Genomic diversity is shaped by the interplay between mutation, genetic drift, recombination, and natural selection. A major goal of evolutionary biology is to understand the relative contribution of these different microevolutionary forces to patterns of genetic variation both within and across species. The advent of massive parallel sequencing technologies opened new avenues to investigate the extent to which alternative evolutionary mechanisms impact the genome and the footprints they leave. We can leverage genomic information to, for example, trace back the demographic trajectory of populations and to identify genomic regions underlying adaptive traits. In this dissertation, I employ genomic data to explore the role of demography and natural selection in two New World bird systems distributed along steep environmental gradients: the Altamira Ori-ole (Icterus gularis), a Mesoamerican bird that exhibits large variation in body size across its range, and the Hairy and Downy woodpecker (Dryobates villosus and D. pubescens), two sympatric species whose phenotypes vary extensively in response to environments in North America. In Chapter 1, I combine ecological niche model, phenotypic and ddRAD sequencing data from several individuals of I. gularis to investigate which spatial processes best explain geographic variation in phenotypes and alleles: (i) isolation by distance, (ii) isolation by history or (iii) isolation by environment. I find that the pronounced genetic and phenotypic variation in I. gularis are only partially correlated and differ regarding spatial predictors. Whereas genomic variation is largely explained by historical barriers to gene flow (IBH), variation in body size can be best predicted by contemporary environmental heterogeneity (IBE), which is consistent with a pattern produced by either natural selection or environmental plasticity. In Chapter 2, I conduct whole genome resequencing on 140 individuals of Downy and Hairy Woodpecker from across North America to more explicitly elucidate the impact of demography and natural selection on the genome. I find that despite spatial congruence in allele frequencies, population structure in these two species has been produced at different temporal scales. Whereas Hairy Woodpeckers were isolated into two east-west glacial refugia, Downy woodpecker populations seem to have expanded from a single ancestral refugium. Demographic analyses suggest large variation in Ne over the past one million years in both Hairy and Downy Woodpeckers, with repeated episodes of bottleneck followed by population expansion, consistent with the onset of the climatic oscillations of the Pleistocene. Nucleotide diversity in both species was positively correlated with recombination rate and negatively correlated with gene density, suggesting the effect of linked selection. The magnitude of this effect, however, seems to have been modulated by the individual demographic trajectory of populations and species. Nevertheless, patterns of nucleotide diversity along the genome are highly correlated between Hairy and Downy Woodpecker, which may be attributed to pervasive selection acting on a conserved genomic landscape of recombination. Finally, in Chapter 3, I use a suite of statistical methods to scan the genome of Hairy and Downy Woodpecker for signatures of natural selection associated with population-specific environmental differences. I test whether climatic adaptation was achieved through selection on the same loci in both species, which would indicate parallel genetic mechanisms for adaptation. I find limited evidence of genomic parallelism at the SNP level, but large parallelism at the gene level. Candidate genes were involved in a broad range of biological processes, including immune response, nutritional metabolism, mitochondrial respiration, and embryonic development. Lastly, I identify potential candidates for key phenotypic traits in Downy and Hairy Woodpecker, such as genes in the IGF signaling pathway, putatively linked to differences in body size, and the melanoregulin gene (MREG), potentially involved in plumage variation. Together, these findings highlight the significant role of demography and natural selection in shaping genomic variation.

A subset of germline mutations that arise de novo each generation are deleterious and may cause severe genetic diseases. Predicting where in the genome and how often we expect to see deleterious mutations requires an understanding both of the distribution of mutation rates and the distribution of fitness effects in the genome. Both aspects are addressed in turn in the two projects described in this thesis. The distribution of mutations in the genome is poorly understood because germline mutations occur very rarely. In Chapter 1 of this work, we investigated the sources of mutations by using the spectrum of low-frequency variants in 13,860 human X chromosomes and autosomes as a proxy for the spectrum of germline de novo mutations. By comparing the mutation spectrum in multiple genomic compartments on the autosomes and between the X and autosomes that have unique biochemical and sex-specific properties, we ascribed specific mutation patterns to replication timing and recombination and identified differences in the types of mutations that accrue in males and females. Understanding mutational mechanisms provides a basis for modeling mutation rate variation in the genome, which is ultimately needed to infer the fitness effects of mutations. In Chapter 2, we used patterns of human genetic variation at methylated CpGsites, known to experience mutations at very high rates, to directly learn about the fitness effects of mutations at these sites. In whole exome sequences now available for 390,000 humans, 99% of putatively-neutral, synonymous CpG sites have experienced a C>T mutation; at current sample sizes, not seeing a C>T mutation at these sites indicates strong selection against that mutation. We leveraged the saturation of neutral C>T mutations and the similarity of mutation rates at methylated CpG sites across annotations to identify the subset of sites in a given functional annotation of interest that are likely to be under strong selection. One implication of this work is that for the vast majority of sites in the genome, there will be little information about strong selection even in samples that are many times larger than at present; the distribution of fitness effects at highly mutable CpG sites may then serve as an anchor for what to expect for other types of sites. Through the two specific cases described, this work illustrates the potential of large contemporary repositories of human genetic variation to inform human genetics and evolution, as well as their limitations in the absence of suitable models of mutation, selection, and other aspects of the evolutionary process.

