A fundamental phenomenon in molecular evolution is the accumulation of mutations in proteins at an approximately constant rate, known as the molecular clock. Remarkably, although this rate remains constant across lineages, it varies by several orders of magnitude across different proteins. The nature of the molecular clock and its variability across proteins is a foundational question in molecular evolution. In addition, understanding the essence of evolutionary constraints provides insights into the principles of biological systems optimization.The primary determinants of the molecular clock have been actively investigated and debated for several decades. It has been established that the strongest predictor of the rate of protein evolution is protein expression. However, the underlying basis for the widely observed anti-correlation between Expression and evolutionary Rate (ER) remains poorly understood. The main goal of this study is to unravel the basic mechanisms of the molecular clock variability across proteins and in particular the nature of ER anti-correlation. We begin by investigating the molecular basis of the ER phenomenon. In this regard, we first addressed the validity of the misfolding avoidance hypothesis, which has dominated related evolutionary discussions for more than a decade. We analyzed multiple recent genome-wide datasets describing protein stability and aggregation propensities – properties predicted to constrain the evolution of highly expressed proteins to avoid toxicity caused by misfolding. We rigorously tested the predictions of the hypothesis, and our results suggest that misfolding avoidance is unlikely to play any substantial role in explaining the variability of the molecular clock across proteins. Thus, other mechanisms should be explored. We focused on the functional hypothesis, which proposes that variability in evolutionary constraints is due to different levels of functional optimization across proteins. We collected data on catalytic efficiency across multiple enzymes in several species to serve as a proxy for protein functional optimality. Notably, we demonstrated that the optimization of protein molecular function substantially constrains the rate of protein evolution. Moreover, up to half of the correlation between protein expression and evolutionary rate can be explained by the level of protein functional efficiency. These findings support to the functional theory of protein evolution. We further investigated the cellular mechanisms behind the ER correlation. To this end, we analyzed how protein expression levels in different tissues of multicellular species or in strains of unicellular species living in different environmental conditions jointly affect protein optimization and evolution. Using tissue- and condition-specific expression data from various animal, plant, and bacterial species, we demonstrated that the protein clock rate and the degree of protein functional optimality are primarily affected by expression in several distinct cell types. Furthermore, the strength of the association between protein expression and evolutionary rate is correlated with the upregulation of specific cellular processes, namely functions related to synaptic transmission in animals and active cellular growth in plants and bacteria. We hypothesize that these cellular properties result in particularly high cost of protein expression, leading to a more pronounced optimization of highly abundant proteins and consequently slowing down the molecular clock. Overall, the study reveals how various constraints from the molecular, cellular, and species’ levels of biological organization jointly affect protein evolution and the level of protein optimization and adaptation.

This investigation explored scientific, religious, and otherwise nonscientific factors that may influence student acceptance of biological evolution and related concepts, how students perceived these factors to have influenced their levels of acceptance of evolution and changes therein, and what patterns arose among students' articulations of how their levels of acceptance of evolution may have changed. This exploration also measured the extent to which students' levels of acceptance changed following a treatment designed to address factors identified as potentially affecting student acceptance of evolution. Acceptance of evolution was measured using the MATE instrument (Rutledge and Warden, 1999; Rutledge and Sadler, 2007) among participants enrolled in a secondary-level academic program during the summer prior to their final year of high school and as they transitioned to the post-secondary level. Student acceptance of evolution was measured to be significantly higher than pre-treatment levels both immediately following and slightly over one year after treatment. Qualitative data from informal questionnaires, from formal course evaluations, and from semi-structured interviews of students engaged in secondary level education and former students at various stages of post-secondary education confirmed that the suspected factors were perceived by participants to have influenced their levels of acceptance of evolution. Furthermore, participant reports provided insight regarding the relative effects they perceived these factors to have had on their evolution acceptance levels. Additionally, many participants reported that their science teachers in public schools had avoided, omitted, or denigrated evolution during instruction, and several of these students expressed frustration regarding what they perceived to have been a lack of education of an important scientific principle. Finally, no students expressed feelings of being offended by having been taught about evolutionary science, and the overwhelming majority of the participants expressed enjoyment of the course and appreciation for having been taught about evolution.

