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A Note On The Denisova Cave mtDNA Sequence Nature Precedings
Niccolo Caldararo; Michael Guthrie.
The recently published Altai fossil sequence from Denisova Cave was purported to be so different from anatomically modern humans, yet have the physiological landmarks of that species designation. When the published sequence was examined it was found that segments in the mtDNA hypervariable regions could be found to align with that of anatomically modern humans if one introduced an insertion at a position found in Neanderthals. Some other points of interest arise from a reconsideration of the sequences for other published samples and Neanderthals from the same perspective.
Tipo: Manuscript Palavras-chave: Genetics & Genomics; Evolutionary Biology.
Ano: 2011 URL: http://precedings.nature.com/documents/5360/version/2
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Mitochondrial Molecular Adaptations and Life History Strategies Coevolve in Plants Nature Precedings
Neeraja M. Krishnan; Basuthkar J. Rao.
Messenger RNA secondary structure prevents mutations at functionally important sites. Mutations at exposed sites would cause micro-adaptations, niche-specialization, and therefore, can be thought to promote K-strategists. Exposing, rather than protecting, conserved sites, is also potentially adaptive because they probably promote macro-adaptive changes. This presumably fits r-strategists: their population dynamics tolerate decreased survival. We found that helix-forming tendencies are greater at evolutionary conserved sites of plant mitochondrial mRNAs than at evolutionary variable sites in a majority (73%) of species–gene combinations. K-strategists preferentially protect conserved sites in short genes, r-strategists protect them most in larger...
Tipo: Manuscript Palavras-chave: Bioinformatics; Plant Biology; Evolutionary Biology.
Ano: 2008 URL: http://precedings.nature.com/documents/1922/version/1
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Publishing re-usable phylogenetic trees, in theory and practice Nature Precedings
Brian O'Meara; Jamie Whitacre; Ross Mounce; Dan F. Rosauer; Rutger A. Vos; Arlin Stoltzfus.
Sharing and re-use of data are essential to the progressive and self-correcting nature of science. In recognition of this principle, journals and funding agencies have adopted policies to encourage sharing of information ('data'), including empirical data as well as computed inferences such as phylogenetic trees. 
Here we summarize an ongoing analysis of 1) current practices for sharing phylogenetic trees and associated data; 2) current barriers to effective sharing and reuse of such data; and 3) prospects for reducing these barriers to promote more widespread sharing and re-use. Currently, the technical infrastructure is available to support (with some limitations) rudimentary archiving in conjunction with manuscript...
Tipo: Presentation Palavras-chave: Bioinformatics; Evolutionary Biology; Data Standards.
Ano: 2011 URL: http://precedings.nature.com/documents/6048/version/1
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Hunter-gatherers in a howling wilderness: Neoliberal capitalism as a language that speaks itself Nature Precedings
Rodrick Wallace.
The 'self-referential' character of evolutionary process noted by Goldenfeld and Woese (2010) can be restated in the context of a generalized Darwinian theory applied to economic process through a 'language' model: The underlying inherited and learned culture of the firm, the short-time cognitive response of the firm to patterns of threat and opportunity that is sculpted by that culture, and the embedding socioeconomic environment, are represented as interacting information sources constrained by the asymptotic limit theorems of information theory. If unregulated, the larger, compound, source that characterizes high probability evolutionary paths of this composite then becomes, literally, a self-dynamic language that...
Tipo: Manuscript Palavras-chave: Ecology; Bioinformatics; Earth & Environment; Evolutionary Biology.
Ano: 2011 URL: http://precedings.nature.com/documents/5650/version/1
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Eco-evolutionary consequences of road adjacency and road salt on the wood frog, Rana sylvatica Nature Precedings
Steven P. Brady.
The network of roads on the landscape is vast, and has wide-reaching ecological influence. Recent investigations have focused on understanding impacts of contaminants from road runoff, especially deicing agents such as road salt. Despite growing research concerning ecological impacts of roads, our understanding of long-term consequences remains nascent. This stems in part from a dearth of investigations, and in part because ecological research typically ignores evolution on contemporary timescales. Yet reports of evolution influencing ecological outcomes are growing, suggesting this influence may be the rule rather than the exception. This may be especially true for species with spatially structured populations. For amphibians, such structuring coupled...
Tipo: Presentation Palavras-chave: Ecology; Earth & Environment; Evolutionary Biology.
Ano: 2009 URL: http://precedings.nature.com/documents/3674/version/1
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It is better than you think: fluid intelligence across the lifespan Nature Precedings
Tracy Packiam Alloway; Ross Alloway.
