Degree

Doctor of Philosophy (PhD)

Department

Department of Biological Sciences

Document Type

Dissertation

Abstract

Although most extant species are parasites, we know relatively little about their diversity and diversification compared to free-living organisms. Exemplifying this research gap is Pneumocystis, a fungal obligate parasite of mammal lungs ubiquitous throughout Mammalia. While Pneumocystis likely contains thousands of host-specific species, only 6 have been formally described, and only ~4% of mammal species have been screened. Broader mammal sampling would certainly uncover many novel species, but this unculturable genus is difficult to study and largely characterized by mitochondrial gene sequences. Pneumocystis evolutionary history therefore remains unclear, with interpretations often falling back on assumptions of strict one-to-one host specificity and cospeciation as the primary drivers of its diversification.

In this dissertation, I re-examined this cospeciation paradigm by analyzing existing single-locus mitochondrial data (Chapter 2). My results showed that neither one-to-one specificity nor cospeciation is supported, and that there are likely between 4,500 and 6,000 extant Pneumocystis species. I then tested for cospeciation in a pair of deermouse sister species (Peromyscus) by sequencing single mitochondrial and nuclear loci from Pneumocystis (Chapter 3), finding that both host species share two distantly related Pneumocystis taxa rather than unique, cospeciated taxa. To expand nuclear sampling, I designed a UCE probe set for Pneumocystis and other members of the Taphrinomycotina, enabling recovery of genome-scale data even from museum and herbarium specimens dominated by host DNA (Chapter 4). I leveraged these data to infer a well-resolved phylogenetic hypothesis and explore the origins of mammalian parasitism through divergence time estimation, which supported an origin of Pneumocystis contemporaneous with placental mammals. Finally, I returned to the question of host specificity by sampling Pneumocystis across North American rodents in the subfamily Neotominae (Chapter 5). Results showed that relaxed multi-host associations are common, and that codiversification, parasite inertia, and spillover events together best explain observed host-parasite associations, rather than strict cospeciation.

By bridging the gap between single-locus sequencing and genome-scale UCE capture for Pneumocystis, this dissertation demonstrates the power of molecular approaches for illuminating the biology of unculturable microbial parasites. Through such approaches, we can better understand the forces that have shaped most branches on the tree of life.

Date

11-11-2025

Committee Chair

Esselstyn, Jacob

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