Abstract

Understanding how evolutionary processes modulate the complex interplay between host genetics, behavior, and the gastrointestinal (GI) microbiome is fundamental to ecological and evolutionary research. This dissertation explores the drivers of multi-kingdom GI microbiome and virome structure and dynamics within a wild baboon hybrid zone, emphasizing the co-evolutionary dynamics both within microbial communities and between hosts and their associated microbes. Chapter One reviews the literature, establishing the critical role of hybridization in shaping primate immune systems and introducing Kinda-Grayfooted chacma hybrid baboons as a compelling model for studying host-microbe co-evolution amid genomic admixture. This chapter details how immune gene introgression, a common consequence of hybridization, can influence host physiology relevant to the GI ecosystem. Furthermore, it examines the composition and function of the gut microbiome, highlighting how microbial diversity and interactions are affected by hybridization and immune gene variations. By integrating these perspectives, the chapter underscores the complex relationships between host genetics, immune responses, and microbial communities within the GI tract. Chapter Two examines the relative contributions of host genetic variation (derived from hybridization), environmental factors, and social behavior, including sex, in shaping overall GI microbiome composition and diversity. I found that direct host genetic ancestry, represented by hybrid category, had a limited impact on overall microbiome structure. Instead, temporal environmental shifts emerged as predominant ecological filters, driving significant changes in microbial diversity and composition. Additionally, biased social interactions, such as mating and grooming, along with sex differences, played pivotal roles in microbial transmission. These interactions contributed to similarities in GI microbiota among frequently interacting individuals, thereby shaping a "social microbiome." Chapter Three delves into the nuanced intra-kingdom microbial relationships, emphasizing niche construction as a central organizing principle. This chapter reveals complex intra-specific cooperation (e.g., quorum sensing, biofilm formation) and competition, alongside diverse inter-specific mutualistic and antagonistic relationships operating within the bacterial, eukaryotic, and viral communities respectively. It highlights how these internal dynamics contribute to the stability and functional capabilities of each microbial kingdom. Chapter Four extends this analysis to inter-kingdom microbial relationships, presenting multi-microbial network analyses that revealed distinct architectures. Bacteria-eukaryote

Committee Chair

Emily Wroblewski

Committee Members

Crickette Sanz; EA Quinn; Elizabeth Mallott; Monica McDonald; Theresa Gildner

Degree

Doctor of Philosophy (PhD)

Author's Department

Anthropology

Author's School

Graduate School of Arts and Sciences

Document Type

Dissertation

Date of Award

12-31-2025

Language

English (en)

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Available for download on Thursday, December 30, 2027

Included in

Anthropology Commons

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