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).

Photocatalytic water splitting using solar irradiation has the potential to produce sustainable hydrogen fuel on a large scale. Practical solar energy conversion requires the development of new, stable photocatalysts that operate efficiently under a broad range of visible wavelengths. Organic semiconductors are increasingly being employed as photocatalysts due to their earth abundance, aqueous stability, and optical absorptions that can be tuned to the solar spectrum. However, much remains unknown about the mechanism of organic semiconductor photocatalysis, and significant efficiency improvements need to be made before organic photocatalysts can achieve practical solar energy conversion. In chapter 2 the effect of residual Pd on hydrogen evolution activity in conjugated polymer photocatalysts was systematically investigated using colloidal poly(9,9- dioctylfluorene-alt-benzothiadiazole) (F8BT) nanoparticles (NPs). Residual Pd, originating from the synthesis of F8BT via Pd catalysed polycondensation polymerisation, was observed in the form of homogenously distributed Pd NPs within the polymer. Residual Pd was essential for any hydrogen evolution to be observed from this polymer, and very low Pd concentrations (<40 ppm) were sufficient to have a significant effect on the hydrogen evolution reaction (HER) rate. The HER rate increased linearly with increasing Pd concentration from <1 ppm to approximately 100 ppm, at which point the rate began to saturate. Transient absorption spectroscopy experiments support these conclusions and suggest that residual Pd mediates electron transfer from the F8BT NPs to protons in the aqueous phase. Photocatalysts formed from a single organic semiconductor typically suffer from inefficient intrinsic charge generation, which leads to low photocatalytic activities. In chapter 3 we demonstrate that incorporating a heterojunction between a donor polymer and non-fullerene acceptor in organic NPs can result in hydrogen evolution photocatalysts with greatly enhanced photocatalytic activity. Control of the nanomorphology of these NPs was achieved by varying the stabilizing surfactant employed during NP fabrication, converting it from a core-shell structure to an intermixed donor/acceptor blend, and increasing H2 evolution by an order of magnitude. The resulting photocatalysts display an unprecedentedly high H2 evolution rate of over 60,000 µmolh-1g -1 under 350 to 800 nm illumination and external quantum efficiencies over 6% in the region of maximum solar photon flux.

Human origins have been debated by evolutionists and creationists. Christian young adults are educated first on creationism and learn of evolution later. This delayed education of evolution leads to potential belief change and stress. This belief change process may be similar to Berry’s acculturation. After belief change, individuals may exhibit belief bias during human origin argument evaluation. Little research has been done to explore a formal belief change model and belief bias in human origin argument evaluation. Data was collected from 121 PSYC 102 and MTurk participants in an online survey measuring evolution and creationist beliefs. Vignettes presented evidence for creationism and evolution. This evidence was evaluated by participants. Cluster analyses, MANOVAs, and ANOVAs were used to determine statistical significance. Results found three groups of individuals exist and these groups differed on age of exposure to evolution and belief change stress measures. These groups evaluated creationism and evolution evidence differently exhibiting belief bias during argument evaluation. These results expand current literature by finding a potential belief change model and preliminary evidence to support earlier teaching of evolution in schools. Limitations include violated statistical assumptions and forced clusters. Further research is needed to explore these three groups in more detail.

Gene trees enable the detailed study of the evolution of genes. These trees can be additive, based purely on mutational counts, or ultrametric, where the branches represent the time elapsed. The purpose of this thesis will be to relate evolutionary rate changes to gene function by examining the effects of a tree transformation on gene trees. The study will focus on the coffee genomes C. arabica, C. eugenioides and C. canephora. Three gene family trees will be studied: N-methyltransferases, FAD2 enzymes and terpenes. An additive tree can be transformed into an ultrametric tree using a transformation method. By taking each additive tree branch length and dividing the branch by the ultrametric branch length we can get a branch mutation rate. To quantify functional divergence, we compared aligned sequences of genes from groups of interest to calculate the ratio of non-synonymous mutations to synonymous mutations (Kn/Ks). Kn/Ks was found to correlate with the branch mutation rate in some but not all groups of interest. In groups in which correlation was present, there was also a correlation between Kn/Ks and branch length. The branch mutation rate can be used in some cases to further prove that functional divergence is present.

