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.

<p>The aim of this project is to examine the relationships between two approaches to the measurement of life history strategies. The traditional method, termed here the biodemographic approach, measures developmental characteristics like birthweight, gestation length, inter-birth intervals, pubertal timing, and sexual debut. The alternative method under exploration, termed here the psychological approach, measures a suite of cognitive and behavioral traits such as altruism, sociosexual orientation, personality, mutualism, familial relationships, and religiosity. Although both approaches are supported by a large body of literature, they remain relatively segregated. This study draws inspiration from both views, integrating measures that assess developmental milestones, including birthweight, prematurity, pubertal timing, and onset of sexual behavior, as well as psychological life history measures such as the Mini-K and a personality inventory. Drawing on previous theoretical work on the fundamental dimensions of environmental risk, these measures are tested in conjunction with several scales assessing the stability of early environmental conditions, including both &ldquo;event-based&rdquo; measures that are defined with an external referent, and measures of internal schemata, or the predicted psychological sequelae of early events. The data are tested in a three-part sequence, beginning with the measurement models under investigation, proceeding to an exploratory analysis of the causal network, and finishing with a cross-validation of the structural model on a new sample. The findings point to exciting new directions for future researchers who seek to integrate the two perspectives. </p>

The purpose of this study is to understand the evolution and diversification of a complex of basioccipital and pharyngeal structures that are important for feeding in cypriniform fishes with special reference to Catostomidae. Fishes in the family Catostomidae are a diverse group inhabiting temperate lotic and lacustrine waters of North America and East Asia. The palatal organ is a muscular pad that forms the roof of the pharynx in catostomids and some cyprinids and functions in separating food items from inorganic debris during feeding. The basioccipital bone forms the postero-ventral part of the neurocranium and part of the skeletal base of the palatal organ. Palatal organ and basioccipital bone morphology is variable among cypriniform families and statistically significant variation exists among catostomids. Subfamily Cycleptinae has the shortest, narrowest, and thinnest palatal organ of all the subfamilies. Subfamily Ictiobinae has the thickest and widest palatal organ. Generally, the shape and size of the palatal organ in Catostominae is intermediate between the other subfamilies. Catostomids possess a ventral and posterior pharyngeal process of the basioccipital bone that is expanded into a fenestrated lattice of bony struts. The pharyngeal process is not fenestrated in cyprinids; however, its ventral portion is modified in to the masticatory plate for attachment of the chewing pad. Only catostomids and cyprinids possess a chewing pad. The chewing pad is lunate in catostomids and generally ovoid in cyprinids. A synonymy of terms used to describe the palatal organ and chewing pad of Cypriniformes is provided. Phylogenetic analysis of mitochondrial and nuclear genes resolve Catostomidae as a monophyletic group with two major clades. Of the two major clades, one comprises Catostominae and the other includes a basal Cycleptinae sister to Myxocyprininae plus Ictiobinae. The sister group of Catostomidae is uncertain because of low bootstrap support at the base of the cypriniform tree. Ancestral character state reconstruction determines that the palatal organs of Catostomidae and Cyprinidae are not homologous. The ancestor of Catostomidae had a palatal organ, fenestrated pharyngeal process, and was probably a large-bodied fish with an inferior or subterminal mouth that occupied benthic habitats / acase@tulane.edu

Complex phenotypes with genetic cause are understood through many processes, including regulatory pathways, but our evolutionary understanding of these critical structures is undermined by poor models which fail to preserve the underlying sequence structure and to incorporate population genetics. In response, this thesis builds a pathway model of evolution from its underlying sequence structure and validates it against a pertinent problem in genome evolution which uniquely leverage the developed model. Specifically, my model preserves sequence characteristics through a novel data structure and pathway-level mutation and recombination rates which are functions of sequence properties. The utility of the model is validated with a study quantifying the advantages and disadvantages of expansive non-coding DNA regions on the establishment of optimal pathways. Because the model presented in this thesis rectifies many fundamental problems in previous models, it may serve as a critical tool for future work in pathway evolution.

Hierarchy is widely observed in biological systems. In this thesis, evidence from nature is presented to show that protein interactions have became increasingly modular as evolution has proceeded over the last four billion years. The evolution of animal body plan development is considered. Results show the genes that determine the phylum and superphylum characters evolve slowly, while those genes that determine classes, families, and speciation evolve more rapidly. This result furnishes support to the hypothesis that the hierarchical structure of developmental regulatory networks provides an organizing structure that guides the evolution of aspects of the body plan. Next, the world trade network is treated as an evolving system. The theory of modularity predicts that the trade network is more sensitive to recessionary shocks and recovers more slowly from them now than it did 40 years ago, due to structural changes in the world trade network induced by globalization. Economic data show that recession-induced change to the world trade network leads to an increased hierarchical structure of the global trade network for a few years after the recession. In the study of influenza virus evolution, an approach for early detection of new dominant strains is presented. This method is shown to be able to identify a cluster around an incipient dominant strain before it becomes dominant. Recently, CRISPR has been suggested to provide adaptive immune response to bacteria. A population dynamics model is proposed that explains the biological observation that the leader-proximal end of CRISPR is more diversified and the leader-distal end of CRISPR is less diversifed. Finally, the creation of diversity of antibody repertoire is investigated. It is commonly believed that a heavy chain is generated by randomly combining V, D and J gene segments. However, using high throughput sequence data in this study, the naive VDJ repertoire is shown to be strongly correlated between individuals, which suggest VDJ recombination involves regulated mechanisms.

