Date of Award

Spring 2021

Project Type


Program or Major

Molecular and Evolutionary Systems Biology

Degree Name

Doctor of Philosophy

First Advisor

David C Plachetzki

Second Advisor

Matthew D MacManes

Third Advisor

M Sabrina Pankey


Over the last 800 million years, animals have evolved an incredible array of diverse forms, life histories, ecologies, and traits. In the age of genome-scale resources for many animal taxa, researchers have a unique opportunity to investigate animal diversity and evolution through comparative genomic methods. These methods allow for studies not only of current diversity and evolutionary relationships, but also of ancient evolutionary dynamics and genomic repertoire. In order to study the evolution of diverse animal traits in a rigorous way however, researchers must not neglect the fundamental components of a robust comparative genomics study: well-supported phylogenies, high-quality genomic resources, and ways of applying comparative genomic methods to a phylogenetic tree. Here, I present three studies of animal trait evolution that address each of the three components above. First, I have leveraged current bioinformatic technologies to identify biases in phylogenomic studies stemming from transcriptome assembly errors, and determined the best practices for processing transcriptomic data for these studies (Chapter 1). I found that high-quality transcriptome assemblies yield richer datasets that are less prone to bias and ambiguity when used to create phylogenetic trees. Second, I have sequenced and assembled a new genomic dataset from a unique marine organism which occupies a crucial position for Cnidarian phylogeny (Chapter 2). This new genomic resource is an important contribution to studies of the evolution of novel cell types and mitochondrial structure. Third, I have investigated the patterns of gene gain and loss that characterize the evolution of one of the earliest-branching metazoan lineages in a well-supported phylogenomic context (Chapter 3). I established that animals in the phylum Porifera have lost traits associated with most other animal lineages, resulting in a derived form in extant sponges. The findings I lay out in this dissertation add to the growing body of knowledge concerning the evolution of non-bilaterian and early-branching metazoan lineages while also providing the scientific community with best practices for the accurate study of diverse traits in Metazoa.