A research report submitted to the Faculty of Humanities, University of the Witwatersrand, in partial fulfillment of the requirements for the degree of Master of Political Studies, March 2017 / Hitler sought to apply Darwinist theories to German social life, under what was regarded as Social Darwinism. In his words; “If I can accept a divine commandment, it’s this one - thou shalt preserve thou species”. His most loyal and undying belief was that the Aryan race was the most superior race on the planet and that it was their right to “starve the weak” in the name of self-preservation. The Nazis saw it as a social obligation to ‘listen’ to the law of nature and embark on a war of territorial expansion and bloodshed. Darwinian thought provided a justification for Germany’s need for incessant colonialism and racial extermination. In this analysis, Lefort’s ‘Other’ becomes synonymous with Darwin’s ‘parasites’ and Hitler’s ‘enemy’. Through Social Darwinism, it is argued that Hitler ultimately achieved his God-given desire and goal, which was to get rid of the poisoners of the planet – the Jews. / XL2018

Despite the extraordinary diversity of behavior across the animal kingdom, the genes and molecules that contribute to such natural diversity are largely unknown. In this thesis, I leverage the dramatic divergence in behavior between two closely related species of deer mice (genus Peromyscus) to investigate the genetic, cellular, and neuroendocrine basis of behavior. In chapter 2, I show that the monogamous oldfield mouse (Peromyscus polionotus subgriseus) has evolved a novel cell type in the adrenal gland that expresses the enzyme AKR1C18, which converts progesterone into 20α-hydroxyprogesterone (20α-OHP). I then demonstrate that 20α-OHP is more abundant in oldfield mice than in the closely-related promiscuous prairie deer mouse (P. maniculatus bairdii) and that it increases monogamous-typical parental behaviors when administered to both monogamous fathers. Using quantitative trait locus mapping in a cross between these species, I discover interspecific genetic variation that drives expression of the glycoprotein tenascin N and ultimately contributes to gain of adrenal AKR1C18 expression in oldfield mice. In chapter 3, I investigate the genetic architecture underlying the striking difference in exploratory behavior between prairie deer mice and oldfield mice. Through congenic fine-mapping, I identify a 15-Mb locus that strongly contributes to species differences in exploratory behavior. I then investigate the potential contributions of one of the 18 genes in the locus, Olfm4, which harbors cis-regulatory variants that drives its expression in the oldfield hypothalamus. Taken together, my research advances our understanding of the genetic and molecular causes that drive rapid behavioral divergence between species.

Phylogenetics is transitioning from a history of deep-time analyses with few genes to a future of full-genome data that allows species-level resolutions at deep and shallow time scales. Accompanying this transition is a new focus on demographic parameters like ancestral population sizes and gene flow events in addition to the bifurcating trees that are the cornerstone of the field. As access to more data has highlighted some shortcomings of traditional phylogenetic methods that do not account for the processes of recombination, selection, population size changes, and inter-species gene flow, the field is exploring new theory and methods to catch up with the data. My thesis focuses on signals of demographic processes in genomic data. In exploring these processes, we attempt to avoid biases involved in simply extending old phylogenetic methods -- which have typically been applied to just a handful of genes -- to genomic datasets. Chapter 1 introduces a tool, ipcoal, for simulating genomic data on phylogenetic trees within a framework that includes recombination and the ability to specify effective population sizes, gene flow events, recombination maps, and differences in generation times. This tool enables, to varying degrees, all further chapters. Chapter 2 studies the effects of species tree demographic parameters on the resulting linkage among nearby local genealogies, including implications for gene tree and species tree inference. Chapter 3 examines turnover in local histories along the genome using a theoretical framework, the MS-SMC, which links topological heterogeneity along the genome to species tree model. Chapter 4 introduces simcat, a machine-learning method that uses genome-wide SNP data to infer admixture events on a phylogeny without relying on gene tree inference. This is an important step toward decreasing gene tree estimation error over deep evolutionary time scales. Behind the scenes, simcat uses ipcoal to train a machine learning model to map patterns in SNP data to the demographic scenarios that produced them. These chapters demonstrate new phylogenetic theory and methods for refining our ability to infer historical processes at phylogenetic scales, while also illuminating the importance of population-scale processes like gene flow and recombination for shaping genomes sampled in the present day.

