The evolution of sexually selected signals has been a major topic of scientific research since Darwin. In recent years, scientists have focused on how elaborate signals can indicate honest information about the quality of their bearers, as predicted by reliability theory. A key concept relating to how mating displays could reliably reveal quality is performance. Animals face limits in display production, and producing high-performance displays depends on the adept coordination of multiple motor systems. Thus, by observing motor performance, signal-receivers can assess the quality of signalers. Birdsong is a prime example of a display that involves motor challenges in its production. In my dissertation, I examined the connections between signal reliability and vocal performance in the swamp sparrow, Melospiza georgiana, and addressed three main questions. First, does vocal performance signal the level of aggressive threat during territorial defense? In wild male swamp sparrows, I measured aggressive response to playback of various performance levels. Males responded with decreased aggression to low-performance stimuli, suggesting these stimuli indicated low threat. Males were as aggressive to control- as to high-performance stimuli, but avoided approaching high-performance stimuli as closely. Additionally, I found that males who possessed high vocal performance were more aggressive. Second, does developmental stress affect adult vocal performance? I found that birds experiencing poor early nutrition had lower vocal performance than did control birds, indicating lasting effects of early stress. Also, males in both groups significantly improved their vocal performance of learned songs between years. Together these results suggest that vocal performance can indicate early condition and age. Third, what factors influence the development of song preferences in females? In two experiments, I raised and tutored females with songs of normal performance. When tested as adults, females displayed stronger preference behavior to tutor than to novel songs, indicating the effects of learning. Females also gave the fewest displays to low-performance and responded more strongly to normal- and high-performance songs, indicating an influence of sexual selection. These experiments provide the first evidence that the development of female preference for sexually selected traits can be guided by an interplay of learning and innate biases.

My dissertation explores several aspects of the relationship between morphological and molecular evolution in amoeboid lineages: Chapter 1—General Introduction. This chapter provides an overview of the most pressing issues in Amoebozoa phylogeny that are dealt with in the remainder of the thesis. Chapter 2—Reducing the impact of PCR-mediated recombination in molecular evolution and environmental studies using a new generation high fidelity DNA polymerase. This chapter addresses the methodological difficulty in the study of large gene families, the generation of artifactual sequences by recombination during PCR Chapter 3—Evolution of the actin gene family in testate lobose amoebae (Arcellinida) is characterized by two distinct clades of paralogs and recent independent expansions. This chapter explores intriging patterns of evolution in the actin gene families of testate amoebae. Chapter 4—Comprehensive phylogenetic reconstruction of Amoebozoa based on concatenated analysis of SSU-rDNA and actin genes. A deep phylogenetic analyses of the Amoebozoa, enables exploration of well supported taxonomic units within the group. Chapter 5—Interpreting the evolutionary history of the Tubulinea (Amoebozoa), in light of a multigene phylogeny. This chapter explores a more restrict taxonomic unit within the Amoebozoa—the Tubulinea—based on an expanded sample of genes and taxa. Chapter 6—The chastity of amoebae: re-evaluating evidence for sex in amoeboid organisms. This chapter asks whether the null-hypothesis that amoebae are asexual is consistent with current phylogenetic evidence.

Tooth cusp radius of curvature (RoC) has been hypothesized to play an important role in food item breakdown, but has remained largely unstudied due to difficulties in measuring and modeling RoC in multicusped teeth. We tested these hypotheses using a parametric model of a four cusped, maxillary, bunodont molar in conjunction with finite element analysis. When our data failed to support existing hypotheses, we put forth and tested the Complex Cusp Hypothesis which states that, during brittle food items breakdown, an optimally shaped molar would be maximizing stresses in the food item while minimizing stresses in the enamel. After gaining support for this hypothesis, we tested the effects of relative food item size on optimal molar morphology and found that the optimal set of RoCs changed as relative food item size changed. However, all optimal morphologies were similar, having one dull cusp that produced high stresses in the food item and three cusps that acted to stabilize the food item. We then set out to measure tooth cusp RoC in several species of extant apes to determine if any of the predicted optimal morphologies existed in nature and whether tooth cusp RoC was correlated with diet. While the optimal morphologies were not found in apes, we did find that tooth cusp RoC was correlated with diet and folivores had duller cusps while frugivores had sharper cusps. We hypothesize that, because of wear patterns, tooth cusp RoC is not providing a mechanical advantage during food item breakdown but is instead causing the tooth to wear in a beneficial fashion. Next, we investigate two possible relationships between tooth cusp RoC and enamel thickness, as enamel thickness plays a significant role in the way a tooth wears, using CT scans from hundreds of unworn cusps. There was no relationship between the two variables, indicating that selection may be acting on both variables independently to create an optimally shaped tooth. Finally, we put forth a framework for testing the functional optimality in teeth that takes into account tooth strength, food item breakdown efficiency, and trapability (the ability to trap and stabilize a food item).