The growth and decline of fluid intelligence is associated with brain structural changes. For example, development of fluid IQ is associated with cortex thickness during the critical period between 6 to 12 years old. On the other end of the lifespan, poor performance in cognitive functioning is attributed to a decrease of frontal gray matter density in elderly populations. In particular, there is a sharp decline in fluid IQ scores after 65 years of age. There is substantial evidence that working memory and fluid intelligence (Gf) share neural substrates, such as the prefrontal and parietal cortices. However, very little research has examined whether the pattern of growth and decline in working memory mirrors that of fluid intelligence. For example, does...
Tipo: Manuscript Palavras-chave: Evolutionary Biology.
Ano: 2010 URL: http://precedings.nature.com/documents/4655/version/1
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A conceptual framework for the evolutionary selection of biologically 'essential' elements Nature Precedings
Mark Conyers.
Standard texts dutifully list 16 essential elements for plant growth, yet the literature indicates that the boundary between essential and nonessential nutrients for plants is not always clear. When animals and 'lower' organisms are considered, the team of 16 is considerably expanded and the notion of essentiality is blurred. Why are some elements more important than others to plants and to organisms in general? Here I propose three criteria by which elements might have been selected in the development of organisms: low atomic weight, at least modest abundance, and ease of assembly into complex structures. Assembly of the structural elements C, N, S, P, and O is based on valency and ionic potential. The selection of monovalent elements...
Tipo: Manuscript Palavras-chave: Earth & Environment; Evolutionary Biology.
Ano: 2009 URL: http://precedings.nature.com/documents/3223/version/1
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On Asymmetry in Biology and Nature Nature Precedings
I. C. Baianu.
Symmetry has attracted a substantial amount of effort because considerable simplifications are possible in the mathematical and physical treatment of phenomena and natural systems that possess a certain degree of symmetry. Among physical and chemical systems the most widely known are those related to crystals and fluids. Whereas crystals have a lattice structure and a symmetry caused by ‘perfect’ order which can be classified by mathematical symmetry groups, most fluids have an average isotropic, highly-disordered ‘structure’ that is often considered to be random.Asymmetry is widely encountered in Biology and ecological systems- from amino acids to trees forests, and tribes, from physiological processes to...
Tipo: Manuscript Palavras-chave: Biotechnology; Chemistry; Developmental Biology; Ecology; Genetics & Genomics; Microbiology; Molecular Cell Biology; Bioinformatics; Earth & Environment; Plant Biology; Evolutionary Biology.
Ano: 2012 URL: http://precedings.nature.com/documents/7134/version/1
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Age and origin of enigmatic megaherbs from the subantarctic islands Nature Precedings
Steven J. Wagstaff; Ilse Breitwieser; Christopher Quinn; Motomi Ito.
Biogeographic relationships in the southern hemisphere have puzzled biologists for the last two centuries. Once joined to form the supercontinent Gondwana, Africa, Antarctica, Australia, New Zealand and South America are widely separated by the Pacific and Indian oceans. Sir Joseph Hooker was the first to suggest that Antarctica served as a corridor for plant migration not unlike the land-bridges in the northern hemisphere. While the Antarctic flora was largely erased by glaciation during the Pleistocene, at least some of these Antarctic plant communities found refuge on the subantarctic islands. Here we provide support for the hypothesis that giant herbs persisted in the subantactic islands prior to the onset of Pleistocene glaciation, then dispersed...
Tipo: Manuscript Palavras-chave: Ecology; Plant Biology; Evolutionary Biology.
Ano: 2007 URL: http://precedings.nature.com/documents/1272/version/1
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Theory of the Origin, Evolution, and Nature of Life Nature Precedings
Erik D. Andrulis.
Life is an inordinately complex unsolved puzzle. Despite significant theoretical progress, experimental anomalies, paradoxes, and enigmas have revealed paradigmatic limitations. Thus, the advancement of scientific understanding requires new models that resolve fundamental problems. Here, I present a theoretical framework that economically fits evidence accumulated from examinations of life. This theory is based upon a straightforward and non-mathematical core model and proposes unique yet empirically consistent explanations for major phenomena including, but not limited to quantum gravity, phase transitions of water, why living systems are predominantly CHNOPS (carbon, hydrogen, nitrogen, oxygen, phosphorus, and sulfur), homochirality of sugars and...
Tipo: Poster Palavras-chave: Evolutionary Biology.
Ano: 2012 URL: http://precedings.nature.com/documents/7050/version/1
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The Size-Weight Illusion Is Not an Illusion When Picking the Best Objects to Throw Nature Precedings
Qin Zhu; Geoffrey Bingham.
