Date of Award

Spring 2021

Document Type

Thesis

Degree Name

Master of Science (MS)

Department

Biological Sciences

Program/Concentration

Biology

Committee Director

Kent E. Carpenter

Committee Member

Daniel Barshis

Committee Member

Christopher E. Bird

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.

DOI

10.25777/xajq-qp11

ORCID

0000-0002-9214-6589

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