http://precedings.nature.com/tags/Evolution Recently posted documents tagged with 'Evolution' Nature Publishing Group en Nature Precedings http://precedings.nature.com/images/header_logo.gif http://precedings.nature.com http://precedings.nature.com/documents/3834/version/1 This report describes the presence of copy genes in plants where the sequence similarity to their parental genes is almost completely limited to limited to the exons. Evidence is presented that indicates that they arose via a novel processing of transcribed precursor RNA during which the introns are replaced rather than excised, followed by reverse transcription and incorporation into the chromosomes. Intron replacement may play an important role in evolution as it results in megagene changes. http://precedings.nature.com/documents/3834/version/1 Wed, 07 Oct 2009 15:36:36 UTC Mega- change gene copies are produced by reverse transcription of precursor RNA with replaced introns. hdl:10101/npre.2009.3834.1 2009-10-07 Drew Schwartz Nature Precedings 2009-10-07T15:36:36Z Manuscript Genetics & Genomics Bioinformatics Plant Biology Evolutionary Biology http://creativecommons.org/licenses/by/3.0/ http://precedings.nature.com/documents/3820/version/1 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 the ability to identify potential epidemic/pandemic viruses before they become widespread. Although the focus here is on influenza surveillance, the described methods are more widely applicable. http://precedings.nature.com/documents/3820/version/1 Mon, 05 Oct 2009 14:18:48 UTC New methods for analyzing serological data with applications to influenza surveillance hdl:10101/npre.2009.3820.1 2009-10-05 Wilfred Ndifon Nature Precedings 2009-10-05T14:18:48Z Manuscript Immunology Evolutionary Biology http://creativecommons.org/licenses/by/3.0/ http://precedings.nature.com/documents/3794/version/1 Interpretations of molecular data by the modern evolution theory are often sharply inconsistent with paleontological results. This is to be expected since the theory is only true for microevolution and yet fossil records are mostly about macroevolution. The maximum genetic diversity (MGD) hypothesis is a more coherent and complete account of evolution that has yet to meet a single contradiction. Here, molecular data were analyzed based on the MGD to resolve key questions of primate phylogeny. A new method was developed from a novel result predicted by the MGD: genetic non-equidistance to a simpler taxon only in slow but not in fast evolving sequences given non-equidistance in time. This ‘slow clock’ method showed that humans are genetically more distant to orangutans than African apes are and separated from the pongid clade (containing orangutan and African apes) 17.3 million years ago. Also, tarsiers are genetically closer to lorises than simian primates are, suggesting a tarsier-loris clade to the exclusion of simian primates. The validity and internal coherence of the primate phylogeny here were independently verified. The molecular split time of human and pongid calibrated from the fossil record of gorilla, or the fossil times for the radiation of anthropoids/mammals at the K/T boundary and for the Eutheria-Metatheria split in the Early Cretaceous, were independently confirmed from molecular dating calibrated using the fossil split times of tarsier-loris and two other pairs of mammals (mouse-rat and opossum-kangaroo). This remarkable and unprecedented concordance between molecules and fossils provides the latest confirmation of the inseparable unity of genotype and phenotype and the unmatched value of MGD in a coherent interpretation of life history. http://precedings.nature.com/documents/3794/version/1 Tue, 22 Sep 2009 16:42:20 UTC Primate phylogeny: molecular evidence for a pongid clade excluding humans and a prosimian clade containing tarsiers hdl:10101/npre.2009.3794.1 2009-09-22 Shi Huang Nature Precedings 2009-09-22T16:42:20Z Manuscript Bioinformatics Evolutionary Biology http://creativecommons.org/licenses/by/3.0/ http://dx.doi.org/10.1038/npre.2009.3647.1 Ready access to data is a key concern in both basic research and problem-solving in the biological sciences, as the scale and scope of the questions that researchers ask expand, and as global problems demand data collected from around the world. With a grant from the National Science Foundation, from 2004 through 2009, the Ecological Society of America (ESA) has led a series of five workshops on data sharing, to help the ecology, evolution, and organismal biology communities find common ground on how to make data more readily discoverable and accessible in their own disciplines. The most recent of these focused in the development of incentives for data sharing, both at the individual and organizational level. This presentation will summarize the workshop recommendations, with a focus on preservation, curation, and access to data; access to analytical and visualization tools; and the need to make data archiving simple