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Collaboration Networks in the Brazilian Scientific Output in Evolutionary Biology: 2000-2012 Anais da ABC (AABC)
Santin,Dirce M.; Vanz,Samile A.S.; Stumpf,Ida R.C..
This article analyzes the existing collaboration networks in the Brazilian scientific output in Evolutionary Biology, considering articles published during the period from 2000 to 2012 in journals indexed by Web of Science. The methodology integrates bibliometric techniques and Social Network Analysis resources to describe the growth of Brazilian scientific output and understand the levels, dynamics and structure of collaboration between authors, institutions and countries. The results unveil an enhancement and consolidation of collaborative relationships over time and suggest the existence of key institutions and authors, whose influence on research is expressed by the variety and intensity of the relationships established in the co-authorship of...
Tipo: Info:eu-repo/semantics/article Palavras-chave: Co-authorship; Collaboration networks; Evolutionary Biology; Scientific collaboration; Scientific output; Scientometrics.
Ano: 2016 URL: http://www.scielo.br/scielo.php?script=sci_arttext&pid=S0001-37652016000100165
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Discovery of the Principal Cystic Fibrosis Mutation (F508del) in Ancient DNA from Iron Age Europeans Nature Precedings
Philip Farrell; Cedric Le Marechal; Claude Ferec; Malika Siker; Maria Teschler-Nicola.
The most common, life-threatening autosomal recessive disease of Europeans and Euro-Americans, cystic fibrosis (CF), occurs predominately in patients with the F508del mutation.1 Although F508del is currently detectable as a single allele in 1/30-1/40 Europeans2-4 and Euro-Americans,5 it has not been determined what heterozygote selective advantage(s) might account for its relatively high prevalence. Indirect evidence6 suggests that this mutation was present in Brittany at least 3000 years ago, but no direct analyses of ancient DNA have been reported to identify F508del and clarify its frequency in prehistoric inhabitants of Europe. Here we show that F508del was present in 3 of 32 Iron Age inhabitants of Austria from whom DNA could be recovered from molar...
Tipo: Manuscript Palavras-chave: Genetics & Genomics; Evolutionary Biology.
Ano: 2007 URL: http://precedings.nature.com/documents/1276/version/1
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Characteristics of oligonucleotide frequencies across genomes: Conservation versus variation, strand symmetry, and evolutionary implications Nature Precedings
Shang-Hong Zhang; Ya-Zhi Huang.
One of the objectives of evolutionary genomics is to reveal the genetic information contained in the primordial genome (called the primary genetic information in this paper, with the primordial genome defined here as the most primitive nucleic acid genome for earth’s life) by searching for primitive traits or relics remained in modern genomes. As the shorter a sequence is, the less probable it would be modified during genome evolution. For that reason, some characteristics of very short nucleotide sequences would have considerable chances to persist during billions of years of evolution. Consequently, conservation of certain genomic features of mononucleotides, dinucleotides, and higher-order oligonucleotides across various genomes may exist;...
Tipo: Manuscript Palavras-chave: Genetics & Genomics; Bioinformatics; Evolutionary Biology.
Ano: 2008 URL: http://precedings.nature.com/documents/2146/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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2011 German Escherichia coli O104:H4 outbreak: Alignment-free whole-genome phylogeny by feature frequency profiles Nature Precedings
Man Kit Cheung; Lei Li; Wenyan Nong; Hoi Shan Kwan.
Accuracy of SNP-based whole-genome phylogeny reconstruction relies heavily on quality of sequence alignment which is particularly hindered by poorly assembled genomes. Alignment-free methods might provide additional insights. Here, we constructed a whole-genome phylogeny of 10 isolates from the current German E. coli outbreak against 30 existing E. coli genomes as well as that of a historical EHEC isolate using the alignment-free feature frequency profile method. Our results revealed a high similarity among E. coli isolates from the current outbreak and the historical EHEC being the most closely related isolate sequenced thus far.
Tipo: Manuscript Palavras-chave: Genetics & Genomics; Microbiology; Bioinformatics; Evolutionary Biology.
Ano: 2011 URL: http://precedings.nature.com/documents/6109/version/2
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Internal conformation of the 'protein folding code' inferred from empirical tertiary structural classifications using Tlusty's topological approach Nature Precedings
Rodrick Wallace.
Tlusty's topological arguments regarding the genetic code are applied to the classification of tertiary irregular protein symmetries. The underlying 'protein folding code network' is found to have one major, highly dominant 'spherical' component, a minor attachment handle in the Morse Theory sense, and as many as two or three additional subminor handles.
Tipo: Manuscript Palavras-chave: Genetics & Genomics; Bioinformatics; Evolutionary Biology.
Ano: 2010 URL: http://precedings.nature.com/documents/4640/version/1
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Structural dynamics and divergence of the polygalacturonase gene family in land plants Nature Precedings
Soon-Jae Kwon; Jae-Han Son; Kyong-Cheul Park; Hae-Young Oh; Pyeung-Hyeun Kim; Woo-Hyeon Byeon; Nam-Soo Kim.