M.Ed. (Science Education) / The topic of evolutionary theory is new to the South African Life Sciences curriculum, having only been introduced in 2008 to the grade 12 cohort. A great deal of controversy and discussion surrounds the teaching and learning of evolution in many countries, and since the introduction of the topic, including South Africa. The primary source of this controversy arises from the conflict that many Christian and Muslim people experience between what their respective religions teach them about the act of Creation by God and the biological theory of evolution. As a result of its recent inception into South African school, not much research has been done to explore how this topic is experienced by Hindu secondary school learners and teachers. The aim of this study is therefore to address two gaps, firstly to add to the almost total lack of information about the Hindu perspective of the topic of evolution. Secondly, to add to the knowledge base of the teaching and learning of evolution in secondary schools since the scant information available on the teaching and learning of evolution in South Africa is mainly confined to tertiary education. Literature was reviewed on various aspects relevant to this study such as the PCK, NOS, CCC, Hinduism and the teaching and learning of evolution overseas and locally. In order to investigate the lived experiences of Hindu Life Sciences teachers and learners to the topic of evolution a qualitative study with elements of phenomenology was the chosen research design. This prompted the need to use a series of focus group and individual interviews with the various role-players as laid out by the overarching conceptual framework CHAT, the lens through which this study was viewed. Triangulation of data increased the reliability and validity of this study and was obtained by interviewing a Hindu priest as well as Hindu parents of Life Sciences learners. Interviews were transcribed, coded using the coding model by Saldana (2009) and analysed according to common themes. The main finding of this study was that Hindu teachers and learners experience no conflict with the topic of evolution thus displaying a lack of major tensions linked to the CHAT model. Many Hindus are however ignorant of their religion and scriptures but nevertheless remain accepting of the theory of evolution. Their acceptance could be attributed to three major tenets of Hinduism that link to evolutionary concepts: the cyclical concept of time; the evolution of the soul during reincarnation and the idea that during times of calamity, God manifests on Earth in the form of Avatāras. Misconceptions of evolutionary theory abound among learners and to a lesser extent the parents and teachers, particularly with respect to the notion of common ancestry. The teachers had adequate PCK but their knowledge of the NOS was limited. Recommendations emerging from these findings therefore warrant greater attention to the NOS in both PRESET and INSET teacher training courses. These courses can also use the lack of tensions between the Hindu religion and the topic of evolution as a case in point to show that religion and science can exist in harmony with each other. The concept of a nearest common ancestor (NCA) should also be emphasised in these courses – thereby helping to dispel the misconception that humans descended directly from apes.

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Thesis (MSc)--Stellenbosch University, 2014. / ENGLISH ABSTRACT: Codes are ubiquitous in culture|and, by implication, in nature. Code biology is the study of these codes. However, the term `code' has assumed a variety of meanings, sowing confusion and cynicism. The rst aim of this study is therefore to de ne what an organic code is. Following from this, I establish a set of criteria that a putative code has to conform to in order to be recognised as a true code. I then o er an information theoretical perspective on how organic codes present a viable method of dealing with biological information, as a logical extension thereof. Once this framework has been established, I proceed to review several of the current organic codes in an attempt to demonstrate how the de nition of and criteria for identifying an organic code may be used to separate the wheat from the cha . I then introduce the `regulatory code' in an e ort to demonstrate how the code biological framework may be applied to novel codes to test their suitability as organic codes and whether they warrant further investigation. Despite the prevalence of codes in the biological world, only a few have been de nitely established as organic codes. I therefore turn to the main aim of this study which is to cement the status of the histone code as a true organic code in the sense of the genetic or signal transduction codes. I provide a full review and analysis of the major histone post-translational modi cations, their biological e ects, and which protein domains are responsible for the translation between these two phenomena. Subsequently I show how these elements can be reliably mapped onto the theoretical framework of code biology. Lastly I discuss the validity of an algorithm-based approach to identifying organic