Cyclic Incrementality in Competitive Coevolution: Evolvability through Pseudo-Baldwinian Switching-Genes

Coevolving systems are notoriously difficult to understand. This is largely due to the Red Queen effect that dictates heterospecific fitness interdependence. In simulation studies of coevolving systems, master tournaments are often used to obtain more informed fitness measures by testing evolved individuals against past and future opponents. However, such tournaments still contain certain ambiguities. We introduce the use of a phenotypic cluster analysis to examine the distribution of opponent categories throughout an evolutionary sequence. This analysis, adopted from widespread usage in the bioinformatics community, can be applied to master tournament data. This allows us to construct behavior-based category trees, obtaining a hierarchical classification of phenotypes that are suspected to interleave during cyclic evolution. We use the cluster data to establish the existence of switching-genes that control opponent specialization, suggesting the retention of dormant genetic adaptations, that is, genetic memory. Our overarching goal is to reiterate how computer simulations may have importance to the broader understanding of evolutionary dynamics in general. We emphasize a further shift from a component-driven to an interaction-driven perspective in understanding coevolving systems. As yet, it is unclear how the sudden development of switching-genes relates to the gradual emergence of genetic adaptability. Likely, context genes gradually provide the appropriate genetic environment wherein the switching-gene effect can be exploite

Art, Shamanism and Animism

Art, shamanism, and animism are mutable, contested terms which, when brought together, present a highly charged package. Debates around these three terms continue to generate interest and strong opinions in the first decades of the twenty-first century. The editors recognise the urgency to explore them together in an unprecedented exercise which, to date, has only been attempted with reference to selected disciplines, periods, or regions. The contributors to this collection reignite debates around the status of ‘things’ identified as ‘art’ through the lens of theories drawn from new materialism, new animism, and multi-species and relational thinking. They are concerned with how and when art-like things may exceed conventional understandings of ‘art’ and ‘representation’ to fully articulate multiple scenarios or ‘manifestations’ in which they interface with academic discourses around animism and shamanism. The authors put in sharp focus the materiality of art-things while stressing their agentive, emotive, and performative aspects, looking beyond their appearances to what they do and who they may be or become in their dealings with diverse interlocutors. The contributors are united in their recognition that things and images are deeply entangled with how different communities, human and other-than-human, experience life, shifting attention from an obsolete concept of worldview to how reality is perceived through all the senses, in all its aspects, both tangible and intangible

Evolutionary forces shaping innate immune gene variation in a bottlenecked population of the Seychelles warbler

In this thesis, I investigated different evolutionary forces in shaping genetic variation within a bottlenecked population of an island species, the Seychelles warbler (Acrocephalus sechellensis). I specifically explore pathogen-mediated selection within this system by using avian beta-defensins and toll-like receptor genes to examine functional variation. First, I characterise variation within both gene groups in this population and show that this species’ demographic history has had an overriding effect on selection and random drift is the predominant evolutionary force. I characterise variation within these gene groups across several other Acrocephalus species, in addition to looking at a specific locus in a prebottlenecked population in order to directly compare genetic variation pre- and postbottleneck. I use population genetic statistical methods to detect selection at several polymorphic genes and evaluate the robustness of these methods when applied to singlelocus sequence data, which may be lacking in power and not meet the demographic assumptions that come with these tests. To overcome this, I designed forward-in-time simulations based on microsatellite markers used in pre- and post-bottleneck populations of the Seychelles warbler. I am able to delineate the evolutionary effects of selection from drift and show that some toll-like receptor genes are indeed under positive balancing selection in spite of the recent bottleneck. I further explore how this variation is maintained by conducting association analyses investigating innate immune gene variation and its relationship with individual survival and malarial susceptibility / resistance. Environmental factors are also considered. By investigating the consequences of functional variation in a bottlenecked species we are able to assess its long-term viability and adaptive potential, whilst elucidating the evolutionary importance of maintaining genetic variation in natural populations

