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

Recent work has shown that microorganisms are surprisingly like animals in having sophisticated behaviours such as cooperation, communication, and recognition, as well as many kinds of symbioses. Here we show first that the social amoeba Dictyostelium discoideum has a primitive farming symbiosis that includes dispersal and prudent harvesting of the crop. About one-third of wild-collected clones engage in husbandry of bacteria. Instead of consuming all bacteria in their patch, they stop feeding early and incorporate bacteria into their fruiting bodies. They then carry bacteria during spore dispersal and can seed a new food crop, which is a major advantage if edible bacteria are lacking at the new site. However, if they arrive at sites already containing appropriate bacteria, the costs of early feeding cessation are not compensated, which may account for the dichotomous nature of this farming symbiosis. We also observed farmer Dictyostelium discoideum clones carry bacteria that they do not use as food. We hypothesized that these bacteria may play a defensive role against other D. discoideum clones. In our second study, we investigated the impact of these bacteria-carrying farmers on non-farming D. discoideum clones. We found that the presence of farming clones reduces spore production in non-farmers. Furthermore, this effect increases with frequency of farming clones, demonstrating the vulnerability of non-farming clones to farmers though in this experiment we had not separated the effects of the farmer clone and the bacteria they carry. In our third study we exposed non-farmers to a filtered supernatant from the most common non-food carried bacterium, Burkholderia xenovorans . This supernatant is likely to carry whatever the bacteria are producing. We treated Dictyostelium clones at the beginning of the social stage and found that the supernatant enhanced spore production of farming clones and hurt spore production of non-farming clones. This study shows that the effects of the bacteria can be restricted to a filtered supernatant alone. This discovery of symbiosis of D. discoideum with bacteria, and its impact on social interactions among D. discoideum clones will provide a fertile ground for further experiments on the evolution of sociality.

The core of sociality and one of the key forces behind the transition to multicellularity is cooperation. The study of social behavior in microorganisms has gained considerable attention in the last decade as researchers have discovered that many of the cooperative social interactions found in higher organisms can also be found in microbes. The dictyostelids are particularly amenable to the study of social evolution because of the potential for conflict and cooperation during multicellular formation. The formation of the multicellular fruiting body may lead to conflict because all nearby cells aggregate together, which may be distinct clones, each trying to increase its own fitness. I first explored how D. discoideum and D. purpureum interact and if either species looks to cheat the other when they interact. I found that both species prefer being clonal but cooperate with each other when it seems the benefits outweigh the costs. Cooperating amoebae are able to make larger fruiting bodies, which are advantageous for migration and dispersal, but both species suffer a cost in producing fewer spores per fruiting body. I next examined short-range social dispersal in the social amoebae, D. discoideum and D. purpureum. It appears that the evolutionary loss of stalked migration gives D. discoideum cells the advantage of delaying specialization and the ability to colonize more distant locations, but has significant costs due to migration distance, such as the fraction of cells that become fertile spores. In my final study, we examine the interaction of different clones of D. discoideum before and after migration. We show that chimerism and migration interact to produce fruiting bodies that have a proportionally higher spore allocation compared to clonal fruiting bodies after migration but were unable to determine whether the results that we see are an indication of clones defecting in a tragedy of the commons or more cooperation. With further study will be able to better explain the affects of cooperation on group dispersal and whether it can be used as a mechanism to reduce local competition.

