<p>The neocortex expanded spectacularly during human origins. That expansion is thought to form the foundation for our cognitive faculties underlying abstract reasoning and socialization. The human neocortex differs from that of other great apes in several notable regards including altered cell cycle, prolonged corticogenesis, and massively increased size. However, despite decades of effort, little progress has been made in uncovering the genetic contributions that underlie these differences that distinguish our species from closely related primate, such as chimpanzees. A subset of highly conserved non-coding regions that show rapid sequence changes along the human lineage are candidate loci for the development and evolution of uniquely human traits. Several studies have identified human-accelerated enhancers, but none have linked an expression difference to a organismal traits, such as brain sizes. Here we report the discovery of a human-accelerated regulatory enhancer (HARE5) near the Wnt receptor FRIZZLED-8 (FZD8). Using a variety of approaches, we demonstrate dramatic differences in human and chimpanzee HARE5 activity, with human HARE5 driving significantly strong expression. We show that HARE5 likely regulates FZD8 and that expression differences influence cell cycle kinetics, cortical layers, and brain size. At present, this would provide the first evidence of a human-chimpanzee genetic difference influencing the evolution of brain size.</p> / Dissertation

<p>For primates, and other arboreal mammals, adopting suspensory locomotion represents one of the strategies an animal can use to prevent toppling off a thin support during arboreal movement and foraging. While numerous studies have reported the incidence of suspensory locomotion in a broad phylogenetic sample of mammals, little research has explored what mechanical transitions must occur in order for an animal to successfully adopt suspensory locomotion. Additionally, many primate species are capable of adopting a highly specialized form of suspensory locomotion referred to as arm-swinging, but few scenarios have been posited to explain how arm-swinging initially evolved. This study takes a comparative experimental approach to explore the mechanics of below branch quadrupedal locomotion in primates and other mammals to determine whether above and below branch quadrupedal locomotion represent neuromuscular mirrors of each other, and whether the patterns below branch quadrupedal locomotion are similar across taxa. Also, this study explores whether the nature of the flexible coupling between the forelimb and hindlimb observed in primates is a uniquely primate feature, and investigates the possibility that this mechanism could be responsible for the evolution of arm-swinging. </p><p> To address these research goals, kinetic, kinematic, and spatiotemporal gait variables were collected from five species of primate (Cebus capucinus, Daubentonia madagascariensis, Lemur catta, Propithecus coquereli, and Varecia variegata) walking quadrupedally above and below branches. Data from these primate species were compared to data collected from three species of non-primate mammals (Choloepus didactylus, Pteropus vampyrus, and Desmodus rotundus) and to three species of arm-swinging primate (Hylobates moloch, Ateles fusciceps, and Pygathrix nemaeus) to determine how varying forms of suspensory locomotion relate to each other and across taxa. </p><p> From the data collected in this study it is evident the specialized gait characteristics present during above branch quadrupedal locomotion in primates are not observed when walking below branches. Instead, gait mechanics closely replicate the characteristic walking patterns of non-primate mammals, with the exception that primates demonstrate an altered limb loading pattern during below branch quadrupedal locomotion, in which the forelimb becomes the primary propulsive and weight-bearing limb; a pattern similar to what is observed during arm-swinging. It is likely that below branch quadrupedal locomotion represents a “mechanical release” from the challenges of moving on top of thin arboreal supports. Additionally, it is possible, that arm-swinging could have evolved from an anatomically-generalized arboreal primate that began to forage and locomote below branches. During these suspensory bouts, weight would have been shifted away from the hindlimbs towards forelimbs, and as the frequency of these boats increased the reliance of the forelimb as the sole form of weight support would have also increased. This form of functional decoupling may have released the hindlimbs from their weight-bearing role during suspensory locomotion, and eventually arm-swinging would have replaced below branch quadrupedal locomotion as the primary mode of suspensory locomotion observed in some primate species. This study provides the first experimental evidence supporting the hypothetical link between below branch quadrupedal locomotion and arm-swinging in primates.</p> / Dissertation

