Bipedalism is commonly assumed to be an adaptive convergence because it has evolved independently three times in small desert rodents. However, the functional benefits of bipedality in this ecosystem have long been unclear. In this thesis I integrate phylogenetics, functional morphology, biomechanics, information theory, and behavior to investigate whether and how bipedality increases fitness in desert ecosystems, and whether bipedal rodents convergently evolved to have the role in their respective ecosystems. Based on the diversity of extant dipodid rodents, I begin by statistically reconstructing the pattern of morphological evolution in jerboas. I find that the strongest indicator of bipedality is metatarsal to humerus length, and that changes in this ratio are associated with increased rates of speciation, supporting a punctuated equilibrium pattern of evolution in this clade. Furthermore, the distinct patterns of morphological evolution suggest that a complex suite of genetic and developmental mechanisms governs the acquisition of bipedality in jerboas. I then use an inverse dynamics approach to characterize the biomechanics of bipedal hopping in a derived jerboa. I find that the dynamics of jerboa hopping are generated predominantly by muscular contractions, rather than tendon--based elastic energy storage and return between strides. Therefore hopping in small rodents favors rapid production and absorption of forces, rather than sustained bouts of steady--state locomotion. By reviewing predator--prey studies in biomechanics, ecology, and evolution I hypothesize that ricochetal locomotion enhances the ability of small rodents to evade predators that hunt via ballistic interception. I then develop Information Theoretic techniques to measure the unpredictability of escape trajectories in sympatric bipedal and quadrupedal rodents. As expected, bipedal rodents use significantly more unpredictable escape trajectories, likely enhancing predator evasion ability and enabling foraging in exposed areas with higher predation risk. I then found that bipedal rodents exhibit a stronger preference for exploring open spaces, matching previously established foraging patterns. These findings suggest that the evolution of bipedality enables spatial resource partitioning to limit interspecific competition in desert rodents. Based on the functional studies in my thesis, I evaluate ecological models to predict the occurrence of convergent bipedal rodents in Myomorpha. I show that diet specialization and aridity are insufficient to predict the locomotor morphology of these rodents and develop novel hypotheses for the convergent evolution of bipedalism in desert rodents. My thesis investigates the functional consequences of morphological evolution in the context of evolutionary ecology. By considering the interconnectedness of ecology, behavior, and evolution, studies in biomechanics can be designed to inform each of these fields. This interdisciplinary approach is necessary to study the adaptive nature of behavioral traits that are governed by myriad genetic, developmental, and environmental factors. / Biology, Organismic and Evolutionary

Hydrothermal vent ecosystems are defined by steep thermal and chemical gradients. Chemosynthetic microorganisms are the primary producers in these systems, utilizing the available chemical energy to support substantial animal biomass. The variety of chemical substrates provided by hydrothermal fluid and surrounding seawater enables a metabolically diverse community of microbes. However, our understanding of how abiotic factors such as temperature, geochemistry, and mineral substrate influence the activity of these microbes is limited. The overarching goal of this dissertation is to examine the influence of these abiotic factors on free-living microbial community composition, structure, and function. In this work I first examined the influence of temperature on primary productivity by using radio isotopic tracer studies to measure rates of carbon fixation by epi- and endolithic microbial communities from vent chimney sulfides. I show evidence that these communities fix more carbon at low temperatures, underscoring the importance of low temperature habitats in these environments commonly characterized by high temperature. I then utilized in situ RNA preservation to examine community-wide microbial activity in low temperature vent fluids throughout a vent field. These data show two distinct activity profiles that cross-cut canonical habitat descriptions, and highlight the importance of the intra-field waters among the discrete vents as regions of high primary productivity bearing similarity in microbial activity to plumes emanating from high temperature chimneys. Finally, I designed novel colonization devices to examine the influence of mineral substrate on microbial community composition, structure, and succession. Mineralogy influenced certain taxa. I also identified potential early and late successional taxa. The combination of metabolic rate measurements, metatranscriptomics, and colonization experiments presented here, all with co-registered geochemistry, underscore the substantial heterogeneity of these systems and offer insights into the relative strengths of the abiotic forces that help to govern these ecosystems. / Biology, Organismic and Evolutionary

