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High rates of molecular evolution in hantaviruses

RAMSDEN, Cadhla; MELO, Fernando L.; FIGUEIREDO, Luiz. M.; HOLMES, Edward C.; ZANOTTO, Paolo M. A.; VGDN Consortium
Fonte: OXFORD UNIV PRESS Publicador: OXFORD UNIV PRESS
Tipo: Artigo de Revista Científica
ENG
Relevância na Pesquisa
65.8%
Hantaviruses are rodent-borne Bunyaviruses that infect the Arvicolinae, Murinae, and Sigmodontinae subfamilies of Muridae. The rate of molecular evolution in the hantaviruses has been previously estimated at approximately 10(-7) nucleotide substitutions per site, per year (substitutions/site/year), based on the assumption of codivergence and hence shared divergence times with their rodent hosts. If substantiated, this would make the hantaviruses among the slowest evolving of all RNA viruses. However, as hantaviruses replicate with an RNA-dependent RNA polymerase, with error rates in the region of one mutation per genome replication, this low rate of nucleotide substitution is anomalous. Here, we use a Bayesian coalescent approach to estimate the rate of nucleotide substitution from serially sampled gene sequence data for hantaviruses known to infect each of the 3 rodent subfamilies: Araraquara virus ( Sigmodontinae), Dobrava virus ( Murinae), Puumala virus ( Arvicolinae), and Tula virus ( Arvicolinae). Our results reveal that hantaviruses exhibit shortterm substitution rates of 10(-2) to 10(-4) substitutions/site/year and so are within the range exhibited by other RNA viruses. The disparity between this substitution rate and that estimated assuming rodent-hantavirus codivergence suggests that the codivergence hypothesis may need to be reevaluated.

Seleção positiva sobre o gene do hormônio do crescimento e sua associação com a diversificação de tamanho nos Platyrrhini; Positive selection on the growth hormone and its association with size evolution in Platyrrhini

Menezes, Elytania Veiga
Fonte: Biblioteca Digitais de Teses e Dissertações da USP Publicador: Biblioteca Digitais de Teses e Dissertações da USP
Tipo: Tese de Doutorado Formato: application/pdf
Publicado em 06/08/2008 PT
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55.92%
As bases moleculares da diversidade fenotipica dentro de espécies são de grande interesse aos biólogos evolutivos porque a evolução morfológica adaptival depende da seleção de variantes genéticas. Entretanto, há poucos exemplos da variação fenotípica cuja a base molecular é compreendida, especialmente entre animais vertebrados. Biólogos em geral concordam que o processo da seleção natural é a fonte predominante de diversificação morfológica. Tem sido documentado previamente que existe diversificação adaptativa da morfologia craniana entre os taxa mais elevados de Platyrrhini e também em espécies e em muitos géneros, que aparentemente diversificaram na morfologia do crânio por seleção natural. O hormônio de crescimento (GH) é um hormônio multifunctional, produzido principalmente pela glândula pituitária de todos os animais vertebrados para regular o metabolismo e para promover o crescimento pos-natal linear. A evolução molecular do GH foi estudada extensivamente em um grande número espécies de vertebrados, incluindo primatas. A evolução rápida do gene do GH em primatas, especiamente em regiões funcionalmente importantes, sugere a seleção darwiniana positiva. Entretanto, o relaxamento da seleção purificadora depois de múltiplas duplicações do locus GH não podem ser descartadas. O objetivo deste estudo era investigar a evolução molecular do gene do GH em primatas neotropicais...

Aspectos de física estatística na evolução e no crescimento molecular.; Aspects of statistical physics on evolution and in molecular growth.

Silva, Wenderson Alexandre de Sousa
Fonte: Biblioteca Digitais de Teses e Dissertações da USP Publicador: Biblioteca Digitais de Teses e Dissertações da USP
Tipo: Dissertação de Mestrado Formato: application/pdf
Publicado em 18/06/2009 PT
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55.89%
A evolução molecular, impulsionada pela Teoria Sintética da Evolução, tornou um assunto indispensável na compreensão da evolução da vida. O crescimento genômico, etapa responsável pelo maior potencial de armazenamento de informação e estabilidade, também foi submetido à indelével ação da seleção natural. Utilizando a metodologia dos ciclos de amplificação-mutação-seleção, tal como o SELEX (systematic evolution of ligands by exponential enrichment), que mimetizam a seleção natural, e ferramentas da Teoria de Informação, foram desenvolvidos e implementados programas para simular a evolução, considerando, além de outros, um parâmetro pouco explorado na literatura: a variação do tamanho do genoma. Foram estudados dois cenários distintos; no primeiro a seleção era dependente da busca exata de uma sequência pré-determinada (o filtro). Além disso, a entropia de Shannon considerada era referente ao alinhamento da molécula toda. Avaliando configurações simples desse modelo, foi possível desenvolver uma equação analítica que descreveu bem os resultados (para tamanho de genoma constante). No segundo cenário, foram exploradas a seleção não específica de uma sequência, o número máximo de bases constante...