Dictyostelium discoideum serves as an ideal system to study social evolution because of the social stage of its lifecycle, where individuals aggregate to build a multicellular structure. However, much of its basic biology remains unknown and this limits its utility. I used three separate projects to fill these gaps. In my first project, I examined how speciation and genetic diversity affects kin discrimination using a related dictyostelid, Polysphondylium violaceum . I sequenced the ribosomal DNA of 90 clones of P. violaceum and found that P. violaceum is split into several morphologically identical groups. When allowed to cooperate in pairwise mixes, I found that some clones cooperated with others in their group, but in mixes between groups, clones did not cooperate. For my second project, I looked at whether D. discoideum has sex in natural populations. While sex has been observed in laboratory clones of D. discoideum , it is unclear whether sex occurs in natural populations, and sex can influence the evolution of traits. I used a dataset of microsatellites in 24 clones of D. discoideum to look for a decrease in linkage disequilibrium as a molecular sign of sex. Linkage disequilibrium is higher between physically close loci than between loci on different chromosomes. From this, I conclude that D. discoideum undergoes recombination in nature. Lastly, I used the genome sequence of D. discoideum to look at large scale patterns of evolution. Mutations tend to be biased towards A/T from G/C so, on average, mutations should lower the nucleotide content of sequences. The removal of these mutations, purifying selection, should preserve nucleotide content. I used the genomes of D. discoideum and Plasmodium falciparum identify classes of sequences that should be under different amounts of purifying selection and compared their nucleotide contents. In all cases, those sequences under more purifying selection had higher GC contents than sequences under less purifying selection. Looking at relative nucleotide content may thus serve as an indicator purifying selection. These three studies add insight on how cooperation works in dictyostelids as well as adding an understanding of how traits, social and otherwise, would evolve in this system.

Cooperation and cheater control have helped shape life as we know it, but there is still much to learn. A eukaryote microbial model organism, like Dictyostelium discoideum , is an excellent system for advancing our understanding. When faced with starvation, multiple genetically distinct clones of D. discoideum aggregate together to form a chimeric fruiting body with a sterile stalk that holds aloft a sorus of hardy reproductive spores. One clone may be able to cheat and form disproportionately more spores, while forcing others to form more stalk. Here we discuss the impact of genetic relatedness on cooperation, and how social actions are temporally organized and can be affected by environmental conditions. First, we documented a potential strategy for facultative cheating within chimeras. We showed that the first cells to starve, and initiate the social stage, cheat cells that starved later. In another paper, we reviewed recent studies of social microbes, which demonstrate the importance of high relatedness in the evolution of cooperation and cheater resistance. In an experimental evolution study, we tested the hypothesis that de novo cheater mutants readily evolve under low relatedness conditions. We found that the majority of our lines evolved to cheat their ancestor. Further, we studied obligate cheaters, which pose a great threat to sociality. They gain a reproductive advantage in chimeras, but cannot cooperate clonally to form fruiting bodies. Wild obligate D. discoideum cheaters have never been documented, but we found that obligate cheaters readily evolved under low relatedness conditions in the laboratory. In another study, we looked at the effects of light level on spore production in D. discoideum and Dictyostelium citrinum . Overall, more spores were produced in the light than in the dark, probably because of reduced movement and cell loss during the motile multicellular slug stage. We found that these effects were species, clone, and environment dependent. Taken together, this work helps us understand how cooperation thrives in nature, despite the threat of cheaters.

A remarkable property of developing organisms is the consistency and robustness within the formation of the body plan. In many animals, morphological pattern formation is orchestrated by conserved signaling pathways, through a process of strict spatio-temporal regulation of cell fate specification. Although morphological patterns have been the focus of both classical and recent studies, little is known about how this robust process is modified throughout evolution to accomodate different morphological adaptations.

