{"id":{"repo_id":"uiuc","oai_identifier":"oai:www.ideals.illinois.edu:2142/120531"},"canonical_url":"https://search.dev.ndltd.org/etd/uiuc/oai:www.ideals.illinois.edu:2142/120531","repository":{"repo_id":"uiuc","name":"University of Illinois - Urbana-Champaign","base_url":"https://www.ideals.illinois.edu/oai-pmh"},"display":{"title":"Using genomics to uncover the evolutionary histories of ectoparasites on birds","abstract":"Submission published under a 24 month embargo labeled 'Closed Access', the embargo will last until 2025-05-01","abstract_html":"Submission published under a 24 month embargo labeled 'Closed Access', the embargo will last until 2025-05-01","abstract_has_math":false,"creators":["Virrueta Herrera, Stephany"],"institution":"University of Illinois at Urbana-Champaign","degree_name":"Ph.D.","degree_level":"Dissertation","degree_discipline":"Ecol, Evol, Conservation Biol","degree_department":null,"school":null,"contributors":["Johnson, Kevin","Hauber, Mark","Dietrich, Christopher","Harmon-Threatt , Alexandra","Heath, Katy"],"advisors":[],"committee_chairs":[],"committee_members":[],"year":2023,"date_issued":"2023-05","date_published":"2023-05","updated_at":"2026-07-22T22:24:57Z","subjects":["Phylogenomics","Lice","Coevolution"],"languages":["en","eng"],"rights":["Copyright 2023 Stephany Virrueta Herrera"],"rights_urls":[],"identifier_entries":[]},"links":{"outbound_url":"https://hdl.handle.net/2142/120531","outbound_label":"Handle","outbound_source":"dc:identifier"},"metadata_groups":[{"id":"people","label":"People","entries":[{"key":"dc:contributor","label":"Contributor","values":["Johnson, Kevin","Hauber, Mark","Dietrich, Christopher","Harmon-Threatt , Alexandra","Heath, Katy"]},{"key":"dc:creator","label":"Author","values":["Virrueta Herrera, Stephany"]}]},{"id":"academic_context","label":"Academic Context","entries":[{"key":"dc:date","label":"Dc Date","values":["2023-05","2023-04-20"]},{"key":"dc:type","label":"Dc Type","values":["text","Thesis"]},{"key":"thesis:degree_discipline","label":"Discipline","values":["Ecol, Evol, Conservation Biol"]},{"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":["Phylogenomics","Lice","Coevolution"]}]},{"id":"language_rights","label":"Language and Rights","entries":[{"key":"dc:language","label":"Dc Language","values":["en","eng"]},{"key":"dc:rights","label":"Dc Rights","values":["Copyright 2023 Stephany Virrueta Herrera"]}]},{"id":"identifiers","label":"Identifiers","entries":[{"key":"dc:identifier","label":"Identifier","values":["https://hdl.handle.net/2142/120531"]}]},{"id":"additional","label":"Additional Metadata","entries":[{"key":"dc:description","label":"Description","values":["Submission published under a 24 month embargo labeled 'Closed Access', the embargo will last until 2025-05-01","The student, Stephany Virrueta Herrera, accepted the attached license on 2023-04-19 at 20:02.","The student, Stephany Virrueta Herrera, submitted this Dissertation for approval on 2023-04-19 at 20:07.","This Dissertation was approved for publication on 2023-04-20 at 13:38.","DSpace SAF Submission Ingestion Package generated from Vireo submission #19055 on 2023-09-01 at 17:21:04","Parasitism is one of the most common life strategies on Earth. While decreasing the fitness of their hosts, parasites are a major component of ecosystems and can regulate host populations. However, much about parasite biology remains unknown. Parasite livelihood is dependent on one or more host species, and this interaction creates complex dynamics between host and parasite. Host parasite systems are ideal for studying coevolutionary mechanisms because of parasite dependence on their hosts and the constant battles to evolve to meet the adaptations of the hosts and vice versa. Ectoparasites of the insect order Phthiraptera, more commonly known as lice, exist on a wide variety of hosts. Genomics allows us to study several aspects of parasite evolution and diversification. I leveraged whole genome sequencing feather lice to study patterns of parasite diversification in relation to host diversification at multiple evolutionary scales. Incorporating datasets of diverse scales allow us to explore the patterns of speciation that are present across these parasites. At a higher taxonomic scale, among genera, I focused on lice from tinamous, a group of paleognath birds, which host some of the greatest diversity of lice. I used genome sequence data from individual lice to estimate phylogenetic trees using both concatenated (RAxML/IQTree) and coalescent (ASTRAL) methods of phylogenetic estimation. The estimated phylogeny provided evidence that tinamou lice are more closely related to each other than previously expected. Our results also indicated diversification of these parasites occurred within tinamous, and not by repeated host switching from other bird lineages. I found one louse genus, Rallicola, in the same broader clade as tinamou lice. Unlike the genera of lice found on tinamous, Rallicola is found on 6 different bird orders and 14 families. We analyzed the phylogenetic, biogeographic, and cophylogenetic relationships of the genus Rallicola and found that the ancestral host of this genus had a New World and most likely South American origin. We also found that