The ways that individuals socialize within groups have evolved to overcome challenges relevant to species-specific socioecology and individuals’ life history state. Studying the drivers, proximate benefits, and fitness consequences of social interaction across life stages therefore helps clarify why and how social behavior has evolved. To date, juvenility is one life stage that field researchers have largely overlooked; however, individual experiences during development are relevant to later behavior and ultimately to fitness. Juvenile animals are subject to unique challenges related to their small size and relative inexperience. They are likely to employ behavioral strategies to overcome these challenges, while developing adult-like behavioral competence according to their species and sex. The research presented in this dissertation draws from long-term behavioral records of adult females and shorter-term behavioral records of juveniles from a population of blue monkeys (Cercopithecus mitis stuhlmanni) in western Kenya. I combine data on social behavior, demography, and biomarkers related to energetic and metabolic status, to assess both short and long term corollaries of social strategies in this gregarious Old World primate. I first explored whether the quality of social ties predicted longevity among adult female blue monkeys. Controlling for any effects of dominance rank, group size, and life history strategy on survival, I used Cox proportional hazards regression to model the both the cumulative and current relationship of social ties and the hazard of mortality in 83 wild adult females of known age, observed 2-8 years each (437 subject-years) in 8 social groups. The strength of bonds with close partners increased mortality risk under certain conditions: females that had strong bonds with partners that were inconsistent over multiple years had a higher risk of mortality than females adopting any other social strategy. Within a single year, females had a higher risk of mortality if they were strongly bonded with partners that were inconsistent from the previous year vs. with partners that were consistent. Dominance rank, number of adult female group-mates, and age at first reproduction did not predict the risk of death. This study demonstrates that costs and benefits of strong social bonds during adulthood can be context-dependent, relating to the consistency of social partners over time. To understand the adaptive value of social behavior among juveniles, it was first necessary to understand the conditions under which their social behavior occurred and with which it co-varied. I examined the social behavior of 41 juvenile blue monkeys, using data collected over 8 consecutive months. I analyzed variation in social activity budgets and partner number related to life history characteristics, socio-demographic conditions, and seasonal environmental change. I examined partner preferences according to kinship, and relative age and rank. Lastly, I explored the stability of juvenile social tendencies over time. Males and females differed strongly in their social activity budgets and partner numbers: males spent more time playing with more partners than females, whereas females spent more time grooming and sitting close with more partners than males. Nevertheless, they were much more similar in terms of their partner preferences. Juveniles generally preferred to interact with partners with whom they were closely related and that were similar in age and maternal rank. Juveniles’ affiliative and aggressive behavior varied seasonally, suggesting that these two types of behavior were related. Rates of agonism given and received were the only types of social behavior to demonstrate repeatable inter-individual differences. This analysis provides a comprehensive examination of juvenile behavior in blue monkeys, synthesizing findings with those in other primate and non-primate species. I then explored the short-term costs and benefits of juveniles’ sociality in terms of their effects on allostatic load. I examined variation in energy balance (as measured by urinary C-peptide), social style, and their influences on allostatic load (as measured by fecal glucocorticoid metabolites, fGCs). Juvenile energy balance varied according to sex, availability of ripe fruit, and rainfall. Both energy balance and social style predicted fGC levels, such that juveniles that had a higher energy balance, groomed less, and played more had lower fGCs. Time spent grooming interacted with energy balance in their effect on fGCs, such that individuals with higher energy balance actually had higher fGCs the more time they groomed. Neither maternal rank nor involvement in agonism corresponded with juvenile fGC levels. These results suggest that juvenile blue monkeys experience energetic stressors and that navigating the social environment via overt affiliative behavior, namely grooming, is a potentially stress-inducing endeavor. Lastly, to further understand variation in social behavior during juvenility, I explored the role of mothers in shaping juveniles’ affiliative tendencies. I examined whether the social behavior of juvenile animals resembled that of their mothers and whether their social behavior was subject to maternal effects, using data from the 41 juveniles and their 29 mothers. Juveniles’ grooming time with peers corresponded with the amount of time they groomed with (primarily being groomed by) mothers as infants, and this relationship varied by sex. Females spent less time grooming with peers the more maternal grooming they received during infancy, whereas males groomed with peers more. The time juveniles spent in other types of association with partners did not correspond with the same behavior in mothers, nor were other types of association subject to maternal effects. This exploratory study suggests limited effects of maternal behavior during infancy, but also that females and males respond differently to maternal investment during the first year. The results of this dissertation emphasize the importance of long-term studies of natural populations in understanding the evolution of social behavior, particularly when examining the causes and consequences of social ties over the life cycle in a long-lived animal. Strategies of affiliation did indeed correspond with costs and benefits over the life cycle, as they were relevant both to mortality in female adults and metabolic hormones among juveniles. Further, individuals socialize during development according to their life trajectory as male or female, what seasonal changes in the physical environment require or allow, and early-life maternal effects.

