Based on dental, cranial, and postcranial anatomy, members of the Permo-Carboniferous clade Diadectidae are generally regarded as the earliest tetrapods capable of processing high-fiber plant material; presented here is a review of diadectid morphology, phylogeny, taxonomy, and paleozoogeography. Phylogenetic analyses support the monophyly of Diadectidae within Diadectomorpha, the sister-group to Amniota, with Limnoscelis as the sister-taxon to Tseajaia + Diadectidae. Analysis of diadectid interrelationships of all known taxa for which adequate specimens and information are known—the first of its kind conducted—positions Ambedus pusillus as the sister-taxon to all other forms, with Diadectes sanmiguelensis, Orobates pabsti, Desmatodon hesperis, Diadectes absitus, and (Diadectes sideropelicus + Diadectes tenuitectes + Diasparactus zenos) representing progressively more derived taxa in a series of nested clades. In light of these results, it is recommended herein that the species Diadectes sanmiguelensis be referred to the new genus Oradectes, Diadectes absitus be referred to the new genus Silvadectes, and Diasparactus be synonymized with Diadectes to produce Diadectes zenos. The phylogenetic hypothesis also reveals an evolutionary history leading to more efficient oral processing within the lineage, with successive nodes characterized by features indicative of a high-fiber diet. Within Diadectomorpha, diadectids constitute the majority of the species, suggesting that the advent of herbivory resulted in a relatively rapid radiation of species within the group, producing a clade that is markedly more species-rich than other, non-herbivorous diadectomorph taxa. An extensive review of Permo-Carboniferous tetrapod-bearing localities does, however, indicate that diadectids were not a key component of the fauna, discovered at fewer than 50 percent of the sites reviewed. These results counter suggestions that the evolution of Diadectidae led to the formation of the modern terrestrial ecosystem—where a large crop of herbivores supports a much smaller number of carnivores—during the Late Carboniferous and Early Permian.

Anthropogenic climate change is expected to dramatically affect boreal forests, not only through warming effects, but through changes in seasonal and diurnal temperature patterns, precipitation, cloud-cover, and direct effects of rising CO2. My doctoral research examines the impact of these changes on dominant boreal forest conifer species, using dendrochronological methods. Through my analysis of white spruce (Picea glauca) and lodgepole pine (Pinus contorta) tree rings across five Yukon Territory sites, I found that white spruce growth is showing growth declines in response to all three measured climate changes, with negative correlations between tree ring increment and spring and summer temperature, spring frost events, and growing season cloud cover. Lodgepole pine populations exhibited growth enhancement with increasing spring maximum daily temperatures, but generally neutral responses to warming summers, higher frost event frequency and increased cloud cover. To evaluate the effect of rising CO2 on boreal forest growth, I examined three representative managed forest stands across Canada, first building a model of climate effects, and examining temporal trends in the residual growth patterns. I found evidence for CO2 fertilization in Ontario black spruce (Picea mariana) and Manitoba white spruce populations, particularly at younger ages, but no growth enhancement in Yukon lodgepole pine. These results taken together suggest that Yukon white spruce may suffer pronounced growth declines under continued climate change, but more eastern spruce populations may be better able to benefit from increased carbon availability. Yukon lodgepole pine populations are less vulnerable to the impacts of climate change, but are also unlikely to exhibit significant growth increases in response to increasing temperature, frost events, cloud cover or rising CO2. The results from this thesis have important implications for future management of the Canadian boreal forest under progressive climate change.

