{"id":{"repo_id":"carleton","oai_identifier":"oai:carleton.scholaris.ca:20.500.14718/38972"},"canonical_url":"https://search.dev.ndltd.org/etd/carleton/oai:carleton.scholaris.ca:20.500.14718/38972","repository":{"repo_id":"carleton","name":"Carleton University","base_url":"https://carleton.scholaris.ca/server/oai/request"},"display":{"title":"Navigating Molecular Evolution Using Substitution Mappings","abstract":"Since first proposed in 2002, Bayesian substitution mappings have found less use than might have been expected in the field of molecular evolution. Here, I first create a sequence simulator capable of generating true substitution mappings for simulated data under any time-reversible model in order to facilitate study of substitution mappings. I then investigate the utility of substitution mappings for two applications: detection of coevolving residues and scoring of amino acid substitution radicality to test the predictions of the nearly neutral theory. I find that mappings perform poorly for coevolution detection, but using mappings to find the radicality of an average amino acid by scoring each observed substitution works well. Overall, substitution mappings look to be a potentially useful tool for some types of molecular evolution studies.","abstract_html":"Since first proposed in 2002, Bayesian substitution mappings have found less use than might have been expected in the field of molecular evolution. Here, I first create a sequence simulator capable of generating true substitution mappings for simulated data under any time-reversible model in order to facilitate study of substitution mappings. I then investigate the utility of substitution mappings for two applications: detection of coevolving residues and scoring of amino acid substitution radicality to test the predictions of the nearly neutral theory. I find that mappings perform poorly for coevolution detection, but using mappings to find the radicality of an average amino acid by scoring each observed substitution works well. Overall, substitution mappings look to be a potentially useful tool for some types of molecular evolution studies.","abstract_has_math":false,"creators":["Low, Andrew"],"institution":"Carleton University","degree_name":"Master of Science (M.Sc.)","degree_level":"Master's","degree_discipline":"Biology","degree_department":null,"school":null,"contributors":[],"advisors":[],"committee_chairs":[],"committee_members":[],"year":2017,"date_issued":"2017","date_published":"2017","updated_at":"2026-07-24T01:34:41Z","subjects":[],"languages":["en"],"rights":["Copyright © 2017 the author(s). Theses may be used for non-commercial research, educational, or related academic purposes only. Such uses include personal study, research, scholarship, and teaching. Theses may only be shared by linking to Carleton University Institutional Repository and no part may be used without proper attribution to the author. No part may be used for commercial purposes directly or indirectly via a for-profit platform; no adaptation or derivative works are permitted without consent from the copyright owner."],"rights_urls":[],"identifier_entries":[{"key":"dc:identifier.doi","label":"DOI","values":["10.22215/etd/2017-12009"],"render_values":[{"text":"10.22215/etd/2017-12009","href":"https://doi.org/10.22215/etd/2017-12009","code":true}]}]},"links":{"outbound_url":"https://hdl.handle.net/20.500.14718/38972","outbound_label":"Handle","outbound_source":"dc:identifier.uri"},"metadata_groups":[{"id":"people","label":"People","entries":[{"key":"dc:creator","label":"Author","values":["Low, Andrew"]}]},{"id":"academic_context","label":"Academic Context","entries":[{"key":"dc:date.accessioned","label":"Dc Date Accessioned","values":["2025-04-08T19:33:20Z"]},{"key":"dc:date.available","label":"Dc Date Available","values":["2025-04-08T19:33:20Z"]},{"key":"dc:date.issued","label":"Date","values":["2017"]},{"key":"dc:publisher","label":"Institution","values":["Carleton University"]},{"key":"dc:type","label":"Dc Type","values":["thesis"]},{"key":"thesis:degree_discipline","label":"Discipline","values":["Biology"]},{"key":"thesis:degree_level","label":"Degree Level","values":["Master's"]},{"key":"thesis:degree_name","label":"Degree Name","values":["Master of Science (M.Sc.)"]}]},{"id":"language_rights","label":"Language and Rights","entries":[{"key":"dc:language.iso","label":"Language (ISO)","values":["en"]},{"key":"dc:rights","label":"Dc Rights","values":["Copyright © 2017 the author(s). Theses may be used for non-commercial research, educational, or related academic purposes only. Such uses include personal study, research, scholarship, and teaching. Theses may only be shared by linking to Carleton University Institutional Repository and no part may be used without proper attribution to the author. No part may be used for commercial purposes directly or indirectly via a for-profit platform; no adaptation or derivative works are permitted without consent from the copyright owner."]}]},{"id":"identifiers","label":"Identifiers","entries":[{"key":"dc:identifier.doi","label":"DOI","values":["10.22215/etd/2017-12009"]},{"key":"dc:identifier.uri","label":"Identifier URI","values":["https://hdl.handle.net/20.500.14718/38972"]}]},{"id":"additional","label":"Additional Metadata","entries":[{"key":"dc:description.abstract","label":"Abstract","values":["Since first proposed in 2002, Bayesian substitution mappings have found less use than might have been expected in the field of molecular evolution. Here, I first create a sequence simulator capable of generating true substitution mappings for simulated data under any time-reversible model in order to facilitate study of substitution mappings. I then investigate the utility of substitution mappings for two applications: detection of coevolving residues and scoring of amino acid substitution radicality to test the predictions of the nearly neutral theory. I find that mappings perform poorly for coevolution detection, but using mappings to find the radicality of an average amino acid by scoring each observed substitution works well. Overall, substitution mappings look to be a potentially useful tool for some types of molecular evolution studies."]},{"key":"dc:title","label":"Title","values":["Navigating Molecular Evolution Using Substitution Mappings"]}]}],"canonical_facts":{"dc:creator":["Low, Andrew"],"dc:date.accessioned":["2025-04-08T19:33:20Z"],"dc:date.available":["2025-04-08T19:33:20Z"],"dc:date.issued":["2017"],"dc:description.abstract":["Since first proposed in 2002, Bayesian substitution mappings have found less use than might have been expected in the field of molecular evolution. Here, I first create a sequence simulator capable of generating true substitution mappings for simulated data under any time-reversible model in order to facilitate study of substitution mappings. I then investigate the utility of substitution mappings for two applications: detection of coevolving residues and scoring of amino acid substitution radicality to test the predictions of the nearly neutral theory. I find that mappings perform poorly for coevolution detection, but using mappings to find the radicality of an average amino acid by scoring each observed substitution works well. Overall, substitution mappings look to be a potentially useful tool for some types of molecular evolution studies."],"dc:identifier.doi":["10.22215/etd/2017-12009"],"dc:identifier.uri":["https://hdl.handle.net/20.500.14718/38972"],"dc:language.iso":["en"],"dc:publisher":["Carleton University"],"dc:rights":["Copyright © 2017 the author(s). Theses may be used for non-commercial research, educational, or related academic purposes only. Such uses include personal study, research, scholarship, and teaching. Theses may only be shared by linking to Carleton University Institutional Repository and no part may be used without proper attribution to the author. No part may be used for commercial purposes directly or indirectly via a for-profit platform; no adaptation or derivative works are permitted without consent from the copyright owner."],"dc:title":["Navigating Molecular Evolution Using Substitution Mappings"],"dc:type":["thesis"],"thesis:degree_discipline":["Biology"],"thesis:degree_level":["Master's"],"thesis:degree_name":["Master of Science (M.Sc.)"]},"updated_at":"2026-07-24T01:34:41Z"}