Many problems in the biological sciences reduce to questions of genetic evolution. Entire classes of medical pathology, such as malignant neoplasia or infectious disease, can be viewed in the light of Darwinian competition of genomes. With the benefit of today's maturing sequencing technologies we can observe and quantify genetic evolution with nucleotide resolution. This provides a molecular view of genetic material that has adapted, or is in the process of adapting, to its local selection pressures. A series of problems will be discussed in this thesis, all involving the mathematical modeling of genomic data derived from clonally evolving populations. We use a variety of computational approaches to characterize over-represented features in the data, with the underlying hypothesis that we may be detecting fitness-conferring features of the biology. In Part I we consider the cross-sectional sampling of human tumors via RNA-sequencing, and devise computational pipelines for detecting oncogenic gene fusions and oncovirus infections. Genomic translocation and oncovirus infection can each be a highly penetrant alteration in a tumor's evolutionary history, with famous examples of both populating the cancer biology literature. In order to exert a transforming influence over the host cell, gene fusions and viral genetic programs need to be expressed and thus can be detected via whole transcriptome sequencing of a malignant cell population. We describe our approaches to predicting oncogenic gene fusions (Chapter 2) and quantifying host-viral interactions (Chapter 3) in large panels of human tumor tissue. The alterations that we characterize prompt the larger question of how the genetics of tumors and viruses might vary in time, leading us to the study of serially sampled populations. In Part II we consider longitudinal sampling of a clonally evolving population. Phylogenetic trees are the standard representation of a clonal process, an evolutionary picture as old as Darwin's voyages on the Beagle. Chapter 4 first reviews phylogenetic inference and then introduces a certain phylogenetic tree space that forms the starting point of our work on the topic. Specifically, Chapter 4 describes the construction of our projective tree space along with an explicit implementation for visualizing point clouds of rescaled trees. The Chapter finishes by defining a method for stable dimensionality reduction of large phylogenies, which is useful for analyzing long genomic time series. In Chapter 5 we consider medically relevant instances of clonal evolution and the longitudinal genetic data sets to which they give rise. We analyze data from (i) the sequencing of cancers along their therapeutic course, (ii) the passaging of a xenografted tumor through a mouse model, and (iii) the seasonal surveillance of H3N2 influenza's hemagglutinin segment. A novel approach to predicting influenza vaccine effectiveness is demonstrated using statistics of point clouds in tree spaces. Our investigations into clonal processes may be extended beyond naturally occurring genomes. In Part III we focus on the directed clonal evolution of populations of synthetic RNAs in vitro. Analogous to the selection pressures exerted upon malignant cells or viral particles, these synthetic RNA genomes can be evolved against a desired fitness objective. We investigate fitness objectives related to reprogramming ribosomal translation. Chapter 6 identifies high fitness RNA pseudoknot geometries capable of inducing ribosomal frameshift, while Chapter 7 takes an unbiased approach to evolving sequence and structural elements that promote stop codon readthrough.

