To maintain high average fitness, populations must effect selection against the deleterious mutations that continuously arise de novo. Theoretical models of mutation-selection balance predict that the maximum tolerable mutation rate is much lower for organisms growing in colonies than for those in well-mixed liquid media due to drift imposed by competition for position along the growing colony front. Simplifying assumptions made in these models, including the irreversibility and fixed fitness cost of mutations, do not strictly hold in extant species. To explore the applicability of these models in natural contexts, we have constructed a yeast strain which undergoes recombinase-mediated irreversible gene excision at a single locus with tunable fitness cost, but also possesses the random genomic mutation profile characteristic of yeast. We find that several theoretical predictions hold for our strain, including the dependence of maximum tolerable mutation rate on growth condition and selective coefficient. These results constitute the first direct biological test of mutation-selection balance theory.

This dissertation investigates the embryonic specification of a specific group of cells: the germ cells. Germ cells, which give rise to sperm and egg, are the only cells in sexually-reproducing animals that directly contribute hereditary information to the next generation. Germ cells are therefore a universal cell type across animals, and represent a profound novelty that likely arose near the base of the animal phylogeny. Yet despite their conserved, essential function in all animals, there is surprising diversity in the mechanisms that specify these cells during embryonic development. In this dissertation, I address the diversity of germ cell specification mechanisms in insects. I focus on two species, the milkweed bug Oncopeltus fasciatus (Hemiptera) and the cricket Gryllus bimaculatus (Orthoptera), which both branch basally to the Holometabola (those insects which undergo metamorphosis, including the well-studied fruit fly Drosophila melanogaster), and thus provide important phylogenetic breadth to our understanding of germ cell specification across insects. Using functional genetic approaches, I show that germ cell specification in both Oncopeltus and Gryllus differs fundamentally from germ cell specification in Drosophila. Specifically, I provide evidence that germ cells arise via inductive cell signaling during mid-embryogenesis, rather than via maternally-supplied cytoplasmic determinants localized in the oocyte, as is the case for Drosophila. These data suggest that Drosophila employs an evolutionarily derived mode of germ cell specification. In further support of this hypothesis, I show that several of the genes required for Drosophila germ cell specification perform other functions in both Oncopeltus and Gryllus. I demonstrate that one of these genes, oskar, which is the only gene both necessary and sufficient for germ cell specification in Drosophila, instead functions in nervous system of the cricket, both during embryonic development and in the adult brain. I suggest that the evolution of the derived mode of germ cell specification seen in Drosophila may have involved co-opting oskar into the germ cell specification pathway from an ancestral role in the nervous system.

Abstract: Archosauria, the "ruling reptiles," characterized along their stem by relatively large, macrocarnivorous animals, are today represented by two enormously successful but divergent extant clades: Aves, the birds, and Crocodylia, the crocodiles and alligators. This thesis seeks to characterize major transformations in the cranial region of archosaurs, a prominent theme in their evolution.

Sexual imprinting, the process of learning mate preferences at a young age, could promote speciation by reducing attraction to individuals from divergent populations or species, consequently creating or maintaining reproductive isolation. Yet, despite the documentation of sexual imprinting in many taxa, its connection to speciation has been understudied. I chose to explore the potential link between sexual imprinting and reproductive isolation and in two North American rodents--the white-footed mouse (Peromyscus leucopus) and its sister species, the cotton mouse (Peromyscus gossypinus). These species have overlapping distributions in nature, possibly allowing interbreeding and admixture. In Chapter 1, I used double-digest restriction-associated DNA sequencing to test for hybridization in sympatric natural populations and found that 1.5% of sampled individuals showed evidence of admixture yet the species have maintained genetic distinctness in sympatry. In the lab, the species hybridize when given no choice of mates but mate more readily with conspecifics, suggesting that mating preferences may prevent hybridization in the wild. In Chapter 2, I tested whether mating preferences create significant reproductive isolation. I measured mating preferences in controlled laboratory conditions and found that both species and sexes preferred conspecific to heterospecific mates in 85% of trials. I then raised offspring with foster parents of the opposite species and found that P. leucopus has a genetically-determined preference while P. gossypinus learns its preference. In Chapter 3, I tested whether sexual imprinting on parental diet could generate assortative mating within a species. I tested this hypothesis by feeding P. gossypinus parents either orange- or garlic-flavored water, thereby exposing their offspring to these flavors through their parents until weaning. I tested the preferences of these offspring as adults and found that P. gossypinus, especially females, had strong assortative mating preferences. This implies that at least females learn parental dietary information and that assortative mating could evolve within a single generation. Together, my results confirm that sexual imprinting on parental traits--possibly mediated through dietary differences--can create assortative mating capable of generating sexual isolation and reducing gene flow between species. My research supports the importance of mating preferences and learning in speciation.

