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| Registros recuperados: 383 | |
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| Guang-Zhong Wang; Martin J. Lercher. |
| Among eubacteria and archeabacteria, amino acid composition is correlated with habitat temperatures. In particular, species living at high temperatures have proteins enriched in the amino acids E-R-K and depleted in D-N-Q-T-S-H-A. Here, we show that this bias is a proteome-wide effect in prokaryotes, and that the same trend is observed in fully sequenced mammals and chicken compared to cold-blooded vertebrates (Reptilia, Amphibia and fish). Thus, warm-blooded vertebrates likely experienced genome-wide weak positive selection on amino acid composition to increase protein thermostability. |
| Tipo: Manuscript |
Palavras-chave: Genetics & Genomics; Bioinformatics; Evolutionary Biology. |
| Ano: 2009 |
URL: http://precedings.nature.com/documents/2974/version/1 |
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| Claudiu I. Bandea. |
| Transmissible spongiform encephalopathies (TSEs), or prion diseases, are a group of incurable neurodegenerative disorders, including Kuru and Creutzfeldt-Jakob disease in humans, “mad cow” disease in cattle, and scrapie in sheep. This paper presents structural, genetic, and evolutionary evidence supporting an endogenous TSE virus model that integrates the three major traditional views on the nature of TSE pathogens, the conventional virus view, the prion hypothesis, and the virino concept, into a novel conceptual and evolutionary framework. According to this model, the TSE pathogens are symbiotic endogenous viruses that inadvertently produce transmissible viral particles that lack the viral genome and are composed primarily of the... |
| Tipo: Manuscript |
Palavras-chave: Microbiology; Neuroscience; Evolutionary Biology. |
| Ano: 2009 |
URL: http://precedings.nature.com/documents/3887/version/1 |
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| Rodrick Wallace. |
| A spontaneous symmetry lifting model based on Tlusty's elegant topological deconstruction suggests that multiple punctuated ecosystem resilience regime changes in metabolic free energy that were broadly similar to the aerobic transition enabled a punctuated sequence of increasingly complex genetic codes and protein translators. In a manner similar to the Serial Endosymbiosis effecting the Eukaryotic transition, codes and translators coevolved until the ancestor of the present narrow spectrum of protein machineries became locked-in by evolutionary path dependence at a relatively modest level of fitness reflecting a modest embedding metabolic free energy ecology. The simplest coevolutionary model of code-translator interaction has high and low... |
| Tipo: Manuscript |
Palavras-chave: Ecology; Molecular Cell Biology; Bioinformatics; Earth & Environment; Evolutionary Biology. |
| Ano: 2010 |
URL: http://precedings.nature.com/documents/4120/version/3 |
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| Gonghua Lin; Fang Zhao; Eviatar Nevo; Tongzuo Zhang; Jianping Su. |
| We report the twining handedness of Codonopsis pilosula, which has either a left- or right-handed helix among different plants, among different tillers within a single plant, and among different branches within a single tiller. The handedness was randomly distributed among different plants, among the tillers within the same plants, but not among the branches within the same tillers. Moreover, the handedness of the stems can be strongly influenced by external forces, i.e. the compulsory left and right forming inclined to produce more left- and right-handed twining stems, respectively, and the reversing could make a left-handed stem to be right-handed and vice versa. We also discuss the probable mechanisms these curious cases happen. |
| Tipo: Manuscript |
Palavras-chave: Ecology; Plant Biology; Evolutionary Biology. |
| Ano: 2012 |
URL: http://precedings.nature.com/documents/7026/version/1 |
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| 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: 2010 |
URL: http://precedings.nature.com/documents/4652/version/1 |
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| Roy J. Britten. |
| 	Sequence comparisons have been made between the proteins of 571 prokaryote species including 46 archaea and 525 bacteria and the set of human proteins. Highly conserved eukaryotic proteins are often strikingly similar in sequence to archaeal and bacterial proteins. Yet in many cases similarity to archaeal proteins is not correlated to the similarity to bacterial proteins. In these comparisons there are hundreds of eukaryote proteins that match well archeal proteins, but do not match recognizably to bacterial proteins, while thousands of proteins match well to bacterial proteins but not recognizably to archeal proteins. Forty percent of the 21,440 human proteins that significantly match prokaryote proteins are in this extreme idiosyncratic... |
| Tipo: Manuscript |
Palavras-chave: Molecular Cell Biology; Evolutionary Biology. |
| Ano: 2008 |
URL: http://precedings.nature.com/documents/1752/version/1 |
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| Rutger Vos. |
| Recent years have seen the emergence of the field of phyloinformatics. In the course of a phyloinformatic analysis, data and metadata are generated, transformed, filtered, analyzed and summarized before they can be interpreted to answer meaningful biological questions. Based on first principles of good science such steps should be reproducible; and, in practice, analysis steps often need to be redone by the researcher multiple times anyway and are too error-prone, tedious and time-consuming to do by hand. Hence, phyloinformatic analyses benefit from increased automation. 