codes developed by G orlich and Dittrich. Unfortunately, the current state of this algorithm and the operationalised de nition of an organic code is such that the process of identifying codes, without the neccessary investigation by a scientist with a biochemical background, is currently not viable. This study therefore demonstrates the utility of code biology as a theoretical framework that provides a synthesis between molecular biology and information theory. It cements the status of the histone code as a true organic code, and criticises the G orlich and Dittrich's method for nding codes by an algorithm based on reaction networks and contingency criteria. / AFRIKAANSE OPSOMMING: Kodes is alomteenwoordig in kultuur|en by implikasie ook in die natuur. Kodebiologie is die studie van hierdie kodes. Tog het die term `kode' 'n verskeidenheid van betekenisse en interpretasies wat heelwat verwarring veroorsaak. Die eerste doel van hierdie studie is dus om te bepaal wat 'n organiese kode is en 'n stel kriteria te formuleer wat 'n vermeende kode aan moet voldoen om as 'n ware kode erken te word. Ek ontwikkel dan 'n inligtings-teoretiese perspektief op hoe organiese kodes `n manier bied om biologiese inligting te hanteer as 'n logiese uitbreiding daarvan. Met hierdie raamwerk as agtergrond gee ek `n oorsig van 'n aantal van die huidige organiese kodes in 'n poging om aan te toon hoe die de nisie van en kriteria vir 'n organiese kode gebruik kan word om die koring van die kaf te skei. Ek stel die `regulering kode' voor in 'n poging om te wys hoe die kode-biologiese raamwerk op nuwe kodes toegepas kan word om hul geskiktheid as organiese kodes te toets en of dit die moeite werd is om hulle verder te ondersoek. Ten spyte daarvan dat kodes algemeen in die biologiese w^ereld voorkom, is relatief min van hulle onomwonde bevestig as organiese kodes. Die hoofdoel van hierdie studie is om vas te stel of die histoonkode 'n ware organiese kode is in die sin van die genetiese of seintransduksie kodes. Ek verskaf 'n volledige oorsig en ontleding van die belangrikste histoon post-translasionele modi kasies, hul biologiese e ekte, en watter prote endomeine verantwoordelik vir die vertaling tussen hierdie twee verskynsels. Ek wys dan hoe hierdie elemente perfek inpas in die teoretiese raamwerk van kodebiologie. Laastens bespreek ek die geldigheid van 'n algoritme-gebaseerde benadering tot die identi sering van organiese kodes wat deur G orlich en Dittrich ontwikkel is. Dit blyk dat hierdie algoritme en die geoperasionaliseerde de nisie van 'n organiese kode sodanig is dat die proses van die identi sering van kodes sonder die nodige ondersoek deur 'n wetenskaplike met 'n biochemiese agtergrond tans nie haalbaar is nie. Hierdie studie bevestig dus die nut van kodebiologie as 'n teoretiese raamwerk vir 'n sintese tussen molekul^ere biologie en inligtingsteorie, bevestig die status van die histoonkode as 'n ware organiese kode, en kritiseer G orlich en Dittrich se poging om organiese kodes te identi seer met 'n algoritme wat gebaseer is op reaksienetwerke en `n kontingensie kriterium.

The extent to which natural selection shapes diversity within populations is a key question for population genetics. Thus, there is considerable interest in quantifying the strength of selection. In this thesis a full likelihood approach for inference about selection at a single site within an otherwise neutral fully-linked sequence of sites is developed. Integral to many of the ideas introduced in this thesis is the reversibility of the diffusion process, and some past approaches to this concept are reviewed. A coalescent model of evolution is used to model the ancestry of a sample of DNA sequences which have the selected site segregating. A novel method for simulating the coalescent with selection, acting at a single biallelic site, is described. Selection is incorporated through modelling the frequency of the selected and neutral allelic classes stochastically back in time. The ancestry is then simulated using a subdivided population model considering the population frequencies through time as variable population sizes. The approach is general and can be used for any selection scheme at a biallelic locus. The mutation model, for the selected and neutral sites, is the infinitely-many-sites model where there is no back or parallel mutation at sites. This allows a unique perfect phylogeny, a gene tree, to be constructed from the configuration of mutations on the sample sequences. An importance sampling algorithm is described to explore over coalescent tree space consistent with this gene tree. The method is used to assess the evidence for selection in a number of data sets. These are as follows: a partial selective sweep in the G6PD gene (Verrelli et al., 2002); a recent full sweep in the Factor IX gene (Harris and Hey, 2001); and balancing selection in the DCP1 gene (Rieder et al., 1999). Little evidence of the action of selection is found in the data set of Verrelli et al. (2002) and the data set of Rieder et al. (1999) seems inconsistent with the model of balancing selection. The patterns of diversity in the data set of Harris and Hey (2001) offer support of the hypothesis of a full sweep.

