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Author ORCID Identifier


Open Access Dissertation

Document Type


Degree Name

Doctor of Philosophy (PhD)

Degree Program

Organismic and Evolutionary Biology

Year Degree Awarded


Month Degree Awarded


First Advisor

Laura A. Katz


Our knowledge about the evolution of eukaryotes and their genomes is very limited because it has largely been based on studies of plants, animals and fungi, which are not a significant representation of the diversity across the eukaryotic tree of life. Advances in sequencing technologies are helping to expand our knowledge by including underrepresented clades and revealing that eukaryotic genomes are much more complex and dynamic than originally thought. In response to the need to explore such levels of complexity in eukaryotic genomes and the earliest events of eukaryotic evolution, this dissertation focuses on the development of bioinformatic and phylogenomic tools to study karyotype evolution and answering deep evolutionary questions. The first chapter covers the development of a phylogenomic chromosome mapper, PhyloChromoMap, and its use to study karyotype evolution in the malaria parasite Plasmodium falciparum. In addition to providing a very flexible and powerful tool to map the phylogenetic history of genes across karyotypes, this chapter reveals very distinctive patterns of evolution between subtelomeric and internal regions of the chromosomes of P. falciparum. The second chapter focuses on the development of PhyloToL, a taxon- and gene-rich phylogenomic pipeline. This chapter presents examples of how to use PhyloToL for phylogenomic studies and studies of gene family evolution, and presents a series of benchmark studies comparing PhyloToL against other popular phylogenomic pipelines. Finally, the third chapter focuses on using PhyloToL to explore one of the most critical questions in field of evolution, the root of the eukaryotic tree of life. The results in this chapter suggest that the root should be placed between Opisthokonta and all other eukaryotes. Overall this dissertation contributes insights of the earliest events of evolution in eukaryotes and provides novel approaches to study this topic. The results of this dissertation are important for comparative biology as it allows to understand the timing and mode of evolution of eukaryotic features across the eukaryotic tree of life