<p>The evolution of reproductive strategies involves a complex calculus of costs and benefits to both parents and offspring. Many marine animals produce embryos packaged in tough egg capsules or gelatinous egg masses attached to benthic surfaces. While these egg structures can protect against environmental stresses, the packaging is energetically costly for parents to produce. In this series of studies, I examined a variety of ecological factors affecting the evolution of benthic development as a life history strategy. I used marine gastropods as my model system because they are incredibly diverse and abundant worldwide, and they exhibit a variety of reproductive and developmental strategies. </p><p>The first study examines predation on benthic egg masses. I investigated: 1) behavioral mechanisms of predation when embryos are targeted (rather than the whole egg mass); 2) the specific role of gelatinous matrix in predation. I hypothesized that gelatinous matrix does not facilitate predation. One study system was the sea slug Olea hansineensis, an obligate egg mass predator, feeding on the sea slug Haminoea vesicula. Olea fed intensely and efficiently on individual Haminoea embryos inside egg masses but showed no response to live embryos removed from gel, suggesting that gelatinous matrix enables predation. This may be due to mechanical support of the feeding predator by the matrix. However, Haminoea egg masses outnumber Olea by two orders of magnitude in the field, and each egg mass can contain many tens of thousands of embryos, so predation pressure on individuals is likely not strong. The second system involved the snail Nassarius vibex, a non-obligate egg mass predator, feeding on the polychaete worm Clymenella mucosa. Gel neither inhibits nor promotes embryo predation for Nassarius, but because it cannot target individual embryos inside an egg mass, its feeding is slow and inefficient, and feeding rates in the field are quite low. However, snails that compete with Nassarius for scavenged food have not been seen to eat egg masses in the field, leaving Nassarius free to exploit the resource. Overall, egg mass predation in these two systems likely benefits the predators much more than it negatively affects the prey. Thus, selection for environmentally protective aspects of egg mass production may be much stronger than selection for defense against predation. </p><p>In the second study, I examined desiccation resistance in intertidal egg masses made by Haminoea vesicula, which preferentially attaches its flat, ribbon-shaped egg masses to submerged substrata. Egg masses occasionally detach and become stranded on exposed sand at low tide. Unlike adults, the encased embryos cannot avoid desiccation by selectively moving about the habitat, and the egg mass shape has high surface-area-to-volume ratio that should make it prone to drying out. Thus, I hypothesized that the embryos would not survive stranding. I tested this by deploying individual egg masses of two age classes on exposed sand bars for the duration of low tide. After rehydration, embryos midway through development showed higher rates of survival than newly-laid embryos, though for both stages survival rates over 25% were frequently observed. Laboratory desiccation trials showed that >75% survival is possible in an egg mass that has lost 65% of its water weight, and some survival (<25%) was observed even after 83% water weight lost. Although many surviving embryos in both experiments showed damage, these data demonstrate that egg mass stranding is not necessarily fatal to embryos. They may be able to survive a far greater range of conditions than they normally encounter, compensating for their lack of ability to move. Also, desiccation tolerance of embryos may reduce pressure on parents to find optimal laying substrata. </p><p>The third study takes a big-picture approach to investigating the evolution of different developmental strategies in cone snails, the largest genus of marine invertebrates. Cone snail species hatch out of their capsules as either swimming larvae or non-dispersing forms, and their developmental mode has direct consequences for biogeographic patterns. Variability in life history strategies among taxa may be influenced by biological, environmental, or phylogenetic factors, or a combination of these. While most prior research has examined these factors singularly, my aim was to investigate the effects of a host of intrinsic, extrinsic, and historical factors on two fundamental aspects of life history: egg size and egg number. I used phylogenetic generalized least-squares regression models to examine relationships between these two egg traits and a variety of hypothesized intrinsic and extrinsic variables. Adult shell morphology and spatial variability in productivity and salinity across a species geographic range had the strongest effects on egg diameter and number of eggs per capsule. Phylogeny had no significant influence. Developmental mode in Conus appears to be influenced mostly by species-level adaptations and niche specificity rather than phylogenetic conservatism. Patterns of egg size and egg number appear to reflect energetic tradeoffs with body size and specific morphologies as well as adaptations to variable environments. Overall, this series of studies highlights the importance of organism-scale biotic and abiotic interactions in evolutionary patterns.</p> / Dissertation