Heaviness perception involves a misperception of weight known, since the 19th century, as the Size-Weight Illusion ^1^. The larger of two objects of equal mass is reported to be lighter than the smaller when they are lifted. The illusion has been found to be reliable and robust. It persists even when people know that the masses are equal and handle objects properly ^2^. It has been exhibited by children of only 2 years of age ^3,4^. All this suggests that the effect might be intrinsic to humans. Although different hypotheses have been advanced to account for the illusion over the 100+ years it has been studied ^5-11^, its origin remains unknown. More recently, people's perception of optimal objects for long distance throwing was found to exhibit a...
Tipo: Manuscript Palavras-chave: Developmental Biology; Ecology; Evolutionary Biology.
Ano: 2010 URL: http://precedings.nature.com/documents/4584/version/1
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Toward a Complete Phyloreferencing Language Nature Precedings
T. Michael Keesey.
A phyloreference is a statement indicating a taxon within a phylogenetic context. A common use for phyloreferences is in phylogenetic definitions, which tie taxonomic names to taxa via such statements. Several conventions for writing phyloreferences have been proposed, but most only cover a few “standard” forms (node‑, branch‑, and perhaps apomorphy‑based clades) without the capacity to represent more “exotic” forms (e.g., ancestor‑based clades and qualified/modified references). In order to build a complete phyloreferencing language, the mathematical underpinnings of phylogenetic contexts must be clarified. A phylogenetic context may be modeled as a directed, acyclic...
Tipo: Presentation Palavras-chave: Bioinformatics; Evolutionary Biology.
Ano: 2011 URL: http://precedings.nature.com/documents/4652/version/2
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Atmospheric hypoxia limits selection for large body size in insects Nature Precedings
C Jaco Klok; Jon Harrison.
Recent geological models indicate a marked increase in atmospheric oxygen partial pressure (aPO~2~) to 32 kPa in the Permo-Carboniferous (approx. 300 million years ago), subsequently falling to 13 kPa in the Triassic^1^.These aPO~2~ changes have been hypothesized to cause multiple major evolutionary events^2^ including the appearance and subsequent extinction of giant insects and other taxa^3, 4^. Patterns of increasing tracheal investment in larger insects support this hypothesis^5^, as do observations of positive relationships between aPO~2~ and body size in single- or multi-generational experiments with _Drosophila melanogaster_ and other insects^6^. Large species likely result from many generations of selection for large body size driven by predation,...
Tipo: Manuscript Palavras-chave: Ecology; Evolutionary Biology.
Ano: 2008 URL: http://precedings.nature.com/documents/1831/version/1
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Transpiration in plants: A thermodynamic imperative Nature Precedings
Carmen Noemi Hernandez Candia; Karo Michaelian.
In this article we determine the importance of transpiration in plants at three different levels of organization: the plant itself, the ecosystem, and the biosphere, all in terms of entropy production due to transpiration. We propose that transpiration is a thermodynamic imperative rather than a physiological burden for the plant. Plants have not replaced their prevalent metabolism C3 with those of less loss of water, C4 or CAM. We argue that the fact that plants retain higher rates of transpiration along evolution could be explained using thermodynamic criteria.

Tipo: Manuscript Palavras-chave: Earth & Environment; Plant Biology; Evolutionary Biology.
Ano: 2010 URL: http://precedings.nature.com/documents/5463/version/1
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Molecular Bio-imprinting of Biocatalysts Nature Precedings
Israr Khan; Muhammad Waheed Akhtar.
Energy conservation is the cry of the day. Attempts are made all over the world to occupy and use energy reserves. Increased industrialization and mechanization has led to the depletion of natural energy reserves. Its unavoidable to search for renewable sources of energy, which may be not used now but can be used by future generations. We are using the expertise of our ancestors. Thus exploiting the nature and newer techniques in this area would yield the best results. Bio-imprinting is one of those techniques whereby chemical modification is done in order to achieve highly expressed protein which can be stored in its highly active form in the specific solvent.
Tipo: Manuscript Palavras-chave: Biotechnology; Cancer; Chemistry; Developmental Biology; Ecology; Genetics & Genomics; Microbiology; Molecular Cell Biology; Neuroscience; Pharmacology; Bioinformatics; Earth & Environment; Plant Biology; Evolutionary Biology.
Ano: 2011 URL: http://precedings.nature.com/documents/5665/version/1
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Biodiversity is a cauliflower under the sunlight Nature Precedings
Roberto Gatti Cazzolla.
