Comparative immunogenetics, microbiomics, and wildlife disease ecology across sympatric imperiled and invasive cottontails

Neil, Kimberly Brooke

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Year:: 2020
Contributor:: Neil, Kimberly Brooke (creator); Rand, David (Advisor); McGreevy, Jr., Thomas (Reader); Ramachandran, Sohini (Reader); Weinreich, Daniel (Reader); Brown University. Biology and Medicine: Ecological and Evolutionary Biology (sponsor)
Genre:: theses
Subject:: Evolution (Biology); microbiome; Wildlife conservation; Immunogenetics; Introduced organisms
Extent:: xxiv, 163 p.

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Abstract:: Knowledge of genetic diversity within natural populations, how this variation is maintained, and its underlying selective drivers are central to both evolutionary ecology and biological conservation. Traditionally, conservation genetics has utilized neutral markers for this purpose, yet with rapid advances in genomic technologies, definitions of wildlife diversity have expanded to include non-neutral sites and host-associated microbes. Indeed, a solely neutral focus may exclude ecologically important processes relevant to species survival, and the critical role of the microbiome in host health is well-accepted. I undertake a comparative approach to investigate immunogenetics, microbiomics, and potential pathogens across a system of conservation concern, that of the imperiled New England cottontail (Sylvilagus transitionalis; NEC) and its closely-related successful invader, the eastern cottontail (S. floridanus; EC). In my first chapter, I investigate population structure and diversity at immune genes within and across these species. I find that EC display exceptional polymorphism at these immune loci relative to genome-wide patterns, and that NEC retain variation despite population decline. Additionally, each species displays different patterns of contemporary selection. In my second chapter, I investigate ear microbiota, potential pathogens, and genetic associations with host microflora. I report that ear microbiota are remarkably similar between species, and a suite of potential rabbit and zoonotic pathogens are identified. Host microbial patterns associate with host genetic elements at single-nucleotide polymorphisms spanning a variety of genes, as well as immune genes specifically. For my third and final chapter, I investigate the role of species and environment in structuring fecal microbiome across NEC and EC. I find that species identity dominates in structuring fecal microbiome, and geography plays a role with intraspecific comparisons only. Collectively this body of work enhances our understanding of how functionally and ecologically significant variation is partitioned and maintained across conservation scenarios of global relevance.
Notes:: Thesis (Ph. D.)--Brown University, 2020

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Citation

Neil, Kimberly Brooke, "Comparative immunogenetics, microbiomics, and wildlife disease ecology across sympatric imperiled and invasive cottontails" (2020). Ecological and Evolutionary Biology Theses and Dissertations. Brown Digital Repository. Brown University Library. https://repository.library.brown.edu/studio/item/bdr:gnfd3zx2/

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Ecological and Evolutionary Biology Theses and Dissertations

Theses and Dissertations for the Ecological and Evolutionary Biology department.
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