Orientador: Renato Eugênio da Silva Diniz / Banca: Marilia Freitas de Campos Tozoni Reis / Banca: Daisi Teresinha Chapani / Resumo: O conteúdo de Evolução Biológica, ao longo de seu desenvolvimento histórico, influenciou de maneira profunda a humanidade, tanto sob o viés científico quanto social. Frente a isso, esse tema é considerado atualmente o eixo unificador das Ciências Biológicas. Muitos são os trabalhos que abordam essa temática, porém poucos apresentam um posicionamento crítico, ou seja, não exploram as relações entre os processos de conhecimento humano e as possibilidades de transformação social. Nosso objetivo, neste trabalho, é compreender as significações dos professores de biologia a respeito do conteúdo de evolução biológica e explorá-las com base nas contribuições da Pedagogia Histórico-Crítica. Entendemos como significação a unidade dialética entre os significados (produtos socioculturais) e os sentidos (produtos subjetivos) que constituem a realidade dos indivíduos. Para alcançar nosso objetivo, elaboramos um roteiro de entrevista semiestruturada e realizamos um total de três entrevistas. Por meio do procedimento metodológico de elaboração de núcleos de significação, analisamos e interpretamos essas entrevistas. Todas as análises e interpretações ocorreram sob os pressupostos da Pedagogia Histórico-Crítica, o que nos permitiu evidenciar os limites e as possibilidades de um ensino de evolução biológica pautado nessa pedagogia. / Abstract: The content of biological evolution, throughout its historical development, profoundly influenced the humanity, both under the scientific and social bias. Therefore, this theme is currently considered the unifying axis of Biological Sciences. Many researchers study this theme, but few present a critical position, that is, they do not explore the relations among the processes of human knowledge and the possibilities of social transformation. The aim of this work is understand the meanings of biology teachers regarding the biological evolution content and to explore them based on the contributions of Historical-Critical Pedagogy. We understand as meaning the dialectical unity among social meanings (sociocultural products) and the personal sense (subjective products) that constitute individuals reality. For this, we developed a semi-structured interview script and conducted a total of three interviews. Through the methodological procedure of elaborating signification cores, we analyzed and interpreted these interviews. All analyzes and interpretations occurred under the assumptions of Historical-Critical Pedagogy, which allowed us to highlight the limits and possibilities of a biological evolution teaching based on this pedagogy. / Mestre

Orientador: Cynthia Peralta de Almeida Prado / Banca: Paula Cabral Eterovick / Banca: Cinthia Aguirre Brasileiro / Banca: Milton Cezar Ribeiro / Banca: Celio Fernando Baptista Haddad / Resumo: A configuração da paisagem e as características fenotípicas associadas ao reconhecimento de parceiros podem influenciar na estrutura genética das populações e nos processos de diversificação de uma espécie. Além disso, interações reprodutivas entre espécies distintas podem alterar a história evolutiva de linhagens com a formação de híbridos viáveis. Para investigar essas interações complexas, estudamos o anuro Bokermannohyla ibitiguara, uma espécie com reprodução prolongada, cantos elaborados, corte complexa, fêmeas seletivas e machos agressivos/territoriais. A espécie é endêmica do Cerrado e tem reprodução associada à vegetação ripária dentro e fora do Parque Nacional da Serra da Canastra (PNSC), uma zona de contato com o congênero B. sazimai. Amostramos vários riachos e desenvolvemos microssatélites para analisar a influência da topografia e cobertura vegetal na diferenciação genética. Comparamos, em seguida, morfologia e cantos através da área de distribuição e examinamos os papéis da seleção sexual, deriva genética e adaptação acústica a ambientes florestados (Hipótese da Adaptação Acústica; HAA) na diferenciação acústica. Testamos também a hipótese de que B. ibitiguara e B. sazimai podem hibridizar devido a semelhanças fenotípicas. Indivíduos de B. ibitiguara mostraram diferença genética significativa entre riachos, exceto naqueles dentro do Parque, os quais apresentaram maiores níveis de riqueza alélica e heterosigozidade. A diferenciação genética foi melhor explicada p... (Resumo completo, clicar acesso eletrônico abaixo) / Abstract: Landscape configuration and phenotypic characteristics linked with mating recognition may influence population genetic structure and diversification processes. Moreover, reproductive interactions among different species may alter the evolutionary history of lineages with the formation of viable hybrids. To investigate these complex interactions we studied the treefrog Bokermannohyla ibitiguara, a species with prolonged reproduction, complex calls, elaborate courtship, choosy females and territorial/aggressive males. It is endemic to the threatened Brazilian Cerrado and breeds in streams associated with riparian forests within and outside the Serra da Canastra National Park (SCNP), a contact zone with the congener B. sazimai. We sampled many streams and developed microsatellite markers to analyze the roles of topography and land cover on genetic differentiation. We then compared morphology and calls throughout the range and examined the roles of sexual selection, genetic drift, and acoustic adaptation to forested habitats (Acoustic Adaptation Hypothesis; AAH) on call differentiation. We also tested the hypothesis that B. ibitiguara and B. sazimai may hybridize due to phenotypic similarities. Individuals of B. ibitiguara showed significant genetic differentiation among streams, except those within the Park, which had higher levels of allelic richness and heterozygosity. Genetic differentiation was best explained by topographic complexity, as were some within-population genetic measures. Calls varied more than morphology, suggesting stronger selective pressures on this behavioral phenotype. Acoustic traits associated with individual discrimination and/or female attraction showed significant population differences. Neither genetic differentiation nor riparian forest cover (the AAH) explained... (Complete abstract click electronic access below) / Doutor

