Date of Award

1-1-2017

Embargo Period

1-1-2020

Document Type

Dissertation

Degree Name

Doctor of Philosophy (PhD)

Department

Marine Biomedical and Environmental Sciences

College

College of Graduate Studies

First Advisor

Gavin J. P. Naylor

Second Advisor

Michael Janech

Third Advisor

Paula Traktman

Fourth Advisor

Daynna Wolff

Fifth Advisor

Gary Hardiman

Abstract

Holocephalan fishes occupy an important phylogenetic position as members of the basal clade of jawed vertebrates, as well as the sister group to bony vertebrates. Thus, they can be used to provide an important reference for comparative studies aimed at understanding early gnathostome genome evolution. However, despite this importance, holocephalans have been understudied, and no comprehensive phylogeny for their inter-relationships has been estimated. A phylogeny will provide information about ancestor-descendant relationships, forming a framework that can be used to test future hypotheses by mapping characters, identifying patterns, and estimating ancestral states. A cross-species hybridization capture method was used to sequence over 1,000 nuclear exons and whole mitochondrial genomes from 55 chimaeroid lineages. Phylogenetic analysis used different methods, partitioning schemes, and character data to estimate and compare trees. Nuclear and mitochondrial data produced mainly congruent results across different data sets and analyses. All trees recovered the same major clades and species within. Major differences among topologies were found in shallower nodes, species-level relationships, and placement of a few clades, and were less resolved. Overall, a robust phylogenetic framework representing the majority of chimaeroid lineages and a consensus tree has been estimated. Divergence times of lineages were estimated, largely congruent between data sets. These results have significant taxonomic implications for the group. Sex determination is an important biological mechanism among organisms. Yet, within chondrichthyans, their sex-determining mechanism is not yet identified nor confirmed. Therefore, restriction site-associated DNA sequencing was used to interrogate the genome of three species, a chimaera, shark, and ray, for sex-linked markers. Candidate sex-specific markers were identified in all three species, consistent with a genetic mechanism of sex determination. Two male-specific markers were identified and validated in Callorhinchus callorynchus, a pattern that is consistent with a male heterogametic, XX/XY sex chromosome system. The shark and ray species were not validated, but their candidate sex-linked marker results also indicate male heterogamety. Estimated evolutionary relationships provides a framework for future research aimed at better understanding this group, and for comparative studies in vertebrate evolution. Specifically, future work can further explore the sex-determining mechanisms and genes among chimaeras and chondrichthyans.

Rights

All rights reserved. Copyright is held by the author.

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