The development of cancer from a population of precancerous cells is a rapid evolutionary process. During progression, cells evolve several new traits for survive and proliferation via a few key `driver' mutations. However, these few driver alterations reside in a cancer genome alongside tens of thousands of additional `passenger' mutations. Passengers are widely believed to have no role in cancer, yet many passengers fall within functional genomic elements that may have potentially deleterious effects on the cancer cells. Here we investigate the potential of moderately deleterious passengers to accumulate and alter neoplastic progression. Evolutionary simulations suggest that moderately-deleterious passengers accumulate during progression and largely evade natural selection. Accumulation is possible because of cancer's unique evolutionary constraints: an initially small population size, an elevated mutation rate, and a need to acquire several driver mutations within a short evolutionary timeframe. Cancer dynamics can be theoretically understood as a tug-of-war between rare, strongly-beneficial drives and frequent mildly-deleterious passengers. In this formalism, passengers present a barrier to cancer progression describable by a critical population size, below which most lesions fail to progress, and a critical mutation rate, above which cancers collapse. In essence, cancer progression can be subverted by its own unique evolutionary constraints. The collective burden of passengers explain several oncological phenomena that are difficult to explain otherwise. Genomics data confirms that many passengers are likely damaging and have largely evaded negative selection, while age-incidence curves and the distribution of mutation totals suggests that drivers and passengers exhibit competing effects. These data also provide estimates of the strength of drivers and passengers. Finally, we use our model to explore cancer treatments. We identify two broad regimes of adaptive evolutionary dynamics and use these regimes to understand outcomes from various treatment strategies. Our theory explains previously paradoxical treatment outcomes and suggest that passengers could serve as a biomarker of response to mutagenic therapies. Deleterious passengers are targetable by either (i) increasing the mutation rate or (ii) exacerbating their deleterious effects. Our results suggest a unique framework for understanding cancer progression as a balance between driver and passenger mutations.

<p>In an ever-changing world, evolution is an essential process that may allow organisms to adapt to their environment through natural selection. All evolutionary processes act through a single fundamental medium: genetic variation. Polyploidy, or whole genome duplication, is a major mechanism for evolutionary change because it is both widespread across taxa and results in a proliferation of genetic material that evolution can act upon. The key questions addressed here are: (1) How does chromosome pairing during meiosis in allopolyploids affect the magnitude of genetic variation?, (2) How does the genome of polyploids evolve following formation, and what genetic mechanisms govern this evolution?, and (3) How does genetic and genomic evolution in polyploids affect phenotypic evolution? I use the shy monkeyflower, <italic>Mimulus sookensis</italic>, a tetraploid of hybrid origin between <italic>Mimulus guttatus</italic> and <italic>Mimulus nasutus</italic>, to address these focal questions. In order to develop a foundation to aid in interpretation of my findings, I first investigate the evolutionary history of <italic>M. sookensis</italic>. Chromosome counts establish that <italic>M. sookensis</italic> is indeed an allotetraploid, and a review of taxonomic literature reveals that this species is heretofore undescribed. By analysing the patterns of genetic variation at chloroplast and nuclear loci in <italic>M. guttatus</italic>, <italic>M. nasutus</italic>, and <italic>M. sookensis</italic>, I show that <italic>M. sookensis</italic> has recurrently formed from <italic>M. guttatus</italic> and <italic>M. nasutus</italic>. Crossing experiments within <italic>M. sookensis</italic> indicate that recurrent origins can contribute to genetic diversity without contributing to reproductive isolation among independently arisen polyploid lineages.</p><p>To address my focal questions, I take advantage of an intriguing and striking difference in flower size among <italic>M. sookensis</italic>, <italic>M. guttatus</italic>, and <italic>M. nasutus</italic>. The flowers of <italic>M. sookensis</italic> and <italic>M. nasutus</italic> are small and remarkably similar to one another, while the flowers of <italic>M. guttatus</italic> and diploid and tetraploid F1 hybrids between <italic>M. guttatus</italic> and <italic>M. nasutus</italic> are large and showy. This phenotypic divergence in flower size between <italic>M. sookensis</italic> and <italic>M. guttatus</italic>-like hybrids indicates that small flower size has evolved in <italic>M. sookensis</italic>. Using genetic marker data and phenotypic measurements from synthetic neoallotetraploid <italic>Mimulus</italic>, I demonstrate that there are low levels of fragment loss and phenotypic variation in neoallotetraploids; this suggests that homeologous pairing and recombination following polyploidization is not a major source of genetic variation or phenotypic evolution in <italic>M. sookensis</italic>. Analysis of the whole genome sequence of two <italic>M. sookensis</italic> lines reveals that <italic>M. sookensis</italic> is a fixed heterozygote throughout its entire genome, in that it has retained both a <italic>M. guttatus</italic>-like and <italic>M. nasutus</italic>-like subgenome, neither of which have been removed through homeologous recombination. These subgenomes have been homogenized by widespread gene conversion, and do not appear to have been differentially affected by deletions or deleterious mutations. Finally, to directly characterize the genetic architecture of flower size in <italic>M. sookensis</italic>, I cross a large-flowered synthetic neoallotetraploid <italic>Mimulus</italic> to small-flowered <italic>M. sookensis</italic>. I then employ a novel genotyping-by-sequencing approach to identify quantitative trait loci (QTL) associated with flower size. I find that there is one locus that accounts for a large proportion of phenotypic variation, and four other loci also contribute to flower size variation between the parental lines. Some of these loci co-localize with previously identified loci for flower size in diploid <italic>Mimulus</italic>, while others do not. Altogether, genetic marker data, phenotypic analysis of neoallotetraploids, whole genome sequence data, and QTL mapping data suggest that the genetic variation necessary for flower size evolution was likely caused by both gene conversion and new mutations, but not homeologous recombination. These results suggest that trait evolution in polyploids may be affected by the unique attributes of polyploids, but that new mutations are always an important source of genetic variation, regardless of ploidy level.</p> / Dissertation