Gnathostome novelties include jaws, paired appendages, and true teeth. Dlx genes encode transcription factors indispensable for embryonic development of these novelties. Gnathostomes possess at least 6 Dlx genes organized in 3 bi-gene clusters, a physical arrangement which is proposed to affect their expression though shared enhancer elements. I studied the Dlx genes of Cyclostomes, the evolutionary sister group of Gnathostomes. I identified 4 novel members of the Dlx gene family in hagfish (Eptatretus stoutii), and confirmed the presence of 6 Dlx genes in lamprey ( Petromyzon marinus). I found that Cyclostomes have only 1 gene cluster and several orphan genes. This lack of conserved arrangement is coincident with an absence of conserved Dlx enhancers. Irregardless, some regulatory conservation is still apparent as lamprey non-coding DNA is able to drive dlx specific expression patterns of reporter genes in zebrafish. Therefore Cyclostome and Gnathostome Dlx are both organized and regulated differently. The causes and consequences of these changes in Chordate evolution are discussed.

<p> The earliest-diverged multicellular animals are decentralized organisms capable of growing to indeterminate sizes and highly variable morphologies. These organisms must coordinate activity among their constitutive cells at the scale of the organism in order to to leverage the benefits of multicellularity, and must do so using decentralized mechanisms that are robust to uncertainty in size and shape. This thesis investigates how coordination within the Placozoa&mdash;arguably the simplest animals&mdash;scales with organism size, quantifies the extent to which different developmental processes affect size regulation, and creates a framework for measuring morphological variability in what had been considered amorphous animals. In Chapter 1 I develop a method by which one can measure coordination and information propagation within an animal's body plan, and investigate how this propagation is affected by changes in size. I argue that such animals are poised at criticality, with evidence presented to suggest that this facilitates optimal information transmission, but that the physical constraints of multicellularity create a size-coordination trade-off in such decentralized organisms. The presence of size-induced trade-offs brings forth the question of how size is regulated, which in Placozoa occurs through growth and asexual fission. In Chapter 2 I investigate whether size is regulated in response to changing environmental nutrient conditions and find that animals adjust their sizes to match their environments. I further find that this change comes about primarily due to changing dynamics of growth rather than fission, and identify that growth is highly dependent on nutrient conditions, but find evidence that asexual fission could be an emergent phenomenon of poor coordination beyond certain sizes. Finally, in Chapter 3 I investigate the morphological variability in Placozoa and find evidence for allometric growth in such animals. In addition, Chapter 3 sets the groundwork for future comparative morphological studies between individuals and for behavioral stereotyping by developing a size and rotation invariant shape representation, which I use to identify the presence of idiosyncratic morphologies. I close the thesis with some remarks regarding future directions in exploring the effects of scaling on coordination, morphology, and behavior in this small yet evolutionarily significant Metazoa phylum.</p><p>