<p>Speciation is a constantly ongoing process whereby reproductive isolating baririer build up over time until groups of organisms can no longer exchange genes with each other. Adaptation is thought to play a major role in the formation of these barriers, although the genetic mechanisms and geographic mode underlying the spread of barriers due to adaptive evolution is poorly understood. Critically, speciation may occur in stages through the formation of intermediate partially reproductively isolated groups. The idea of such widespread ecotypes has been the subject of great controversy over the last century. Even so, we have relatively little understanding about whether widespread ecotypes exist, wheather they are reproductively isolated, and how adaptive alleles are distributed among partially isolated groups. In this dissertation, I examined these issues in widespread coastal perennial and inland annual ecotypes of the yellow monkeyflower, Mimulus guttatus. First, I determined that coastal and inland populations comprise distinct ecotypic groups. I then determined that these ecotypes are adapted to their respective habitats through genetically based flowering time and salt tolerance differences. I assessed the genetic architecture of these adaptations through quantitative trait loci (QTL) analysis and determined the geographic distribution of the underlying alleles through latitudinally replicated mapping populations. I quantified the contribution of these loci to adaptation in the field through the incorporation of advance generation hybrids in reciprocal transplant experiments. In the process, I discovered a widespread chromosomal inversion to be involved in the adaptive flowering time and annual/perennial life-history shift among the ecotypes. Overall, the results of this study suggest that widespread reproductively isolated ecotypes can form through the spread adaptive standing genetic variation between habitats and that chromosomal rearrangements can integral to this process.</p> / Dissertation

<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

<p>What evolutionary processes and ecological patterns underlie the maintenance of asexual reproduction in natural populations? Although a vast body of literature offers theory to explain the existence of sexual and asexual reproduction, there has been little study of these forms of reproduction in the natural environment. In this dissertation I use a combination of field experiments, greenhouse studies, and genetic techniques to answer this question in the model plant system Boechera. </p><p>In Chapter 1, I review the utility of this system for studying ecological and evolutionary questions in general. Boechera offers an array of genetic and genomic tools, facilitated in part by a close evolutionary relationship with the model plant Arabidopsis thaliana, as well as undisturbed ecology and habitat that extends across much of North America. Additionally, the presence of apomixis (asexual reproduction via parthenogenetic formation of seeds) at the diploid level makes Boechera an ideal system for studying sex without the often-confounding factor of polyploidy; Boechera is one of very few plant groups in which this is possible. </p><p>In Chapter 2, I use a combination of microsatellite markers, flow cytometry, chromosome squashes, and morphological work to characterize apomixis, polyploidy, and species diversity in over 100 natural populations collected from central Idaho and western Montana. As in many other apomictic systems, I find that apomixis in Boechera is strongly linked to hybridization between species or between genetically divergent intraspecific lineages. I then explore associations between apomixis and ecological and topographical variables, as well as variables underlying differentiation between apomictic and sexual lineages. I find that ecological variables associated with apomixis are largely in congruence with the hypothesis of geographic parthenogenesis, and that geographic parthenogenesis is likely driven by the consequences of interspecific hybridization. We also find that apomixis is linked with disturbance and slope, with apomicts occurring in flatter locations than sexuals. </p><p>In Chapter 3, I use a large-scale field experiment comprising three years of data from two cohorts of sexual and asexual lineages to compare fitness between these two groups. I find that, despite herbivory levels that are much higher in apomicts than sexuals, apomictic fitness is consistently higher than sexual. Viability selection strongly favors apomicts, which results in a total fitness advantage for apomicts, despite variable fecundity selection. Selection varies in intensity between cohorts and among gardens. The results of a complementary greenhouse experiment show that the effects of herbivory differ by reproductive mode. Together, these experiments suggest that Red Queen dynamics may contribute to the coexistence of sex and asex in this group.</p><p>In Chapter 4, I use inter- and intraspecific F2 crosses to conduct a greenhouse study and a field experiment to explore the effects of hybridization and heterozygosity on fitness. I find that heterozygosity is favored in the field, with viability selection strongly favoring outcrossed over inbred lineages. However, hybridization results in lower survival, reproduction, and total fitness of interspecific F2 crosses, although hybrids that do reproduce produce more fruits than selfed parental lineages of both species, resulting in fecundity selection for hybrids. It is clear that the benefits of apomixis are due to hybridization, as hybrids are less fit overall. Evidence for both heterosis and outbreeding depression, dependent on lineage and on trait, are found in the field; these phenomena are not clearly associated with geographic distance between parental populations. Ongoing SNP genotyping will facilitate assessment of heterozygosity-fitness correlations as well as correlation of fitness and heterozygosity.</p> / Dissertation

