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Bio-Communication of Bacteria and its Evolutionary Interrelations to Natural Genome Editing Competences of Viruses Nature Precedings
Guenther Witzany.
Communicative competences enable bacteria to develop, organise and coordinate rich social life with a great variety of behavioral patterns even in which they organise themselves like multicellular organisms. They have existed for almost four billion years and still survive, being part of the most dramatic changes in evolutionary history such as DNA invention, cellular life, invention of nearly all protein types, partial constitution of eukaryotic cells, vertical colonisation of all eukaryotes, high adaptability through horizontal gene transfer and co-operative multispecies colonisation of all ecological niches. Recent research demonstrates that these bacterial competences derive from the aptitude of viruses for natural genome editing....
Tipo: Manuscript Palavras-chave: Molecular Cell Biology; Evolutionary Biology.
Ano: 2008 URL: http://precedings.nature.com/documents/1738/version/2
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Frequency-dependent selection predicts patterns of radiations and biodiversity Nature Precedings
Carlos Melian; David Alonso; Diego Vazquez; James Regetz; Stefano Allesina.
Most empirical studies support a decline in speciation rates through time, although evidence for constant speciation rates also exists. Declining rates have been explained by invoking niche-filling processes, whereas constant rates have been attributed to non-adaptive processes such as sexual selection, mutation, and dispersal. Trends in speciation rate and the processes underlying it remain unclear, representing a critical information gap in understanding patterns of global diversity. Here we show that the speciation rate is driven by frequency dependent selection. We used a frequency-dependent and DNA sequence-based model of populations and genetic-distance-based speciation, in the absence of adaptation to ecological niches. We tested the...
Tipo: Manuscript Palavras-chave: Ecology; Genetics & Genomics; Bioinformatics; Earth & Environment; Evolutionary Biology.
Ano: 2009 URL: http://precedings.nature.com/documents/3752/version/1
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Evolution signatures in genome network properties Nature Precedings
Rita de Almeida; Leonardo Brunnet; José Luiz Rybarczyk-Filho; Ricardo Ferreira; Jose Claudio Moreira; Mauro Castro; Rodrigo Dalmolin.
Genomes maybe organized as networks where protein-protein association plays the role of network links. The resulting networks are far from being random and their topological properties are a consequence of the underlying mechanisms for genome evolution. Considering data on protein-protein association networks from STRING database, we present experimental evidence that degree distribution is not scale free, presenting an increased probability for high degree nodes. We also show that the degree distribution approaches a scale invariant state as the number of genes in the network increases, although real genomes still present finite size effects. Based on the experimental evidence unveiled by these data analyses, we propose a simulation model for genome...
Tipo: Manuscript Palavras-chave: Genetics & Genomics; Bioinformatics; Evolutionary Biology.
Ano: 2011 URL: http://precedings.nature.com/documents/6653/version/1
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Circadian Preference and Sexual Selection: A Novel Evolutionary Approach Nature Precedings
Davide Piffer.
Human sleep patterns differ across age groups and between males and females, and their association with age and gender suggest that they might have been the target of sexual selection during human evolutionary history. In this study, I will test the hypothesis that a phase-delayed circadian phase is a sexually selected trait in humans. A short version of the Horne and Ostberg questionnaire and a questionnaire on sexual behaviour were administered to 134 males and 140 females. A significant negative relationship was found between the MEQ score and the number of sexual partners among males, with evening types reporting more sexual partners than morning types. No significant relationship between females MEQ and number of sexual partners was found. Findings...
Tipo: Manuscript Palavras-chave: Evolutionary Biology.
Ano: 2010 URL: http://precedings.nature.com/documents/2964/version/2
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Why are women smaller than men? When anthropology meets evolutionary biology Nature Precedings
Priscille Touraille; Pierre-Henri Gouyon.
There are large variations of size among humans but in all populations, men are larger on average than women. For most biologists this fact can be easily explained by the same processes that explain the size dimorphism in large mammals in general and in apes in particular. Due to fights between males for the possession of females, sexual selection has favoured bigger males. Indeed, this factor certainly explains why males are selected for being large but lets aside the question of selection on the female side. Actually, it has been shown that larger females are also favoured by natural selection. This is particularly relevant for women because their probability of dying when giving birth is then reduced. In this paper, the common view that size dimorphism...
Tipo: Manuscript Palavras-chave: Evolutionary Biology.
