Degree Type

Dissertation

Date of Award

2012

Degree Name

Doctor of Philosophy

Department

Ecology, Evolution, and Organismal Biology

Major

Ecology and Evolutionary Biology

First Advisor

Dennis V. Lavrov

Abstract

The mitochondrial DNA (mtDNA) in animals (Metazoa) is a favorite molecule for phylogenetic studies given its relative uniformity in both size and organization. Yet, as the depth coverage of representative animal groups increases sharply thanks to recent advances in sequencing technology, some clades remain stubbornly under sampled, if even represented at all. Difficulties associated with data collection from problematic taxa can arise from highly derived sequences, fragmented genomes, unusual structure, or any combination of these. Particularly illustrative examples are found in non-bilaterian animals (placozoans, sponges, cnidarians, comb jellies) where the mtDNA is more variable in size and structure. The present dissertation provides several case studies of what is considered “unusual” mtDNA for animals. First, we describe some unusual characteristics of the mitochondrial genomes found in calcareous sponges (Calcarea, Porifera), where one, potentially two, novel genetic codes are inferred, transfer RNAs (tRNAs) are edited, and ribosomal RNA (rRNA) genes are in pieces. We also hypothesize that the mtDNA is linear and multipartite. Then, we explore the evolution of the mtDNA in medusozoan cnidarians (Medusozoa, Cnidaria). The mtDNA in Medusozoa is linear, and encodes two extra protein genes (lost in one clade) putatively involved in the maintenance and replication of the linear chromosomes. In addition, secondary segmentalization has occurred independently in some hydras (Hydridae) and box jellies (Cubozoa). Using the sequences from these mito-genomes, we propose a new phylogeny for Cnidaria, providing additional support for the clade [Medusozoa + Octocorallia], rendering Anthozoa (Hexacorallia + Octocorallia) paraphyletic. Finally, this dissertation concludes by a mini review stating the current state of knowledge of metazoan mtDNA and some of the pitfalls in the field of mitogenomics. In particular, the new findings further challenge the classical idea of a uniform mtDNA organization (frozen genome) in animals, and question any directional explanation of the evolution of the mtDNA in animals.

DOI

https://doi.org/10.31274/etd-180810-938

Copyright Owner

Ehsan Kayal

Language

en

File Format

application/pdf

File Size

180 pages

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