Genotyping-in-Thousands by sequencing panel development and application for informing multi-scaled kokanee salmon (Oncorhynchus nerka) fisheries management
department or school: Science, Irving K. Barber Faculty of (Okanagan)
department or school: Biology, Department of (Okanagan)
data provider: DSpace
degree campus: UBCO
creator: Chang, Sarah Lu
issued: 2021-07-02T15:33:50Z
issued: 2021
related degree: Master of Science - MSc
degree grantor: University of British Columbia
description: The ability to differentiate life history variants is vital for estimating fisheries management parameters, yet traditional survey methods can be inaccurate in mixed-stock fisheries. Such is the case for kokanee, the resident freshwater form of sockeye salmon (Oncorhynchus nerka), which exhibits various reproductive ecotypes (stream-, shore-, deep-spawning) that co-occur with each other and/or anadromous O. nerka in some systems across their pan-Pacific distribution. Additionally, stocking programs have been implemented to re-establish extirpated species to their historical ranges and can affect recipient ecosystems. Here, we developed and applied two Genotyping-in-Thousands by Sequencing (GT-seq) panels with targeted single nucleotide polymorphisms (SNPs) to enable accurate kokanee stock identification by geographic basin, migratory form, and reproductive ecotype across British Columbia, Canada, as well as further investigation of the genetic outcomes of an anadromous sockeye salmon (Oncorhynchus nerka) stocking program in Skaha Lake, British Columbia. The broad-scale GT-seq panel exhibited high self-assignment accuracy (93.3%), perfect assignment of individuals not included in the baseline to their geographic basin and life history form. The panel was subsequently applied to Wood Lake, a valuable mixed-stock fishery, revealing high concordance (>98%) with previous assignments to ecotype using microsatellites and TaqMan® SNP genotyping assays and improving resolution, extending a long-term time series, and demonstrating the scalability of this approach for this system and others. The O. nerka hybrid panel exhibited high efficiency, accuracy, and power (>94.5%) of assignment to pure-stock sockeye/kokanee, F₁ F₂ and B₂ backcross-sockeye/kokanee. We genetically re-assigned 91 individuals that had previously been assessed with otolith microchemistry analysis and TaqMan® SNP assay genetic assignment to evaluate panel power with known individuals and found that our panel…
aggregated CHO: https://circle.library.ubc.ca/rest/handle/2429/78849
note: Genotyping-in-Thousands by sequencing panel development and application for informing multi-scaled kokanee salmon (Oncorhynchus nerka) fisheries management by Sarah Lu Chang B.Sc., University of California Los Angeles, 2016 A THESIS SUBMITTED IN PARTIAL FULFILLMENT OF THE REQUIREMENTS FOR THE DEGREE OF MASTER OF SCIENCE in THE COLLEGE OF GRADUATE STUDIES (Biology) THE UNIVERSITY OF BRITISH COLUMBIA (Okanagan) June 2021 © Sarah Lu Chang, 2021 ii The following individuals certify that they have read, and recommend to the College of Graduate Studies for acceptance, a thesis/dissertation entitled: Genotyping-in-Thousands by sequencing panel development and application for informing multi-scaled kokanee salmon (Oncorhynchus nerka) fisheries management submitted by Sarah Lu Chang in partial fulfillment of the requirements of the degree of Masters of Science . Dr. Michael Russello, Department of Biology, Irving K. Barber Faculty of Science Supervisor Dr. Hillary Ward, British Columbia Ministry of Forests, Lands, Natural Resource Operations and Rural Development, Penticton, BC Supervisory Committee Member Dr. Robert Lalonde, Department of Biology, Irving K. Barber Faculty of Science Supervisory Committee Member Dr. Federic Menard, Department of Chemistry, Irving K. Barber Faculty of Science University Examiner iii Abstract The ability to differentiate life history variants is vital for estimating fisheries management parameters, yet traditional survey methods can be inaccurate in mixed-stock fisheries. Such is the case for kokanee, the resident freshwater form of sockeye salmon (Oncorhynchus nerka), which exhibits various reproductive ecotypes (stream-, shore-, deep-spawning) that co-occur with each other and/or anadromous O. nerka in some systems across their pan-Pacific distribution. Additionally, stocking programs have been implemented to re-establish extirpated species to their historical ranges and can affect recipient ecosystems. Here, we developed and applied two Gen…
has type: Thesis/Dissertation
date issued: 2021-09
is shown at: 10.14288/1.0400038
language: eng
degree discipline: Biology
provider: Vancouver : University of British Columbia Library
publisher: University of British Columbia
rights: Attribution-NonCommercial-NoDerivatives 4.0 International
rights URI: http://creativecommons.org/licenses/by-nc-nd/4.0/
scholar level: Graduate
contributor: Russello, Michael A.
type: Text
identifier URI: http://hdl.handle.net/2429/78849