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Discovering the targets of selection in a genome is fundamental for understanding how adaptation has affected the biological processes that lead to population and species diversity. However, very few variants in proteins are known to be adaptive. For example, in humans, fewer than 30 such adaptive missense variants are known. It is surprising that in the 5-6 million years since human divergence from chimpanzee so few adaptive missense variants would have accumulated, and so it is unclear whether such adaptive variants have never occurred or whether current methods cannot detect such changes. Are there such adaptive variants in the coding region of the genome? Alternatively, is everything found in non-coding regions, which is often largely thought of as “junk DNA”? These questions represent a grand challenge in the field of evolutionary biology. This work helps to resolve this paradox and shows that there, in fact, may be much more coding adaptation that was previously not detectable. We do this by developing and testing the idea that long term evolutionary patterns of genomic differences between species can be used to identify alleles that affect the fitness of individuals in a population.Many methods that aim to detect selection are often limited as to the timescale during which they are applicable, e.g., long-term or short-term only. In bridging this gap, we build on the Evolutionary Probability (EP) method, a method that uniquely integrates long term evolutionary history to provide a probability of observation under neutrality. We develop an approach that benefits from the strengths of both types of methods by leveraging long term evolutionary information from EP and short-term evolutionary information from population polymorphisms to identify alleles affected by selection. High-throughput analysis of variation for functional change is not possible given the immense sequencing data output that is increasing each day. Thus, we employ an in silico approach. We perform simulations of neutral evolution to identify thresholds of neutrality for EP. We also analyze various bona fide datasets of both neutral, adaptive, and deleterious variation found in humans comprising of hundreds of thousands of individual variants in humans alone. We find that our approach is reliably able to identify evolutionarily unexpected, non-neutral (affected by selection) alleles and requires only sequence alignments. Known adaptive variants are successfully identified, and a vast majority of disease variants are found to be evolutionarily forbidden underscoring the role of coding variation in human divergence as much more than previously thought. In fact, applying our approach across the human exome, we find that the amount of adaptation in humans is likely multiple orders of magnitude greater than previously believed. A catalog of the discovered candidate adaptive polymorphisms is available through an online personal genomics web resource. The new approach has also been shown to be generalizable to any sequence alignment, given that sufficient evolutionary time has elapsed among the species. Overall, our findings offer insight into the adaptive landscape of coding variants in humans, as well as provide a look into the role of long-term evolutionary history into generating disease in contemporary human populations, prompting a rethinking of the role of adaptation in human evolution. / Biology

<p> This thesis examines literal and metaphorical correlations between suppression of grey wolves in ecological systems and suppression of emotions related to trauma in the landscape of the human psyche. Similar interconnected cascading patterns arise subsequent to repression of perceived adverse conditions. Hermeneutic research methodology was employed to contrast studies of predator extirpation/reintroduction with emotional suppression/resiliency in humans. Evidence points toward value in allowing the shadow in the form of adversity to function dynamically within ecological and psychfological systems. Creativity, resiliency, and altruism are possible resulting factors that surface in the human psyche. These characteristics are believed to promote increased adaptability and communal cooperation toward greater probability of group survival and social evolution. Alternative approaches to accepting imperfection and the shadow are examined through the lens of Eastern philosophy, illustrating how integration of dual polarities may help achieve a more vital state in ecology and in the human psyche.</p>

<p>North American <i>Speyeria </i>butterflies are a group whose species hypotheses are confounded by shared wing color patterns between sympatric populations of closely related recognized species due to a putatively recent origin in evolutionary time. Previous studies of this group and the closely related Palearctic genus <i>Argynnis</i>, suggest that <i>Speyeria </i>is monophyletic but derived from within <i>Argynnis</i>. Sampling in these studies has either involved few basal <i>Speyeria</i> species, or too few <i>Argynnis</i> species (Simonsen 2006, Simonsen <i>et al. </i>2006). Thus, no comprehensive phylogenetic analysis exists for all members that answers the question of monophyly of <i>Speyeria</i>, or other subgeneric taxa,and their relationship to <i>Argynnis </i>species. A phylogenetic analysis was completed of all North American <i>Speyeria </i>species and nearly all species within <i>Argynnis</i>, using one mitochondrial (CO1) and four nuclear genes (EF1?, WG, GAPDH, and RPS5). The results indicate that North American <i>Speyeria</i> is a monophyletic group, but that Palearctic <i>Argynnis</i> is paraphyletic. Three major lineages are identified within <i>Argynnis sensu lato</i>: two Palearctic and one containing both Palearctic and Nearctic species. <i>Argynnis</i> species representing the subgenera <i>Argyreus</i>, <i>Argyronome</i>, <i>Childrena</i>, <i>Damora</i>,<i> Pandoriana, </i>and <i>Nephargynnis</i>, belong to a well-supported lineage that split early in the evolution of the group and is comprised of species with long branches. <i>Fabriciana</i> and <i>Mesoacidalia</i> were both recovered as strongly supported lineages, except for <i>A. clara</i> which was recovered as sister to <i>Speyeria</i>. In summary, the phylogenetic analyses suggest the need for reorganization into three genera: <i>Argynnis</i>, <i>Fabriciana</i>, and <i>Speyeria</i>. The results have implications for the conservation of these butterflies across the temperate zone by providing a framework for understanding potential gene flow between sympatric species complexes, proper taxonomic validity, and the natural history of threatened populations of <i>Speyeria </i>and <i>Argynnis </i>butterflies.

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