The evolution of snakes (Squamata: Serpentes) represents a major transition in squamate reptiles and involves extensive modifications in the body plan. Functional morphology and phylogeny are integrated to discuss adaptive morphological traits in the origin of snakes and in the evolution of the venom-injecting apparatus among lizards, which is convergent with that in snakes. The focus of these analyses is to determine how to best optimize morphological traits on the phylogeny and to use character distribution in terminal taxa to estimate ecological adaptation in ancestral nodes. To study the locomotion transition from lizards to snakes, 45 virtual models of the squamate bony labyrinth in the inner ear were reconstructed. The results show morphological diversifications of the vestibular region among burrowers, generalists and marine swimmers. The vestibule is enlarged in fossorial species, and reduced in marine snakes and the marine lizard Platecarpus coryphaeus. To quantify the morphological differences and provide tractable methods to reconstruct locomotion in ancestral snakes, I performed three-dimensional geometric morphometric analysis of the 45 samples, using six landmarks and 22 semilandmarks. ANOVA tests on the Procrustes coordinates supported differences among fossorial, generalist, and aquatic locomotion categories. Phylogenetic signal was insignificant in the Procrustes coordinates. Using a phylogeny with the 44 extant samples as terminal taxa, I reconstructed shape coordinates of all internal nodes. Reconstructed shape of the vestibular region of key ancestral nodes in snakes preferred a terrestrial origin for crown-group snakes. Morphological proxies used in this study can be applied to stem snakes to estimate locomotion. Methodologically, this study provides a novel approach to resolve the question whether snakes become limbless on land or in the oceans. Evolution of the venom-injection apparatus in lizards is discussed, based on new material of Estesia mongoliensis. A total-evidence phylogenetic analysis of anguimorph lizards is performed with 86 anguimorph taxa coded to 435 morphological characters and four genes. The matrix includes eight new morphological characters. The total-evidence phylogeny suggests that Estesia Mongoliensis is a basal monstersaur whose crown groups are Heloderma, the only living venomous lizards. Presence of tooth flanges with venom grooves is recognized as a new monstersaurian synapomorphy in this study. Estesia mongoliensis has venom grooves comparable to extant Heloderma, but has a deeper root-to-tip groove in the caudal tooth carina, revealing morphological variations of lizard venom delivery apparatus that are not recorded in extant species.

The standard representation of evolutionary relationships is a bifurcating tree. However, many types of genetic exchange, collectively referred to as reticulate evolution, involve processes that cannot be modeled as trees. Increasing genomic data has pointed to the prevalence of reticulate processes, particularly in microorganisms, and underscored the need for new approaches to capture and represent the scale and frequency of these events. This thesis contains results from applying new techniques from applied and computational topology, under the heading topological data analysis, to the problem of characterizing reticulate evolution in molecular sequence data. First, we develop approaches for analyzing sequence data using topology. We propose new topological constructions specific to molecular sequence data that generalize standard constructions such as Vietoris-Rips. We draw on previous work in phylogenetic networks and use homology to provide a quantitative measure of reticulate events. We develop methods for performing statistical inference using topological summary statistics. Next, we apply our approach to several types of molecular sequence data. First, we examine the mosaic genome structure in phages. We recover inconsistencies in existing morphology-based taxonomies, use a network approach to construct a genome-based representation of phage relationships, and identify conserved gene families within phage populations. Second, we study influenza, a common human pathogen. We capture widespread patterns of reassortment, including nonrandom cosegregation of segments and barriers to subtype mixing. In contrast to traditional influenza studies, which focus on the phylogenetic branching patterns of only the two surface-marker proteins, we use whole-genome data to represent influenza molecular relationships. Using this representation, we identify unexpected relationships between divergent influenza subtypes. Finally, we examine a set of pathogenic bacteria. We use two sources of data to measure rates of reticulation in both the core genome and the mobile genome across a range of species. Network approaches are used to represent the population of S. aureus and analyze the spread of antibiotic resistance genes. The presence of antibiotic resistance genes in the human microbiome is investigated.