Multiple rounds of whole genome duplication (WGD) have played a pivotal role in the expansion, elaboration, and evolutionary diversification of vertebrate genomes. In addition to sharing two rounds of whole genome duplication with all other vertebrates, a teleost-specific genome duplication (TGD) occurred in the stem of the teleost lineage ~350 million years ago (MYA) and is thus a genomic synapomorphy shared by all ~26,000 extant species. The TGD has variously been implicated in accelerated speciation, evolution of morphological complexity, increased rates of molecular evolution, and the evolution of novelty, and therefore is therefore of significant interest for its impact on teleost evolution and also as a model for understanding the evolutionary patterns and processes which accompany WGDs more generally. Investigation of the TGD has contributed extensively to the general understanding of WGDs however, until the present work, a relatively narrow taxonomic sampling of species within a single teleost subdivision, Clupeocephala, have been investigated. This taxonomic bias has left potentially relevant evolutionary changes to the teleost genome in the immediate wake of the TGD obscured. Due to their deeply branching ancestry, species belonging to the two other major teleost subdivisions, Osteoglossomorpha and Elopomorpha, are well positioned for deeper comparative genomic analyses of the TGD and the accompanying phenomenon of diploidization. The focus of the present work has been to develop the first genomic resources specifically for osteoglossomorphs and to investigate the evolutionary patterns and processes which accompanied diploidization prior the deep divergence of the three extant teleost subdivisions. To this end, I have generated de novo genome and transcriptome data from four osteoglossomorph taxa (Pantodon buchholzi, Osteoglossum bicirrhosum, Chitala ornata, and Gnathonemus petersii) and conducted comparative genomic and phylogenetic analysis with other teleosts and pre-TGD vertebrates including the gar Lepisosteus oculeatus. With a focus on Hox and other ANTP class homeobox-containing transcription factor families I provide evidence that speciation of the major teleost subdivisions occurred prior to the termination of the diploidization process following TGD and discuss the evolutionary implications of this model. Beginning with an analysis of the Hox clusters in P. buchholzi I show that divergent resolution of TGD-generated Hox duplicates occurred both at the individual gene level as well as at the level of whole cluster losses. Detailed phylogenetic analyses of the P. buchholzi Hox clusters further revealed that the transition from polyploid alleles to full paralogs during the diploidization process can occur independently in different lineages when speciation rapidly follows WGDs, causing duplicated genes to exhibit a special case of four-way gene homology which I have termed 'tetralogy'. A genome-wide survey of ANTP class homeobox genes in a de novo assembly of the P. buchholzi genome revealed that ancient TGD duplicates of at least 14 subfamilies were preserved uniquely in the P. buchholzi genome and lost from clupeocephalan teleosts. Finally, by comparing the Hox complements in gar and P. buchholzi with three additional osteoglossomorphs I show that the diversity in potential duplicate resolution patterns is also highly variable between osteoglossomorph families. Overall, this work highlights the importance of considering not only the relative timing of gene duplication and speciation in comparative genomic analyses but also their timing relative to diploidization. Going forward, the research community will need to carefully evaluate the effects differences in diploidization rate and pattern, both between lineages and across the genome, have had in influencing the fate of individual gene duplicates as well as upon the macroevolutionary phenomena frequently correlated with WGDs more generally.

The aim of this dissertation is to explore the nature of scientific progress and to broaden existing theories of what constitutes progress in science. I do this by means of a close analysis of the main post-Kuhnian philosophical accounts of scientific progress, namely those put forward by Imre Lakatos, Larry Laudan and Philip Kitcher. I test these three accounts by reconstructing a series of scientific episodes in evolutionary ecology in terms of each account and then assessing the degree to which each account incorporates what is progressive. The episodes I have selected concern the resource competition research of Dolph Schluter on Galapagos finches and related work leading up to it. After distinguishing between macroscopic and microscopic levels in science, I attend carefully to the microscopic level of each episode as it relates to epistemic progress. This investigation demonstrates that some important aspects of scientific progress have been overlooked. I conclude that there are three main ways in which the philosophies of science surveyed do not adequately represent instances of scientific progress. First, the accumulation of factual knowledge is not well accommodated. Second, the role of evidence and argument in scientific theories is not adequately captured. Third, the fine-grained level at which much important epistemic progress in science occurs is often not accounted for. These criticisms relate to a more general tendency of contemporary philosophical accounts to emphasize the macroscopic level of entire research programmes and traditions while failing to attend to the microscopic level of progress inherent in a detailed case study. I end by offering a positive account of scientific progress in light of these criticisms. / Arts, Faculty of / Philosophy, Department of / Graduate