Madagascar’s lemurs are the most endangered group of mammals in the world, with 94% of species threatened with extinction. Forest loss is one the greatest threat to these arboreal primates, but hunting, habitat degradation, and climate change also threaten their survival. Lemurs are a diverse group of more than 100 species; and their ecological traits shape how species respond to anthropogenic pressure. Incorporating knowledge of species’ ecological niches and evolutionary histories can contextualize threats and improve conservation assessments. In this dissertation, I investigate what constitutes suitable habitat for lemurs in light of the threats present, their sensitivity to forest fragmentation, their dispersal ability, and their ecological uniqueness. I obtained data about lemur distributions in two ways. First, I conducted field surveys of the Critically Endangered blue-eyed black lemur (Eulemur flavifrons), which only occurs in the ecotone between eastern rainforest and western dry forest in the Sahamalaza region. I also surveyed the range of sister species, the black lemur (E. macaco), which inhabits nearby eastern rainforest in the Manogarivo region. I focused on areas that have not been surveyed recently and on the poorly studied boundary between the species to collect observations from the breadth of these species’ ecological ranges. I also documented threats, including incursions into protected areas, and collected fecal samples to test whether whole genomes could be obtained noninvasively for analyses of local adaptation in these species. Second, I searched online databases and published literature for GPS localities for all species of lemur. I used these records, along with the ones collected in the field, to construct ecological niche models for nearly all species of lemur using Maxent. For the blue-eyed black lemur and the black lemur, I estimated the remaining area they can occupy based on these models and the threat survey data. Next, I examined the role of not just forest loss, but forest degradation, in determining where lemur species occur. I used high-resolution forest cover maps to determine lemurs’ tolerance for characteristics of degraded forest, including distance to the edge and mean patch size. I then limited species niche model to only intact, forested habitat. Lastly, using the sportive lemurs (genus Lepilemur) as an example, I evaluate how the inability to disperse across large rivers has influenced ecological niche diversity. I also examine what limited dispersal ability will mean for these species as climate change causes their ranges to shift. Field surveys in the Sahamalaza and Manongarivo regions revealed extensive threats to blue-eyed black lemurs, from traps to cattle incursions and fire. I found no evidence of sympatry, but did locate an undocumented population of E. flavifrons north of the Andranomalaza River. Madagascar National Parks (MNP) managed protected areas appear to have less human incursion than NGO-managed protected areas. Further investigation of the ecological distinctiveness of these species is possible via non-invasive methods: I sequenced whole genomes at 2.3x coverage from eight of the fecal samples collected during this study. While SNPs indicating a loss of function did not reveal any patterns, sequencing additional samples could make studies of local adaptation and population genetic diversity possible. At the regional scale, forest conversion is a grave threat to lemurs. When forest loss and degradation are considered in habitat models, lemur species have lost 51% of their habitat in the last 30 years. Proximity to a forest edge rendered more forested areas too degraded for lemurs than did mean patch size. This result is likely the influence of human contact nearer the forest edge. I recommend urgent support for reserves like Beanka, Tsimembo Forest, Ranobe PK 32, and Amoron’i Onilahy, which have highly suitable, intact forest for many lemur species. Spaces like these will be important for conserving the remarkable diversity within the sportive lemur clade. Though their distribution is largely explained by riverine barriers, I show a role for ecological niche divergence and local adaptation in accelerating allopatric speciation. These same rivers will limit their ability to track climatically suitable areas as climate change progresses: sportive lemurs as a group will lose nearly a quarter of their accessible habitat to climate change by the 2070s. While my results are focused on the particulars of lemur conservation in Madagascar, the methods I have presented here are broadly applicable to other threatened species. Piggybacking fecal sample collection onto rapid field surveys is straightforward. The possibility of obtaining whole genomes from non-invasive samples presents a new way to answer questions about local adaptation without risking injury to other arboreal study subjects, like Neotropical monkeys, or for elusive species like big cats. For threatened species, their climatic niche only dictates part of their distribution. The habitat quantification pipeline presented here takes advantage of thirty-five years of research in Madagascar to estimate species’ tolerance for forest fragmentation. While these records are impressive for primates, they are dwarfed by those available for passerines, through scientific literature and online repositories like eBird. By integrating field surveys, ecological niche modeling, and non-invasive genomics, we can begin to understand the complex threats facing species like lemurs and the options for ensuring their survival.