<p> Over the last half-century, previously undescribed tick-borne pathogens including the Lyme disease bacteria, <i>Borrelia burgdorferi</i>, have rapidly spread across the Northeast and Midwest United States. Lyme disease is now the most commonly reported vector-borne disease in North America, with over 300,000 estimated cases each year in the United States. Despite its epidemiological importance, many questions remain about this ongoing invasion. Does the observed spread of human cases reflect the ecological spread of the Lyme disease bacteria or does it reflect changes in case reporting and recognition? How do ticks and tick-borne pathogens spread across space and why are tick-borne pathogens currently invading the US? A better understanding of the ecological and evolutionary history of Lyme disease in North America will inform predictions about its future spread and how control measures might be implemented.</p><p> Reconstructing the invasion of Lyme disease is challenging because <i> B. burgdorferi</i> circulates in an enzootic cycle; humans are only incidental hosts. This means that reported cases of disease may not reflect the underlying ecological spread of <i>B. burgdorferi</i>. Pathogen genomes offer an alternative data source for reconstructing the history of pathogen invasion. However, this requires large population-scale samples of pathogen genomes that are difficult to generate from field samples. Further, for pathogen genomes to be informative, pathogens must evolve on similar timescales to ecological spread.</p><p> My dissertation work integrates diverse data sources&ndash;human case reports and pathogen genomic data&ndash;to reconstruct the history of <i> B. burgdorferi</i> in North America. In Chapter One, I present a spatio-temporal model for the spread of human cases of Lyme disease and babesiosis, another tick-borne disease, across New England. Our model uses use the best available longitudinal data&ndash;human surveillance data&ndash;to model the underlying ecological spread of tick-borne pathogens. Our model predicts that tick- borne diseases spread in a diffusion-like manner, at approximately 10 km per year, with occasional long-distance dispersal, likely due to spread by avian hosts. The remaining studies rely on pathogen genomic data. In Chapter Two, I tackle the methodological challenge of generating genomic data from mixed template samples by developing a method to capture multiple pathogen genomes from individual field-collected tick samples. This approach allowed us to efficiently differentiate between pathogen DNA versus tick and other exogenous DNA, enabling efficient deep sequencing and population genomic study. In Chapter Three, I examined the genomic diversity of <i>B. burgdorferi</i> within individual field-collected ticks. I found that 70% of ticks are infected with multiple strains of the Lyme disease bacteria, indicating that humans may be exposed to and infected with more than one strain of the bacteria from a single tick bite. I also find evidence that the Lyme disease bacteria is evolving in response to the immune defenses of its natural hosts (including rodents and birds). Finally, in Chapter Four, I examined patterns of <i>B. burgdorferi</i> genomic variation across space. I find that <i>B. burgdorferi</i> diversity is ancient and predates not only the reported emergence of Lyme disease in humans over the last ~40 years, but also the last glacial maximum, ~20,000 years ago. Ultimately, population genomic data reveal that the recent emergence of Lyme disease in North America is not driven by a recent introduction or evolution of <i>B. burgdorferi</i>. Instead, the recent epidemic of human Lyme disease is likely driven by environmental and ecological changes that have increased the density of ticks, infected ticks, and/or frequency of human exposures to infected ticks in the past century.</p><p>

In this thesis, I use 10 populations of Drosophila melanogaster, each fixed for a different visible recessive mutation to investigate two outstanding issues in sexual selection research. First, to quantifty indirect benefits of female mate choice and explore the nature of genotype x environment interactions for different fitness components, I estimated the effects of these mutations on male sexual fitness and productivity in the population's ancestral laboratory environment, as well as a novel food environment. Indirect benefits in the ancestral environment were lacking, suggesting that a good genes process is not acting. Cross-environment correlations were not conducive to indirect benefits following colonization of a novel environment. Second, to investigate the contribution of variable search effort to variance among males in mating success, I conducted mate choice trials to compare the relative mating success of mutant males in small vs. large arenas. Sexual selection against mutant males was stronger when search effort was included than when it was excluded, indicating that varying ability to find mates may increase the strength of selection against deleterious alleles.

The Cariceae (Carex & Kobresia; Cyperaceae) account for ca. 10% of Canada's native vascular plants, yet diversity within the tribe is overlooked due to its taxonomically-difficult floral morphology. DNA barcoding is a useful tool for identifying animals and the technique is currently being adapted for use in plants. This thesis develops a reference barcode database for the Cariceae of North America, north of Mexico, using the chloroplast gene matK. A species resolution rate of 39% is reported, although when broken down into political regions, this can increase to 75%. Unknown tissue samples from across North America were then identified using this reference database; 50% of these were identified to a single species matching the morphological identification, and 50% were identified to a group of taxa containing the correct identification. An ecogeographical regional database for the Arctic Archipelago was also challenged with 230 unknown samples and identified 98% to a single species.

The taxonomic status of the 25 nominal species of the Indo-Pacific flatfish genus Zebrias (Pleuronectiformes: Soleidae) was revised based on a morphological study of 531 specimens, including 36 type specimens. Two distinct, monophyletic groups were identified differing in the confluence and attachment of the caudal fin to adjacent dorsal and anal fins. Species most closely associated to the type species Pleuronectes zebra were included in the genus Zebrias while the remaining species were assigned to the genus Pseudaesopia to accommodate Zebrias species having a shallowly confluent caudal fin with adjacent fins, among other characters. Ten species are now recognized and re-described in Zebrias while six species are recognized and redescribed in Pseudaesopia. Comprehensive generic definitions and identification keys to species are provided. In addition, the closely related and monospecific genus Aesopia is briefly discussed. Finally, potentially useful characters for a future phylogenetic study are discussed.