This dissertation reveals that the American reception of evolution often hinged on the theory's implications for gender and that Darwinian ideas significantly shaped feminist thought in the U.S. While the impact of evolution on American culture has been widely studied, few scholars have done so using gender as a category of analysis. Similarly, evolutionary theory is largely absent from histories of American feminist thought. Yet, Darwin's ideas, specifically those in The Descent of Man, and Selection in Relation to Sex (1871), had profound ramifications for gender and sex. Nineteenth century scientists and laypeople alike eagerly applied Darwin's theories to the "woman question," generally to the detriment of women. At the same time, key female activists embraced evolution as an appealing alternative to biblical gender strictures (namely the story of Adam and Eve) and enthusiastically incorporated it into their speeches and writings. My work describes how women including Antoinette Brown Blackwell, Elizabeth Cady Stanton, and Charlotte Perkins Gilman utilized Darwinian principles to challenge traditional justifications for female subordination and bolster their arguments for women's rights. Furthermore, my research demonstrates that gender roles, particularly those pertaining to courtship, marriage, and reproduction, were reformulated in accordance with Darwin's theory of sexual selection, altering popular ideas about motherhood and paving the way for eugenics and birth control. My interdisciplinary project draws on scientific and mainstream publications, the feminist press, prescriptive literature, fiction, popular culture, and archival materials, and it explores both intellectual developments and their impact on people's daily lives. I argue that evolution shifted the terms of debate from women's souls to women's bodies, encouraged feminists to claim "equivalence" rather than "equality," inspired opponents and proponents of women's rights to ground their arguments in science (most frequently biology and zoology), destigmatized sex as a topic of scientific inquiry, and galvanized support for greater female autonomy in reproductive decisions. Looking at gender, religion, and evolutionary theory in concert not only helps us more fully comprehend the construction of gender and the development of American feminism, especially its troubled relationships with religion and science, it also enriches our understanding of the American reception of Darwin. / text

M.Ed. (Science Education) / Evolution was introduced as a new section of Life Sciences in the National Curriculum Statement in 2008, anecdotal evidence indicating that this incorporation was not welcomed by all teachers, learners, parents and schools with the same enthusiasm. For example, many Christian teachers and learners seem to have religious objections, but while there is ample research available in the United States of America and Great Britain on their views of evolution, that on the South African Life Sciences classroom is limited. Therefore, this study strives to determine the lived experiences of these teachers and learners and how they relate to the topic. The objectives were to investigate how Christian teachers of Life Sciences experience the teaching of evolution in the classroom; the knowledge and skills they have in order to teach natural selection and evolutionary biology, as prescribed by the National Curriculum Statement; and the barriers they face in the teaching of evolution and natural selection. Meanwhile, Grade 12 learners completed a questionnaire before and after receiving tuition on evolution in order to determine their lived experiences. This study is part of a trilogy within a Research Niche Area of the University of Johannesburg, with the other two researchers focusing on Islam perspectives (Yalvac, 2011) and the Hindu perspective (Reddy, 2012). This is an explanatory sequential mixed method study with an element of phenomenology. Quantitative data was collected which informed the qualitative research, the latter being used to examine the lived experiences of Life Sciences teachers, the former to determine learners’ attitudes toward evolution as well as gauging the teachers’ general understanding of the theory of evolution. Third generation Cultural Historical Activity theory (CHAT) was used as the theoretical framework through which the lived experiences of Christian teachers and learners were analysed. This is appropriate for this study as it views the teachers and learners holistically, by taking their culture and history into account, and it provides a vehicle for looking at what Pintrich, Marx and Boyle (1993) call, the “hot” factors associated with controversial conceptual change. The findings of my study show that many Christian teachers and learners experience conflict between their religion and evolution and many tensions arise in the activity system when using CHAT as a lens. These tensions mainly arise due to a lack of the teachers’ PCK and the conflict arising because of religious objections. The findings furthermore show that learners have a relative naïve understanding of evolution before tuition and have many misconceptions regarding it. A clear polarisation can be seen after tuition as learners move from a neutral stance with regards to evolution to either a more creationistic or scientific point of view. In the final chapter I make recommendations on how the teaching and learning of evolution can be improved in the South African classroom.