Creatine kinase (CK) and arginine kinase (AK) are members of a highly conserved family of phosphoryl transferase enzymes known as phosphagen kinases. CK and AK play a central role in cells that display high and variable rates of ATP turnover such as neurons, muscle fibers, spermatozoa, and transport epithelia. All CK isoforms exhibit targeting to specific tissues. In vertebrates CK exists as two dimeric, cytoplasmic isoforms, B (brain) and M (muscle) and two octameric, mitochondrial isoforms termed sarcomeric (SarMtCK) and ubiquitous (UbiMtCK). In some groups cytoplasmic dimers and mitochondrial octamers are found as well as a contiguous trimeric form, flagellar CK (flgCK). This latter isoform is found in the primitive-type spermatozoa of protochordates and certain protostome and deuterostome invertebrates. FlgCKs are myristolated and are found anchored to the flagellar membrane. AK isoforms are found as monomers, dimers, and contiguous dimers. AK is present in protozoans, protostome and deuterostome invertebrates, and protochordates, but not in craniates. Recently, a dimeric mitochondrial creatine kinase (MtCK) and a protoflagellar creatine kinase (protoflgCK) have been cloned and sequenced from the demosponge Tethya aurantia (Sona et al. 2004) and AK has been cloned and sequenced from the demosponge Suberites domuncula (Perovic-Ottstadt et al. 2005). Based on this earlier work we have surveyed all three classes of the poriferans, arguably the most primitive, basal metazoans, for the presence of CK and AK using spectrophotometric assays of tissue extracts as well as molecular biology protocols. Total RNA was isolated from three demosponges and three hexactinellids. RT-PCR was performed and cDNAs were amplified consisting of both mitochondrial and protoflagellar CK isoforms for two demosponges and two out of three hexactinellids tested. A gene for protoflgCK was amplified from a third hexactinellid. AKs were amplified from two demosponges and one hexactinellid. Our results show that AK is widely distributed in all three sponge classes. CK is present in two of the sponge classes and the genes for the mitochondrial and protoflagellar isoforms evolved prior to the divergence of the hexactinellids. It is highly probable that CK evolved in the sponges or in their immediate ancestors, the urmetazoans, or possibly even earlier. The deduced amino acid sequences from the amplified cDNAs were aligned and used in phylogenetic analyses along with CKs from other invertebrates and vertebrates and AKs from protozoans, invertebrates, and protochordates to elucidate the early evolution of the CK and AK gene families. Maximum Likelihood analysis using PHYLIP produced a CK tree with two distinct clades: mitochondrial and cytoplasmic-protoflagellar-flagellar. Using an outgroup composed of AKs, GKs, LKs, and TKs for evolutionary direction, our tree suggests that the ancestral CK dimer was MtCK-like and strongly suggests that the MtCK isoform was the first to evolve. Cyt, protoflg, and flgCK are closely related as well and phylogenetic evidence supports the idea that protoflgCKs are ancestral to flgCKs. The phylogenetic analysis completed in this effort provides the strongest evidence yet for a gene duplication event producing the true CytCKs and protoflgCKs. Maximum Likelihood analysis produced an AK tree with a base of protozoan, poriferan, and cnidarian AKs, and a clade of higher ecdysozoan and lophotrochozoan invertebrate AKs. To supplement this phylogenetic data and to further understand the early evolution of the CK isoforms, genomic DNA was isolated from Suberites ficus and the mitochondrial and protoflagellar genes were amplified by PCR. The gene organization data provides additional support that protoflgCKs are ancestral to flgCKs and that MtCKs are highly conserved in terms of their intron:exon organization. The present effort focuses on the distribution and early evolution of AK and CK in the poriferans, the pattern of gene duplication and divergence responsible for CK isoform diversity, and the development of intracellular targeting. The location and physiological roles of AK and CK will also be hypothesized and well as examining the utility of CK and AK as characters for sponge systematics. We will also explore structure-function relationships of these proteins and propose an evolutionary pathway for phosphagen kinases. / A Thesis Submitted to the Department of Biological Science in Partial Fulfillment of the Requirements for the Degree of Master of Science. / Spring Semester, 2006. / March 31, 2006. / Molecular Evolution / Includes bibliographical references. / W. Ross Ellington, Professor Directing Thesis; Gavin J. P. Naylor, Committee Member; Janie Wulff, Committee Member.