Botany_Theory Lectures_Pharmacy degree-UV_IsaacGarridoBenavent

El document forma part dels materials docents programats mitjançant l'ajut del Servei de Política Lingüística de la Universitat de València.This document contains the teaching material corresponding to the subject Botany, which is taught in the first year of the Degree in Pharmacy at the University of Valencia. More specifically, this material is designed for the high performance group (ARA). It contains basic botany lessons (structure and reproduction) as well as others dedicated to describing the diversity of different botanical groups, such as plants, algae and fungi

Exploring the molecular footprints of natural selection in threespine stickleback

The primordial and prevailing goal of evolutionary biology is to elucidate how biological diversity emerges from the interaction of organisms and environments. Nowadays, we have the technology and analytical power to ask the same question at a much deeper scope and aim to identify the genomic processes underlying the adaptation of species to spatially and temporally changing environments. This has recently led to the emergence of a new research field – evolutionary genomics, which focuses on understanding the genetic basis of adaptive evolutionary change and ultimately establish the molecular links between phenotype, genome, development and ecology. Population genomic investigations embedded in strong ecological frameworks are still sparse but arguably represent the only way to empirically establish those links. My thesis focused on exploring the genomic and phenotypic footprints of natural selection, in threespine stickleback, contributing to further our understanding of the tempo and mode of natural adaptive change

Writing a way home : Cherokee narratives of critical and ethical nationhood

textWriting a Way Home examines ways that Cherokees in the latter half of the 20th century who have been marginalized through the privileging of state narratives have deployed literature as a way to challenge narratives of state domination and to imagine and work toward more critical, ethical Cherokee nationhood. I examine the ways that Robert K. Thomas and Natachee Scott Momaday used literature during the federal Termination and Relocation programs to imagine functioning tribal nations against the United States' assimilation narrative of the time. I further delve into how the Cherokee Nation's state narrative of the Cherokee Freedmen has denationalized Freedmen descendants and how, by using the WPA narratives of former Cherokee slaves and Tom Holm and Thomas' Peoplehood Matrix, we can re-narrate the Freedmen descendants into a more ethical Cherokee Nation. Finally, I close the study with an examination of Daniel Heath Justice's Way of Thorn and Thunder trilogy that uses storytelling to re-imagine a place of reverence for gay and queer-identified Cherokees at a time when the Cherokee Nation passed a ban on same-sex marriage, claiming that such relationships defied what the Cherokee state narrates as tribal tradition. I aim to show in this study the danger of uncritically accepting the state model for tribal nations and the importance of periodically challenging tribal nations when leaders behave unethically. Likewise, this study demonstrates the power of story to not only check the excesses of state sovereignty that marginalize people based on their history, politics, race and sexuality, but also the power to re-imagine a nation -- a home -- that welcomes all its relations.Englis

The Laplace transform in population genetics: from theory to efficient algorithms

Extracting information on the selective and demographic past of populations contained in samples of genome sequences requires a description of the distribution of the underlying genealogies. Using the Laplace transform, this distribution can be generated with a simple recursive procedure, regardless of model complexity. Assuming an infinite-sites mutation model, the probability of observing specific configurations of linked variants within small haplotype blocks can be recovered from the Laplace transform of the joint distribution of branch lengths. However, the repeated differentiation required to compute these probabilities has proven to be a serious computational bottleneck in earlier implementations. In this thesis, I extend existing work on this theoretical framework in three ways. First, I incorporate a description of the impact of hard sweeps on the genealogies of nearby neutral sites. Secondly, the recursive nature of this approach not only makes the theory easily extendable, but also implies the possibility of graph-based algorithms to query the joint distribution of branch lengths. I devise algorithms that drastically reduce the computational cost of deriving mutation configuration probabilities. This work has been implemented in an open-source Python module, agemo. Finally, the efficient library is used to develop a fully fledged demographic inference tool for fitting models of isolation with migration (IM) to genomic data. Fitting these models to smaller chunks of sequence allows us to also infer both background selection and barriers to gene flow. The software is designed to be modular and user-friendly. It facilitates the entire model fitting workflow, from parsing variants to a simulation-based bootstrap on the model estimates