Ultraviolet B radiation (UVBR) and chemical pollutants are environmental stressors that may affect amphibian populations. While adverse effects of UVBR and chemicals on amphibians are documented, few studies examined the effects of interactions between stressors on amphibian health. Gosner stage 25 Rana pipiers tadpoles were chronically exposed to environmentally relevant levels of UVBR (0.15-0.22 W/m2) and the estrogenic chemical 4-tert-octylphenol (OP) (0.01 nM or 10 nM) alone and in combination. Tadpoles exposed to UVBR and/or OP exhibited significantly delayed development at stage 29. Significantly fewer UVBR-treated tadpoles developed past stage 34 and metamorphosed. Effects of UVBR/OP on the thyroid system were assessed because it is the main regulator of amphibian metamorphosis. Stage 29 and 34 tadpoles were collected for gene expression analysis in tail and T3 (triiodothyronine) whole body levels (minus tail). Moreover, we examined whether pre-exposure to UVBR/OP affected the molecular and morphological responses of tadpoles to exogenous T3. OP increased the expression of several genes in tail and brain and/or their response to T3 (e.g., deiodinase 2), and the addition of UVBR can alter the effect of OP. Although UVBR had no observable effect on gene expression, developmentally delayed UVBR-treated stage 31 tadpoles exposed to T3 exhibited slowed tail resorption and accelerated hind limb development. UVBR and/or OP did not affect T3 levels of stage 29 and 34 tadpoles. However, a decrease and increase in deiodinase 2 and 3 (D2 and D3) mRNA levels, respectively, were observed in groups of tadpoles with slowed developmental rates at those stages. Since D2 activates and D3 inactivates thyroid hormones (TH), UVBR/OP mediated disruptions in development are likely caused by dysfunctions in the localized metabolism of THs. These results indicate that environmental levels of UVBR and/or OP can affect metamorphosis, potentially by disrupting the biological action of T3 and deiodinases in peripheral tissues, which could contribute to population declines.

It has long been recognized that climate can influence the diversity and dynamics of communities and regional assemblages. Within this thesis, I ask three questions: (1) which processes are most important in mediating climate-species richness relationships; (2) are predictions of spatial climate-richness models temporally consistent, and (3) is local community structure determined primarily by regional or local processes. Metabolic theory proposes that climate-richness relationships arise due to the temperature dependence of metabolic rate. I tested the theory's predictions for six taxa in North America. Contrary to the theory's predictions, temperature-richness relationships were curvilinear and their slopes deviated from the predicted value. This suggests that the mechanism proposed by metabolic theory does not underlie climate-richness relationships. If climate determines species richness, then climate should predict how species richness will change over time. To test this, I compared alternative methods (regression and niche modelling) of forecasting shifts in species richness given global climate change. Models were trained on butterfly richness data from the early 20th century and their predictions were compared to observed changes throughout the 20th century. Overall, regression-based approaches that incorporated spatial autocorrelation outperformed other methods. Broad-scale richness gradients could arise from climatic niche conservatism. I tested this hypothesis for treefrogs (Hylidae) by combining data on species' distributions and phylogeny. I found that while niches were conserved with respect to cold tolerance, species richness was determined by precipitation, not temperature. This suggests that the processes determining regional species composition and richness are controlled by fundamentally different climatic components. I evaluated the relative importance of regional and local processes and how there were affected by climatic gradients by examining patterns of body size dispersion at local and regional scales for hylid frogs. On average, communities were over-dispersed, but there was no increased signature of competition in the tropics. Dispersion of regional assemblages decreased in cold areas, but this was not due to an elevated tropical rate of body size evolution. Overall, regional processes explained twice as much variance in body size dispersion than did local processes. This thesis rejected several hypotheses for the link between climate and macroevolutionary patterns. In doing so, it provided new insight to the role of ecological and evolutionary processes along broad-climatic gradients.

