the laboratory to investigate genome-wide inter-species recombination rates. A combination of high-throughput genome sequencing and novel computational tools determined that recombination rates do not vary significantly across the genome. This contrasts with the natural population study, implying that environmental selection acts against inter-species hybrids to reinforce species boundaries. Finally, antagonistic interactions among these ten genome strains, as well as an expanded set of strains isolated from multiple hot springs and time points were catalogued and shown to correlate with genetic distance. Characterization of the genetic underpinnings and mechanism of the antagonism have begun, but definitive conclusions will require further work and alternative approaches.","abstract_has_math":false,"creators":["Krause, David Joseph"],"institution":"University of Illinois at Urbana-Champaign","degree_name":"Ph.D.","degree_level":"Dissertation","degree_discipline":"Microbiology","degree_department":null,"school":null,"contributors":["Whitaker, Rachel J.","Metcalf, William W.","Farrand, Stephen K.","Kuzminov, Andrei"],"advisors":[],"committee_chairs":[],"committee_members":[],"year":2016,"date_issued":"2016-11-10T18:43:02Z","date_published":"2016-11-10T18:43:02Z","updated_at":"2026-07-22T22:26:35Z","subjects":["Population genomics","Archaea","Recombination"],"languages":["en"],"rights":["Copyright 2016 David Krause"],"rights_urls":[],"identifier_entries":[]},"links":{"outbound_url":"http://hdl.handle.net/2142/93068","outbound_label":"Handle","outbound_source":"dc:identifier"},"metadata_groups":[{"id":"people","label":"People","entries":[{"key":"dc:contributor","label":"Contributor","values":["Whitaker, Rachel J.","Metcalf, William W.","Farrand, Stephen K.","Kuzminov, Andrei"]},{"key":"dc:creator","label":"Author","values":["Krause, David Joseph"]}]},{"id":"academic_context","label":"Academic Context","entries":[{"key":"dc:date","label":"Dc Date","values":["2016-11-10T18:43:02Z","2018-11-11T10:15:36Z","2016-07-15","2016-08"]},{"key":"dc:type","label":"Dc Type","values":["text"]},{"key":"thesis:degree_discipline","label":"Discipline","values":["Microbiology"]},{"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":["Population genomics","Archaea","Recombination"]}]},{"id":"language_rights","label":"Language and Rights","entries":[{"key":"dc:language","label":"Dc Language","values":["en"]},{"key":"dc:rights","label":"Dc Rights","values":["Copyright 2016 David Krause"]}]},{"id":"identifiers","label":"Identifiers","entries":[{"key":"dc:identifier","label":"Identifier","values":["http://hdl.handle.net/2142/93068"]}]},{"id":"additional","label":"Additional Metadata","entries":[{"key":"dc:description","label":"Description","values":["Microbial speciation is a topic of great debate, given that bacteria and archaea are generally asexually reproducing organisms that occasionally engage in genetic transfer and recombination. With the onset of the era of genomic sequencing of natural populations of microorganisms, it has been revealed that genetic recombination is not just a useful laboratory tool for microbial geneticists, but instead a prominent feature of microbial population biology. Conceptual models of how microbial species may form, especially those that incorporate genetic recombination, are currently being tested using the rapidly accumulating wealth of sequence data from entire microbial populations and communities. Sulfolobus islandicus is a model organism for studying microbial population biology due to its island population structure that isolates endemic populations to specific regions. A single population from the Mutnovsky Volcano region of Kamchatka, Russia was studied in-depth to determine why diverging species showed large 'continents' of fixation between co-existing 'species'. The effects of mutation, selection, and recombination were analyzed genome-wide using a set of ten genomes from the two species that co-exist in this population. Although mutation rates had no correlation with patterns of genetic diversity, the interplay between recombination and selection were shown to define the non-uniform distribution of genetic diversity in the S. islandicus chromosome. The analysis also identified large genomic regions (>100Kb) of low recombination. To follow up on this result, strains were brought into the laboratory to investigate genome-wide inter-species recombination rates. A combination of high-throughput genome sequencing and novel computational tools determined that recombination rates do not vary significantly across the genome. This contrasts with the natural population study, implying that environmental selection acts against inter-species hybrids to reinforce species boundaries. Finally, antagonistic interactions among these ten genome strains, as well as an expanded set of strains isolated from multiple hot springs and time points were catalogued and shown to correlate with genetic distance. Characterization of the genetic underpinnings and mechanism of the antagonism have begun, but definitive conclusions will require further work and alternative approaches.","Submission published under a 24 month embargo labeled 'U of I Access', the embargo will last until 2018-08-01","The student, David Krause, accepted the attached license on 2016-07-15 at 10:04.","The student, David Krause, submitted this Dissertation for approval on 2016-07-15 at 10:10.","This Dissertation was approved for publication on 2016-07-15 at 13:29.","DSpace SAF Submission Ingestion Package generated from Vireo submission #9958 on 2016-11-10 at 12:25:28","Made available in DSpace on 2016-11-10T18:43:02Z (GMT). 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With the onset of the era of genomic sequencing of natural populations of microorganisms, it has been revealed that genetic recombination is not just a useful laboratory tool for microbial geneticists, but instead a prominent feature of microbial population biology. Conceptual models of how microbial species may form, especially those that incorporate genetic recombination, are currently being tested using the rapidly accumulating wealth of sequence data from entire microbial populations and communities. Sulfolobus islandicus is a model organism for studying microbial population biology due to its island population structure that isolates endemic populations to specific regions. A single population from the Mutnovsky Volcano region of Kamchatka, Russia was studied in-depth to determine why diverging species showed large 'continents' of fixation between co-existing 'species'. The effects of mutation, selection, and recombination were analyzed genome-wide using a set of ten genomes from the two species that co-exist in this population. Although mutation rates had no correlation with patterns of genetic diversity, the interplay between recombination and selection were shown to define the non-uniform distribution of genetic diversity in the S. islandicus chromosome. The analysis also identified large genomic regions (>100Kb) of low recombination. To follow up on this result, strains were brought into the laboratory to investigate genome-wide inter-species recombination rates. A combination of high-throughput genome sequencing and novel computational tools determined that recombination rates do not vary significantly across the genome. This contrasts with the natural population study, implying that environmental selection acts against inter-species hybrids to reinforce species boundaries. Finally, antagonistic interactions among these ten genome strains, as well as an expanded set of strains isolated from multiple hot springs and time points were catalogued and shown to correlate with genetic distance. Characterization of the genetic underpinnings and mechanism of the antagonism have begun, but definitive conclusions will require further work and alternative approaches.","Submission published under a 24 month embargo labeled 'U of I Access', the embargo will last until 2018-08-01","The student, David Krause, accepted the attached license on 2016-07-15 at 10:04.","The student, David Krause, submitted this Dissertation for approval on 2016-07-15 at 10:10.","This Dissertation was approved for publication on 2016-07-15 at 13:29.","DSpace SAF Submission Ingestion Package generated from Vireo submission #9958 on 2016-11-10 at 12:25:28","Made available in DSpace on 2016-11-10T18:43:02Z (GMT). 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