Over the past few decades, it has become increasingly apparent that host-associated microbial communities play an integral role in the development, physiology, and health of their host organisms. All hosts have evolved mechanisms to filter the microbial taxa that comprise their resident intestinal microbial community, or gut microbiota. Utilizing the zebrafish as a model host organism, we documented the development of the gut microbiota through time, and found a significant shift in the composition of the gut microbiota after the onset of adaptive immunity. This led us to hypothesize that adaptive immunity is an important determinant of gut microbiota composition. We tested this hypothesis using wild type and rag1-/- zebrafish, which lack a functional adaptive immune system. Additionally we tested the robustness of the effects of adaptive immunity to dispersal of microbes between immune-compromised and immune-competent genotypes. We found that adaptive immunity had less of an effect on the composition of the gut microbiota than we expected, although there were intriguing differences in the nature of selection imposed when adaptive immunity was present than when it was absent. Because “westernization”, or market-integration, has been associated with significant changes in the human microbiota and certain health risks, we used similar analyses to those we applied to the zebrafish system to determine whether market-integration alters the filtering effects of inflammation and intestinal helminth parasites on the intestinal microbial community. We found that market-integration increased inter-subject dissimilarity and reduced inter-subject dispersal. Even small changes in the inflammation marker, CRP, were associated with differences in the gut microbiota, but these effects were reduced in the presence of helminth infection, which has been hypothesized to affect the microbiota by reducing inflammation. In total, this dissertation provides evidence for the nature and importance of host filters of the gut microbiota across two vertebrate species, as well as providing a framework for future studies of the effects of such filters on the assembly of the gut microbiota. This dissertation includes previously published, and unpublished, co-authored material.

Multiple ecological factors can simultaneously affect species activity and community structure. The goal of my dissertation was to examine the effects of abiotic factors, biotic factors, and succession on anuran communities. I took a three pronged approach dividing the study into three major chapters. First I focused on abiotic factors that affect anuran breeding activity. I found that weather, rainfall and temperature affect the breeding activity of each species differently, and species in my study area can be placed into 5 different groups based on their association with weather and season: 1) breed within a predictable season (summer) independent of local weather patterns 2) breed opportunistically within a predictable season (summer) dependent on local rainfall 3) breed opportunistically within a predictable season (winter) dependent on local temperature 4) breed opportunistically dependent on local flood level rainfall events and 5) breed opportunistically year round dependent on local temperature in the winter and local rainfall in the summer. In the second part of the study, I created a simulation model of an anuran community using published life history parameters of the anuran species in my study system. Results of the model suggest colonizing ability is important for species with low fecundity and high susceptibility to predation. These early succession species tend to be constrained from later stages of succession by predators. Species that are resistant to predators are generally poor colonizers and tend to arrive late in succession, but once they colonize a pond they tend to persist and recruit successfully. Finally, I explored biotic mechanisms that might be important in structuring anuran communities. I found that with the exception of Rana sphenocephala, anuran species occupying sites with shorter hydroperiods had higher activity rates and were more susceptible to predation. Rana sphenocephala appeared to be better at escaping predation than the other species despite a relatively high activity rate. Examination of published phylogenies indicates R. sphenocephala is derived from a species group that uses permanent water suggesting that R. sphenocephala has retained many anti-predator defenses inherited from its ancestors, even though the species now exploits sites with low predator densities.

The skin microbiome is a critical component of human health, however, little is understood about the daily dynamics of skin microbiome community assembly and the skin’s potential to acquire microorganisms from the external environment. I performed a series of microbial transfers using three skin habitat types (dry, moist, sebaceous) on human subject volunteers. Microbial communities were transferred to recipient skin using a sterile swab 1) from other skin sites on the same individual, 2) from other skin sites on a different individual, 3) and from two environmental donor sources (plant leaf surfaces and farm soil). With these experiments I was able to test for the presence of initial transfer effects and for the persistence of those effects over the time period sampled (2-, 4-, 8-, and 24-hours post-transfer). The sebaceous skin community was associated with the strongest initial effect of transfer and persistence on the moist recipient skin site, and to a lesser extent the dry skin site. The soil donor community when transferred to dry skin resulted in the strongest initial transfer effect and was persistent over 8- and even 24-hours post-transfer. These experiments are the first in scope and scale to directly demonstrate that dispersal from other human or environmental microbial communities are plausible drivers of community dynamics in the skin microbiome.

