Anthropology, and other disciplines have searched for isomorphic principles and rules operating in information systems. This thesis locates and describes this deep structure applicable to all information systems. It presents a model for information flow as a set of ordering principles revealing universal patterns inherent in nature, a set of transformation rules functioning to increase organization and complexity, and a structure for this activity. The model is isomorphic: it demonstrates similar operational behavior in different systems. Major features of the model include polarity, emergent or transformational phenomena, self-organization, and a trajectory traveling through a hierarchical structure representing the flow of information. Polar opposition is the primary functional mechanism, and has two critical roles. It initiates and maintains the trajectory through time and stabilizes the system by representing existence in time. The author applies the model to consciousness, neurogenesis, ontogeny, social behavior, mythology, rites of passage, and other systems. / Department of Anthropology

Recent genetic studies have confirmed that there was admixture between African early modern humans and archaic populations throughout the Old World. In this dissertation, I examine European early modern human dental morphology to assess the evidence for Neandertal-human admixture. The focus of this study is not on the question of taxonomic designations of Late Pleistocene Homo, but rather on the interactions of these populations in Europe. This focus on gene flow itself redefines the Neandertal question. Rather than asking if Neandertals are a different species from H. sapiens, I focus on the nature of the interactions between archaic and modern populations, which is essential to understanding the history of modern H. sapiens regardless of species definitions. I recorded dental metric measurements and morphology observations on 85 fossil Neandertals and early modern humans and a recent modern human comparative sample of 330 Native Americans and Spaniards. I examined each trait distribution individually and through the use of Mahalanobis D2, mean measure of divergence, principle components analysis, discriminant function analysis, k-means cluster analysis, and a population genetics program, structure. Through these methods, I found evidence of admixture in the dental trait distributions of European early modern humans. However, it is not evident in traditional distance measures or cluster analyses. The earliest European modern humans do not follow the trend of dental reduction found throughout the Pleistocene and into the Holocene and do not uniformly classify with any fossil population in discriminant function analysis of metric traits. The non-metric trait sample size is too small to make any definitive conclusions, but a mosaic pattern of trait frequencies also suggests admixture. The recent modern human sample shows that while increased variation and a mosaic of non-metric traits persist through many generations after admixture has ceased, traditional methods of distance analysis cannot detect low levels of admixture within 200 years. The program structure is effective in finding patterns of variation within and among populations using morphological data. It will be useful for future analyses of dental traits and other fossil data, given the ability to use it with an incomplete data set.

abstract: The pattern and strength of genetic covariation is shaped by selection so that it is strong among functionally related characters and weak among functionally unrelated characters. Genetic covariation is expressed as phenotypic covariation within species and acts as a constraint on evolution by limiting the ability of linked characters to evolve independently of one another. Such linked characters are "constrained" and are expected to express covariation both within and among species. In this study, the pattern and magnitude of covariation among aspects of dental size and shape are investigated in anthropoid primates. Pleiotropy has been hypothesized to play a significant role in derivation of derived hominin morphologies. This study tests a series of hypotheses; including 1) that negative within- and among-species covariation exists between the anterior (incisors and canines) and postcanine teeth, 2) that covariation is strong and positive between the canines and incisors, 3) that there is a dimorphic pattern of within-species covariation and coevolution for characters of the canine honing complex, 4) that patterns of covariation are stable among anthropoids, and 5) that genetic constraints have been a strong bias on the diversification of anthropoid dental morphology. The study finds that patterns of variance-covariance are conserved among species. Despite these shared patterns of variance-covariance, dental diversification has frequently occurred along dimensions not aligned with the vector of genetic constraint. As regards the canine honing complex, there is no evidence for a difference in the pleiotropic organization or the coevolution of characters of the complex in males and females, which undermines arguments that the complex is selectively important only in males. Finally, there is no evidence for strong or negative pleiotropy between any dental characters, which falsifies hypotheses that predict such relationships between incisors and postcanine teeth or between the canines and the postcanine teeth. / Dissertation/Thesis / Ph.D. Anthropology 2011