host switching events were very common in this group of lice, and then we decided to study cospeciation pattens at a deeper level and focused on Rallicola on woodcreepers, ovenbirds, and leaftossers (one bird family). Cophylogenetic analysis of Rallicola on these specific hosts revealed several cospeciation events, but also equally as many host switching events. In general, avian lice show evidence of occasional cospeciation with their hosts, but there also appears to be considerable host switching, both between and within major groups of birds. Studying diversification patterns at shorter scales allowed us to gain insight on what we may have been missing with broader sampling and scales. Genomics, and specifically phylogenomics and cophylogenetic analyses, allow us to begin to tease apart these complex relationships."]},{"key":"dc:format","label":"Dc Format","values":["application/pdf"]},{"key":"dc:title","label":"Title","values":["Using genomics to uncover the evolutionary histories of ectoparasites on birds"]}]}],"canonical_facts":{"dc:contributor":["Johnson, Kevin","Hauber, Mark","Dietrich, Christopher","Harmon-Threatt , Alexandra","Heath, Katy"],"dc:creator":["Virrueta Herrera, Stephany"],"dc:date":["2023-05","2023-04-20"],"dc:description":["Submission published under a 24 month embargo labeled 'Closed Access', the embargo will last until 2025-05-01","The student, Stephany Virrueta Herrera, accepted the attached license on 2023-04-19 at 20:02.","The student, Stephany Virrueta Herrera, submitted this Dissertation for approval on 2023-04-19 at 20:07.","This Dissertation was approved for publication on 2023-04-20 at 13:38.","DSpace SAF Submission Ingestion Package generated from Vireo submission #19055 on 2023-09-01 at 17:21:04","Parasitism is one of the most common life strategies on Earth. While decreasing the fitness of their hosts, parasites are a major component of ecosystems and can regulate host populations. However, much about parasite biology remains unknown. Parasite livelihood is dependent on one or more host species, and this interaction creates complex dynamics between host and parasite. Host parasite systems are ideal for studying coevolutionary mechanisms because of parasite dependence on their hosts and the constant battles to evolve to meet the adaptations of the hosts and vice versa. Ectoparasites of the insect order Phthiraptera, more commonly known as lice, exist on a wide variety of hosts. Genomics allows us to study several aspects of parasite evolution and diversification. I leveraged whole genome sequencing feather lice to study patterns of parasite diversification in relation to host diversification at multiple evolutionary scales. Incorporating datasets of diverse scales allow us to explore the patterns of speciation that are present across these parasites. At a higher taxonomic scale, among genera, I focused on lice from tinamous, a group of paleognath birds, which host some of the greatest diversity of lice. I used genome sequence data from individual lice to estimate phylogenetic trees using both concatenated (RAxML/IQTree) and coalescent (ASTRAL) methods of phylogenetic estimation. The estimated phylogeny provided evidence that tinamou lice are more closely related to each other than previously expected. Our results also indicated diversification of these parasites occurred within tinamous, and not by repeated host switching from other bird lineages. I found one louse genus, Rallicola, in the same broader clade as tinamou lice. Unlike the genera of lice found on tinamous, Rallicola is found on 6 different bird orders and 14 families. We analyzed the phylogenetic, biogeographic, and cophylogenetic relationships of the genus Rallicola and found that the ancestral host of this genus had a New World and most likely South American origin. We also found that host switching events were very common in this group of lice, and then we decided to study cospeciation pattens at a deeper level and focused on Rallicola on woodcreepers, ovenbirds, and leaftossers (one bird family). Cophylogenetic analysis of Rallicola on these specific hosts revealed several cospeciation events, but also equally as many host switching events. In general, avian lice show evidence of occasional cospeciation with their hosts, but there also appears to be considerable host switching, both between and within major groups of birds. Studying diversification patterns at shorter scales allowed us to gain insight on what we may have been missing with broader sampling and scales. Genomics, and specifically phylogenomics and cophylogenetic analyses, allow us to begin to tease apart these complex relationships."],"dc:format":["application/pdf"],"dc:identifier":["https://hdl.handle.net/2142/120531"],"dc:language":["en","eng"],"dc:rights":["Copyright 2023 Stephany Virrueta Herrera"],"dc:subject":["Phylogenomics","Lice","Coevolution"],"dc:title":["Using genomics to uncover the evolutionary histories of ectoparasites on birds"],"dc:type":["text","Thesis"],"thesis:degree_discipline":["Ecol, Evol, Conservation Biol"],"thesis:degree_level":["Dissertation"],"thesis:degree_name":["Ph.D."],"thesis:institution_name":["University of Illinois at Urbana-Champaign"]},"updated_at":"2026-07-22T22:24:57Z"}