Ano: 2008 URL: http://precedings.nature.com/documents/1832/version/1
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Deciphering the genome structure and paleohistory of _Theobroma cacao_ Nature Precedings
Xavier Argout; Jerome Salse; Jean Marc Aury; Gaetan Droc; Jerome Gouzy; Mathilde Allegre; Cristian Chaparro; Thierry Legavre; Mark Guiltinan; Siela Maximova; Michael Abrouk; Florent Murat; Olivier Fouet; Julie Poulain; Manuel Ruiz; Yolande Roguet; Maguy Rodier-Goud; Jose Fernandes Barbosa-Neto; Francois Sabot; Dave Kudrna; Jetty Siva S. Ammiraju; Stephan C. Schuster; John E. Carlson; Erika Sallet; Schiex T.; Anne Dievart; Melissa Kramer; Laura Gelley; Zi Sh; Aurélie Bérard; Christopher Viot; Michel Boccara; Ange Marie Risterucci; Valentin Guignon; Xavier Sabau; Michael Axtell; Zhaorong Ma; Yufan Zhang; Spencer Brown; Mickael Bourge; Wolfgang Golser; Xiang Song; Didier Clement; Ronan Rivalan; Mathias Tahi; Joseph Moroh Akaza; Bertrand Pitollat; Karina Gramacho; Angélique D’Hont; Dominique Brunel; Diogenes Infante; Ismael Kebe; Pierre Costet; Rod Wing; W. Richard McCombie; Emmanuel Guiderdoni; Francis Quetier; Olivier Panaud; Patrick Wincker; Stephanie Sidibe-Bocs; Claire Lanaud.
We sequenced and assembled the genome of _Theobroma cacao_, an economically important tropical fruit tree crop that is the source of chocolate. The assembly corresponds to 76% of the estimated genome size and contains almost all previously described genes, with 82% of them anchored on the 10 _T. cacao_ chromosomes. Analysis of this sequence information highlighted specific expansion of some gene families during evolution, for example flavonoid-related genes. It also provides a major source of candidate genes for _T. cacao_ disease resistance and quality improvement. Based on the inferred paleohistory of the T. cacao genome, we propose an evolutionary scenario whereby the ten _T. cacao_ chromosomes were shaped from an ancestor through eleven chromosome...
Tipo: Marker Paper / Data Plan Palavras-chave: Genetics & Genomics; Plant Biology; Evolutionary Biology; Data Standards.
Ano: 2010 URL: http://precedings.nature.com/documents/4908/version/1
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Extreme energy lability in human children: An overlooked and central aspect of human biology Nature Precedings
John Skoyles.
A four year old child devotes half their total energy expenditure (TEE) to their brains. Even by 10 years-of-age it is still 30% (compared to an adult’s ≈12%). This extreme energy use results from a high brain/body size ratio – combined with a doubling of cerebral gray matter energy utilization (due to synaptic exuberance during cognitive neuromaturation). 

With extreme energy expenditure goes extreme vulnerability to hypoglycemia: (1) children become hypoglycemic after 24-36 hours of fast (compared to 60-72 hours in adults), and (2) their brains suffer neurological impairment (shown in disrupted P300 potentials) at a lower decrease in plasma glucose: 3.6 - 4.2 mmol L-1 in children rather...
Tipo: Presentation Palavras-chave: Developmental Biology; Neuroscience; Evolutionary Biology.
Ano: 2012 URL: http://precedings.nature.com/documents/7097/version/1
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The Dryad Digital Repository: Published evolutionary data as part of the greater data ecosystem Nature Precedings
Todd Vision.
Here we describe the motivation and workings of Dryad, a digital repository for data underlying published articles in the biosciences, that grew out of a grassroots effort to support a joint data archiving policy adopted by a consortium of journals in ecology and evolutionary biology.
Tipo: Manuscript Palavras-chave: Ecology; Bioinformatics; Evolutionary Biology.
Ano: 2010 URL: http://precedings.nature.com/documents/4595/version/1
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The existence of species rests on a metastable equilibrium between inbreeding and outbreeding Nature Precedings
Etienne Joly.
Background: Speciation corresponds to the progressive establishment of reproductive barriers between groups of individuals derived from an ancestral stock. Since Darwin did not believe that reproductive barriers could be selected for, he proposed that most events of speciation would occur through a process of separation and divergence, and this point of view is still shared by most evolutionary biologists today. 

Results: I do, however, contend that, if so much speciation occurs, it must result from a process of natural selection, whereby it is advantageous for individuals to reproduce preferentially within a group and reduce their breeding with the rest of the population, leading to a model whereby new species arise not...
Tipo: Manuscript Palavras-chave: Ecology; Genetics & Genomics; Earth & Environment; Evolutionary Biology.