Análise estatística da teoria de quase-espécies de evolução molecular; Statistical analysis of the quasispecies theory of molecular evolution

Alves, Domingos
Fonte: Biblioteca Digitais de Teses e Dissertações da USP Publicador: Biblioteca Digitais de Teses e Dissertações da USP
Tipo: Tese de Doutorado Formato: application/pdf
Publicado em 24/03/1999 PT
Relevância na Pesquisa
65.86%
Nesta tese propomos e estudamos um modelo alternativo para investigar a evolução de quase-espécies moleculares, no qual supomos que a população seja uma combinação aleatória das moléculas constituintes em cada geração. Essa aleatoriedade deve-se a inclusão de um procedimento adicional de amostragem da população além dos procedimentos usuais de mutação e reprodução diferenciada. O modelo, denominado modelo de amostragens, é baseado em um algoritmo que mimetiza procedimentos experimentais que usam técnicas de transferências em série para reproduzir o processo de evolução de microorganismos in vitro. Além do modelo reproduzir a solução exata do estado estacionário do modelo de quase-espécies no regime determinístico, ele permite o estudo da evolução da quase-espécie molecular em todo espaço de parâmetros de controle, incluindo o caso em que a população é finita. A generalização dessa formulação alternativa para uma classe geral de relevos de replicação permite-nos realizar um estudo bastante completo do fenômeno do limiar de erro, levando-nos a uma análise crítica sobre a generalidade desse fenômeno; In this thesis we propose and study an alternative model to investigate the evolution of a molecular quasispecies...

Hepatitis C virus molecular evolution: Transmission, disease progression and antiviral therapy

Victoria Preciado, Maria; Valva, Pamela; Escobar-Gutierrez, Alejandro; Rahal, Paula; Ruiz-Tovar, Karina; Yamasaki, Lilian; Vazquez-Chacon, Carlos; Martinez-Guarneros, Armando; Carlos Carpio-Pedroza, Juan; Fonseca-Coronado, Salvador; Cruz-Rivera, Mayra
Fonte: Baishideng Publishing Group Inc Publicador: Baishideng Publishing Group Inc
Tipo: Artigo de Revista Científica Formato: 15992-16013
ENG
Relevância na Pesquisa
55.8%
Hepatitis C virus (HCV) infection represents an important public health problem worldwide. Reduction of HCV morbidity and mortality is a current challenge owned to several viral and host factors. Virus molecular evolution plays an important role in HCV transmission, disease progression and therapy outcome. The high degree of genetic heterogeneity characteristic of HCV is a key element for the rapid adaptation of the intrahost viral population to different selection pressures (e.g., host immune responses and antiviral therapy). HCV molecular evolution is shaped by different mechanisms including a high mutation rate, genetic bottlenecks, genetic drift, recombination, temporal variations and compartmentalization. These evolutionary processes constantly rearrange the composition of the HCV intrahost population in a staging manner. Remarkable advances in the understanding of the molecular mechanism controlling HCV replication have facilitated the development of a plethora of direct-acting antiviral agents against HCV. As a result, superior sustained viral responses have been attained. The rapidly evolving field of anti-HCV therapy is expected to broad its landscape even further with newer, more potent antivirals, bringing us one step closer to the interferon-free era. (C) 2014 Baishideng Publishing Group Inc. All rights reserved.