Patterns in the distribution of homoplasy are investigated from theoretical and empirical perspectives. The history of the term "homoplasy" as used by morphologists, evolutionary systematists, cladists, and others is reviewed, especially in relation to its complement, "homology." Homoplasy is defined relative to homology, which is viewed as any similarity shared through an unbroken line of common ancestry. An investigation of levels of homoplasy based on a statistical analysis of 60 published phylogenies reveals a strong dependence of homoplasy on the number of taxa included. This relation is independent of number of characters, type of data, taxonomic rank, or organism, and suggests that large taxa should be the focus of empirical studies of homoplasy. Hence, a phylogenetic analysis of the large genus Astragalus was undertaken using 113 representative species (and varieties) found in North America. Fifty-seven binary and multistate characters were scored and the resulting matrix was subjected to numerical cladistic analysis. Two large sets of equally parsimonious trees were found at 595 and 596 steps. The sets were analyzed using consensus methods, robust clades were discussed in detail, and the phylogenies were compared to previous classifications. Character evolution of a large set of taxonomically important and morphologically varied traits was investigated. Statistical tests were developed to detect patterns of topological clustering of homoplastic character changes in cladograms. The tests use Monte-Carlo computer simulations of four null models of character evolution in an attempt to reject the hypothesis of random homoplastic distributions. For the Astragalus data set only two of 17 characters were significantly clustered, and this is close to random expectation. Another data set from the literature was also tested, and in it no characters were clustered at the 5 percent level. The explanation for these negative findings regarding homoplastic "tendencies" is explored with respect to "scope", "scale", and character "resolution," factors believed to play an important role in the analysis of character evolution.

A dissertation submitted to the Faculty of Science, University of Witwatersrand, in fulfilment of the requirements for the degree of Master of Science. Johannesburg, 10 October 2016. / This research explores the potential influence of Life Sciences teacher curriculum support materials on unscientific ideas about evolution by natural selection. The Curriculum and Assessment Policy Statement document, seven learner Life Sciences textbooks and their seven teacher guides were investigated by content analysis to find out firstly, the nature and extent of misconceptions about evolution; secondly, the nature and extent of latent problems associated with the topic of evolution; thirdly, the extent to which the Grade 12 Life Sciences textbooks pointed out common misconceptions and went on to provide the correct scientific explanations to counter the misconceptions; and fourthly, the extent to which teacher guides address teachers’ pedagogical content knowledge (PCK) for teaching the topic of evolution by a) pointing out common misconceptions; b) providing the correct science to counter a specific misconception; c) pointing out pre-requisite knowledge which ought to be learnt first in order to understand the topic of evolution; d) pointing out typical difficulties students encounter when learning the topic of evolution. The Grade 10 and 11 textbooks and teacher guides were analysed for fragmentation and sequencing by use of a checklist. The results show the presence of manifest errors and latent problems in the CAPS document, textbooks and teacher guides. The CAPS document had one manifest error and five instances of latent problems. The section on alternatives to evolution was judged to be a manifest error because religious ideas are not regarded as science by the scientific community. The manifest error found in the CAPS document was also found in the textbooks and teacher guides. Frequent manifest errors occurred in the textbooks, averaging 11 per publisher. The CAPS document had fragmented evolution ideas and probably because textbook authors use this document to write their books, the evolution content in textbooks was also found to be fragmented. Whilst some of the teacher guides were found to address the issue of teacher PCK for teaching the topic of evolution in different ways, some of them were found to be deficient in that respect. The presence of latent problems across all the three curriculum support materials investigated is a cause for concern. Latent problems are problematic if not handled with care because they pose a risk of being misinterpreted, and this may in turn cause the development of evolution misconceptions. An investigation of whether the unscientific evolution ideas in the curriculum documents actually influenced learners’ evolution ideas was not part of this study. However, because textbooks are generally considered as authoritative sources of knowledge upon which teachers and students rely, the presence of misconceptions in these curriculum support materials poses a risk that users of such documents could pick up these misconceptions during teaching and learning. The study highlights the need for a multifaceted approach involving all relevant stakeholders (teachers, authors, publishers and the Department of Education officials) working together in an attempt to address the problem of evolution misconceptions in the Life Sciences curriculum support materials. / TG2016

The human prefrontal cortex (PFC) is associated with complex cognitive behaviors such as planning for the future, memory for serial order, social information processing and language. Understanding how the PFC has changed through time is central to the study of human neural evolution. Here we investigate the expansion of the PFC by measuring relative surface area of the PFC in Pan troglodytes and Homo sapiens. Magnetic resonance images (MRI's) from 8 preserved chimpanzee brains (3 male and 5 female adults) were segmented and measured. The results of this study indicate that there are gross anatomical differences between the chimpanzee and human prefrontal cortex beyond absolute size. The lower surface area to volume ratio in PFC of the chimpanzee when compared to a human indicates less gyral white matter in this region and thus, less associative connectivity. This anatomical evidence of a difference corresponds with the lesser cognitive complexity observed in chimpanzees. / by Ian D. George. / Thesis (M.A.)--Florida Atlantic University, 2009. / Includes bibliography. / Electronic reproduction. Boca Raton, Fla., 2009. Mode of access: World Wide Web.