and routine. The roles of funders and publishers of research are also key and will be highlighted. Background/Question/MethodsReady access to data is a key concern in both basic research and problem-solving in the biological sciences, as the scale and scope of the questions that researchers ask expand, and as global problems demand data collected from around the world. With a grant from the National Science Foundation, from 2004 through 2009, the Ecological Society of America (ESA) has led a series of five workshops on data sharing, to help the ecology, evolution, and organismal biology communities find common ground on how to make data more readily discoverable and accessible in their own disciplines. The most recent of these focused in the development of incentives for data sharing, both at the individual and organizational level. Results/ConclusionsThis presentation will summarize the workshop recommendations, with a focus on preservation, curation, and access to data; access to analytical and visualization tools; and the need to make data archiving simple and routine. The roles of funders and publishers of research are also key and will be highlighted. http://dx.doi.org/10.1038/npre.2009.3647.1 Wed, 19 Aug 2009 09:23:08 UTC Development of Incentives for Data Sharing in Ecology, Evolution, and Organismal Biology doi:10.1038/npre.2009.3647.1 2009-08-19 Clifford S. Duke Nature Precedings 2009-08-19T09:23:08Z Presentation Ecology Evolutionary Biology http://creativecommons.org/licenses/by/3.0/ http://dx.doi.org/10.1038/npre.2009.1866.2 Withdrawn http://dx.doi.org/10.1038/npre.2009.1866.2 Thu, 16 Jul 2009 17:43:53 UTC A Study on the Origin of Peroxisomes: Possibility of Actinobacteria Symbiosis doi:10.1038/npre.2009.1866.2 2009-07-16 Duhita Narendra Nature Precedings 2009-07-16T17:43:53Z Manuscript Genetics & Genomics Evolutionary Biology http://creativecommons.org/licenses/by/3.0/ http://precedings.nature.com/documents/3206/version/1 Prospect of changes in such umbilical structures as Lip, Portici and Tegilla throughout Turonian-Campanian was also investigated. The phylogenic trend show that Lip structure in primary morphogroups turns gradually to tegilla in more developed forms in which the opening become also entirely umbilical. Statistical an analysis showed that the trends of changes are correlatable with increase in water depth while a decrease in depth result in development of lip in the planktonic foraminifera studied. The changes are considered to be in accord with Pascal law. http://precedings.nature.com/documents/3206/version/1 Thu, 30 Apr 2009 19:21:45 UTC The study of the umbilical system in planktonic foraminifera in relation with depth of the Abderaz Formation at type section, IRAN hdl:10101/npre.2009.3206.1 2009-04-30 Meysam Shafiee Ardestani Nature Precedings 2009-04-30T19:21:45Z Manuscript Ecology Earth & Environment Evolutionary Biology http://creativecommons.org/licenses/by/3.0/ http://dx.doi.org/10.1038/npre.2009.3152.1 Linear motifs are short and evolutionarily variable sequence patterns associated with particular functions often involving post-translational modifications, such as phosphorylation, acetylation, glycosylation, targeting signals for cellular compartments, protein cleavage sites and protein–protein interaction.Experimentally they are often neglected because their short length (4-10 residues long), and the fact that they often reside in disordered regions in proteins makes them difficult to detect. For a similar reason, using the sole regular expression to detect linear motifs matches in sequences has almost no predictive power because they are both statistically insignificant and prone to massive over-prediction.The Eukaryotic Linear Motif resource (ELM – http://elm.eu.org) is a bioinformatics facility for investigating candidate short functional motifs in eukaryotic proteins. The ELM database to date has collected more than 140 motifs and their regular expressions patterns as well as information about their instances of occurrence, distribution, crystal structure, publications, etc.In order to reduce the over-prediction inherent to pattern matching against protein sequences and to discriminate true from false positive motif matches, context-based rules and logical filters are applied. The current version includes cell compartment, phylogeny, globular domain clash filters and the more recent structural filter based on known three-dimensional information that relies on structural information, such as residue solvent accessibility and secondary structure features. This implies that a candidate motif can be excluded from further consideration if the protein resides in the wrong cellular compartment or the motif is buried in the core of a globular domain. By considering additional types of context information, we expect that prediction of functional sites by ELM can be considerably improved. In cases where the user cannot provide relevant context information, we consider providing predictions of