The evolution of antibiotic resistance is shaped by interactions between genes, the chemical environment, and an antibiotic's mechanism of action. This thesis explores these interactions with experiments, theory, and analysis, seeking a mechanistic understanding of how different interactions between genes and drugs can enhance or constrain the evolution of antibiotic resistance. Chapter 1 investigates the effects of the chemical decay of an antibiotic. Tetracycline resistant and sensitive bacteria were grown competitively in the presence of tetracycline and its decay products. Antibiotic decay did not only remove selection for resistance, but long-lived decay products favored tetracycline sensitivity by inducing costly drug efflux pumps in the resistant strain. Selection against resistance by antibiotic-related compounds may contribute to the coexistence of drug-sensitive and resistant bacteria in nature. Chapter 2 investigates how genetic interactions can favor particular combinations of resistance-conferring mutations. All possible combinations of a set of trimethoprim resistance-conferring mutations in the drug's target gene were constructed and phenotyped. Incompatibilities between mutations arose in a high-order, not pairwise, manner. One mutation was found to induce this ruggedness and create a multi-peaked adaptive landscape. Chapters 1 and 2 observed that non-optimal expression of a drug resistance gene or a drug's target could compromise antibiotic resistance. Chapter 3 broadly characterizes non-optimal gene expression under antibiotic treatment, using a functional genetic screen to identify over one hundred pathways to antibiotic resistance through positive and negative changes in gene expression. Genes with the potential to confer antibiotic resistance were found to often go unused during antibiotic stress. The optimization of gene expression for drug-free growth was found to cause non-optimal expression under drug treatment, creating a situation where regulatory mutations can confer resistance by correcting errors in gene expression. Chapter 4 investigates whether it is beneficial to up-regulate the genes encoding antibiotic targets when they are inhibited. Drug target genes were quantitatively over-expressed, and drug resistance was found to not always increase, but alternatively to remain unchanged or even decrease. These diverse effects were explained by simple models that consider toxicity arising from gene over-expression, and mechanisms of drug action in which drugs induce harmful enzymatic reactions.

The major histocompatibility complex region (MHC) is a multi gene family present in all jawed vertebrates, with a fundamental role in vertebrate immunity. More than two decades of studies have resulted in the characterization of over a dozen MHC regions, and models of evolution explaining that the MHC has gradually increased in size and gene content since its origins without addressing their genomic context or the environmental selective forces. Furthermore, a compelling reconstruction of the evolutionary history of the MHC has been hampered due to phylogenetic gaps and the absence of comparative phylogenetic methods applied to comparative genomics. Here I reconstruct 320 MY of MHC evolution using 42 amniote genomes using improved gene annotations, genomic alignments and phylogenetic algorithms to reconstruct the evolution of the MHC at three levels of phylogenetic resolution. The first one describes 25 MY of evolution of the primate MHC using eight Human and four non-Human primate MHC haplotypes. Results suggests that highly dense gene segments have a strikingly conserved gene organization, and six conserved and highly rearranging segments overlap genes that are most commonly associated to disease. Phylogenomic analysis implies that the MHC has remained stable in gene content and size, with significantly increased duplication rates in the primate ancestors. The second one describes 280 MY of MHC evolution through the first characterization of reptilian MHC region, which combines mammalian, reptilian, Bird and amphibian characteristics, which favors the hypothesis of the existence of a primordial MHC in which natural killer receptors, CD1 and lectin genes co-exist. The Anolis MHC expands our understanding of the origins of the exceptionally small Bird MHC regions and provides further information about the organization and size of the ancestral amniote MHC. The third one compares 42 amniote MHC regions and map gene duplications and losses to further evaluate the mode and tempo of the evolution of the region. Comparative phylogenetic methods imply that the genomic and environmental factors affect the diversification of MHC during 320 My of evolution.