Made available in DSpace on 2014-06-11T19:25:28Z (GMT). No. of bitstreams: 0 Previous issue date: 2009-06-24Bitstream added on 2014-06-13T20:33:06Z : No. of bitstreams: 1 costa_obr_me_mar.pdf: 498825 bytes, checksum: 3ae7c7c5aaf9ff0bb10fcc4e44418866 (MD5) / Considera-se a espécie humana como caracterizada por uma cognição diferenciada, que inclui aprendizado constante, uso de linguagem simbólica e auto-consciência. Que fatores evolutivos teriam engendrado tal fenômeno? Nesse trabalho, são discutidos alguns dados e conjecturas da Neuroantropologia Cognitiva, que sugerem uma configuração de fatores, como a adoção do bipedalismo, uso de instrumentos rudimentares, emergência da linguagem e da cooperação social, na origem do fenômeno da cognição humana. A explicação do processo evolutivo humano aponta no sentido da operação de mecanismos de causalidade circular, pelos quais desenvolvimentos incipientes da técnica, da linguagem e da sociabilidade teriam progressivamente causado novos desenvolvimentos nestas mesmas esferas de atividade humana, conduzindo às formas sofisticadas de tecnologia, comunicação e relacionamento humano que caracterizam o período histórico contemporâneo / The human species displays peculiar cognitive abilities that includes continuous learning capacity, symbolic language and self-consciousness. Which evolutionary factors could have engendered this condition? In this work, we discuss evolutionary facts and conjectures from Cognitive Neuroanthropology, suggesting a configuration of several factors - as the adoption of bipedalism, use of rudimentary tools, the emergence of language and social cooperation - in origin of human cognition. An explanation of the process of human evolution could then be achieved from the operation of a mechanism of circular causality, by which incipient developments of technique, language and sociability would progressively cause more complex developments of the same kinds of activity, leading to the sophisticated forms of technology, communication and human relations found in the contemporary epoch

Orientador: Alfredo Pereira Junior / Banca: Jonas Gonçalves Coelho / Banca: Marcelo Carbone / Resumo: Considera-se a espécie humana como caracterizada por uma cognição diferenciada, que inclui aprendizado constante, uso de linguagem simbólica e auto-consciência. Que fatores evolutivos teriam engendrado tal fenômeno? Nesse trabalho, são discutidos alguns dados e conjecturas da Neuroantropologia Cognitiva, que sugerem uma configuração de fatores, como a adoção do bipedalismo, uso de instrumentos rudimentares, emergência da linguagem e da cooperação social, na origem do fenômeno da cognição humana. A explicação do processo evolutivo humano aponta no sentido da operação de mecanismos de causalidade circular, pelos quais desenvolvimentos incipientes da técnica, da linguagem e da sociabilidade teriam progressivamente causado novos desenvolvimentos nestas mesmas esferas de atividade humana, conduzindo às formas sofisticadas de tecnologia, comunicação e relacionamento humano que caracterizam o período histórico contemporâneo / Abstract: The human species displays peculiar cognitive abilities that includes continuous learning capacity, symbolic language and self-consciousness. Which evolutionary factors could have engendered this condition? In this work, we discuss evolutionary facts and conjectures from Cognitive Neuroanthropology, suggesting a configuration of several factors - as the adoption of bipedalism, use of rudimentary tools, the emergence of language and social cooperation - in origin of human cognition. An explanation of the process of human evolution could then be achieved from the operation of a mechanism of circular causality, by which incipient developments of technique, language and sociability would progressively cause more complex developments of the same kinds of activity, leading to the sophisticated forms of technology, communication and human relations found in the contemporary epoch / Mestre