The Bio::Phylo toolkit promotes this by giving easy access to phylogenetic data objects (trees, taxa, character state matrices) read from a variety of... |
| Tipo: Manuscript |
Palavras-chave: Bioinformatics; Evolutionary Biology. |
| Ano: 2010 |
URL: http://precedings.nature.com/documents/4601/version/1 |
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| Melissa Amarello; Jeffrey J. Smith. |
| Coloration may serve a variety of behavioral (e.g., crypsis, communication) and physiological (e.g., thermoregulation, protection) functions for terrestrial ectotherms. However, optimal coloration for a given function may vary over environments (spatial or temporal) or conflict with other functions. Physiological color change (rapid change due to movement of pigment granules within chromatophores) may be an adaptation to resolve conflicting selective pressures on coloration. The proximate factors related to physiological color change are well known in many animals, but few studies have investigated the ecological or evolutionary implications of this behavior. Here, we present alternative hypotheses for physiological color change and discuss biotic and... |
| Tipo: Poster |
Palavras-chave: Ecology; Evolutionary Biology. |
| Ano: 2011 |
URL: http://precedings.nature.com/documents/6711/version/1 |
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| Shawn Vincent; Matthew Brandley; Takeo Kuriyama; Akira Mori; Anthony Herrel; Masami Hasegawa. |
| In biology, spandrels are phenotypic traits that evolve through their underlying developmental, genetic, and/or structural links to another trait under selection^1, 2, 3^. Despite the importance of the concept of spandrels in biology, empirical examples of spandrels are exceedingly rare at the organismal level^2, 3^. Here we test whether body size evolution in insular populations of a snake (_Elaphe quadrivirgata_) is the result of an adaptive response to differences in available prey, or the result of a non-adaptive spandrel resulting from selection on gape size. In contrast to previous hypotheses, Mantel tests show that body size does not coevolve with diet. However, gape size tightly matches diet (birds vs. lizards) across populations, even after... |
| Tipo: Manuscript |
Palavras-chave: Ecology; Evolutionary Biology. |
| Ano: 2009 |
URL: http://precedings.nature.com/documents/3360/version/1 |
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| Wilfred Ndifon. |
| Two important challenges to the use of serological assays for influenza surveillance include the substantial amount of experimental effort involved, and the inherent noisiness of serological data. Here, informed by the observation that log-transformed serological data (obtained from the hemagglutination-inhibition assay) exist in an effectively one-dimensional space, computational methods are developed for accurately and efficiently recovering unmeasured serological data from a sample of measured data, and systematically minimizing noise found in the measured data. Careful application of these methods would enable the collection of better-quality serological data on a greater number of circulating influenza viruses than is currently possible, and improve... |
| Tipo: Manuscript |
Palavras-chave: Immunology; Evolutionary Biology. |
| Ano: 2009 |
URL: http://precedings.nature.com/documents/3820/version/1 |
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| Kushal Shah. |
| A plot of the correlation function of a given DNA sequence has certain characteristic features common to almost all organisms. One common feature is that the correlation values at distances that are multiples of three is higher than correlation values at other distances. Because of this such a correlation plot can be divided into two or three curves with different scalings. P. falciparum has a rare correlation property which is probably unique. I have analyzed genomes of many bacteria, fungi and protozoa and found that P. falciparum is the only organism whose DNA sequence correlation plot can be divided into four curves with different scalings. This property is neither shared by other species of the Plasmodium genus nor by other AT rich genomes. This could... |
| Tipo: Manuscript |
Palavras-chave: Genetics & Genomics; Bioinformatics; Evolutionary Biology. |
| Ano: 2012 |
URL: http://precedings.nature.com/documents/6817/version/1 |
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| Marko Prous. |