Indigenous Knowledge Production

Despite many scholars noting the interdisciplinary approach of Aboriginal knowledge production as a methodology within a broad range of subjects – including quantum mathematics, biodiversity, sociology and the humanities - the academic study of Indigenous knowledge and people is struggling to become interdisciplinary in its approach and move beyond its current label of ‘Indigenous Studies’. Indigenous Knowledge Production specifically demonstrates the use of autobiographical ethnicity as a methodological approach, where the writer draws on lived experience and ethnic background towards creative and academic writing. Indeed, in this insightful volume, Marcus Woolombi Waters investigates the historical connection and continuity that have led to the present state of hostility witnessed in race relations around the world; seeking to further one’s understanding of the motives and methods that have led to a rise in white supremacy associated with ultra-conservatism. Above all, Indigenous Knowledge Production aims to deconstruct the cultural lens applied within the West which denies the true reflection of Aboriginal and Black consciousness, and leads to the open hostility witnessed across the world. This monograph will appeal to undergraduate and postgraduate students, as well as postdoctoral researchers, interested in fields such as Sociology of Knowledge, Anthropology, Cultural Studies, Ethnography and Methodology

Blonde Indian: Manuscript, Author's Notes, and Correspondence

Item 1. Author's notes on structure -- Item 2. Draft versions of Acknowledgements, Book Summary and About the Author sections -- Item 3. Draft version of portion of "The Bog" section -- Item 4. Completed manuscript appraisal forms from reviewers -- Item 5. Letter from Ernestine Hayes to University of Arizona Press -- Item 6. Letter from editor at University of Arizona Press to Hayes -- Item 7. Copyedited "redline" manuscript sent to Ernestine Hayes in September 2005, with publisher's suggested edits shown in-line and comments from author's proofreader in margins: part 1, pages 1-58 -- Item 8. Copyedited "redline" manuscript: part 2, pages 59-92 -- Item 9. Copyedited "redline" manuscript: part 3, pages 93-156 -- Item 10. Copyedited "redline" manuscript: part 4, pages 157-217 -- Item 11. Letter from Hayes to editor, University of Arizona Press

Society, ritual and symbolism in Umeda village (West Sepik District, New Guinea)