The ability to retrieve DNA from the skeletal remains of ancient humans has yielded many insights into the relationship between humans living today and our nearest evolutionary relatives, the Neandertals and Denisovans. Two important insights emerged from the first high-quality genome sequences of Neandertals and Denisovans: 1) these archaic humans had very low genetic diversity in comparison to most populations of present-day humans, and 2) there was gene flow from archaic humans into the ancestors of present-day people. In my thesis, I explored aspects of both these insights. In my first project, I analysed the consequences of low genetic diversity of archaic humans for immune genes, using genetic diversity in protein-coding genes (‘gene diversity’) as a proxy for functional diversity. I conclude that low gene diversity in archaic humans did not affect immune genes more severely than any other class of protein-coding genes. I then show that the MHC genes, that typical have high genetic diversity and are a component of the adaptive immune system, have substantially higher gene diversity than expected from the genome-wide gene diversity in archaic humans. Moreover, I find no detectable reduction in gene diversity between two Neandertals that lived more than 70,000 years apart. This is first evidence indicating that diversity in late Neandertals did not decrease over the last ~100,000 years of their existence, which would be expected if low gene diversity had played a considerable role in Neandertal extinction, as has been proposed. In my second project I analysed genomic regions depleted of both Neandertal and Denisovan ancestry in the genomes of humans living today (‘shared deserts’). It has been suggested that shared deserts reflect incompatibilities between archaic humans and the ancestors of present-day humans, and were created by negative selection against archaic alleles. By analysing archaic ancestry in almost 2,000 published present-day human genomes, including 155 published genomes from Oceania, I generated a further refined set of genomic regions that are most depleted of archaic ancestry. I discuss candidate variants in these regions that may underlie important phenotypic or functional differences between archaic and modern humans, such as in the brain-expressed genes CADM2 and KCND2, and propose this refined list as a set of candidates for future molecular testing.:Bibliographische Darstellung iii Table of contents iv Summary 8 Zusammenfassung 14 1. Introduction 21 1.1. A strange fossil and its genome 21 1.2. Archaic humans had low genetic diversity 26 1.3. Evidence of gene flow between archaic humans and AMH 29 1.3.1. Identification of archaic sequence and its impact on humans today 32 1.3.1.1. The distribution of archaic sequence in AMH is heterogeneous 34 1.3.1.2. Negative selection against introgressed archaic sequence 37 1.3.1.3. Adaptive introgression: Archaic sequence under positive selection in AMH 39 1.3.1.4. Association of introgressed variants with phenotypes of present-day people 41 1.3.2. Deserts: Gene flow left regions depleted of archaic introgression 43 2. Thesis outline 46 3. Methods 47 3.1. Methods for study of immune gene diversity 47 3.1.1. Data 47 3.1.2. Measure of gene diversity 47 3.1.3. Diversity in innate immune and MHC genes 48 3.1.4. GO enrichment analysis 49 3.2. Methods for study of deserts of archaic ancestry 50 3.2.1. Data sets and processing 50 3.2.2. Identification of introgressed haplotypes 51 3.2.2.1. Hidden Markov Model (HMM) 51 3.2.2.2. Probability cut-off for haplotypes to be archaic 51 3.2.3. Reanalysis of published deserts of archaic ancestry 52 3.2.3.1. Shared deserts 52 3.2.3.2. Sliding windows 52 3.2.3.3. Mean percentage introgression 53 3.2.3.4. Comparison to random regions 53 3.2.3.5. Definition of refined shared desert regions 54 3.2.3.6. Overlap of refined shared deserts with genes 54 3.2.3.7. Enrichment analyses in refined shared desert regions 55 3.2.3.8. Overlap with regions under ancient positive selection on the AMH lineage 55 3.2.3.9. Overlap with (nearly) fixed differences between present-day and archaic humans 56 4. Results 57 4.1. Immune gene diversity in archaic and present-day humans 57 4.1.1. Abstract 58 4.1.2. Introduction 59 4.1.3. Results 61 4.1.3.1. Archaic humans had lower overall gene diversity than present-day humans 61 4.1.3.2. Archaic humans had similarly low gene diversity in innate immune genes compared with non-immune genes 62 4.1.3.3. High MHC gene diversity in archaic humans 64 4.1.3.4. Genes with highest/lowest diversity show similar GO enrichments in archaic and present-day humans 66 4.1.4. Discussion 69 4.1.5. Supplementary results 71 4.1.6. Acknowledgements and author contributions 72 4.2. Refining deserts of archaic ancestry 73 4.2.1. Abstract 73 4.2.2. Introduction 75 4.2.3. Results 78 4.2.3.1. Genome-wide patterns of archaic introgression are consistent with previous maps 78 4.2.3.2. The published shared desert regions are not the most depleted regions in the genome 79 4.2.3.3. Levels of archaic introgression in shared deserts for the IGDP data set are comparable 82 4.2.3.4. Shared deserts unique to either the Vernot or Sankararaman set have lower mean percentage introgression 84 4.2.3.5. Refined shared deserts 84 4.2.3.6. Overlap of refined shared deserts with genes 87 4.2.3.7. Enrichment analyses 88 4.2.3.8. Overlap with regions under ancient positive selection on the AMH lineage 89 4.2.3.9. Overlap of refined shared deserts with (nearly) fixed differences (nFD) 89 4.2.4. Discussion 94 4.2.5. Acknowledgements 98 5. Discussion and outlook 99 5.1. Interpreting immune gene diversity in archaic humans 99 5.2. Implications from refined deserts of archaic ancestry 104 5.2.1. Comments on the origin of desert regions 106 5.2.2. Candidates for functional molecular testing in refined deserts 107 5.2.3. Future directions in the characterisation and definition of shared deserts 110 5.3. Future directions beyond shared deserts 115 6. Outlook: Molecular functional testing of candidate variants 118 7. Conclusions and final remark 122 8. Supplementary information (SI) 124 8.1. SI: Immune gene diversity in archaic and present-day humans 124 8.2. SI: Refining deserts of archaic ancestry 152 Index of figures 216 Index of tables 218 Index of supplementary data files 220 References 221 Abbreviations 240 Acknowledgements/Danksagungen 242 Curriculum vitae 244 Publications 248 Selected talks 249 Poster presentations 249 Selbstständigkeitserklärung 250 Nachweis über Anteile der Co-Autor:innen 251