Ano: 2011 URL: http://precedings.nature.com/documents/5003/version/4
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Positive Darwinian Selection And The Birth Of An Olfactory Receptor Clade In Teleost Fish Nature Precedings
Ashiq Hussain; Luis Saraiva; Sigrun Korsching.
Trace amine-associated receptors (TAARs) in mammals recently have been shown to function as olfactory receptors. We have delineated the taar gene family in jawless, cartilaginous and bony fish (zero, two, and more than hundred genes, respectively). We conclude that taar genes are evolutionary much younger than the related OR and ORA/V1R olfactory receptor families, which are present already in lamprey, a jawless vertebrate. The two cartilaginous fish genes appear to be ancestral for two taar classes, each with mammalian and bony fish (teleost) representatives. Unexpectedly, a whole new clade, class III, of taar genes originated even later, within the teleost lineage. Taar genes from all three classes are expressed in subsets of zebrafish olfactory receptor...
Tipo: Poster Palavras-chave: Neuroscience; Evolutionary Biology.
Ano: 2011 URL: http://precedings.nature.com/documents/6448/version/1
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Variety in evolutionary strategies favours biodiversity in habitats of moderate productivity Nature Precedings
Simon Pierce.
The mechanism whereby biodiversity varies between habitats differing in productivity is a missing link between ecological and evolutionary theory with vital implications for biodiversity conservation, management and the assessment of ecosystem services. A unimodal, humped-back relationship, with biodiversity greatest at intermediate productivities, is evident when plant, animal and microbial communities are compared across productivities in nature. However, the mechanistic, evolutionary basis of this observation remains enigmatic. We show, for natural and semi-natural plant communities across a range of bioclimatic zones, that biodiversity is greatest where communities include species with widely divergent values for phenotypic traits involved in resource...
Tipo: Manuscript Palavras-chave: Ecology; Plant Biology; Evolutionary Biology.
Ano: 2011 URL: http://precedings.nature.com/documents/6618/version/1
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Can ABC be Used for Model Selection? Nature Precedings
Xavier Didelot; Rich Everitt; Adam Johansen; Dan Lawson.
Over the past ten years, Approximate Bayesian Computation (ABC) has become hugely popular to estimate the parameters of a model when the likelihood function cannot be computed in a reasonable amount of time. ABC can in principle be used also to perform Bayesian model comparison, but this raises the question of which summary statistic should be used for such applications. Here we present a general method for constructing a summary statistic that is sufficient for the model choice problem. We apply this construction to models from the exponential family. Unfortunately, in more complex models, our construct often results in statistics with too high dimensionality to use in ABC. We therefore discuss the possibility of applying ABC with non-sufficient...
Tipo: Presentation Palavras-chave: Bioinformatics; Evolutionary Biology.
Ano: 2011 URL: http://precedings.nature.com/documents/5955/version/1
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Effective Phylogenetic Compression with TreeZip Nature Precedings
Suzanne J. Matthews; SeungJin Sul; Tiffani L. Williams.
Phylogenetic trees are family trees that represent the relationships between a group of organisms, or taxa. The most popular techniques for reconstructing phylogenetic trees intelligently navigate an exponentially-sized tree space by solving NP-hard optimization problems that that best hypothesize the evolutionary history for a given set of taxa. Instead of reconstructing a single tree, these heuristics often return tens to hundreds of thousands of trees that represent equally-plausible hypotheses for how the taxa of interest evolved from a common ancestor. As biologists attempt to reconstruct increasingly larger phylogenies, these tree collections only continue to grow in size. To combat the cost of storage and to facilitate the transfer of these large...
Tipo: Manuscript Palavras-chave: Bioinformatics; Evolutionary Biology.
Ano: 2010 URL: http://precedings.nature.com/documents/4613/version/1
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Molecular Models of DNA Structures and Dynamics: Principles, Techniques and Applications Nature Precedings
I. C. Baianu.
Molecular models of DNA structures are representations of the molecular geometry and topology of Deoxyribonucleic acid (DNA) molecules using one of several means, such as: closely packed spheres (CPK models) made of plastic, metal wires for 'skeletal models', graphic computations and animations by computers, artistic rendering, and so on, with the aim of simplifying and presenting the essential, physical and chemical, properties of DNA molecular structures either in vivo or in vitro. Computer molecular models also allow animations and molecular dynamics simulations that are very important for understanding how DNA functions in vivo.
Tipo: Manuscript Palavras-chave: Biotechnology; Cancer; Chemistry; Developmental Biology; Genetics & Genomics; Microbiology; Molecular Cell Biology; Bioinformatics; Plant Biology; Evolutionary Biology.