Understanding the success of the human species is central to evolutionary anthropology. While we share many traits with our relatives the great apes, only humans migrated to all corners of the earth and domesticated other species, leading to the emergence of complex societies. Investigations into human genomes have shown that they are a rich source of information for insights into our past. However, for a complete understanding of human evolution it is necessary to look beyond our own genomes. This thesis is about using comparative genomics to place human evolution within a wider context by studying adaptation in our closest living relatives and in the species that we domesticated. In the first study, I investigate the genetic changes involved in the earliest stages of dog domestication. Using a global sample of dog and wolf genomes I identify regions that are highly diverged between these species. I find that selection in the initial stages of dog domestication likely involved genes involved in the fight-or-flight response, advancing our understanding of this process. In the second study, I look for commonalities in the genetic changes that occurred during animal domestication across species. I compare genome sequences from experimentally and historically domesticated species. I identify genes and variants that may underlie the phenotypic changes that occurred during domestication. I find evidence of biological pathways that appear to always be involved in the domestication process. In the third study, I characterise the signatures of natural selection in all major Hominidae lineages using population genomic data. I find that most signatures of positive selection are species specific, although some loci appear to be selected across several lineages. I determine that the efficacy of selection varies between species and is significantly correlated with long-term effective population size. These results contribute to a more complete understanding of human evolution. i This thesis is based on the following manuscripts: 1. Cagan A & Blass T. (2016) Identification of genomic variants putatively targeted by selection during dog domestication. BMC Evolutionary Biology,16:1. 2. Cagan A, Albert FW, Plyusnina I, Trut L, Renaud G, Romagné F, Wiebe V, Kozhemjakina R, Gulevich R, Trapezov O, Yudin N, Alekhina T, Aitnazarov R, Trapezova L, Herbeck Y, Schöneberg T, Pääbo S. Genes and pathways selected during animal domestication. Submitted to eLife. 3. Cagan A, Theunert C, Laayouni H, Santpere G, Pybus M, Casals F, Prüfer K, Navarro A, Marques-Bonet T, Bertranpetit J, Andrés AM. (2016). Natural Selection in the Great Apes. Molecular Biology and Evolution, 33:3268-3283.:Summary 1 Zusammenfassung 8 Chapter 1 Identification of genomic variants putatively targeted by selection during dog domestication 16 Chapter 2 Genes and pathways selected during animal domestication 38 Chapter 3 Natural Selection in the Great Apes 73 References 149 Acknowledgments 152 Curriculum Vitae 153 Declaration of Independence 156 Author Contribution Statements 157

Estimates of the time-varying standard deviation of the surface EMG signal (EMGσ) are extensively used in the field of EMG-torque estimation. The use of a whitening filter can substantially improve the accuracy of EMGσ estimation by removing the signal correlation and increasing the statistical bandwidth. However, a subject-specific whitening filter which is calibrated to each subject, is quite complex and inconvenient. To solve this problem, we first calibrated a 60th-order “Universal” FIR whitening filter by using the ensemble mean of the inverse of the square root of the power spectral density (PSD) of the noise-free EMG signal. Pre-existing data from elbow contraction of 64 subjects, providing 512 recording trials were used. The test error on an EMG-torque task based on the “Universal” FIR whitening filter had a mean error of 4.80% maximum voluntary contraction (MVC) with a standard deviation of 2.03% MVC. Meanwhile the subject-specific whitening filter had performance of 4.84±1.98% MVC (both have a whitening band limit at 600 Hz). These two methods had no statistical difference. Furthermore, a 2nd-order IIR whitening filter was designed based on the magnitude response of the “Universal” FIR whitening filter, via the differential evolution algorithm. The performance of this IIR whitening filter was very similar to the FIR filter, with a performance of 4.81±2.12% MVC. A statistical test showed that these two methods had no significant difference either. Additionally, a complete theory of EMG in additive measured noise contraction modeling is described. Results show that subtracting the variance of whitened noise by computing the root difference of the square (RDS) is the correct way to remove noise from the EMG signal.

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