<p>Islands have been the inspiration for some of evolutionary biology's most important advances. This is largely due to the unique properties of islands that promote the differentiation of island species from their mainland counterparts. Rodents are widely distributed across even the most remote islands, a rarity among mammals, making them uniquely suited to study the factors leading to the divergence of insular species. In this dissertation, I use two case studies to examine the morphological and genetic divergences that take place in an insular environment.</p><p>In chapters one and two, I examine how different factors influence insular body size change in rodents. In chapter one, I examine factors influencing the direction of island body size change using classification tree and random forest (CART) analyses. I observe strong consistency in the direction of size change within islands and within species, but little consistency at broader taxonomic scales. Including island and species traits in the CART analyses, I find mainland body mass to be the most important factor influencing size change. Other variables are significant, though their roles seem to be context-dependent.</p><p>In chapter two, I use the distributions of mainland rodent population body sizes to identify `extreme' insular rodent populations and compare traits associated with those populations and their islands with those island populations of a more typical size. I find that althought there is no trend among all insular rodents towards a larger or smaller size, `extreme' populations are more likely to increase in size. Using CART methods, I develop a predictive model for insular size change that identifies resource limitations as the main driver when insular rodent populations become `extremely small'. </p><p>Chapters three and four shift their focus to a single rodent species, the deer mouse <italic>Peromyscus maniculatus</italic>, as they examine the genetic differentiation of deer mice across the California Channel Islands and the nearby mainland. In chapter three, I sequence a region of the mitochondrial control region for individuals from 8 populations across the northern Channel Islands and two mainland sites, and I analyze these sequences by calculating population genetics parameters and creating a Bayesian inference tree and a statistical parsimony haplotype network. All of these analyses reveal significant divergences between island and mainland populations. Among the islands, Santa Barbara and Anacapa islands both display unique genetic signatures, but the other northern islands remain relatively undifferentiated.</p><p>In chapter four, I genotype individuals from the previous chapter at 5 microsatellite loci, I calculate additional population genetics parameters and I utilize a Bayesian clustering algorithm to examine the similarities and differences between nuclear and mitochondrial analyses. I find the nuclear data to be largely congruent with the mitochondrial analyses; there are significant differences between island and mainland populations, and Anacapa Island is significantly differentiated from the other islands. Unlike the previous analyses, Santa Barbara Island is not significantly different from the northern islands, yet San Miguel Island has a unique genetic signature. </p><p>These studies underscore the importance of ecological processes and historical biogeography in the generation of diversity, and they highlight the role of islands as drivers of evolutionary divergence.</p> / Dissertation

<p>In an attempt to gain more insight on functional evolution of cAMP-PKA pathway I have taken a comparative approach and examined functional interactions of cAMP-PKA signaling in well-studied yeast developmental programs and closely related <italic>Saccharomyces sensu stricto<italic/>. species. I have shown that variation in cAMP-PKA signaling contributes significantly to variation in developmental responses in <italic>S cerevisiae. Variation in pseudohyphal growth and sporulation, two inversely correlated developmental strategies to nutrient limitation in yeast, proportional to variation in intracellular cAMP levels. <italic>S. cerevisiae strains proficient in pseudohyphal growth have higher intracellular cAMP concentrations relative to strains that sporulate efficiently. Phenotypic, genetic and signaling data presented here suggest that the cAMP-PKA signaling underlies a phenotypic trade-off between sporulation and pseudohyphal growth in <italic>S. cerevisiae<italic/>.</p><p>Further investigation into the role of cAMP-PKA signaling in closely related <italic>S paradoxus<italic/> and <italic>S bayanus revealed an antagonistic function of cAMP-PKA signaling for developmental responses in <italic>S. bayanus. Unlike in <italic>S. cerevisiae, increased cAMP concentrations surprisingly inhibit pseudohyphal response in <italic>S. bayanus<italic/>. Another unanticipated finding in this work is that in <italic>S. bayanus<italic/>. Flo11, required for pseudohyphal differentiation in S. cerevisiae, is dispensable. Additionally, interactions of cAMP-PKA signaling and the general-stress response mechanism appear reversed in <italic>S. bayanus<italic/>. As shown by deletion mutation, gene expression and pharmacological treatment data, altered interactions and alternative targets downstream of cAMP-PKA could critically contribute to alternative regulation of nutrient-induced development in <italic>S. bayanus<italic/>.</p><p>Intracellular cAMP concentrations show decaying oscillations upon glucose replenishment in derepressed yeast cells. The quantitative characteristics of oscillations are distinct within and between Saccharomyces species. Given the tight regulation of cAMP levels and its critical role, the variation in cAMP oscillatory dynamics could be reflective of differential interactions of cAMP-PKA signaling that also underlie induction of developmental programs to changing environments. As such, intracellular cAMP levels and dynamics could potentially be used as molecular phenotypes.</p> / Dissertation