Anthropogenic climate change is expected to dramatically affect boreal forests, not only through warming effects, but through changes in seasonal and diurnal temperature patterns, precipitation, cloud-cover, and direct effects of rising CO2. My doctoral research examines the impact of these changes on dominant boreal forest conifer species, using dendrochronological methods. Through my analysis of white spruce (Picea glauca) and lodgepole pine (Pinus contorta) tree rings across five Yukon Territory sites, I found that white spruce growth is showing growth declines in response to all three measured climate changes, with negative correlations between tree ring increment and spring and summer temperature, spring frost events, and growing season cloud cover. Lodgepole pine populations exhibited growth enhancement with increasing spring maximum daily temperatures, but generally neutral responses to warming summers, higher frost event frequency and increased cloud cover. To evaluate the effect of rising CO2 on boreal forest growth, I examined three representative managed forest stands across Canada, first building a model of climate effects, and examining temporal trends in the residual growth patterns. I found evidence for CO2 fertilization in Ontario black spruce (Picea mariana) and Manitoba white spruce populations, particularly at younger ages, but no growth enhancement in Yukon lodgepole pine. These results taken together suggest that Yukon white spruce may suffer pronounced growth declines under continued climate change, but more eastern spruce populations may be better able to benefit from increased carbon availability. Yukon lodgepole pine populations are less vulnerable to the impacts of climate change, but are also unlikely to exhibit significant growth increases in response to increasing temperature, frost events, cloud cover or rising CO2. The results from this thesis have important implications for future management of the Canadian boreal forest under progressive climate change.

Evolutionary history has been recognized as an important factor in studying ecological communities. Lake fish communities have had limited consideration from a community phylogenetics perspective and present the opportunity to include trophic interactions in the analysis. For the species under study, I used known phylogenies from the literature and genetic information to determine relative branch lengths and phylogenetic relationships by Bayesian inference. Using the resultant phylogenetic tree and fish community data, the phylogenetic community structure was determined for the lakes in the Manitoulin Island and LaCloche regions of Ontario, Canada. Evidence of phylogenetic structuring was found, particularly associated with piscivory, winter hypoxia tolerance, and thermal preferences for deep coldwater lakes. Although the majority of the lakes were weakly structured from a phylogenetic perspective, significant trends were nonetheless apparent; especially when further informed by examining species-specific trends, demonstrating that evolutionary history can play a role in structuring freshwater fish communities.

Evolutionary history has been recognized as an important factor in studying ecological communities. Lake fish communities have had limited consideration from a community phylogenetics perspective and present the opportunity to include trophic interactions in the analysis. For the species under study, I used known phylogenies from the literature and genetic information to determine relative branch lengths and phylogenetic relationships by Bayesian inference. Using the resultant phylogenetic tree and fish community data, the phylogenetic community structure was determined for the lakes in the Manitoulin Island and LaCloche regions of Ontario, Canada. Evidence of phylogenetic structuring was found, particularly associated with piscivory, winter hypoxia tolerance, and thermal preferences for deep coldwater lakes. Although the majority of the lakes were weakly structured from a phylogenetic perspective, significant trends were nonetheless apparent; especially when further informed by examining species-specific trends, demonstrating that evolutionary history can play a role in structuring freshwater fish communities.

The inherent complexity of the natural world has long been a central theme in ecological research, as the patterns and processes that govern ecosystems can operate at multiple spatial and temporal scales. It is clear that to develop general ecological frameworks, we must consider many different factors at different scales, and incorporate ideas from other disciplines. This thesis touches on several of these ideas, first through an analysis of literature, and then with field research examining the role of broad-scale abiotic factors on lotic systems. To determine how integrated aquatic science is currently understood among different researchers, I provide an analysis on communication and exchange of ideas among various subfields in aquatic science. I show that there are clear divisions within the aquatic science literature, suggesting that there is progress to be made on the integration of methods and ideas. Next, I examine the impact of a large-scale geological feature, the Canadian Precambrian Shield, on abiotic conditions in lotic systems, and how these conditions in turn influence the species assemblages of aquatic organisms. This is addressed with both historical survey data, as well as contemporary data, and as a whole, incorporates ideas concerning the relative influence of regional versus local factors, the importance of historical factors on species distributions, and the relationship between the abiotic environment and biological communities. These analyses show that there are distinct fish and macroinvertebrate communities in Shield lotic systems compared to those found in nearby off-Shield sites, indicating that the Shield is an important broad-scale factor influencing local biological communities. This finding, in conjunction with previous knowledge on the influence of historical factors, provides further insight on the structuring of lotic fish and macroinvertebrate communities in Ontario.