Ciliates are model organisms for studying programmed genome rearrangement because each cell houses two distinct genomes. During postzygotic development, the somatic genome rearranges from a copy of the germline genome via extensive genome remodeling, including DNA elimination, religation and sometimes translocation or inversion of genomic regions. Previous studies of this process were restricted to a few model ciliates including Tetrahymena thermophila, Paramecium tetraurelia and Oxytricha trifallax. Oxytricha diverged from Tetrahymena and Paramecium over one billion years ago, and it possesses a massively fragmented and scrambled germline genome. My thesis compares Oxytricha to more closely related ciliates to address the evolutionary origin of genome complexity. Chapter 1 provides a general introduction to genome architecture, comparison of well-studied ciliate genomes and challenges of studying genome rearrangement in non-model ciliates. Chapter 2 describes a computational pipeline, SIGAR (Split-read Inference of Genome Architecture and Rearrangements), which infers genome rearrangement features without a germline genome assembly. We validated the pipeline using a published Oxytricha dataset, and also applied it to six diverse ciliate species including Ichthyophthirius multifiliis, a fish pathogen. This pipeline enables pilot surveys or exploration of chromosomal rearrangement in ciliates with limited germline DNA access, thereby providing new insights into the evolution of DNA rearrangement. Chapter 3 presents a comparative genomic study of three ciliate species including Oxytricha trifallax, Tetmemena sp. and Euplotes woodruffi. Collaborating with my colleagues, I assembled and annotated germline genomes in Tetmemena and E. woodruffi, as well as E. woodruffi’s somatic genome. We identified scrambled genes in all three species, especially the earlier-diverged E. woodruffi, though at a lower level (7.3% of gene loci) compared to Oxytricha (15.6%) and Tetmemena (13.6%). E. woodruffi may therefore represent an intermediate between the nonscrambled ancestral genome and more massively scrambled genomes as can be seen in Oxytricha and Tetmemena. We also found that scrambled genes tend to have more paralogs or have partial MDS duplications, suggesting that local duplications might play a role in the evolutionary origin of scrambled genes. Chapter 4 reports a new genetic code identified in a basal spirotrich ciliate, Licnophora macfarlandi. Ciliates have been a hot spot for the evolution of alternative genetic codes. All variant genetic codes in ciliates reassign canonical stop codons to amino acids, and in most cases the UAA and UAG are reassigned to the same amino acid, or are both used as stop codons. The codon usage analysis in Licnophora revealed an unprecedented genetic code that translates the UAA to glutamic acid and the UAG to glutamine. We also detected candidate tRNAs from the somatic genome which can recognize the UAA and UAG. Chapter 5 describes possible future directions to understand the genome complexity of ciliates.

Cooperatively breeding societies, in which one or more non-parental individuals (“alloparents”) care for young alongside the parents, show considerable variation in social structure. Traditionally, such societies have been thought to comprise small, kin-based family groups where offspring from previous broods delay dispersal and help raise closely-related offspring to gain indirect fitness benefits when independent breeding opportunities are unavailable or yield lower fitness outcomes. However, genetic evidence is increasingly revealing cooperatively breeding species whose social groups comprise unrelated individuals as co-breeders or alloparents or both (for e.g., 45% of all avian cooperative breeders). Such social groups exhibit complexity in social structure such as large group size, multiple breeders, and low and varied group kin structure. To understand why such complex societies form and how are they maintained when the opportunity to gain indirect benefits via kin selection is low and variable, I investigated the direct and indirect benefits driving a key demographic process, dispersal, and the resulting variation in group social structure on the individual, group, and population levels in an obligate, avian cooperative breeder, the superb starling (Lamprotornis superbus). I used a combination of long-term, individual-level data spanning 15 years from nine groups monitored at the Mpala Research Centre in Kenya and fine-scale genetic and environmental data sampled across 22 social groups that included the long-term study population. In Chapter 1, I show that (i) dispersal decisions in superb starling males are driven by temporal environmental variation experienced by their parents pre-laying, (ii) both dispersal and philopatry result in equivalent lifetime inclusive fitness outcomes, and (iii) oscillating selection due to high temporal variability in the environment likely maintains the two alternative dispersal tactics, resulting in the formation of mixed-kin groups. In Chapter 2, I show that (i) immigrants are vital to the stability of superb starling social groups in light of low and variable offspring recruitment in a harsh, unpredictable environment, (ii) plural breeding likely arises as a result of reproductive concessions provided by group members as joining incentives to recruit immigrants, and (iii) despite smaller groups providing more reproductive concessions, immigrants gain higher fitness in larger social groups and thus prefer to immigrate into larger groups which are found in higher-quality territories. Finally, in Chapter 3, I find genetic signatures of directional dispersal from social groups in low- to high-quality territories across an environmental gradient which likely generates considerable within-population variation in group social structure. Overall, my dissertation underscores the importance of direct benefits derived from group augmentation in the formation and maintenance of cooperative social groups with a complex social structure in a harsh and unpredictable environment.