| To test the monophyly of Opisthokonta (animal-fungal clade) and Ecdysozoa (nematode-arthropod clade), Philip et al [Mol. Biol. Evol. 22: 1175–1184 (2005)] used sequence data from 10 eukaryotic genomes (an alveolate, a plant, two ascomycetous yeasts, a nematode, two dipterans, and three vertebrates). Strict criteria were used to select genes for phylogenetic analyses: single-gene families were identified and from these families, genes capable of recovering the uncontroversial parts of the phylogenetic tree (for example animal and vertebrate monophyly) were selected. Only five single-copy genes were found to be universally distributed across the analyzed taxa and capable of recovering all the uncontroversial parts of the tree. Phylogenetic... |
| Tipo: Poster |
Palavras-chave: Evolutionary Biology. |
| Ano: 2009 |
URL: http://precedings.nature.com/documents/3306/version/1 |
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| Ralph Catalano. |
| Much literature invokes natural selection to explain the pervasive deficit in the average lifespan of men compared to women.^1^ The explanation assumes that mothers, not fathers, provisioned children over much of human existence, and that women who lived long enough to help their children and grand children survive to reproductive age had more grandchildren and great-grandchildren than did shorter-lived women.^2^ Although this argument implies that natural selection would conserve mutations that conferred longevity on mothers but not fathers,^3,4^ it offers no explanation of the considerable changes over historic time in the male longevity deficit thereby implying that these arise solely from culture.^5^ I show, however, that natural selection _in utero_... |
| Tipo: Manuscript |
Palavras-chave: Evolutionary Biology. |
| Ano: 2009 |
URL: http://precedings.nature.com/documents/3915/version/1 |
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| Paul Fearnhead; Dennis Prangle. |
| To analyze complex datasets efficiently, ABC algorithms require well-chosen low dimensional summary statistics of the data. We present a method to construct appropriate summary statistics for ABC in a semi-automatic manner. Previous attempts at this have been based around constructing statistics that are sufficient (or approximately sufficient). However, in most real applications it is difficult to know if low-dimensional sufficient statistics exist, or how to approximate them if they do. We take an alternative approach of aiming for summary statistics which will enable inference about certain parameters of interest to be as accurate as possible.  This talk describes our method, the underpinning theory, and promising empirical results on a range... |
| Tipo: Presentation |
Palavras-chave: Evolutionary Biology. |
| Ano: 2011 |
URL: http://precedings.nature.com/documents/5959/version/1 |
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| Ilana Agmon; Chen Davidovich; Anat Bashan; Ada Yonath. |
| A structural element that could have existed independently in the prebiotic era was identified at the active site of the contemporary ribosome. It is suggested to have functioned as a proto-ribosome catalyzing peptide bond formation and non-coded elongation in the same manner that contemporary ribosomes exert positional catalysis, namely by accommodating the reactants in stereochemistry favourable for inline nucleophilic attack. This simple apparatus is a dimer of self-folding RNA units that could have assembled spontaneously into a symmetrical pocket-like structure, sufficiently efficient to be preserved throughout evolution as the active site of modern ribosomes, thus presenting a conceivable starting point for translation.Here we discuss the... |
| Tipo: Manuscript |
Palavras-chave: Molecular Cell Biology; Evolutionary Biology. |
| Ano: 2009 |
URL: http://precedings.nature.com/documents/2921/version/1 |
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| Brian C. O'Meara. |
| 1) Rates of phenotypic evolution have changed throughout the history of life, producing variation in levels of morphological, functional, and ecological diversity among groups. Testing for the presence of these rate shifts is a key component of evaluating hypotheses about what causes them. General predictions regarding changes in phenotypic diversity as a function of evolutionary history and rates are developed, and tests are derived to evaluate rate changes. Simulations show that these tests are more powerful than existing tests using standardized contrasts. 
2) Species delimitation and species tree inference are difficult problems in the case of recent divergences, especially when different loci have different histories. I quantify the... |
| Tipo: Manuscript |
Palavras-chave: Ecology; Evolutionary Biology. |
| Ano: 2008 |
URL: http://precedings.nature.com/documents/2261/version/1 |
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| Registros recuperados: 383 | |
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