Understanding the relationship between ecological characteristics and genetic change in natural populations in different time scales can reveal how anthropogenic stressors affect natural populations and can improve the success of conservation strategies. The purpose of the Philippines Partnerships for International Research and Education (PIRE) project is to examine levels of genetic change between historical fish samples collected by the USS Albatross expedition in the early 1900s in the Philippines and contemporary populations collected at the same localities. This study tests genetic protocols to process historical and contemporary DNA for simultaneous comparison. Two DNA library preparation methods, single digest RADseq (“un-baited” sequences) and Rapture or capture probes designed from the initial RADseq tags (“baited” sequences), and two filtering pipelines, dDocentHPC and ANGSD are tested using four fishes with different life history traits. Sequencing RADseq libraries produced a range of contigs from contemporary and historic DNA across species. Sequencing baited libraries did not improve the depth of coverage for either Albatross or contemporary results. However, the ANGSD pipeline did improve our ability to work with and conduct analyses on the resulting low-coverage data, unlike dDocentHPC where fewer sequences passed all respective filters. This study was successful in providing the first assessment of sequencing and bioinformatics methodologies and paves the way for developing methods to improve data that can be obtained from the historical Albatross specimens for future PIRE project research.
","abstract_html":"<p>Understanding the relationship between ecological characteristics and genetic change in natural populations in different time scales can reveal how anthropogenic stressors affect natural populations and can improve the success of conservation strategies. The purpose of the Philippines Partnerships for International Research and Education (PIRE) project is to examine levels of genetic change between historical fish samples collected by the USS <em>Albatross</em> expedition in the early 1900s in the Philippines and contemporary populations collected at the same localities. This study tests genetic protocols to process historical and contemporary DNA for simultaneous comparison. Two DNA library preparation methods, single digest RADseq (“un-baited” sequences) and Rapture or capture probes designed from the initial RADseq tags (“baited” sequences), and two filtering pipelines, dDocentHPC and ANGSD are tested using four fishes with different life history traits. Sequencing RADseq libraries produced a range of contigs from contemporary and historic DNA across species. Sequencing baited libraries did not improve the depth of coverage for either <em>Albatross</em> or contemporary results. However, the ANGSD pipeline did improve our ability to work with and conduct analyses on the resulting low-coverage data, unlike dDocentHPC where fewer sequences passed all respective filters. This study was successful in providing the first assessment of sequencing and bioinformatics methodologies and paves the way for developing methods to improve data that can be obtained from the historical<em> Albatross</em> specimens for future PIRE project research.</p>","abstract_has_math":false,"creators":["Kenton, Madeleine I."],"institution":null,"degree_name":"Master of Science (MS)","degree_level":"Thesis","degree_discipline":"Biological Sciences","degree_department":null,"school":null,"contributors":["Kent E. Carpenter","Daniel Barshis","Christopher E. Bird"],"advisors":[],"committee_chairs":[],"committee_members":[],"year":2021,"date_issued":"2021-04-01T07:00:00Z","date_published":"2021-04-01T07:00:00Z","updated_at":"2026-07-24T03:35:38Z","subjects":["Albatross","Anthropogenic impacts","Bioinformatics","Ichthyology","Molecular ecology","Rad capture","Ecology and Evolutionary Biology","Molecular Biology"],"languages":[],"rights":["In Copyright. URI: http://rightsstatements.org/vocab/InC/1.0/ This Item is protected by copyright and/or related rights. You are free to use this Item in any way that is permitted by the copyright and related rights legislation that applies to your use. For other uses you need to obtain permission from the rights-holder(s).
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"]},{"key":"dc:title","label":"Title","values":["A Test of Rad Capture Sequencing on Ethanol-Preserved Centennial and Contemporary Specimens of Philippine Fishes"]}]}],"canonical_facts":{"dc:contributor":["Kent E. Carpenter","Daniel Barshis","Christopher E. Bird"],"dc:creator":["Kenton, Madeleine I."],"dc:date.available":["2021-06-11T07:00:00Z"],"dc:description.abstract":["Understanding the relationship between ecological characteristics and genetic change in natural populations in different time scales can reveal how anthropogenic stressors affect natural populations and can improve the success of conservation strategies. The purpose of the Philippines Partnerships for International Research and Education (PIRE) project is to examine levels of genetic change between historical fish samples collected by the USS Albatross expedition in the early 1900s in the Philippines and contemporary populations collected at the same localities. This study tests genetic protocols to process historical and contemporary DNA for simultaneous comparison. Two DNA library preparation methods, single digest RADseq (“un-baited” sequences) and Rapture or capture probes designed from the initial RADseq tags (“baited” sequences), and two filtering pipelines, dDocentHPC and ANGSD are tested using four fishes with different life history traits. Sequencing RADseq libraries produced a range of contigs from contemporary and historic DNA across species. Sequencing baited libraries did not improve the depth of coverage for either Albatross or contemporary results. However, the ANGSD pipeline did improve our ability to work with and conduct analyses on the resulting low-coverage data, unlike dDocentHPC where fewer sequences passed all respective filters. This study was successful in providing the first assessment of sequencing and bioinformatics methodologies and paves the way for developing methods to improve data that can be obtained from the historical Albatross specimens for future PIRE project research.
"],"dc:identifier":["9798515226312","https://digitalcommons.odu.edu/biology_etds/122"],"dc:rights":["In Copyright. URI: http://rightsstatements.org/vocab/InC/1.0/ This Item is protected by copyright and/or related rights. You are free to use this Item in any way that is permitted by the copyright and related rights legislation that applies to your use. For other uses you need to obtain permission from the rights-holder(s).
"],"dc:subject":["Albatross","Anthropogenic impacts","Bioinformatics","Ichthyology","Molecular ecology","Rad capture","Ecology and Evolutionary Biology","Molecular Biology"],"dc:title":["A Test of Rad Capture Sequencing on Ethanol-Preserved Centennial and Contemporary Specimens of Philippine Fishes"],"thesis:degree_discipline":["Biological Sciences"],"thesis:degree_level":["Thesis"],"thesis:degree_name":["Master of Science (MS)"]},"updated_at":"2026-07-24T03:35:38Z"}