Littoral zone primary production is under-studied relative to the pelagic zone, despite recent work indicating its importance to the lake as a whole. Benthic extracellular material, shown to be important for food web dynamics and stabilization of the surrounding ecosystem in the marine intertidal, is even less frequently studied in lakes. I examined the environmental and community level drivers of benthic primary production, and found production to increase over the summer and to decrease with disturbance. I also found that maximum photosynthesis and efficiency under sub-saturating light both increased with depth, contrary to the existing, laboratory-derived paradigm of a trade-off between the two. I also examined how benthic primary production and environmental factors were correlated with the amount of extracellular material. I found that loosely bound colloidal extracellular material decreased with in situ photosynthesis and was affected by algal community composition, whereas tightly bound capsular extracellular material was affected only by date, indicating that capsular material is refractory in lakes just as it is in marine systems. Contrary to what is seen in marine systems, however, there were no direct effects of the environmental factors, possibly the result of physical differences between these systems. I also performed the first cross-ecosystem comparison of extracellular material. Despite relatively few studies from lakes and streams, and methods which have not been standardized, I found that lakes were similar to marine intertidal zones both in their median amounts of extracellular material and their relationships between extracellular material and chlorophyll a. This relationship appeared to be quite different in streams, with very low amounts of extracellular material found at sites with either high or low chlorophyll a concentrations. While the above studies will improve future estimates of lake carbon budgets and whole-lake production, my development of a permutation test for path analysis, and a novel application of the Bayesian principal components analysis, will assist all ecological studies that are often restricted in their sample sizes or compromised by missing data.

Although boreal forest management typically results in an increased frequency of even-aged forest stands in managed landscapes, fire history research suggests that much of the natural forest mosaic is composed of stands characterised by multiple cohorts of trees. To aid in the development of multicohort management, I investigated stand structural characteristics and small mammal communities as a function of their tree cohort structures. I also tested key alternatives: stand age, productivity, and tree species composition, as correlates of structural variation and small mammal communities. Results reveal that in mixedwood and black spruce forests, three-dimensional structure of boreal forests is strongly correlated with small mammal community structure, and indicate that tree diameter distribution is a succinct descriptor of such structural variation, performing better than alternative stand characteristics. This represents a new approach to characterising habitat supply as a function of within-stand heterogeneity, contrasting with existing approaches that focus on among-stand characteristics.

Bioassessment can be performed through several methods and with different bioindicators. In Canadian Areas of Concern (AOC), fishes are used as a proxy for site condition. The Index of Biotic Integrity (IBI), a multimetric index for biological assessment, has been applied to fish data across Canadian AOCs to detect recovery. Previous studies, however, have indicated the IBI is not sensitive to assemblage changes characteristic of later stages of recovery. In this study, the IBI and multivariate methods were applied to data from two AOCs, the Detroit and St. Clair rivers. The results revealed that the IBI is susceptible to species substitutions within metric categories. The substitutions produced high variability within narrative ranks and rendered the IBI insensitive to changes, detected by multivariate methods, in the fish assemblage. In the absence of reference sites, the multivariate analyses were supplemented with the development of a reference condition based on best professional judgment.

To monitor and assess direct anthropogenic impacts on an aquatic system requires knowledge of its natural variation. The goal of this study explored natural variation in the lake fish communities of the northern Bruce Peninsula, which may act as a reference condition for other studies. The results of this study indicated there has been a shift towards more small-bodied, native species present in the fish communities, potentially a result of beaver activity in the area. A second goal was to calculate gear sampling efficiencies to enable the design of efficient monitoring protocols for fish communities in small, shallow lakes. It was concluded that a wide variety of gears are required to assess the fish species composition in a lake. Fine-mesh hoops were the most effective gear; however, saturation was never obtained for boat electrofishing; therefore, additional research is required to determine effectiveness relative to the fine-mesh hoop net.