contextual information in order to improve the ELM performance. For example, since the ELM motif database has been annotated with biological process GO terms, the system could be prepared for addition of a new context filter using biological process. http://dx.doi.org/10.1038/npre.2009.3152.1 Thu, 23 Apr 2009 17:20:38 UTC The Eukaryotic Linear Motif Resource (ELM): Regulatory Sites in Proteins doi:10.1038/npre.2009.3152.1 2009-04-23 Francesca Diella Nature Precedings 2009-04-23T17:20:38Z Poster Bioinformatics http://creativecommons.org/licenses/by/3.0/ http://precedings.nature.com/documents/3071/version/1 Explaining the evolution of cooperative behavior has been one of main challenges in evo- lutionary theory1-6. Cooperation may collapse a surge of defectors who enjoy the benefit without cooperation in situation called prisoner’s dilemma. In the concept of evolutionary game theory, there are many proposals to explain the evolution of cooperation by adding further mechanism such as, kin selection1, reciprocity7, punishment8,9 and the finiteness of the population6. In evolutionary game theory, a pair is randomly picked from population, and play a prisoner’s dilemma game. Here we also show the finiteness encourages cooperation but use different approach: in spite of random-pick, individuals join and leave a spot or territory with a limited capacity to form a pair and play prisoner’s dilemma game during their stay in the spot. We use a simple finite-state continuous-time Markov chain to analyze the dynamics in the spot and find that, given large cooperation benefit, just leaving together from the spot is enough for cooperation to be emerged. Further, we show that the coexistence of cooperators and defectors may become stable in highly congested spots. http://precedings.nature.com/documents/3071/version/1 Thu, 16 Apr 2009 09:34:51 UTC Evolution of Cooperation on Playing Prisoner's Dilemma Game in the Finite-Capacity Spot hdl:10101/npre.2009.3071.1 2009-04-16 Hiroshi Toyoizumi Nature Precedings 2009-04-16T09:34:51Z Manuscript Evolutionary Biology http://creativecommons.org/licenses/by/3.0/ http://dx.doi.org/10.1038/npre.2009.3028.1 Natural selection is often regarded as a result of severe competition. Defect seems beneficial for a single individual in many cases.However, cooperation is observed in many levels of biological systems ranging from single cells to animals, including human society. We have yet known that in unstructured populations, evolution favors defectors over cooperators. On the other hand, there have been much interest on evolutionary games1,2 on structured population and on graphs3-16. Structures of biological systems and societies of animals can be taken as networks. They discover that network structures determine results of the games. Together with the recent interest of complex networks17,18, many researchers investigate real network structures. Recently even economists study firms' transactions structure19. Seminal work11 derives the condition of favoring cooperation for evolutionary games on networks, that is, benefit divided by cost, b/c, exceeds average degree, (k). Although this condition has been believed so far20, we find the condition is b/c (knm) instead. knm is the mean nearest neighbor degree. Our condition enables us to compare how network structure enhances cooperation across different kinds of networks. Regular network favors most, scale free network least. On ideal scale free networks, cooperation is unfeasible. We could say that (k) is the degree of itself, while knm is that of others. One of the most interesting points in network theory is that results depend not only on itself but also on others. In evolutionary games on network, we find the same characteristic. http://dx.doi.org/10.1038/npre.2009.3028.1 Mon, 06 Apr 2009 09:36:52 UTC A condition of cooperation. Games on network doi:10.1038/npre.2009.3028.1 2009-04-06 Tomohiko Konno Nature Precedings 2009-04-06T09:36:52Z Manuscript Evolutionary Biology http://creativecommons.org/licenses/by/3.0/ http://precedings.nature.com/documents/2887/version/1 February 12th, 2009 was Charles Darwin’s 200th birthday, and November 2009 represents the 150th anniversary of the publication of his transformative book, The Origin of Species. It seems a good time to look back and assess Darwin’s legacy within the perspective of current knowledge of genetics, cytogenetics, and molecular biology in general. Although a comprehensive understanding of evolution would no doubt have emerged eventually, it is difficult to imagine how anyone could have matched Darwin’s prodigious and sustained efforts, as well as his talent for explaining things in simple terms. http://precedings.nature.com/documents/2887/version/1 Mon, 23 Feb 2009 19:45:11 UTC The Necessity of Darwin hdl:10101/npre.2009.2887.1 2009-02-23 Herbert C. Macgregor Nature Precedings 2009-02-23T19:45:11Z Manuscript Genetics & Genomics Molecular Cell Biology Evolutionary Biology http://creativecommons.org/licenses/by/3.0/