Ano: 2012 URL: http://precedings.nature.com/documents/7075/version/1
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Music can reduce cognitive dissonance Nature Precedings
Nobuo Masataka; Leonid Perlovsky.
The fundamental cognitive functions of music in the brain have not been known and evolutionary reasons for musical abilities seem mysterious. A recent hypothesis suggested that a fundamental function of music has been to help mitigating cognitive dissonances. A cognitive dissonance is "a discomfort caused by holding conflicting cognitions" simultaneously; it usually leads to devaluation of conflicting knowledge. Since every concept implies some degree of contradictions to other knowledge, unmitigated cognitive dissonances could prevent evolution of cognition. Thus music might be fundamental for the evolution of cognition. Here we provide experimental confirmation of this hypothesis using a classical paradigm known to induce a cognitive...
Tipo: Manuscript Palavras-chave: Neuroscience; Evolutionary Biology.
Ano: 2012 URL: http://precedings.nature.com/documents/7080/version/1
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Universal Features in the Genome-level Evolution of Protein Domains Nature Precedings
Marco Cosentino Lagomarsino; Alessandro L. Sellerio; Philip D. Heijning; Bruno Bassetti.
Protein domains are found on genomes with notable statistical distributions, which bear a high degree of similarity. Previous work has shown how these distributions can be accounted for by simple models, where the main ingredients are probabilities of duplication, innovation, and loss of domains. However, no one so far has addressed the issue that these distributions follow definite trends depending on protein-coding genome size only. We present a stochastic duplication/innovation model, falling in the class of so-called Chinese Restaurant Processes, able to explain this feature of the data. Using only two universal parameters, related to a minimal number of domains and to the relative weight of innovation to duplication, the model reproduces two...
Tipo: Manuscript Palavras-chave: Genetics & Genomics; Bioinformatics; Evolutionary Biology.
Ano: 2008 URL: http://precedings.nature.com/documents/1376/version/2
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ABC for ancestral inference Nature Precedings
Richard Wilkinson; Simon Tavare.
ABC for ancestral inference
Tipo: Presentation Palavras-chave: Bioinformatics; Evolutionary Biology.
Ano: 2011 URL: http://precedings.nature.com/documents/5963/version/1
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Comment to "Endogenous Viral Etiology of Prion Diseases" Nature Precedings
Claudiu Bandea.
This note is intended as a comment to a paper in Nature Precedings entitled "Endogenous viral etiology of prion diseases":http://precedings.nature.com/documents/3887/version/1 . Because it contains illustrations that could not be displayed in the comments section of that paper, I’m posting this comment here as a PDF document.
Tipo: Manuscript Palavras-chave: Genetics & Genomics; Immunology; Microbiology; Neuroscience; Evolutionary Biology.
Ano: 2009 URL: http://precedings.nature.com/documents/4101/version/1
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Deciphering the phylogenetic history of neuroserpin orthologs across metazoans by analysis of synteny and rare genomic characters Nature Precedings
Abhishek Kumar; Hermann Ragg.
The superfamily of serine proteinase inhibitors (serpins) is involved in wide arrays of fundamental biological processes such as blood coagulation, complement activation, fibrinolysis, angiogenesis, inflammation and tumor suppression. The average protein size of a serpin family member is 350-400 amino acids, but gene structure varies in terms of number and position of exons and introns. All known serpins can be grouped into 16 clades and 10 orphan sequences. Vertebrate serpins can be conveniently classified into six sub-groups, based on three independent biological features - genomic organization, diagnostic amino acid sites and rare indels.
The objective of this study was to elucidate the phylogenetic kinships of serpins involved in...
Tipo: Poster Palavras-chave: Bioinformatics; Evolutionary Biology.
Ano: 2008 URL: http://precedings.nature.com/documents/2496/version/1
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On the close relationship between speciation, inbreeding and recessive mutations. Nature Precedings
Etienne Joly.
Whilst the principle of adaptive evolution is unanimously recognised as being caused by the process of natural selection favouring the survival and/or reproduction of individuals having acquired new advantageous traits, a consensus has proven much harder to find regarding the actual origin of species. Indeed, since speciation corresponds to the establishment of reproductive barriers, it is difficult to see how it could bring a selective advantage because it amounts to a restriction in the opportunities to breed with as many and/or as diverse partners as possible. In this regard, Darwin himself did not believe that reproductive barriers could be selected for, and today most evolutionary biologists still believe that speciation can only occur through a...
Tipo: Manuscript Palavras-chave: Genetics & Genomics; Evolutionary Biology.
Ano: 2010 URL: http://precedings.nature.com/documents/5003/version/3
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