All eukaryotes contain at least three homologous RNA polymerases (RNAPI, RNAPII, and RNAPIII), which are directed towards their target genes by interactions with RNAP-specific general transcription factors (GTFs). Although the RNAPs transcribe a subset of nuclear genes, it is unknown if they have evolved altered functionality. An in silico approach to identify putative differences in the three RNAPs was used to identify whether any functional differences likely exist by identifying amino acids that have experienced shifts in evolutionary rates and by identifying length differences between the cleft loops of the RNAPs. The difference in the levels of concerted evolution experienced by the genes transcribed by RNAPs was then exploited to test the molecular coevolution hypothesis of Dover and Flavell (1984. Cell . 38:622-623.). According to the molecular coevolution hypothesis, concertedly evolving DNA increases the evolutionary rate of any interacting proteins. We thus compared the evolutionary rates of the three RNAPs and their GTFs, since their target genes undergo different levels of concerted evolution. Finally, the origins of the 5 subunits that are specific to RNAPIII were examined, since no homologous relationships have been identified thus far for any of these subunits. Several sites that have experienced shifts in substitution rates in the ancestral RNAPs were found in all three enzymes and these sites were clustered near the active sites in all cases. Several cleft loops with different lengths (in amino acids) between the three RNAPs were also identified. The validity of the molecular coevolution hypothesis was largely confirmed via the demonstration that most subunits of RNAPI evolve faster than those of RNAPIII and most subunits of RNAPIII evolve faster than RNAPII. This is consistent with the molecular coevolution hypothesis because RNAPI experiences higher levels of concerted evolution than the target genes of RNAPIII. The evolutionary rates of the GTFs of RNAPI and RNAPIII were also higher than those of RNAPII. Finally, four of the five RNAPIII-specific subunits were identified as homologs of RNAPII GTFs, indicating that several of the GTF paralogs existed in ancestral RNAPIII and were subsequently recruited to the enzyme before the diversification of eukaryotes.

<p> The deep sea is the Earth&rsquo;s largest ecosystem and harbors a unique and largely endemic fauna. Although most research has focused on the ecological mechanisms that allow coexistence, recent studies have begun to investigate how this remarkable fauna evolved.. My work quantifies geographic patterns of genetic variation and investigates potential mechanisms that shape evolution in the deep ocean. </p><p> Bathymetric genetic divergence is common in the deep sea with population structure typically decreasing with depth. The evolutionary mechanisms that underlie these patterns are poorly understood. Geographic patterns of genetic variation indicated that the protobranch bivalve <i>Neilonella salicensis </i> was composed of two distinct lineages separated bathymetrically. Genetic diversity was greater in the lower-bathyal clade of <i>N. salicensis </i> than the upper to mid-bathyal clade. In a co-occurring mid-bathyal protobranch <i>Malletia johnsoni,</i> population differentiation was greater among samples than the confamilial lower-bathyal <i>Clencharia abyssorum,</i> though, genetic diversity was similar. These patterns suggest general trends do not always hold and fine scale patterns of gene flow need to be thoroughly investigated. </p><p> Little is known about the ecological or evolutionary mechanisms that might promote divergence or maintain population structure. Oxygen minimum zones (OMZs), which cover enormous regions of the deep ocean, might hamper gene flow by precluding larval dispersal. To test this, genetic patterns of the wood-boring bivalve <i>Xylophaga washington</i> were quantified across the northeastern Pacific OMZ. Results indicate two clades were apparent, one throughout the OMZ and one within and below it, possibly segregated by a historically stronger OMZ or other environmental factors that vary with depth. A similarly uninvestigated evolutionary factor with potentially large impacts is selection on mitochondrial DNA. Positive selection is apparent in the mitochondrial DNA of shallow water and deep-sea crabs, shrimp, and fishes, possibly related to any of the myriad factors that differ between the two habitats. </p><p> The deep sea is biogeochemically important and is highly impacted by climate change and anthropogenic factors. Genetic patterns in this habitat are very complex. This work suggests gene flow is inhibited at many scales, both across bathymetric gradients and within small bathymetric ranges.</p><p>