Complex interactions between mammalian hosts and their gut microbes have evolved over many millennia and have established a sophisticated communication system that is essential for symbiosis and mutualism. Perturbations to host-microbiota homeostasis in the context of a genetically susceptible host are central to the development of inflammatory bowel disease (IBD). In-depth understanding of the underlying mechanisms that control homeostasis and dysbiosis are essential for determining how to reliably modulate the host-microbiota continuum to prevent and treat disease. However, deciphering whether alterations in the microbiota are a cause or consequence of IBD remains a considerable challenge, as is defining the role of specific microbes in the pathogenesis of disease. This thesis explores the gut microbiome in mouse models of experimental colitis and evaluates the contribution of specific microbial clades and pathways in potentiating mucosal inflammation with the goal of identifying novel microbiome-targeted interventions for disease management. To improve our understanding of microbial dysbiosis and dysfunction in IBD, we use the TRUC (T-bet-/-RAG2-/- ulcerative colitis) mouse model to profile the gut microbiome in active disease versus treatment-induced remission. 16S ribosomal RNA gene surveys of stool from mice treated with antibiotics, immunodulatory therapies, or a fermented-milk dietary intervention reveal microbial features modified among health and disease states. Discriminatory biomarkers of active disease included increased Enterobacteriaceae and shifts from carbohydrate and energy metabolism to pathways favoring bacterial pathogenesis, specifically cell motility and two-component systems. An unexpected observation is a significant enrichment in genes for microbial benzoate degradation in active colitis. Intermediates of benzoate metabolism – catechols – share the same backbone as host catecholamines, which can signal through two-component systems to promote virulence in pathogenic Enterobacteriaceae. Based on expansions in Enterobacteriaceae and increased gene abundances for benzoate degradation, two-component systems, and bacterial motility proteins, we identify a potential signaling axis linking host adrenergic stress with enhanced bacterial virulence in a preclinical model of colitis. Enterobacteriaceae sense and respond to microbiota-generated signals and host-derived catecholamines through the QseBC two-component quorum sensing system. QseC is a membrane-bound sensor kinase that surveys the external milieu and, upon signal detection, activates its cognate response regulator, QseB, to induce expression of virulence genes. To investigate whether blocking QseC signaling could reduce disease severity, we test the effects of a QseC inhibitor (LED209) in the TRUC, Il-10-/-, and dextran sodium-sulfate models of experimental colitis. LED209 attenuates disease across all three models, with the most striking protective effect in TRUC and dextran sodium sulfate-treated mice. LED209 also prevents the expansion of Enterobacteriaceae in Il-10-/-and dextran sodium-sulfate-exposed mice, but not in TRUC mice, indicating a potential difference in microbiota responses based on genetic context. Moreover, measuring catecholamines in cecal content and stool show that LED209 does not significantly affect the luminal catecholamine pool and thus, may not disrupt host or microbial catecholamine metabolism. Collectively, these data show that QseC inhibition can ameliorate disease in distinct models of experimental colitis and suggest a role for QseC-mediated bacterial virulence in the pathogenesis of IBD. Although a single pathogen has not been identified as a causative agent, several bacteria continue to be implicated in the initiation and progression of IBD, including adherent-invasive Escherichia coli (AIEC). As a proof-of-principle, we genetically inactivate qseC in the Crohn’s disease-associated AIEC strain LF82. We show that absence of qseC leads to downregulated virulence gene expression and defects in flagellar assembly and motility in vitro and reduced colonization efficiency in vivo. Overall, these studies provide evidence that QseC may be an upstream virulence node utilized by colitogenic bacteria to survey their host and potentiate disease and may be a useful target for microbiota-directed therapies in IBD. / Biological Sciences in Public Health