I aimed to expand our understanding of community assembly and species co-existence by examining the implications of phylogenetic robustness on metrics describing phylogenetic community structure, as well as the phylogenetic patterns of co-occurring insect species in Churchill, MB. Using a variety of tree reconstruction methods, I found that cytochrome c oxidase subunit I (COI) was able to accurately estimate phylogenetic community structure metrics calculated from a multi-gene phylogeny when using more biologically realistic approaches. This included incorporating known phylogenetic relationships among families, and methods that employ best-fit models of molecular evolution (i.e. Bayesian inference). My second study examined the phylogenetic community patterns of freshwater insects. Overall communities were phylogenetically clustered suggesting environmental filtering, but community structure varied with time, habitat, taxonomic group, and water chemistry (particularly pH and turbidity). My thesis has suggested more robust techniques for calculating phylogenetic community structure, and described patterns of phylogenetic community composition in subarctic freshwater insects. / Natural Sciences and Engineering Research Council of Canada (NSERC), International Barcode of Life (iBOL), Genome Canada, Ontario Genomics Institute, Canadian Foundation for Innovation, Ontario Ministry of Research and Innovation, Churchill Northern Studies Centre, and Aboriginal Affairs and Northern Development Canada.

Identifying the processes and mechanisms that govern communities of organisms is the main goal of community ecology. Locally operating mechanisms such as environmental filtering, in which the environment determines what species are found in a given location, as well as regional processes such as dispersal have all been identified as potential drivers of community processes. However, the relative importance of these drivers may vary temporally and spatially. In dendritic stream networks, headwater streams are isolated when compared to more centrally located mainstem stream sections. I investigated the potential for stream networks to influence the relative influence of local and regional processes via a survey and field experiment based approaches. I found that headwater streams can influence mainstem stream communities, potentially as a result of the dispersal of organisms or abiotic materials. Additionally, I demonstrated that macroinvertebrate communities in headwater streams respond more strongly to manipulations of local environment than do mainstem streams, both in terms of community composition as determined taxonomically and as functional traits. These results indicate that headwater streams may be affected differently than mainstem streams by anthropogenic activity and as such, management strategies and restorations may need to be specifically tailored to address the relative influences of local and regional processes at varying points within a stream network. / Ph. D.

One of the original goals of phylogeography was to use genetic data to identify historical events that might contribute to breaks among biotic communities. In this study, we examine the phylogeography of a common livebearing fish (Poecilia gillii) from Costa Rica. Our goal was to see if phylogeographic breaks in this species were congruent with previously-defined boundaries among four fish community provinces. We hypothesized that if abiotic factors influence both community boundaries and genetic structuring in P. gillii then we would find four monophyletic clades within our focal species that were geographically separated along community boundary lines. Similarly, we expected to find most of the genetic variation in P. gillii partitioned among these four geographic regions. We generated DNA sequence data (mitochondrial cyt b and nuclear S7 small ribosomal subunit) for 260 individuals from 42 populations distributed across Costa Rica. We analyzed these data using phylogenetic (parsimony and likelihood) and coalescent approaches to estimate phylogenetic relationships among haplotypes, patterns of gene flow, and effective population size. Contrary to our expectations, we did not find four monophyletic groups that mapped cleanly to our geographic community provinces. However, one of our clades was restricted to a single province, suggesting that common earth history events could be responsible for both genetic structuring in P. gillii and fish community composition in this area. However, our results show a complex pattern of gene flow throughout other regions in Costa Rica where genetic structuring is not governed by community province boundaries.

With the introduction of metacommunity theory, the field of community ecology expanded its scope to include patterns and processes beyond the scale of local communities. Dispersal, or the movement of organisms between sites, can play an influential role in generating patterns of community assembly and stability. However, little is known about the role of dispersal in structuring and stabilizing freshwater communities. For my dissertation, I conducted a literature review of dispersal in stream metapopulations and metacommunities. Our current knowledge of the movement of freshwater taxa is limited due to difficulties in accurately monitoring dispersal. We have inferred the role of dispersal based primarily on organismal-based and graph-based proxies, although the body of work in modeling and experimental research is growing. Future research should incorporate innovative methods to directly monitor dispersal at finer spatial and temporal scales. To address this knowledge gap, we experimentally manipulated dispersal mode (aerial and drift) alongside the magnitude of dispersal (network location as a proxy) to investigate the role of these components of dispersal in community assembly and multiple metrics of stability. The results of my experiment suggest both factors may play a role in community assembly and stability patterns in stream metacommunities. Lastly, I conducted a mesocosm experiment with zooplankton mesocosms to investigate if biodiversity can generate asynchronous patterns of community dynamics that contribute to stability. There was a positive biodiversity-asynchrony relationship that, in turn, generated higher levels of stability. This effect was strongest in communities connected via dispersal. Overall, my dissertation demonstrates that dispersal plays a role in the assembly and stability of freshwater communities. / Doctor of Philosophy / Freshwater ecosystems and the abundance and richness of life that they support are threatened under global environmental change. One factor that may help maintain the diversity of stream-dwelling species is dispersal, or the movement of organisms between sites within networks of freshwater communities. The influence of dispersal on the formation and stability of freshwater communities is poorly understood. To determine the state of the science, I conducted a literature review on the study of dispersal in stream networks. We have only recently developed a limited knowledge of the direct movement of freshwater species within networks. The majority of what we know is deduced from patterns of diversity, the traits of organisms, or theoretical modeling. More direct measures of dispersal are needed to understand the dispersal of freshwater organisms. To address this knowledge gap, I conducted an experiment with streamside flumes throughout a stream network where I manipulated how a macroinvertebrate could colonize, or join, a stream community. I found that both position in a network and the use of various methods of colonization affect patterns of diversity and how stable stream communities are. Finally, I conducted an experiment where I manipulated the number of zooplankton and environmental conditions to detect the influence of dispersal on community dynamics and stability. Communities connected via dispersal had the highest level of asynchrony in dynamics and these community dynamics, in turn, produced the greatest amount of community stability. Overall, these findings demonstrate the role of dispersal in the biodiversity and stability of freshwater communities.