<p>This thesis concerns the use of protein structure to improve phylogenetic inference. There has been growing interest in phylogenetics as the number of available DNA and protein sequences continues to grow rapidly and demand from other scientific fields increases. It is now well understood that phylogenies should be inferred jointly with alignment through use of stochastic evolutionary models. It has not been possible, however, to incorporate protein structure in this framework. Protein structure is more strongly conserved than sequence over long distances, so an important source of information, particularly for alignment, has been left out of analyses.</p><p>I present a stochastic process model for the joint evolution of protein primary and tertiary structure, suitable for use in alignment and estimation of phylogeny. Indels arise from a classic Links model and mutations follow a standard substitution matrix, while backbone atoms diffuse in three-dimensional space according to an Ornstein-Uhlenbeck process. The model allows for simultaneous estimation of evolutionary distances, indel rates, structural drift rates, and alignments, while fully accounting for uncertainty. The inclusion of structural information enables pairwise evolutionary distance estimation on time scales not previously attainable with sequence evolution models. Ideally inference should not be performed in a pairwise fashion between proteins, but in a fully Bayesian setting simultaneously estimating the phylogenetic tree, alignment, and model parameters. I extend the initial pairwise model to this framework and explore model variants which improve agreement between sequence and structure information. The model also allows for estimation of heterogeneous rates of structural evolution throughout the tree, identifying groups of proteins structurally evolving at different speeds. In order to explore the posterior over topologies by Markov chain Monte Carlo sampling, I also introduce novel topology + alignment proposals which greatly improve mixing of the underlying Markov chain. I show that the inclusion of structural information reduces both alignment and topology uncertainty. The software is available as plugin to the package StatAlign. </p><p>Finally, I also examine limits on statistical inference of phylogeny through sequence information models. These limits arise due to the `cutoff phenomenon,' a term from probability which describes processes which remain far from their equilibrium distribution for some period of time before swiftly transitioning to stationarity. Evolutionary sequence models all exhibit a cutoff; I show how to find the cutoff for specific models and sequences and relate the cutoff explicitly to increased uncertainty in inference of evolutionary distances. I give theoretical results for symmetric models, and demonstrate with simulations that these results apply to more realistic and widespread models as well. This analysis also highlights several drawbacks to common default priors for phylogenetic analysis, I and suggest a more useful class of priors.</p> / Dissertation

<p>Sex determination is a critical biological process for all sexually reproducing animals. Despite its significance, evolution has provided a vast array of mechanisms by which sexual phenotype is determined and elaborated even within amniote vertebrates. The most prevalent systems of sex determination in this clade are genetic and temperature dependent sex determination. These two systems are sometimes consistent within large groups of species, such as the mammals who nearly ubiquitously utilize XY genetic sex determination, or they can be much more mixed as in reptiles that use genetic or temperature dependent systems and even both simultaneously. The turtles are a particularly diverse group in the way they determine sex with multiple different genetic and temperature based systems having been described. We investigated the nature of the temperature based sex determination system in Trachemys scripta elegans to ascertain whether it behaved as a purely temperature based system or if some other global source of sex determining information might be apparent within thermal regions insufficient to fully induce male or female development. These experiments found that sex determination in this species is much more complex and early acting than previously thought and that each gonad within an individual has the same sexual fate established enough that it can persist even without further communication between. We established a best practice for the assembly and annotation of de novo whole transcriptomes from T. scripta RNA-seq and utilized the technique to quantify the gene regulatory events that occur across the thermal sensitive period.</p><p>Evidence is entirely lacking on the resolution of TSD when eggs are incubated at the pivitol temperature in which equal numbers or males and females are produces. We have produced a timecourse data set that allowed for the elucidation of the gene expression events that occur at both the MPT and FPT over the course of the thermal sensitive period. Our data suggests that early establishment of a male or female fate is possible when temperature is sufficiently strong enough as at MPT and FPT. We see a strong pattern of mutually antagonistic gene expression patterns emerging early and expanding over time through the end of the period of gonad plasticity. In addition, we have identified a strong pattern of differential expression in the early embryo at stages prior to the formation of the gonad. Even without the known systemic signaling attributed to sex hormones emanating from the gonad, the early embryo has a clear male and female gene expression pattern. We discuss how this early potential masculinization or feminization of the embryo may indicate that the influence of temperature may extend beyond the determination of gonadal sex or even metabolic adjustments and how this challenges the well-defined paradigm in which gonadal sex determines peripheral sexual characteristics.</p> / Dissertation