Natural selection gives rise to biodiversity by purging the less-fit among variants that are too similar (a principle known as character displacement), but to predict how fit or different an organism needs to be to survive is hard. In the simplest theoretical case, the probability whether one lineage versus another survives depends only on their relative fitness and random fluctuations. In more complex scenarios, this probability may depend on the fitness of all the other lineages in the population, mutations that these and other lineages acquire before the outcome of competition is decided, and additional ecological interactions. These complexities evolve readily in laboratory microbial populations, suggesting that they are the norm in Nature, and have been extensively studied theoretically. This thesis provides one of the few empirical examples in which the evolution and mechanism of some of these complexities have been characterized and modeled sufficiently to make basic predictions, such as whether a mutation will fix or go extinct, which competing lineages may or may not coexist, and how do these processes relate? This work was carried out in an established system for experimental evolution, populations of asexual budding yeast (S. cerevisiae) in microtiter plates. Chapter 2 demonstrates an experimental design and modeling approach to infer the distribution of fitness effects of beneficial mutations from the population-dynamics of genetic markers. The inferred distribution accurately predicts fixation probabilities of lineages and adaptation rates of populations. Chapter 3 describes a new example of spontaneously-evolved coexistence between types competing for the same resources, including the physical mechanism, genetic basis and a mathematical model of the coexistence. The conclusion provides additional analyses to connect the findings from these two chapters and discusses their implications for microbial evolution more generally and directions for future work. / Biophysics

Mutualistic symbioses have enabled the colonization of novel habitats and niches in a large array of eukaryotic and bacterial taxa. Reliable mechanisms of symbiont transmission between host generations are necessary to stabilize these associations over evolutionary time. Historically, symbionts have been categorized as either vertically transmitted from the parents to offspring or horizontally transmitted through the environment. The route between hosts influences how symbiont populations are connected between hosts and between geographic localities. Over evolutionary time vertical transmission leads to gene loss and genome erosion. Growing evidence from diverse associations suggests that modes utilizing both horizontal and vertical strategies exist, raising the question of how these “mixed modes” influence symbiont genome evolution. The overarching goal of my dissertation was to determine whether the mode of symbiont transmission in an obligate mutualism is consistent over evolutionary time and what impact transmission mode fidelity has on symbiont genome evolution. To test these questions, I used the chemosynthetic symbiosis between the marine bivalve Solemya velum and its gammaproteobacterial symbionts, which has been reported to transmit its symbionts vertically through the ovary, but bears none of the genomic hallmarks of strict vertical transmission. In this work, I used population genomics of S. velum subpopulations sampled from five localities along the New England coast, from Massachusetts to North Carolina, to test for evidence of horizontal transmission in the evolutionary history of this species. These analyses revealed that symbionts and mitochondria do not exhibit concordant genealogies, divergent symbiont lineages have come into contact and recombined, and symbiont genomes have experienced large-scale structural changes mediated by mobile elements and horizontal gene transfer. In total, these lines of evidence indicate that a substantial amount of horizontal transmission has occurred in the recent history of this association. The vertical transmission route through host tissues was characterized via in situ hybridization to symbiont 16S rRNA in adult host tissues and by qPCR of the rhlE gene in spawned eggs. These data showed that symbionts are present at low abundance in the ovary, associated with the supportive cells and mature oocytes, and each spawned egg contains approximately 50-100 copies of the symbiont genome. Lastly, I tested for evidence of mixed transmission modes in symbiont populations contained within host tissues (each host gill contains more than a billion symbiont cells), by deep-coverage whole genome sequencing. Using a novel variant-calling procedure, I detected low amounts of genetic variation among symbiont genomes within a host relative to between hosts. However, the variant sites that were present were correlated in position along the genome, present on the same chromosome, and segregating in the symbiont population at large, suggesting that these variants arose via recombination with a variant symbiont genotype introduced by horizontal transmission. In total, this work supports the existence of mixed transmission modes in symbiotic associations and indicates they have distinct consequences for symbiont evolution. Mixed modes may provide a best-of-both-worlds strategy to ensure that hosts acquire symbionts every generation while maintaining opportunities for recombination and acquisition of novel genetic elements. These results are relevant to understanding the impact of symbiont transmission mode on genome evolution in associations ranging from mutualisms to pathogenic infections. / Biology, Organismic and Evolutionary

