Genome-wide analysis to investigate patterns of ecotype divergence, population structure and life history changes in deep-spawning sockeye salmon, Oncorhynchus nerka
department or school: Science, Irving K. Barber Faculty of (Okanagan)
department or school: Biology, Department of (Okanagan)
data provider: DSpace
degree campus: UBCO
creator: Samad-zada, Farida
issued: 2021-03-12T17:47:49Z
issued: 2021
related degree: Master of Science - MSc
degree grantor: University of British Columbia
description: Sockeye salmon (Oncorhynchus nerka) have been a classic study system for investigating ecotype divergence due to their tremendous life history variation. Multiple independent lineages of freshwater O. nerka (kokanee) have evolved from anadromous sockeye, and these migratory forms are further divided into reproductive ecotypes, depending on spawning location (shore-, stream- and deep-spawners). Deep-spawning O. nerka in Canada and Japan share unique phenotypic traits, but little is known about the origin and genomic basis of this ecotype. Here, we conducted genome-wide analyses of deep-spawning O. nerka on multiple scales, from regional populations in British Columbia, Canada, to those that span the pan Pacific distribution. First, we analyzed the Alouette Lake (British Columbia) O. nerka population, which (a) consists of both migrant and resident individuals, and (b) is the only known O. nerka population where migrants exhibit deep-spawning behaviour, leading to questions regarding the true ecotype of this population. To investigate the genomic basis of life history variation in this system, we collected SNP data (n = 7,709) for migrant and resident Alouette O. nerka (n = 163) and analyzed these samples relative to each other and O. nerka (n = 149) from known anadromous sockeye salmon and kokanee populations across the Fraser River drainage. Population structure analyses revealed five distinct clusters, primarily associated with geography, and no evidence for differentiation between resident and migrant Alouette O. nerka at the neutral loci. However, we identified eight high-confidence outlier loci divergent between migrant and resident Alouette O. nerka that were located on sex chromosomes, suggesting an association between migratory behaviour and sex in this system. We conclude that Alouette O. nerka likely represents a single stock best characterized as land-locked sockeye salmon, with individuals that retain the ability to migrate. Second, we genotyped deep- and…
aggregated CHO: https://circle.library.ubc.ca/rest/handle/2429/77515
note: Genome-wide analysis to investigate patterns of ecotype divergence, population structure and life history changes in deep-spawning sockeye salmon, Oncorhynchus nerka by Farida Samad-zada B.Sc. (Hon.), University of Toronto, 2018 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) March 2021 © Farida Samad-zada, 2021 ii The following individuals certify that they have read, and recommend to the College of Graduate Studies for acceptance, a thesis/dissertation entitled: Genome-wide analysis to investigate patterns of ecotype divergence, population structure and life history changes in deep-spawning sockeye salmon, Oncorhynchus nerka submitted by Farida Samad-zada in partial fulfillment of the requirements of the degree of Master of Science. Dr. Michael Russello, Department of Biology, Irving K. Barber Faculty of Science Supervisor Dr. Brett van Poorten, Resource and Environmental Management, Simon Fraser University Supervisory Committee Member Dr. Sepideh Pakpour, School of Engineering, Faculty of Applied Science Supervisory Committee Member Dr. Adam Wei, Department of Earth, Environmental, and Geographic Sciences, Irving K. Barber Faculty of Science University Examiner iii Abstract Sockeye salmon (Oncorhynchus nerka) have been a classic study system for investigating ecotype divergence due to their tremendous life history variation. Multiple independent lineages of freshwater O. nerka (kokanee) have evolved from anadromous sockeye, and these migratory forms are further divided into reproductive ecotypes, depending on spawning location (shore-, stream- and deep-spawners). Deep-spawning O. nerka in Canada and Japan share unique phenotypic traits, but little is known about the origin and genomic basis of this ecotype. Here, we conducted genome-wide analyses of deep-spawning O. nerka on multiple scales, from regional populations in Brit…
has type: Thesis/Dissertation
date issued: 2021-05
is shown at: 10.14288/1.0396109
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
type: Text
identifier URI: http://hdl.handle.net/2429/77515