<p>This dissertation examines the processes that generate phenotypic variation in life cycles in seasonal environments. Collectively, a life cycle describes the stages an organism passes through during a generation. The timing, or phenology, of these transitions is often influenced by both environmental and allelic variation. Using the model organism Arabidopsis thaliana and both empirical and modeling approaches, I examine how correlations between life-cycle transitions, environment-dependent allelic effects, and epistasis generate patterns of life-cycle variation both within and between generations. In my first chapter, I use experiments to determine that many combinations of genetic, environmental, and developmental factors can create similar germination phenotypes, that maternal effects can influence phenotypes more than genetic differences, and that cross-generational effects can reduce variation in germination timing despite variation in flowering and dispersal time. In my second chapter, I use a modeling approach to consider the entire life cycle. I find that environmental variation is a major driver of phenotypic variation, and that considering the known geographic distribution of allelic variation across the range improves the match of model predictions to phenotypes expressed in natural populations. Specifically, variation in dormancy generated in the previous generation is predicted to cause life-cycle differences within a location, and the geographic distribution of allelic variation in dormancy interacts with local climatic environments to canalize an annual life history across the range. Finally, I test if allelic and environmental variation that affects early life stages can influence the environment experienced during reproduction. This environment determines both the time available for reproduction and the environment experienced during senescence. By implementing simple survival rules for flowering plants in the model, I show that time available for a plant to reproduce depends on earlier phenological traits and varies widely from year to year, location to location, and genotype to genotype. If reproductive trade-offs that underlie the evolution of senescence are environmentally sensitive, these results suggest that genetic variation in earlier life-stage transitions might shape senescence rates and whether they are environmentally responsive. In sum, my dissertation demonstrates the importance of pleiotropy, environment-dependent allelic expression, and epistasis in defining life-cycle variation, and proposes a novel way of predicting these relationships and complex life cycles under seasonal conditions.</p> / Dissertation

<p>Primates in the wild face complex foraging decisions where they must assess the most valuable of different potential resources to exploit, as well recall the location of options that can be widely distributed. While differences in diet and ecology have long been thought to be an important factor influencing brain evolution in primates, it is less well understood what psychological abilities animals actually use when making foraging decisions. This dissertation examines cognitive domains that play a crucial role in supporting foraging behaviors--spatial memory and decision-making--by integrating both psychological and biological approaches to behavior. In particular, the research presented here examines multiple species of primates to address the cognitive skills that different animals use to solve foraging problems (at the proximate level of analysis), as well as why some species appear to solve such problems differently than other species (at the ultimate level of analysis).</p><p>The first goal of the dissertation is to compare closely-related species that vary in ecological characteristics, in order to illuminate how evolution shapes the cognitive skills used in foraging contexts. This component focuses on comparisons between chimpanzees (Pan troglodytes) and bonobos (Pan paniscus), humans' closest extant relatives. In addition, this component reports comparisons amongst strepsirrhines (Lemur catta, Eulemur mongoz, Propithecus coquereli, and Varecia subsp.) to model cognitive evolution in a taxonomic group with greater ecological diversity than Pan. The first two chapters test the hypothesis that more frugivorous species exhibit more accurate spatial memory skills, first by comparing apes' spatial memory abilities (Chapter 2), and then by comparing four species of lemurs on a related set of spatial memory tasks (Chapter 3). In subsequent chapters, I examine apes' decision-making strategies to test the hypothesis that chimpanzees are more willing to pay decision-making costs than are bonobos, due to differences in their feeding ecology. I focus on preferences about the timing of payoffs (Chapter 4); preferences about risk, or the variability in payoffs (Chapters 4 and 5); and preferences about ambiguity, or knowledge about available options (Chapter 6). </p><p>The second goal of the dissertation is to compare the psychological mechanisms that human and nonhuman great apes use for foraging, in order to identify potentially human-unique cognitive abilities. In terms of spatial memory, I examine whether other apes also exhibit human-like patterns of spatial memory development (Chapter 2). In terms of decision-making, I examine whether apes exhibit a suite of human-like biases when making value-based choices. In particular, I test whether emotional and motivational processes, which are critical components of human decision-making, also play a role in apes' choices (Chapters 4); whether apes are sensitive to social context when making economic decisions (Chapter 5); and whether apes are sensitive to their degree of knowledge when making choices under uncertainty (Chapter 6). Finally, I directly compare human and ape preferences on a matched task to assess whether humans use any unique psychological abilities when making decisions about risk (Chapter 7). In sum, this dissertation links studies of mechanism with hypotheses about function in order to illuminate the evolutionary roots of human's unique cognitive phenotype.</p> / Dissertation