Life history theory assumes that organisms allocate energetic resources (i.e., calories) to primary life functions such as maintenance, growth, reproduction, and physical activity in a manner that maximizes fitness. Under this conceptual framework, energy is limited, resource allocation is dynamic, and functional tradeoffs between competing metabolic processes are expected to occur. Life history tradeoffs have been invoked to explain biological variation across a range of species and ecological contexts. However, few studies have examined patterns of energy allocation and tradeoffs during human development, restricting fundamental understandings of human life history, phenotypic plasticity, and health. This dissertation investigates human energy allocation and life history tradeoffs in the context of physical growth among the Shuar, a small-scale indigenous population from Amazonian Ecuador. Mixed-longitudinal anthropometric data were collected from 2,553 Shuar between the ages of 0-29 years. Additional market integration (i.e., production for and consumption from a market-based economy) and immune activity (i.e., finger-prick blood biomarker) data were obtained from a subset of children and adolescents. Analysis was performed to explore variation in physical growth at the population, regional, household, and individual levels. Results demonstrate that, as a population, the Shuar grow significantly more slowly than international references and experience several unique developmental characteristics that may be explained by energetic life history tradeoffs. Between-individual variation in Shuar growth, however, is substantial. A large portion of this variation is explained by household-level market integration factors associated with differences in diet, lifestyle, and pathogen exposure. Among Shuar children, linear growth is negatively related to several diverse biomarkers of immune function, such that growth is reduced by as much as 83% during intermittent periods of elevated immune activity. These tradeoffs occur over timeframes as short as one week and are typically avoided by children with adequate energy reserves (i.e., high levels of subcutaneous body fat). Taken together, these findings provide evidence for an important role of energetic tradeoffs in shaping patterns of human ontogeny and health. / Human Evolutionary Biology

In the context of declining populations of freshwater eels in Europe and North America and inspired by observations of Japanese eel spawning near seamounts, this study explored a possible spatial relationship between spawning American and European eels (Anguilla rostrata and A. anguilla) and geophysical features in the Sargasso Sea. A spatial analysis of positive and null catch sampling data from 1863 to 2007 found observations of young eel larvae significantly clustered over magnetic anomalies with higher than average intensities. These larval clusters occurred above the southwest Bermuda Rise and in the vicinity of the Vema Gap, a constricted abyssal channel connecting the Nares and Hatteras Abyssal Plains and directing flow of the abyssal bottom current. In this area, newly hatched larvae were positioned on either side, but not within, a 170 km wide high-magnetic gradient band located on the M0 anomaly. This gradient separated the centers of the distributions of the two species when they were ≤ 5 mm in length. Standard deviations of directional trends indicated probabilities in dispersal patterns, highlighting a potential tool for modeling larval distributions. Like other species undergoing oceanic migrations, eels have demonstrated a magnetic sensory ability and may rely on magnetic cues for navigation. The geomagnetism of the ocean floor, which attenuates at a cubic rate with distance, may provide a clue to eel migratory routes and depth preferences or play a role in larval dispersal, metamorphosis and recruitment. Spatial analyses open new opportunities to study anguillid distributions in relation to geomagnetic and oceanographic features.

This biogeographical study documents the modern distribution of ostracodes in the southwest Yukon Territory and northern British Columbia, Canada. The study tested the hypothesis that dissolved ion composition and concentrations of the lake water are the primary determinants of the distribution of modern ostracodes in this region. A total of 28 freshwater species representing 8 genera were identified in the 33 study lakes. Species common in the southwest Yukon are widely distributed throughout North America, and include Cyclocypris ampla, Candona candida, Cypria turneri, Cypria ophtalmica, and Candona protzi. Concentrations of ostracode valves were highest in four lakes with moderate conductivity values ranging between 330 and 397 muS/cm. Rarefaction estimated species richness was low (3 to 8), and the highest estimated species richness was found in four lakes, three of which were within 1 km of each other. Conductivities in these lakes ranged between 320 and 397 muS/cm. There is little geographic pattern in either species richness or in the distribution of common species. The dissolved ion composition is the primary control determining the species that will be present in a particular lake.