No description available.

A long-standing question in ecology is understanding how the environment structures species occupancy in space and time. Specifically, identifying associations between environmental drivers - climate and land cover - and species occupancy is crucial to predicting species distributional dynamics in the future. Over the last century, research on the abiotic drivers of species occupancy has largely focused on temperate regions. Tropical mountain ecosystems harbor extraordinary levels of diversity and face some of the highest anthropogenic pressures of climate and land cover change. Yet, such regions have remained historically understudied. Bird species, due to their sheer diversity and occurrence across climatic zones and land cover types, are an ideal model for understanding how climate and land cover structure occupancy in space and time. The goal of this dissertation is to disentangle spatial and temporal associations between environmental drivers - climate and land cover - and bird species occupancy along a tropical montane gradient. I use an integrative approach that relies on citizen science, historical ecology, and bioacoustics to study bird communities in the Western Ghats biodiversity hotspot of southern India. In Chapter 1, we used observations from the world’s largest citizen science database, eBird, to ask how contemporary climate and land cover are associated with bird species occupancy across the Nilgiri and the Anamalai hills of the Western Ghats. We show that the occupancy of several forest specialist birds was negatively associated with temperature seasonality, highlighting narrow thermal niches for such species. We also show that a small number of generalist bird species are positively associated with human-modified land cover types. In Chapter 2, we combined colonial-era and modern datasets on bird species observations and land cover to ask how a century of landscape change across the Nilgiri hills has impacted bird communities. Between 1848 and 2017, 75% of grassland habitat across the Nilgiri hills was lost toward timber plantation and cash crop expansion. Such drastic declines in grassland habitat have resulted in declines in species persistence and relative abundance of grassland specialist birds over the last century. As a result, the functional trait space has undergone biotic homogenization. In Chapter 3, we ask if the reversal of landscape changes significantly affects bird communities. Using passive acoustic monitoring, we examined the impacts of ecological restoration on bird communities and other vocalizing fauna along a gradient of forest regeneration (consisting of actively restored, naturally regenerating, and mature benchmark sites) in the Anamalai hills. Encouragingly, we show that the bird community composition of actively restored sites is transitioning toward mature benchmark sites. However, when we moved beyond birds, we found that vocalizations at higher frequencies (> 12 kHz) were largely missing from actively restored and naturally regenerating sites, while the same frequency space was occupied in mature benchmark sites. Taken together, we find that climate and land cover are key determinants of bird species occupancy in the Western Ghats, and in a globally changing world, conservation interventions such as ecological restoration along with the preservation of naturally occurring land cover types are key to sustaining montane avifauna in the long run.

The early environment impacts many aspects of an individual’s developing phenotype. In particular, early environmental conditions are important for shaping the hypothalamic-pituitary-adrenal (HPA) axis, which coordinates an individual’s stress response. These developmental changes are likely mediated by epigenetic modifications, functional changes to the genome that can alter gene expression in response to environmental variation, resulting in significant phenotypic differences (Kundakovic and Champagne 2015; Richards 2006). Determining how early life variation alters epigenetic modifications (such as DNA methylation) of genes throughout the HPA axis, and how these marks change over time, in wild organisms is important for understanding their potential long-term fitness consequences. Here, I examine DNA methylation modifications in the HPA axis in relation to early environmental variation in free-living house sparrows (Passer domesticus). In Chapter 1, I show a relationship between natural variation in the early environment and DNA methylation marks of numerous genes related to HPA axis function, which in turn predict growth trajectories. In Chapter 2, I show that early life stress in particular impacts DNA methylation in genes critical to HPA axis function, but does so differently depending on the life history stage in which stress is encountered. Finally, in Chapter 3, I find that these early life marks have long-term effects past the developmental period, predicting longevity as well as lifetime reproductive output in a sex-specific manner. Overall, my dissertation adds to a growing understanding of the dynamic role of epigenetic modifications in mediating phenotypic responses to the early life environment in wild birds, and demonstrates the potential long-term fitness outcomes of these changes.

