The impact of late Pleistocene mammal extinctions on microbe transmission and pathogen diversity

Prys-Jones, Tomos Oliver (2023) The impact of late Pleistocene mammal extinctions on microbe transmission and pathogen diversity. Doctoral thesis, Northern Arizona University.

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Abstract

Large-scale extinctions of vertebrate species occurred 10 – 50,000 years ago, during two time periods known as the late Pleistocene and early Holocene. Human influences and climate change are the most widely accepted drivers of these extinctions, which removed a large proportion of the biggest terrestrial species, known as megafauna, from many continents outside Africa. A recent study by Doughty et al. (2020) found that these extinctions are associated with an increased risk of zoonotic disease outbreaks in contemporary times. However, the credibility of this link is debatable since it was based on a limited number of disease outbreaks. In my first study, I examine the author's overarching conclusion that losses of host species can cause long-lasting changes to pathogen populations. Specifically, I test the hypothesis that mammalian species, which previously shared their habitats with closely related but now extinct late Pleistocene species, are likely to carry a higher number of parasites (viruses, bacteria, and helminths). The results supported this hypothesis. We then identified geographic areas predicted to have an elevated parasite richness due to the extinctions. When theorizing about the impacts of late Pleistocene extinctions on microbial communities, Doughty et al. (2020) assumed that there was an easy transfer of microbes between different species of megafauna. However, this assumption has been insufficiently investigated in previous research. In my second study, I assess microbe transmission between wild, free-ranging megafauna species. These species undergo annual migrations, congregating in a single region each year, a pattern that mirrors the movement of extinct hosts in prehistoric ecosystems. I find that the microbiomes of these wild megafauna species become more similar after periods of close contact, suggestive of inter-species microbe transmission. In summary, results from both the first and second studies support the findings of Doughty et al. (2020), leading us to propose further mechanisms for how the late Pleistocene extinctions impacted microbe populations and evolution. We envisage that these may become distinguishable with advancements in the methods used for analyzing ancient DNA from paleontological samples. In the fourth chapter we identify the taxa present within the coprolites deposited by three megafauna species during the late Pleistocene (approx. 10-20,000 YBP). We find that beta diversity of coprolite microbiomes are closest to dried modern fecal samples, suggesting further research is needed to understand which taxa that are endogenous to host guts are detectable in their desiccated feces, as this will determine the upper limit of what analyses of coprolites will be able to find. A better understanding of how host extinctions impact microbe populations is needed, as we are currently witnessing another large-scale extinction of host species, driven by anthropogenic pressures. While these will likely go hand in hand with the extinction of micro and macro-organisms carried by these hosts, some may spread in ways that are currently unpredictable at present, such as the recent global pandemic caused by SARS-CoV-2.

Item Type:	Thesis (Doctoral)
Publisher’s Statement:	© Copyright is held by the author. Digital access to this material is made possible by the Cline Library, Northern Arizona University. Further transmission, reproduction or presentation of protected items is prohibited except with permission of the author.
Keywords:	Extinction; Late Pleistocene; Megafauna; Microbe transmission; Microbiome; Pathogen richness
Subjects:	Q Science > QL Zoology
NAU Depositing Author Academic Status:	Student
Department/Unit:	Graduate College > Theses and Dissertations College of Engineering, Informatics, and Applied Sciences > School of Informatics, Computing, and Cyber Systems
Date Deposited:	28 Jul 2026 16:53
Last Modified:	28 Jul 2026 16:53
URI:	https://openknowledge.nau.edu/id/eprint/6320

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