Methylmercury (MeHg) enters most aquatic food webs primarily at the phytoplankton level. However, in the complex aquatic ecosystem, it is difficult to fully examine specific pathways. Consequently, in this study, the uptake of environmentally realistic levels of added MeHg concentrations (0.21 to 20 ng Hg L-1 ) by the freshwater green alga Pseudokirchniriella subcapitata grown in batch and semi-continuous cultures at biomass levels of (0.03, 0.15, 0.3 and 3 mg (dw) L-1) was investigated. In algal culture media without dissolved organic carbon (DOC) and in river water samples with DOC concentration of (2.8 mg L-1) uptake, uptake rate constant, algal concentration of MeHg and the bioconcentration factor (BCF) after 48 h was measured. MeHg uptake was biphasic, with rapid uptake of at least 50% of the total uptake taking place over the first 2 h of incubation followed by a more gradual uptake for the remaining 46 h. Desorption of MeHg from algal cells by re-suspension in acidic medium (pH 3) was < 10% of the total uptake at 48 h. Uptake rate constants of MeHg (ku) increased with aqueous MeHg concentration (r2 = 0.99). At 48 h, algal concentration of MeHg (MeHg (ng) divided by dry weight of algal biomass (g)) increased with aqueous MeHg concentration (r2 = 0.98) but decreased with increasing biomass (r2 = 0.75). This was shown to be a biomass dilution effect as the total uptake of MeHg did increase with biomass. Log MeHg BCF decreased with increasing algal biomass (r 2 = 0.99) with values of 6.9, 6.2 and 5.2 at 0.03, 0.3 and 3 mg (dw) L-1 respectively at all concentrations of MeHg added (0.5, 1.0 and 20 ng L-1).

Numerous forest fires occurred during the summer of 2004 in the Klondike Goldfields region of the Yukon Territory, an area of extensive discontinuous permafrost. More than 35 shallow detachment failure landslides developed in subsequent weeks in Steele Creek, a small drainage basin located about 60 km south of Dawson City. Preliminary observations of the failures and near-surface thermal regime were made through freeze-up of 2004 and continued in the summers of 2005 and 2006. Detachment failures were mapped and individual sites were surveyed. Air and ground temperatures were measured in burned and unburned areas. In addition, two-dimensional DC resistivity transects were used to examine subsurface conditions in the area. Forest fire contributed to detachment failure activity on permafrost slopes by destroying the surface organic mat, causing burned surface temperatures to rise, thawing active layers by up to 20 cm (+31%) deeper than unburned slopes and weakening the surface root structures. Deeper thaw melted transient layer ground ice, raising soil porewater pressures. The thermal differences between burned and unburned sites were greater at the north-facing than south-facing sites, and active layer freezing and thawing processes varied according to both aspect and burned status. More southerly-facing and/or burned sites generally thawed earlier, refroze later and had warmer temperatures than more northerly and/or unburned sites. Thaw of burned areas with high ground surface temperatures can be expected to continue, depending on climatic conditions, until sufficient revegetation occurs to shade the surface and rebuild the insulating organic mat. The detachment failures occurred from a few weeks to two years after forest fire, and only on slopes where permafrost was extensive. They were not similar to others in the literature in that almost all occurred in coarse-gained soils and had failure planes elevated above the permafrost table. These landslides were flow-type failures that rafted portions of the organic mat on top of deforming, non-cohesive sediment. They occurred in areas of deeper thaw but their distribution and the resistivity data suggest that they were associated with supra-permafrost taliks which concentrated groundwater flow. In an unglaciated area like the Klondike region this landsliding process has likely occurred thousands of times during the Pleistocene and may be responsible for elements of the form of the region's slopes. Predicted increases in the frequency and magnitude of forest fire in the boreal forest due to warming climates may increase incidence of these types of failures.