As a primary factor in human evolution, natural selection is an important component of genetic research. Studies of lactase persistence suggest that positive selection has played a powerful role in the adaptation to a lifelong consumption of fresh milk. Using multiple research studies of lactase persistence and suspected corresponding single nucleotide genetic polymorphisms, this study combines data sources to determine whether evidence exists for natural selection of a specific cytosine-to-thymine genetic mutation located 13,910 base pairs (T-13910) upstream from the lactase gene. This polymorphism has potential to be a causal element for lactase persistence, and data suggest that natural selection has played a role in the rising frequency and distribution of this allele, if only in some regions. European and neighboring regions appear to have the highest frequencies with little or no frequency in Asia, Africa and Indonesia; however the presence of lactase persistence in those areas suggests convergent evolution may be occurring on a phenotypic level. To examine this possibility several other identified polymorphisms in the same region as the T-13910 will be included in this study

The genetic variation among extant life forms reflects the outcomes of evolution. The fodder of evolution – germline mutations – is shaped by the interplay among evolutionary forces – notably natural selection and random genetic drift. In turn, these forces leave footprints recorded in the genetic variation of extant life forms. Characterizing these footprints to understand how evolution works is at the heart of population genetics. To this end, massive datasets of genetic variation have opened new avenues of research, around how mutation rates evolve for instance, and reinvigorated long standing questions in population genetics, notably about the genetic basis of adaptation. In turn, theoretical models of evolution inform what kind of footprints we expect evolution to leave behind in such data. Two theoretical models that investigate open questions in population genetics are described in this thesis. In Chapter 1, I consider the evolution of germline mutation rates, particularly on short evolutionary timescales, and ask if recently observed variation in mutation rates among human lineages could be explained by evolution at genetic modifiers of mutation rates. Genetic modifiers of mutation rates are expected to evolve under purifying selection: mutations at modifiers that increase mutation rates (“mutator alleles”) should be selected against, because they increase the burden of deleterious mutations in individuals who carry them. The frequencies of mutator alleles are also affected by mutation, genetic drift, and demographic processes. We model the evolution of mutator alleles under the interplay of these forces and characterize the dynamics at mutation rate modifiers as a function of the efficacy of selection acting on them. We find that modifiers under intermediate selection have the greatest contribution to variation in mutation rates between distantly related populations, but only variation at strongly selected modifiers turns over fast enough to explain variation in mutation rates among human lineages. We also predict that strongly selected modifiers could be potentially identified in the contemporary datasets of human pedigrees used to study germline mutations. In Chapter 2, I consider a central and enduring question in evolutionary biology: whether adaptation typically arises from few large effect changes or from many small effect changes. Both sides are supported by ample evidence. Yet it is unclear how to translate this evidence into general answers about the genetic basis of adaptation, in part because different methodologies have different limitations and ask different questions. Theory may offer a way out of this quagmire or at least a start. To this end, we reframe the question in terms of traits and ask: how does the genetic basis of adaptation depend on the ecological and genetic attributes of a trait? To start answering this question, I model adaptation in a simple yet highly relevant setting. I consider a trait under stabilizing selection and assume the distribution of trait values in the population is initially at mutation-selection-drift-balance. I then characterize the adaptive response that is elicited by a sudden change in the environment. I find that the adaptive response, and notably the probability that adaptation arises from the fixation of large effect alleles, depends on the size of the environmental change and the genetic architecture of the trait. These attributes are measurable and can be directly related to the disparate evidence that we have about the genetic basis of adaptation. Thus, this kind of modeling may help translate such evidence into general conclusions about how traits evolve. My thesis work was interrupted by the global COVID-19 pandemic, and in response to this pandemic, governments around the world implemented shelter-in-place protocols. However, essential workers were exempt from these protocols, potentially decreasing their efficacy. In Chapter 3, we describe our epidemiological project, aimed at understanding the impact of essential workers on epidemic control. To this end, we model three different archetypes of essential workers under a reasonably realistic SEIR model of the COVID-19 pandemic. We find that the different social interactions that essential workers maintain qualitatively changes their personal risk of infection and the spread of the overall epidemic. These results highlight the utility of not considering essential workers as a monolithic group but instead distinguishing between the impact of different types of essential workers on epidemic control.

Argues that, without the publication of Charles Darwin's "Origin of Species," Bram Stoker's novel "Dracula" and Oscar Wilde's novel "The Picture of Dorian Gray" would not have been written with their distinct style and themes, as evolution clashes with degeneration and female power (and the sexuality derived from that power) clashes with the new science. Stoker and Wilde combine the science of the late 19th century with the characters of their imaginations. Natural and sexual selection plays a part in these characters' core development. The mixture of sexuality, science and power in these two novels all combine to formulate what is known as Victorian sexology.