Evolution and diversity of stramenopiles
department or school: Science, Faculty of
department or school: Botany, Department of
data provider: DSpace
degree campus: UBCV
creator: Cho, Anna
issued: 2024-05-21T16:12:43Z
issued: 2024
related degree: Doctor of Philosophy - PhD
degree grantor: University of British Columbia
description: Stramenopiles are a diverse eukaryotic supergroup with considerable genomic information available. Nevertheless, the relationships between major stramenopiles subgroups remain unresolved and incongruent between analyses, in part due to a lack of data from small nanoflagellates that make up much of the genetic diversity of the group, under-represented ochrophyte classes, and a rapid radiation leading to eroded phylogenetic signals in the tree. As a result, assessing genetic diversity and distribution, addressing character evolution, and investigating interactions of these lineages with other organisms are limited. To resolve phylogenomic relationships of stramenopiles, I generated 23 transcriptomes from the most under-sampled subgroups, such as Bigyromonadea, MAST-6, Placididea, and some classes of ochrophytes that had been scarcely represented in phylogenomic data. Of these, 11 are new species of stramenopiles, some of which have helped resolving phylogenomic relationships of Bigyromonadea and the backbone of deep-branching lineages. Some of these species were found to be abundant in sediment sampled across different geographic locations, while others can tolerate a broad range of salinities. I also described behaviours and morphological characters of these species including the ability to form pseudopods and cell-aggregates observed in some bigyromonads. This updated phylogenomic dataset now represents 14 out of 17 classes of ochrophytes and demonstrates robust support for previously contentious or under-tested lineages such as Eustigmatophyceae, Pinguiophyceae, and Olisthodiscophyceae. To address phylogenomic incongruence between multi- or single-gene trees, I explored various gene filtering criteria to identify the phylogenetically informative genes. Selecting genes with long internal phylogenetic branches or removing genes with high levels of phylogenetic noise recovered more topologies that were found in other phylogenomic analyses. Finally, I investigated the …
aggregated CHO: https://circle.library.ubc.ca/rest/handle/2429/88338
note: EVOLUTION AND DIVERSITY OF STRAMENOPILES by Anna Cho M.Sc, The University of British Columbia, 2019 B.Sc (Hon.), Trent University, 2015 B.Sc., McGill University, 2010 A THESIS SUBMITTED IN PARTIAL FULFILLMENT OF THE REQUIREMENTS FOR THE DEGREE OF DOCTOR OF PHILOSOPHY in The Faculty of Graduate and Postdoctoral Studies (Botany) THE UNIVERSITY OF BRITISH COLUMBIA (Vancouver) May 2024 © Anna Cho, 2024 ii The following individuals certify that they have read, and recommend to the Faculty of Graduate and Postdoctoral Studies for acceptance, the dissertation entitled: Evolution and diversity of stramenopiles submitted by Anna Cho in partial fulfilment of the requirements for the degree of Doctor of Philosophy in Botany Examining Committee: Patrick Keeling, Professor, Botany, UBC Supervisor Brian Leander, Professor, Botany and Zoology, UBC Supervisory Committee Member Sean Graham, Professor, Botany, UBC University Examiner Dolph Schluter, Professor, Zoology. UBC University Examiner Heroen Verbruggen, Professor, School of BioSciences, University of Melbourne External Examiner Additional Supervisory Committee Members: Patrick Martone, Professor, Botany, UBC Supervisory Committee Member iii Abstract Stramenopiles are a diverse eukaryotic supergroup with considerable genomic information available. Nevertheless, the relationships between major stramenopiles subgroups remain unresolved and incongruent between analyses, in part due to a lack of data from small nanoflagellates that make up much of the genetic diversity of the group, under-represented ochrophyte classes, and a rapid radiation leading to eroded phylogenetic signals in the tree. As a result, assessing genetic diversity and distribution, addressing character evolution, and investigating interactions of these lineages with other organisms are limited. To resolve phylogenomic relationships of stramenopiles, I generated 23 transcriptomes from the most under-sampled subgroups, such as Bigyromonadea, MAST-6, Placididea, an…
has type: Thesis/Dissertation
date issued: 2024-11
is shown at: 10.14288/1.0443571
language: eng
degree discipline: Botany
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: Keeling, Patrick J. (Patrick John), 1969-
type: Text
identifier URI: http://hdl.handle.net/2429/88338