For a long time ecologists have questioned the variations of biodiversity across the latitudinal gradient. Recently it has emerged that the changes in [beta]-diversity are caused simply by changes in the sizes of species pools. I combined the species pool size and the fractal nature of ecosystems to clarify some general patterns of this gradient. Considering temperature, humidity and NPP as the main variables of an ecosystem niche and as the axis of the polygon in the Cartesian plane, it is possible to build fractal hypervolumes, whose the fractal dimension rises up to three, moving towards the equator. It follows that the best figure that graphically synthesizes the evolutionary forces that fit this ecosystem hypervolume is the fractal cauliflower.
Tipo: Manuscript Palavras-chave: Ecology; Evolutionary Biology.
Ano: 2012 URL: http://precedings.nature.com/documents/6917/version/1
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SNP analysis reveals an evolutionary acceleration of the human-specific microRNAs Nature Precedings
Qipeng Zhang; Ming Lu; Qinghua Cui.
MicroRNAs are one class of important gene regulators at the post-transcriptional level by binding to the 3’UTRs of target mRNAs. It has been reported that human microRNAs are evolutionary conserved and show lower single nucleotide polymorphisms (SNPs) than their flanking regions. However, in this study, we report that the human-specific microRNAs show a higher SNP density than both the conserved microRNAs and other control regions, suggesting rapid evolution and positive selection has occurred in these regions. Furthermore, we observe that the human-specific microRNAs show greater SNPs minor allele frequency and the SNPs in the human-specific microRNAs show fewer effects on the stability of the microRNA secondary structure, indicating that the...
Tipo: Manuscript Palavras-chave: Genetics & Genomics; Bioinformatics; Evolutionary Biology.
Ano: 2008 URL: http://precedings.nature.com/documents/2127/version/1
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Independent elaboration of steroid hormone signaling pathways in Metazoans Nature Precedings
Gabriel V. Markov; Raquel Tavares; Chantal Dauphin-Villemant; Barbara A. Demeneix; Michael E. Baker; Vincent Laudet.
Steroid hormones regulate many physiological processes in vertebrates, nematodes and arthropods through binding to nuclear receptors (NR), a metazoan-specific family of ligand-activated transcription factors. The main steps controlling the diversification of this family are now well understood. In contrast, the origin and evolution of steroid ligands remain mysterious although this is crucial for understanding the emergence of modern endocrine systems. Using a comparative genomic approach, we analyzed complete metazoan genomes to provide a comprehensive view of the evolution of major enzymatic players implicated in steroidogenesis at the whole Metazoan scale. Our analysis reveals that steroidogenesis has been independently elaborated in the three main...
Tipo: Manuscript Palavras-chave: Cancer; Developmental Biology; Bioinformatics; Earth & Environment; Evolutionary Biology.
Ano: 2009 URL: http://precedings.nature.com/documents/3374/version/1
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Birth Control Does Not Significantly Alter Women’s Preferences for Variants of Men’s Voices Nature Precedings
Jason W. J. W. W. Whitaker; Ryan R. S. Setten; Ulv U. A. Ankerstjerne.
Research shows that women‘s preferences for masculine voices (low pitch) vary as a function of the menstrual cycle, becoming positively augmented around ovulation. The proximate cause catalyzing this effect is attributed to fluctuating estrogen levels. Thus, the introduction of hormonally based birth control has been to shown to have a dampening effect in experiments researching women‘s preference of dimorphic secondary sexual characteristics. However, this dampening effect has not yet been explored in respect to women‘s preferences for masculine voice types. This experiment sought, first, to investigate the effect of birth control on subjects off and on birth control; and, second, to replicate past findings:...
Tipo: Poster Palavras-chave: Evolutionary Biology.
Ano: 2011 URL: http://precedings.nature.com/documents/5895/version/1
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P-POD, The Princeton Protein Orthology Database, as a Tool for Identifying Gene Function Nature Precedings
Michael S. Livstone; Rose Oughtred; Sven Heinicke; Fan Kang; Benjamin Vernot; Aiton Goldman; Dannie Durand; David Botstein; Kara Dolinski.
P-POD, the Princeton Protein Orthology Database, classifies proteins from model organisms and medically-important organisms into families of homologs and provides curated evidence from the literature addressing these relationships. The web page for each protein family includes a phylogenetic tree, sequence alignment, and cross-references to disease-related papers from SGD, papers describing complementation experiments, and OMIM gene and disease information.

As participants in the Gene Ontology Consortium’s Reference Genome project, we seek to provide a consistent centralized method to identify orthologous proteins. We have expanded P-POD to include the protein complement of the twelve Reference Genomes. In...
Tipo: Poster Palavras-chave: Genetics & Genomics; Bioinformatics; Evolutionary Biology.
Ano: 2009 URL: http://precedings.nature.com/documents/3119/version/1
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