abstract: Given the success of science, weak forms of mind-brain dependence are commonly treated as uncontroversial within contemporary philosophies of mind. More controversial are the different metaphysical claims inferred from this dependence, many ascribing ontological priority to the brain. Consider the following three propositions: (i) neurological events are essentially identified by their role in material systems, laws, and causes that are constitutively non-rational; (ii) at least some mental events are essentially identified in virtue of their role in the use of reason; (iii) all mental events are realized by, identical to, or composed out of, neurological events. (i) is uncontroversial. However, (iii) is strictly materialistic. (i), (ii) and (iii) taken together appear incoherent. A fruitful task for philosophy is to resolve this apparent incoherence. In his 1997 book The Last Word Thomas Nagel offers an explication of reason that conceptually transcends the nature of material substrate. In his 2010 article "Modest Dualism" Tyler Burge offers reasons to think of propositional thought as irreducible to the concepts of the material sciences. Both focus on rationality as a unique form of intentionality. Both philosophers also reject materialism (iii). On their accounts it's reasonable to take 'rational intentionality' as exhibiting a logical priority of the mind with respect to the brain in inquiries into the nature of mind. Granting this, the diminished conception of mind presupposed by prevailing contemporary theories is seen to be the result of a more general failure to recognize the logical priority and intricate nature of rationality. The robust views of rationality expressed by Nagel and Burge constitute grounds for argument against even the weakest form of materialism. I develop such an argument in this thesis, showing that the propositional attitudes exhibited in thought and speech preclude all materialistic notions of mind. Furthermore, I take the nature of propositional attitudes to suggest a perspective for exploring the fundamental nature of mind, one that focuses not on composition but on rational powers. / Dissertation/Thesis / M.A. Philosophy 2011

abstract: The pattern and strength of genetic covariation is shaped by selection so that it is strong among functionally related characters and weak among functionally unrelated characters. Genetic covariation is expressed as phenotypic covariation within species and acts as a constraint on evolution by limiting the ability of linked characters to evolve independently of one another. Such linked characters are "constrained" and are expected to express covariation both within and among species. In this study, the pattern and magnitude of covariation among aspects of dental size and shape are investigated in anthropoid primates. Pleiotropy has been hypothesized to play a significant role in derivation of derived hominin morphologies. This study tests a series of hypotheses; including 1) that negative within- and among-species covariation exists between the anterior (incisors and canines) and postcanine teeth, 2) that covariation is strong and positive between the canines and incisors, 3) that there is a dimorphic pattern of within-species covariation and coevolution for characters of the canine honing complex, 4) that patterns of covariation are stable among anthropoids, and 5) that genetic constraints have been a strong bias on the diversification of anthropoid dental morphology. The study finds that patterns of variance-covariance are conserved among species. Despite these shared patterns of variance-covariance, dental diversification has frequently occurred along dimensions not aligned with the vector of genetic constraint. As regards the canine honing complex, there is no evidence for a difference in the pleiotropic organization or the coevolution of characters of the complex in males and females, which undermines arguments that the complex is selectively important only in males. Finally, there is no evidence for strong or negative pleiotropy between any dental characters, which falsifies hypotheses that predict such relationships between incisors and postcanine teeth or between the canines and the postcanine teeth. / Dissertation/Thesis / Ph.D. Anthropology 2011