<p>How organisms adapt and survive in continuously fluctuating environments is a central question of evolutionary biology. Additionally, organisms have to deal with the inherent stochasticity in all cellular processes. The purpose of this thesis is to gain insights into how organisms can use epigenetics and the stochasticity of gene expression to deal with a fluctuating environment. To accomplish this, two cases at different temporal and structural scales were explored: (1) the early transcriptional response to an environmental stimulus in single cells, and (2) the evolutionary dynamics of a population adapting to a recurring fluctuating environment. Mathematical models of stochastic gene expression, population dynamics, and evolution were developed to explore these systems.</p><p>First, the information available in sparse single cell measurements was analyzed to better characterize the intrinsic stochasticity of gene expression regulation. A mathematical and statistical model was developed to characterize the kinetics of a single cell, single gene behavior in response to a single environmental stimulus. Bayesian inference approach was used to deduce the contribution of multiple gene promoter states on the experimentally measured cell-to-cell variability. The developed algorithm robustly estimated the kinetic parameters describing the early gene expression dynamics in response a stimulus in single neurons, even when the experimental samples were small and sparse. Additionally, this algorithm allowed testing and comparing different biological hypotheses, and can potentially be applied to a variety of systems.</p><p>Second, the evolutionary adaptation dynamics of epigenetic switches in a recurrent fluctuating environment were studied by observing the evolution of gene regulatory circuit in a population under multiple environmental cycles. The evolutionary advantage of using epigenetics to exploit the natural noise in gene expression was tested by competing this strategy against the classical genetic adaptation through mutations in a variety of evolutionary conditions. A trade-off between minimizing the adaptation time after each environmental transition and increasing the robustness of the phenotype during the constant environment between transitions was observed. Surviving lineages evolved bistable, epigenetic switching to adapt quickly in fast fluctuating environments, whereas genetic adaptation with high robustness was favored in slowly fluctuating environments.</p> / Dissertation

Parental care is important to offspring survival in many species. Because care benefits young and is often costly to parents, it can generate fitness trade-offs that influence the evolution of family life. In particular, interactions within families are predicted to generate variation in care, which in turn causes selection on traits used to give, receive, and influence care. My dissertation examines whether such socially dynamic processes have influenced the evolution of parental and embryo behavior in glassfrogs (Centrolenidae). These Neotropical frogs have terrestrial eggs, aquatic larvae, and multiple origins of male-only care. Embryos can plastically alter hatching age, which might allow them to adaptively respond to variation in egg care. I test for parent–embryo coevolution by combining field observations (40 species), experiments (8 species), and phylogenetic comparative analyses. First, I test historical and functional hypotheses of parental care evolution. I found that uniparental egg-care is ubiquitous in centrolenids, can be provided by either sex, and benefits young. Elaborate male-only care evolved repeatedly from simpler female-only care, a pattern consistent with constraints on female-care levels. Second, I examine the diversification of male-only care, testing whether maternal changes to egg-clutch traits influence embryo dependency and if such changes are associated with male-only care. Evidence indicates that reduced female expenditure on egg-jelly evolved with, and increases the importance of, elaborate male care. Next, I evaluate whether embryos respond to behavioral and evolutionary changes in parenting. Embryos behaviorally delay hatching when parents continue caring, and evidence indicates that evolutionary increases in hatching plasticity evolved with increases in care duration. I tested if male mating success causes variation in male care, and thereby influences embryo behavior. I found that increased mating success extends male care, making nests safer, and embryos delay hatching accordingly. Finally, I examine selective tradeoffs influencing hatching plasticity by measuring hatchling phenotypes and fitness correlates. Across species, delayed hatching provides performance benefits during the larval stage. Overall, my work reveals coevolutionary interactions among mothers, fathers, and embryos. It supports that embryos respond to parentally mediated changes in egg environments and elucidates how family life alters selection on parental and embryo traits.

abstract: Weevils are among the most diverse and evolutionarily successful animal lineages on Earth. Their success is driven in part by a structure called the rostrum, which gives weevil heads a characteristic "snout-like" appearance. Nut weevils in the genus Curculio use the rostrum to drill holes into developing fruits and nuts, wherein they deposit their eggs. During oviposition this exceedingly slender structure is bent into a straightened configuration - in some species up to 90° - but does not suffer any damage during this process. The performance of the snout is explained in terms of cuticle biomechanics and rostral curvature, as presented in a series of four interconnected studies. First, a micromechanical constitutive model of the cuticle is defined to predict and reconstruct the mechanical behavior of each region in the exoskeleton. Second, the effect of increased endocuticle thickness on the stiffness and fracture strength of the rostrum is assessed using force-controlled tensile testing. In the third chapter, these studies are integrated into finite element models of the snout, demonstrating that the Curculio rostrum is only able to withstand repeated, extreme bending because of modifications to the composite structure of the cuticle in the rostral apex. Finally, interspecific differences in the differential geometry of the snout are characterized to elucidate the role of biomechanical constraint in the evolution of rostral morphology for both males and females. Together these studies highlight the significance of cuticle biomechanics - heretofore unconsidered by others - as a source of constraint on the evolution of the rostrum and the mechanobiology of the genus Curculio. / Dissertation/Thesis / Doctoral Dissertation Evolutionary Biology 2009