This thesis began as an investigation into evolution of the platypus family (Ornithorhynchidae, Monotremata), now known from both Australia and South America. The thesis broadened its scope with inclusion of non-ornithorhynchid Mesozoic monotremes from Lightning Ridge, NSW. This change in direction brought an unexpected result: a fossil mammal from Lightning Ridge investigated for this thesis (presumed to be monotreme: Flannery et al., 1995) appears to be a new and unique type of mammal. Specimens were procured through Queensland Museum (Riversleigh material); Australian Museum (Lightning Ridge material); and Museum of Victoria and the South Australian Museum (fossil ornithorhynchids). Specimens were examined under a light microscope and scanning electron microscope; specimens were photographed using light photography and a scanning electron microscope; and illustrations and reconstructions were done with a camera lucida microscope attachment and photographic references. Parsimony analysis utilised the computer programs PAUP and MacClade. Major conclusions: 1) analysis and reconstruction of the skull of the Miocene platypus Obdurodon dicksoni suggest this robust, large-billed platypus was a derived northern offshoot off the main line of ornithorhynchid evolution; 2) the well-preserved skull of Obdurodon dicksoni shows aspects of soft anatomy previously unknown for fossil ornithorhynchids; 3) two upper molars from Mammalon Hill (Etadunna Formation, late Oligocene, central Australia) represent a third species of Obdurodon; 4) the South American ornithorhynchid Monotrematum sudamericanum from the Paleocene of Argentina is very close in form to the Oligocene-Miocene Obdurodon species from Australia and should be considered congeneric; 5) a revised diagnosis of the lower jaw of the Early Cretaceous monotreme Steropodon galmani includes the presence of two previously undescribed archaic features: the probable presence of postdentary bones and a meckelian groove; 6) morphological evidence is presented supporting a separate family Steropodontidae; and 7) analysis of new fossil material for Kollikodon ritchiei suggests that this taxon is not a monotreme mammal as originally identified but is a basal mammal with close relationships to allotherian mammals (Morganucodonta; Haramiyida). Kollikodon is provisionally placed as basal allotherian mammal (Allotheria sensu Butler 2000) and is unique at the ordinal level, being neither haramiyid nor multituberculate. A new allotherian order ??? Kollikodonta ??? is proposed.

PROBLEMS INVESTIGATED:This thesis responds to a significant gap in modern Greek literary scholarship in relation to the Darwinian, post-Darwinian and other evolutionary theories and ideas in the works of Greek writers. My preliminary investigations show that there have been Greek writers who were influenced by Darwinian ideas. However, histories of modern Greek literature do not include Darwinism as a distinct influence in its own right, instead it only appears within the Greek naturalist school of the late 19th century; even when they discuss naturalist works influenced by evolutionary thought. This thesis primarily examines the Darwinian and post- Darwinian influence in select writings of Grigorios Xenopoulos in the period from 1900 to at least 1930. In doing so it attempts to reassess the status of these works and to argue for their importance in the context of other Greek and non-Greek literature. PROCEDURES FOLLOWED: This thesis takes on a cross-disciplinary approach drawing on the histories of science and of literature, on the biological sciences and other sciences. So as to establish a context for Xenopoulos' work, I discuss the themes and issues associated with evolutionary ideas and draw on Greek and non-Greek writers from the 19th century first wave of Darwinism to the first decades of the twentieth century. GENERAL RESULTS: I am able to document that while there appears to have been a general delay in the transmission of Darwinian ideas to Greek creative writers, certain themes in their writings arise, responding to Darwinism, which are common to those of non-Greek writers. While there are differences in the treatments of these themes amongst writers, there are a number of main issues which arise from them which include class, gender and race, and are shown to be important in Greek society at the time. In addition, the direct implications of Darwin's theory of evolution are debated in Greece by science and religion, and are discussed in the writings of Xenopoulos and his peers. MAJOR CONCLUSIONS: My examination of responses to Darwinism by Xenopoulos in the context of other Greek and non-Greek writers aims, firstly, to emphasise the importance of Xenopoulos and his work as a key literary influence in Greek society at the time; and secondly, to play a part in bringing modern Greek literature into the mainstream of European culture. The responses to Darwinism in literature, fiction and non-fiction, past and present, encompass a fascinating and controversial field of investigation which, in view of our scientific knowledge today, continues to address issues such as the nature-nurture debate, creationism versus evolution and man's place in nature. Hence it is important that literary responses to the Darwinism of the late 19th and early 20th centuries in Greece be documented as a foundation for present literary responses.