This thesis is about the pedagogical transformation of modern scientific knowledge from the field of palaeoanthropology and evolution anthropology to the teaching about human at the first and high schools in the Czech Republic. The main objective of this thesis (realised through four constituent research studies) is to analyse and to describe this complex and multilevel process. The first step was the content analyse of 32 textbooks. We also analysed the framework of the whole process. We realise questionnaire survey among 217 teachers and also interview with 10 teachers. The last research study about student's attitude and knowledge was questionnaire survey among 660 students. We found that there are no serious obstacles in the teaching of (human) evolution from the field of believers in the Czech Republic like in some other countries. It takes usually few decades to get new findings and conceptions into the textbooks, despite it some exceptions exist. Teachers seem to be the key participants of the process of pedagogical transformation. It is not only about the information they teach in their lessons but also about the way how they teach and about the attitude the build-up towards the topic among their students.

Islands have been considered natural laboratories to study evolutionary processes. Ibiza is a  small island in Spain whose population stands out from other Spanish populations due to its  particular demographic and historical processes. War, famine, and several epidemics have af fected Ibizans, and these phenomena could have left signatures of positive selection in their  genomes. Here, we used three different methodologies to detect positive selection: The Popu lation Branch Statistic (PBS), the Integrated Haplotype Score (iHS), and the Cross-Population  Extended Haplotype Homozygosity (XP-EHH). We used a sliding windows approach to control  for spurious results. The candidate windows for selection were chosen using three different  criteria for each test: maximum and mean score within each window, and proportion of high  scores in each window. Only the windows being simultaneously on the top of each of the three  criteria were selected for annotation and enrichment analyses. The most common traits asso ciated with the SNPs present in the candidate windows were blood function, cardiovascular  diseases, body mass measures, lipid metabolism, renal function, and skin diseases. We sug gest some hypotheses to explain the selection signatures related to some of these traits and  some recommendations for further studies to overcome the present research's limitations.

Among the American population, there is a general misunderstanding of human evolution and human life in the Paleolithic. Beyond the mechanics of biological evolution, there is confusion over what sorts of modern-day behaviors are vestiges from humans’ evolutionary past. My master’s thesis explores what kind of misconceptions about Paleo-life and human evolution circulate in popular discourse and where these misconceptions stem from. Drawing on the experiences of community members in upstate New York, I conducted a multimodal discourse analysis via surveys, interviews, and a reflexive media analysis to triangulate my findings. Through these two discourses – that of the everyday understanding of human evolution and Paleo-life versus what kinds of messages popular media portrays on these same issues – I determined that popular media constitutes a large resource of information gathering for the general public. Furthermore, the media highlighted by my research participants to exhibit themes of human evolution had clear messages on race, gender, and violence that research participants largely believe to be successful modes of “survival of the fittest” and thus cultural “survivals” from when we were evolving to our modern form. Participant and media messages regarding race, gender, and violence mirror the logics behind white American Exceptionalism; though these everyday epistemologies are argued by my participants to be biological in nature, they merely reflect today’s values and are logics used to successfully participate in American society. That is to say, the repetitive, naturalizing messages portrayed by popular media on human evolution and paleo-life both construct and reify the popular understanding that modern concepts of race, gender and violence are biological and have led to the success of our species. With these findings, I offer science educators recommendations on how to best utilize edutainment to correct these outdated narratives. / Graduate

In the past, efforts to prove or disprove stasis in hominids have relied upon univariate tests such as Students's t-test. Severe methodological and interpretive problems arise from the misapplication of univariate statistics to questions concerning variation in shape through time. These are questions best addressed using the multivariate approach of morphometrics. Eighteen cranial dimensions drawn from 33 mid and late Pleistocene Homo sapiens were examined using principal component analysis (PCA). PCA divided the sample into two distinct morphologies. Archaic Homo sapiens of the mid Pleistocene clustered with Wurm I neanderthals and apart from post Gottweig early anatomically modern Homo sapiens. ANOVA and Cluster analysis confirm the groups represent two different morphologies rather than a single spectrum of morphological change. These results support stasis rather than phyletic gradualism during this period of hominid evolution.