<p>Speciation has occurred countless times throughout history, and yet the genetic mechanisms that lead to speciation are still missing pieces. Here, we describe the genetics of two processes that can act alone or together to cause speciation: hybrid sterility and meiotic drive. We use the <italic>Drosophila pseudoobscura/D, persimilis</italic> species as a model system to study these processes. We expanded on a prior study and saw little variation in strength of previously known hybrid sterility alleles between distinct strains of <italic>D. persimilis</italic> and the Bogota subspecies of <italic>D. pseudoobscura</italic>. Introgression of an autosomal, noninverted hybrid sterility allele from the USA subspecies of <italic>D. pseudoobscura</italic> into <italic>D. persimilis</italic> demonstrated that the <italic>D. pseudoobscura</italic> copy of a <italic>D. persimilis</italic> hybrid sterility factor also causes hybrid male sterility in a <italic>D. pseudoobscura bogotana</italic> background. This allelism suggests that the introgressed allele is ancestral, but was lost in the Bogota lineage, or that gene flow between <italic>D. pseudoobscura</italic> USA and <italic>D. persimilis</italic> moved the sterility-conferring allele from <italic>D. persimilis</italic> into <italic>D. pseudoobscura</italic>. To further understand the genetic basis of speciation, we asked if meiotic drive in <italic>D. persimilis</italic> is associated with hybrid sterility seen in <italic>D. persimilis/D. pseudoobscura</italic> hybrids. QTL mapping of both traits along the right arm of the X chromosome, where both drive and hybrid sterility loci are found, suggest that some of the causal loci overlap and may be allelic.</p> / Dissertation

<p>Morphological characters from the gametophyte and sporophyte generations have been used in land plants to infer relationships and construct classifications, but sporophytes provide the vast majority of data for the systematics of vascular plants. In bryophytes both generations are well developed and characters from both are commonly used to classify these organisms. However, because morphological traits of gametophytes and sporophytes can have different genetic bases and experience different selective pressures, taxonomic emphasis on one generation or the other may yield incongruent classifications. The moss order Hookeriales has a controversial taxonomic history because previous classifications have focused almost exclusively on either gametophytes or sporophytes. The Hookeriales provide a model for comparing morphological evolution in gametophytes and sporophytes, and its impact on alternative classification systems. Sometimes, placement of certain groups within Hookeriales remains challenging even at the molecular level. That is the case of the genus <italic>Calyptrochaeta</italic>. We study diversification dynamics in this genus to elucidate possible mechanisms obscuring its placement and we address biogeographic questions using the Tropical Conservatism scenario as our null hypothesis. Furthermore, to better understand biogeographic patterns in the Southern Hemisphere, infraspecific molecular patterns are compared in two species of the genus <italic>Calyptrochaeta</italic> (i.e., <italic>C. apiculata</italic> and <italic>C. asplenioides</italic>) and vicariance and recent long distance dispersal are tested to explain the disjunct distributions observed in these species. </p><p>In this study we reconstruct relationships among pleurocarpous mosses in or associated to the Hookeriales, in <italic>Calyptrochaeta</italic>, and within <italic>Calyptrochaeta</italic>. Six molecular markers are explored in total from all three genome compartments to reconstruct the evolution of morphological characters and habitat preferences in our phylogenies. Divergence times are estimated in a Bayesian framework using a relaxed molecular clock, and diversification rates are calculated on the chronograms resulting from these estimations. </p><p>As a result, we found that the Hookeriales, as currently circumscribed, are monophyletic and that both sporophyte and gametophyte characters are labile. We documented parallel changes and reversals in traits from both generations. We show that diversification rates in <italic>Calyptrochaeta</italic> have changed through its history. Also, though we lack support to clearly reject the tropical conservatism hypothesis, our data point to a more complex scenario where both temperate and tropical species can be ancient and give rise to one another, since shifts between tropical and temperate regions seem to be possible in any direction. Finally, we have show that recent long distance dispersal best explains the distribution of both <italic>C. apiculata</italic> and <italic>C. asplenioides</italic> in the Southern Hemisphere.</p> / Dissertation