We report a new chameleon-like Anolis species from Hispaniola that is ecomorphologically similar to congeners found only on Cuba. Lizards from both clades possess short limbs and a short tail and utilize relatively narrow perches, leading us to recognize a novel example of ecomorphological matching among islands in the well-known Greater Antillean anole radiation. This discovery supports the hypothesis that the assembly of island faunas can be substantially deterministic and highlights the continued potential for basic discovery to reveal new insights in well-studied groups. Restricted to a threatened band of midelevation transitional forest near the border of the Dominican Republic and Haiti, this new species appears to be highly endangered.

Most of the seafloor is soft sediment, so hard substrata are isolated and island-like. In this dissertation, I explore how species distribution patterns on isolated marine hard substrata resemble terrestrial island communities, drawing on classical island biogeography theory and assembly rules, and describe how benthic invertebrate communities assemble in these island-like habitats. Higher species richness occurred on larger substrata (dropstones and shipwrecks), paralleling terrestrial island communities. However, while larger islands have greater habitat diversity and primary productivity, marine hard substrata are simpler habitats. Greater elevation in the benthic boundary layer may expose fauna to faster current, higher food supply and larval flux. Substrata located closer together had more similar communities, another pattern that resembles terrestrial islands. Dropstone fauna had a clumped distribution, indicating that larvae may disperse among substrata located close together, resulting in similar communities. In Svalbard fjords, benthic megafaunal communities were significantly different between Arctic- and Atlantic-influenced fjords. Depth and temperature had the greatest influence, with the highest diversity occurring in cold Rijpfjorden and on the north Svalbard shelf. Recruitment in Svalbard fjords was spatially and temporally variable, with lower recruitment in Rijpfjorden than in Atlantic-influenced fjords and lower recruitment at greater depth. Most of the recruits in Svalbard fjords were fast-growing, poor-competitive opportunists. On shipwrecks, communities showed two mechanisms of colonization: mobile fauna with long-dispersing planktotrophic larvae, and encrusting fauna with lecithotrophic larvae. Encrusting species reproduce asexually to cover the wreck surface, and philopatry may build up dense populations, leading to uneven communities. On terrestrial islands, non-random co-occurrence is attributed to interspecific competition, but for marine substrata, there may not be a relationship. Fauna were distributed randomly on settlement plates in Svalbard fjords, even when interspecific competition was observed. On dropstones, some morphotypes co-occurred non-randomly in the absence of overgrowth competition. Non-random co-occurrence on isolated marine hard substrata may be a result of restricted larval dispersal (for pairs co-occurring less than by chance) or epibiontism (for pairs co-occurring more often than by chance). While species distribution patterns on island-like marine hard substrata resemble terrestrial islands, the mechanisms are not necessarily the same.

In many habitats, species’ traits correspond strongly to local environmental conditions. The cause of this pattern may be in-situ evolution, where initially mal-adapted resident species evolved traits that increased their fitness. Alternatively, species with suitable traits may have colonized the focal habitat and replaced resident species. Since theories in the fields of evolutionary biology and community ecology developed independently, few guidelines tell us when to expect evolutionary adaptation or ecological species replacement as the primary driver of species and trait composition in a given habitat. The goal of my dissertation research was to explain how evolutionary adaptation and ecological species replacement together determine the composition of pond zooplankton communities. I combined theoretical models with thorough surveys of natural pond communities and manipulative experiments. I discovered that one particular zooplankton species, Daphnia pulex, evolved to have different trait values in ponds with different environments. The evolutionary divergence within D. pulex profoundly affected its ecological interactions with other zooplankton species. D. pulex populations diverged from one another so much that they differed in their ability to successfully colonize ponds full of competing zooplankton species. I also used a computer simulation model to determine when a community’s trait changes were explained by evolutionary adaptation or ecological species replacement. The dispersal rate of species among habitats and the amount of genetic variance within these species both influenced adaptive trait change in a community. The group of research studies that indicate evolutionary and ecological processes operate on a similar time scale is small but growing. My dissertation research provides another crucial demonstration that evolution within individual species, such as D. pulex, influences their community ecological interactions with other species. I also identified key parameters (dispersal rate among and genetic variance within species) that may help biologists predict whether evolution or ecological species replacement explained adaptive trait change. My projects mostly concern the community and trait distributions that result from the assembly of species in new habitats. However, this framework may inform studies of community response to environmental changes such as invasive species or habitat destruction. / text