Thesis (Ph. D.)--University of Chicago, Committee on Evolutionary Biology, August 2003. / Includes bibliographical references. Also available on the Internet.

Mutation is a fundamental process in evolution because affects the amount of genetic variation in evolving populations. Molecular-structure models offer significant advantages over traditional population-genetics models for studying mutation, mainly because such models incorporate simple, tractable genotype-to-phenotype maps. Here, I use RNA secondary structure models to study four basic properties of mutation. The first section of this thesis studies the statistical properties of beneficial mutations. According to population genetics theory, the fitness effects of new beneficial mutations will be exponentially distributed. I show that in RNA there is sufficient correlation between a genotype and its point mutant neighbors to produce non-exponential distributions of fitness effects of beneficial mutations. These results suggest that more sophisticated statistical models may be necessary to adequately describe the distribution of fitness effects of new beneficial mutations. The second section of this thesis addresses the dynamics of deleterious mutations in evolving populations. There is a vast body of theoretical work addressing deleterious mutations that almost universally assumes that the fitness effects of deleterious mutations are static. I use an RNA simulation model to show that, at moderately high mutation rates, initially deleterious mutations may ultimately confer beneficial effects to the individuals harboring them. This result suggests that deleterious mutations may play a more important role in evolution than previously thought. The third section of this thesis studies the global patterns of mutations connecting phenotypes in fitness landscapes. I developed a network model to describe global characteristics of the relationship between sequence and structure in RNA fitness landscapes. I show that phenotype abundance varies in a predictable manner and critically influences evolutionary dynamics. A study of naturally occurring functional RNA molecules using a new structural statistic suggests that these molecules are biased towards abundant phenotypes. These results are consistent with an "ascent of the abundant" hypothesis, in which evolution yields abundant phenotypes even when they are not the most fit. The final section of this thesis addresses the evolution of mutation rates infinite asexual populations. I developed an RNA-based simulation model in which each individual's mutation rate is controlled by a neutral modifier locus. Using this model, I show that smaller populations maintain higher mutation rates than larger populations. I also show that genome length and shape of the fitness function do not significantly determine the evolved mutation rate. Lastly, I show that intermediate rates of environmental change favor evolution of the largest mutation rates. / text

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This dissertation critiques and rejects Elliott Sober's dismissal of intelligent design as a scientific hypothesis. Sober builds the case for this dismissal in chapter 2 of his 2008 book Evidence and Evolution. Sober's case against intelligent design as science is a philosophical one, emerging from a Bayesian likelihood approach. Sober claims that unlike neo-Darwinian processes, intelligent design cannot supply independent evidence to support the claim that it is a measurably likely cause responsible for the emergence of biological organisms and the structures or processes of which they are composed. Without an assessable likelihood, Sober asserts that intelligent design (again, unlike neo-Darwinian mechanisms) is not testable, and since it is not testable, it does not qualify as a scientific hypothesis. This dissertation argues however, that according to Sober's own standards in Evidence, because intelligent design and the neo-Darwinian hypothesis both address unrepeated, major biological changes in the unobservable past, and because they both depend upon crucial analogies in order to support either inductive arguments or likelihood assessments, the two hypotheses stand on equivalent evidential and logical grounds. Either Sober must reject both neo-Darwinism and intelligent design, or he must allow them both as equivalent, rival hypotheses based upon a fair application of his argumentation requirements. In addition, after explaining important basics of analogy theory, and its crucial, even unavoidable role in the historical (or "origins") sciences, the dissertation goes on to show how intelligent design's empirical support, based upon analogy with humanly designed artifacts, machines and increasingly cell-like creations in the laboratory, is continuing to grow stronger by the year in both likelihood and in explanatory power. The dissertation thus concludes that intelligent design should be treated as a viable scientific explanation for the dramatic examples of specified complexity being discovered in biology, and indeed should be regarded as an increasingly vigorous rival to the neo-Darwinian explanation of such complexity.