A distinct feature of eukaryotic genomes is the presence of gene families. The polygalacturonase (PG) (EC3.2.1.15) gene family is one of the largest gene families in plants. PG is a pectin-digesting enzyme with a glycoside hydrolase 28 domain. It is involved in numerous plant developmental processes. The evolutionary processes accounting for the functional divergence and the specialized functions of PGs in land plants are unclear. Here, phylogenetic and gene structure analysis of PG genes in algae and land plants revealed that land plant PG genes resulted from differential intron gain and loss, with the latter event predominating. PG genes in land plants contained 15 homologous intron blocks and 13 novel intron blocks. Intron position and phase were not...
Tipo: Manuscript Palavras-chave: Genetics & Genomics; Plant Biology; Evolutionary Biology.
Ano: 2008 URL: http://precedings.nature.com/documents/1608/version/1
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CDAO-Store: A New Vision in Data Integration Nature Precedings
Brandon Chisham; Trung Le; Enrico Pontelli; Tran Son; Ben Wright.
The Comparative Data Analysis Ontology (CDAO) 1 is an ontology developed, as part of the EvoInfo2 and EvoIO3 groups supported by NESCent4, to provide semantics to the descriptions of data and transformations commonly found in the domain of phylogenetic inference. The core concepts of the ontology enables the description of phylogenetic 
trees and associated character data matrices. 

Tipo: Manuscript Palavras-chave: Bioinformatics; Evolutionary Biology.
Ano: 2010 URL: http://precedings.nature.com/documents/4585/version/1
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Phyloinformatics in the age of Wikipedia Nature Precedings
Roderic Page.
This talk describes a mapping between the NCBI taxonomy database and Wikipedia. These two databases were chosen because the NCBI taxonomy contains all the taxa for which sequences are publicly available, and for many taxa Wikipedia is the first site returned in a Google search on that taxon's scientific name. The NCBI web pages for nearly 53,000 NCBI taxa now have a link to the corresponding page in Wikipedia.
Tipo: Manuscript Palavras-chave: Bioinformatics; Evolutionary Biology.
Ano: 2010 URL: http://precedings.nature.com/documents/4583/version/1
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Enhancing Jatropha Productivity by Canopy Management Nature Precedings
Chalapathy K. Reddy; Vishal V. Naole.
Jatropha seed and oil yield is function of planting material used, growing conditions, plant architecture development and maintenance. Jatropha is hardy plant; thrives well in arid and semi arid regions with an average rainfall ranging from 500 to 1200 mm. It has been planted in varied soil types, marginal and waste lands; where in utilization of in situ resources by agronomic practices and development and management of canopy by pruning are very crucial for harvesting higher seed for biodiesel production. Building ideal canopy by pruning during first growing season is very important. Pruning is done during winter season when plants are in dormant condition.
Tipo: Manuscript Palavras-chave: Developmental Biology; Earth & Environment; Plant Biology; Evolutionary Biology.
Ano: 2009 URL: http://precedings.nature.com/documents/3700/version/1
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Recombination modulates how selection affects linked sites in Drosophila Nature Precedings
Suzanne E. McGaugh; Caiti S. Smukowski; Brenda Manzano-Winkler; Tiffany L. Himmel; Mohamed A. F. Noor.
One of the most influential observations in molecular evolution has been a strong association between regional recombination rate and amount of nucleotide polymorphism in those genomic regions, interpreted as evidence for ubiquitous natural selection. The alternative explanation, that recombination is mutagenic, has been rejected by the absence of a similar association between regional recombination rate and nucleotide divergence between species. However, many recent studies show that recombination rates are often very different even in closely related species, questioning whether an association between recombination rate and divergence between species has been tested satisfactorily. To circumvent this problem, we directly surveyed recombination across...
Tipo: Manuscript Palavras-chave: Genetics & Genomics; Evolutionary Biology.
Ano: 2012 URL: http://precedings.nature.com/documents/7005/version/1
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Structural Analysis of Polarizing Indels Argues the Root of the Tree of Life is Near the Chloroflexi Nature Precedings
Ruben E. Valas; Philip E. Bourne.
Determining which branches of the tree of life have derived features narrows down the possible location of the root. Currently the polarization of indels done by Lake _et al_.^1-5^ and the polarizing transitions of Cavalier-Smith^6^ arrive at contradictory positions for the root of the tree. We have analyzed the sequence based indel arguments using protein structure wherever possible. Structure strongly supports some of the polarizations, but in other indels it argues for a different conclusion. We conclude that there is no contradiction between Lake _et al_. and Cavalier-Smith; the root of the tree of life must be near the Chloroflexi.

Tipo: Poster Palavras-chave: Genetics & Genomics; Bioinformatics; Evolutionary Biology.
Ano: 2009 URL: http://precedings.nature.com/documents/3290/version/1
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Ediacaran Macro Body Fossils Nature Precedings
Timothy D. Huang; Jei-Fu Shaw; Liang Zheng; Chun-Lan Huang; YiLung Chang; ChuanWei Yang.