This thesis concerns the people of Umeda village, one of the four villages which make up the Waina-Sowanda Census district of the West Sepik district of New Guinea. The thesis falls into three major parts. In the first part (Chapters 1 and 2) the major features of the social structure are outlined. The economy (based on Sago, hunting, and gardening) is described. The discussion of Social Structure looks at various 'levels' of organisation starting with the cost inclusive and working downwards. These levels are 1) the connubium, 2) the village, 3) Village societies 4) Bush associations 5) the hamlet 6) hamlet societies 7) clans and sub-clans, and 8) the household. The main theme of the discussion is the role of marriage alliance, set up through sister-exchanges between exogamous (patrilineal) clan-hamlets, as the 'lateral’ bonding element in the social structure. It is shown, for instance, that members of the society conceptualise its overall structure in terms of 'compatibilities’ set up by alliance relationships. These alliance relations, though actually shifting slightly with each generation are seen as permanent structural features. This is given symbolic expression in the Village- and Hamlet-moiety organisation. The opposition of kinship relations (within the clan-hamlet) and alliance relations (outside it) is postulated as the basis of a pervasive opposition between ‘central’ and 'lateral' -- an opposition which underlies the moiety organisation, and which is also of crucial importance in understanding the Symbolic System as found e.g. in Ritual. Later sections of Chapter 2 (viii - xi) discuss interpersonal relations in more detail. The problems posed by sorcery beliefs are discussed in relation to marriage and sexual relations generally. The concept of 'tadv' - relations (killing, eating, shooting, and copulating with the other} are discussed as the basic modality of ego-alter relations across sociological boundaries. Sorcery is the reciprocal of marriage. Chapter 3 takes up the second major theme of the Thesis. This chapter is devoted to linguistic symbolism, particularly in relation to the basic social and kinship roles. Three forms of linguistic symbolism (or 'lexical motivation’) are distinguished; 1) semantic motivation 2) morphological motivation 3) psychological motivation. Chapter 3 concerns itself only with the first two kinds, Phonological motivation in Umeda being explored in Appendix I as it poses problems which go beyond the purely Anthropological. It is shown that the Umeda vocabulary contains many implicit clues as to the symbolic system of the people. A system of analogies is demonstrated, using lexical evidence, between the structure of the body, the structure of botanical entities such as trees and the overall structure of the society. Once again the ‘central/lateral’ opposition is shown to be crucial, but this is further elaborated into a notion of ‘organic structure’ -- a structural model applicable both to biological and sociological organisms. Considerable attention is devoted to an analysis of Umeda tree symbolism: for instance, the fact that the Mother's Brother is (lexically) identified with the Sago Palm, the Ancestors with the Coconut palm and so on. Chapter 3 thus performs a 'bridging’ function between the first part of the thesis which is basically concerned with Sociological questions, and the second part which is concerned with Ritual Symbolism. Through a consideration of language, an understanding is gained both of the 'organic' metaphor at the heart of Umeda symbolism, and of the way in which this kind of metaphor meshes in with the details of the functioning of the social system, dominated by certain basic kinship roles. Chapter 4 is mainly descriptive. The Ida fertility rites, performed annually to increase the productivity of the sago palms are described in detail. A discussion of the actual ceremonies is preceded by an account of the many months of preparations for the ritual. It is argued that the ritual, and the need to accumulate supplies of food for its performance, imposes pattern and discipline on mundane economic activity. The ceremonies themselves consist of the appearance, over the course of a night and the subsequent two days, of a sequence of masked dancers (all male) representing various ritual roles. The most important roles are those of 1) cassowaries, 2) fish --- of which there are two kinds, the one red, the other black, 3) sago, 4) termites and 5) ipele bowmen, representing neophytes accompanied by preceptors. Chapter 5 takes the various ritual roles in order of their appearance and analyses their symbolic significance. A preliminary discussion is devoted to methodological issues. Subsequent sections discuss ritual roles under a number of rubrics e.g. the significance in practical or mythological terms of the animal or species represented, the significance of the constraints on actors taking certain roles, the significance of body-paint styles and mask styles, the (significances of various methods of dancing etc. All these ‘role attributes’ are set out in Tabular diagram-form (Table 5). The problem then becomes the analysis of the ritual process, seen as a sequence of transformations taking place in the attributes of successive ritual actors over the course of the total rite. It is demonstrated that the Ida ritual can be best understood as a concrete and dramatic representation of the overall process of bio-social regeneration. The cassowaries, who open the ritual, are shown transformed, and regenerated, as the (neophyte) bowmen, whose loosing off of magical arrows (ipele) is the culmination, and concluding, act of the ritual cycle. This finding is supported by detailed analyses of the transformations of mask-styles and body paint styles throughout the ritual. An extended account is given of Umeda colour symbolism. This leads, finally, to a discussion of the ritual representation of Time. It is argued that the ritual is a means of (symbolically) renewing Time. Certain contradictions inherent in the notion of temporality are specified, and the ritual is seen as a means of overcoming these contradictions within the cultural and symbolic milieu of Umeda. This chapter concludes the main part of the thesis. Two appendices deal I) with phonological motivation in Umeda – it is argued that articulatory features are employed expressively in the structure of Umeda lexical items. II) An appendix gives the complete Pul-tod Myth – a myth referred to at various points in the structure in the thesis, concerning the adventures of the ‘Oedipal’ hero, Pul-tod (Areca-man)