In this thesis I contend that evolutionary scientific discourses were integral to the work of "New Woman" writers of late Victorian literary culture in Britain. In the cultural debates that raged over the new gender politics and their relationship to social and moral values at the fin de siècle, the questions raised about femininity, modernity and the "woman question" were also central to the "new sciences" of sexology, eugenics, psychology and anthropology. This thesis investigates the issue of whether the new sciences offered an enabling set of discourses to New Women through which to produce new artistic, professional and personal feminine identities and to campaign for feminist goals. An understanding of the field of cultural production informs this discussion; I argue that science functions as cultural and symbolic capital in literary production of the period, and consider the dynamics between constructs of value, status, and the feminine in the literary market-place and their relationship to scientific narratives. This analysis is developed through the illumination of the relationship between New Woman novelists and poets, female aesthetes, and other forces in the field, in discussion of the thematic concerns and literary strategies of those participating in these debates: amongst others, Mona Caird, "Iota" (Katherine Mannington Caffyn), Victoria Cross(e) (Annie Sophie Cory), Sarah Grand (Frances Elizabeth McFall), Vernon Lee (Violet Paget), Alice Meynell, May Kendall, Constance Naden, and the anti-New Woman male writer, Grant Allen. An examination of a variety of literary forms and genres, in addition to the novel — the principal focus for much scholarship on the New Woman — such as the feminist periodicals, poetry, journalism and the short story, is central to the thesis and enables identification of shared literary strategies and techniques as well as consideration of readers and critical contexts. The roles and representation of "woman" in this period were produced within biological determinist concepts of sex and Nature. The study concentrates on ways in which essentialist dichotomies of cultural and biological reproduction redefined notions of literary and artistic "genius", motherhood and female citizenship, as they intersect with "race" and sexuality in imperial contexts. Women's critique and construct of these subjectivities differed; study of the women's journals reveals a consumer culture saturated in discourses of health and hygiene, negotiated by a divided community of readers. Focus on theories and representation of the child in late Victorian culture finds that Alice Meynell's writing challenged evolutionary psychology, and relates Sarah Grand's child genius to emergent Galtonian eugenics. I argue that late nineteenth-century feminism was intimately involved in imperialism and eugenics, and suggest that current feminist scholarship must confront and analyse these investments. In this thesis I find that boundaries between the groups' identities are fluid; points of intercourse and affiliation are revealed, such as the ways in which scientific constructs of "race", as in Mona Caird's use of the Celtic, are deployed in order to comment on literary value. I have highlighted the ambivalences at work in these appropriations, and suggest that the New Woman text was not always polemical, nor did it reject "high art" values, and that the female aesthetes also express feminist convictions. I contend that for many feminist writers, participation in these late nineteenth-century debates was a necessary and productive critical intervention, with radical, if not always progressive, implications.