This paper, Ediacaran Macro Body Fossils, reports a new discovery of well preserved three dimensional macro body fossils of the Ediacaran Period in central YunNan province in the People's Republic of China. These body fossils will enable more detailed and in-depth exploration of the evolution of multi-cellular macro organisms on this planet, whereas in the past, researches could only rely on cast or imprint fossils.
Tipo: Manuscript Palavras-chave: Earth & Environment; Evolutionary Biology.
Ano: 2010 URL: http://precedings.nature.com/documents/4423/version/1
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DNA^+Pro^: an Improved Progressive Multiple Sequence Alignment Algorithm for Evolutionary Analysis Using Combined DNA-Protein Sequences Nature Precedings
Xiaolong Wang; Shuang-yong Xu; Deming Gou.
Alignment of DNA and protein sequences is a basic tool in the study of evolutionary, structural and functional relationship among macromolecules. Present sequence alignment methods are somewhat error-prone, often producing systematic bias. Errors in sequence alignments sometimes lead to subsequent misinterpretation of evolutionary, structural and functional information in genes, proteins and genomes. In traditional sequence alignment algorithms, alignments of DNA and protein sequences are conducted separately. It has been long believed that the phylogenetic signal disappears more rapidly from DNA sequences than from encoded proteins. It is therefore generally preferable to align sequences at the amino acid level. Here we present a new...
Tipo: Manuscript Palavras-chave: Biotechnology; Genetics & Genomics; Microbiology; Bioinformatics; Evolutionary Biology.
Ano: 2010 URL: http://precedings.nature.com/documents/4898/version/1
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Telomeres in Evolution and Development from Biosemiotic Perspective Nature Precedings
Guenther Witzany.
Whereas telomeres protect terminal ends of linear chromosomes, telomerases identify natural chromosome ends being different from broken DNA. Although telomeres play a crucial role in the linear chromosome organisation of eukaryotic cells, their molecular syntax descended from an ancient retroviral competence. This is an indicator for the early retroviral colonization of large double stranded DNA viruses, which are putative ancestors of the eukaryotic nucleus.

This contribution will demonstrate an advantage of the biosemiotic approach towards our evolutionary understanding of telomeres: focus on the genetic/genomic structures as language-like text which follows combinatorial (syntactic), context-sensitive (pragmatic) and...
Tipo: Poster Palavras-chave: Genetics & Genomics; Evolutionary Biology.
Ano: 2007 URL: http://precedings.nature.com/documents/932/version/2
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Living unicellular eukaryote Tetrahymena pyriformis as a model for study Nature Precedings
Elena N. Mokhova.
Some animals are able to survive for a long time under conditions of drastically reduced oxidative metabolism, called metabolic depression. The most investigated type of metabolic depression is hibernation. Research into the basic properties of liver mitochondria energetics during hibernation is essential for fundamental biology and medicine. However, the absence of a suitable hepatocyte culture makes it impossible to study the characteristic features of mitochondrial metabolic states in living cells during hibernation. We proposed that under selected conditions, the unicellular eukaryote Tetrahymena pyriformis resembles hepatocytes under hibernation, as (i) both cell types survive under condition of restricted food supply, hypoxia, and accumulation of...
Tipo: Manuscript Palavras-chave: Molecular Cell Biology; Evolutionary Biology.
Ano: 2011 URL: http://precedings.nature.com/documents/4521/version/4
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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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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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EvolveAGene 3: A DNA coding sequence evolution simulation program Nature Precedings
Barry G. Hall.
EvolveAGene 3 is a realistic coding sequence simulation program that separates mutation from selection and allows the user to set selection conditions, including variable regions of selection intensity within the sequence and variation in intensity of selection over branches. Variation includes base substitutions, insertions and deletions. Output includes a log file, the true tree and both unaligned coding sequence and protein sequences and the true DNA and protein alignments.
Tipo: Manuscript Palavras-chave: Ecology; Genetics & Genomics; Bioinformatics; Evolutionary Biology.
Ano: 2007 URL: http://precedings.nature.com/documents/1230/version/1
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Ecological, phenological and biochemical significance of bimodal fruiting of Boletus alutaceus morgan Nature Precedings
Nandkumar Kamat.
Boletus alutaceus Morgan an ectomycorrhizal species was extensively studied from an ecologically fragmented microhabitt colonized by its' host plant Ficus benghalensis L. in the Goa University campus, Taleigao, Goa, India. Qualitatively the fruiting cycles were monitored for three years and thereafter detail ecological and morphological investigations were carried out in May and November 2004. A bimodal temporal fruting pattern emerged which may have significant ecological, phenological and biochemical role in EM dynamics.
Tipo: Presentation Palavras-chave: Biotechnology; Developmental Biology; Ecology; Genetics & Genomics; Microbiology; Plant Biology; Evolutionary Biology.
Ano: 2009 URL: http://precedings.nature.com/documents/2835/version/1
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