Browsing by Author "Stothart, Mason R."

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    Shades of grey: host phenotype dependent effect of urbanization on the bacterial microbiome of a wild mammal
    (2021-07-05) Stothart, Mason R.; Newman, Amy E. M.
    Abstract Background Host-associated microbiota are integral to the ecology of their host and may help wildlife species cope with rapid environmental change. Urbanization is a globally replicated form of severe environmental change which we can leverage to better understand wildlife microbiomes. Does the colonization of separate cities result in parallel changes in the intestinal microbiome of wildlife, and if so, does within-city habitat heterogeneity matter? Using 16S rRNA gene amplicon sequencing, we quantified the effect of urbanization (across three cities) on the microbiome of eastern grey squirrels (Sciurus carolinensis). Grey squirrels are ubiquitous in rural and urban environments throughout their native range, across which they display an apparent coat colour polymorphism (agouti, black, intermediate). Results Grey squirrel microbiomes differed between rural and city environments; however, comparable variation was explained by habitat heterogeneity within cities. Our analyses suggest that operational taxonomic unit (OTU) community structure was more strongly influenced by local environmental conditions (rural and city forests versus human built habitats) than urbanization of the broader landscape (city versus rural). The bacterial genera characterizing the microbiomes of built-environment squirrels are thought to specialize on host-derived products and have been linked in previous research to low fibre diets. However, despite an effect of urbanization at fine spatial scales, phylogenetic patterns in the microbiome were coat colour phenotype dependent. City and built-environment agouti squirrels displayed greater phylogenetic beta-dispersion than those in rural or forest environments, and null modelling results indicated that the phylogenetic structure of urban agouti squirrels did not differ greatly from stochastic expectations. Conclusions Squirrel microbiomes differed between city and rural environments, but differences of comparable magnitude were observed between land classes at a within-city scale. We did not observe strong evidence that inter-environmental differences were the result of disparate selective pressures. Rather, our results suggest that microbiota dispersal and ecological drift are integral to shaping the inter-environmental differences we observed. However, these processes were partly mediated by squirrel coat colour phenotype. Given a well-known urban cline in squirrel coat colour melanism, grey squirrels provide a useful free-living system with which to study how host genetics mediate environment x microbiome interactions.
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    The ecology and fitness consequences of gut microbiome variation in Sable Island feral horses (Equus caballus)
    (2023-09-12) Stothart, Mason R.; Poissant, Jocelyn; Fox, Jeremy; McLoughlin, Philip Dunstan; Reimer De Bruyn, Raylene A; Wasmuth, James; Sycuro, Laura K; Archie, Elizabeth A
    Gut microbiomes are understood to be integral to the ecology and evolution of animal life, but until very recently, the scientific literature has lacked robust empirical characterization of the host genetic basis and fitness consequences of microbiome variation within wild animal populations. As a closed population of free-living but exhaustively surveyed fate-known individuals which are obligately reliant on their gut microbiomes, the feral horses of Sable Island (Nova Scotia) provide a tractable study system in which to study the ecology, host-to-host transmission, and fitness consequences of microbiome variation in the wild. In this thesis, I begin by characterizing the ecological determinants of the Sable Island horse hindgut microbiome (Chapter 2) and validate the use of shallow shotgun metagenomic sequencing methods for characterizing diverse microbial communities in the horse hindgut (Chapter 3). In applying a shallow shotgun metagenomic sequencing method to a dataset of 2394 fecal samples from 794 individuals spanning 7 years of collection, I find evidence that variation the gut microbiome is visible to host-level selection (Chapter 4). Further quantitative genetic analyses of these data reveal that microbiome features are weakly heritable on average (Chapter 5), suggesting a limited capacity for the microbiome to rapidly respond to selection; but animal model and eco-phylogenetic null model results independently provide evidence that the social dispersal of microbes between horses is an important determinant of microbiome structure. Furthermore, the microbiota which show the strongest evidence for social structuring are those which are most consequential for horse survival. These findings support hypotheses that non-genetic inheritance mechanisms (microbe dispersal) could critically underlie the ability for microbiomes to adaptively respond to selection on ecologically-relevant timescales. However, host inbreeding may constrain the capacity for microbiome variation to adaptively respond to host-level selection, since microbe responses to inbreeding were negatively associated with the estimated effects of those same microbiota on horse survival (Chapter 6). The proximate environmental and host genetic mechanisms underpinning microbiome variation, patterns of context-specific selection, and strain-level transmission remain to be characterized in detail. Nonetheless, this thesis contains tentative but important empirical milestones in describing the eco-evolutionary significance of host-associated microbiomes in the wild.