Biodiversity and molecular evolution of malacostraca; Biodiversidade e evolução molecular da classe malacostraca

Silva, Joana Rafael Matzen Neves da
Fonte: Universidade de Aveiro Publicador: Universidade de Aveiro
Tipo: Tese de Doutorado
ENG
Relevância na Pesquisa
55.84%
No actual cenário de perda acelerada de biodiversidade, o nosso conhecimento dos ecossistemas marinhos, apesar da sua extensão e complexidade, continua muito inferior ao dos ecossistemas terrestres. A classe Malacostraca (Arthropoda, Crustacea), um grupo dos mais representativos nos ecossistemas marinhos, apresenta um elevado nível de diversidade morfológica e ecológica, mas difícil sua identificação ao nível de espécie requer frequentemente a ajuda de especialistas em taxonomia. A utilização recente do “barcoding” (código de barras do ADN), revelou ser um método rápido e eficaz para a identificação de espécies em diversos grupos de metazoários, incluindo os Malacostraca. No âmbito desta tese foi construída uma base de dados de código de barras de ADN envolvendo 132 espécies de Malacostraca vários locais de amostragem no Atlântico Nordeste e Mediterrâneo. As sequências de ADN mitocondrial provenientes de 601 espécimes formaram, em 95% dos casos, grupos congruentes com as identificações baseadas em características morfológicas. No entanto, foi detectado polimorfismo em seis casos e a divergência intra-específica foi elevada em exemplares pertencentes a duas espécies morfológicas, sugerindo, neste caso...

Molecular evolution in bacteria: cell division

Trevors,J.T.
Fonte: Sociedade Brasileira de Microbiologia Publicador: Sociedade Brasileira de Microbiologia
Tipo: Artigo de Revista Científica Formato: text/html
Publicado em 01/10/1998 EN
Relevância na Pesquisa
65.8%
Molecular evolution in bacteria is examined with an emphasis on the self-assembly of cells capable of primitive division and growth during early molecular evolution. Also, the possibility that some type of encapsulation structure preceeded biochemical pathways and the assembly of genetic material is examined. These aspects will be considered from an evolutionary perspective.

Functional Evolution of cis-Regulatory Modules at a Homeotic Gene in Drosophila

Ho, Margaret C. W.; Goetz, Sara E.; Schiller, Benjamin J.; Bae, Esther; Tran, Diana A.; Shur, Andrey S.; Rau, Christoph; Celniker, Susan E.; Drewell, Robert A.; Johnsen, Holly; Allen, John M; Bender, Welcome W.; Fisher, William W.
Fonte: Public Library of Science Publicador: Public Library of Science
Tipo: Artigo de Revista Científica
EN_US
Relevância na Pesquisa
55.87%
It is a long-held belief in evolutionary biology that the rate of molecular evolution for a given DNA sequence is inversely related to the level of functional constraint. This belief holds true for the protein-coding homeotic (Hox) genes originally discovered in Drosophila melanogaster. Expression of the Hox genes in Drosophila embryos is essential for body patterning and is controlled by an extensive array of cis-regulatory modules (CRMs). How the regulatory modules functionally evolve in different species is not clear. A comparison of the CRMs for the Abdominal-B gene from different Drosophila species reveals relatively low levels of overall sequence conservation. However, embryonic enhancer CRMs from other Drosophila species direct transgenic reporter gene expression in the same spatial and temporal patterns during development as their D. melanogaster orthologs. Bioinformatic analysis reveals the presence of short conserved sequences within defined CRMs, representing gap and pair-rule transcription factor binding sites. One predicted binding site for the gap transcription factor KRUPPEL in the IAB5 CRM was found to be altered in Superabdominal (Sab) mutations. In Sab mutant flies, the third abdominal segment is transformed into a copy of the fifth abdominal segment. A model for KRUPPEL-mediated repression at this binding site is presented. These findings challenge our current understanding of the relationship between sequence evolution at the molecular level and functional activity of a CRM. While the overall sequence conservation at Drosophila CRMs is not distinctive from neighboring genomic regions...

Contrasting rates of mitochondrial molecular evolution in parasitic diptera and hymenoptera

Castro, L.; Austin, A.; Dowton, M.
Fonte: Soc Molecular Biology Evolution Publicador: Soc Molecular Biology Evolution
Tipo: Artigo de Revista Científica
Publicado em //2002 EN
Relevância na Pesquisa
65.89%
We investigated the putative association between the parasitic lifestyle and an accelerated rate of mt genetic divergence, compositional bias, and gene rearrangement, employing a range of parasitic and nonparasitic Diptera and Hymenoptera. Sequences were obtained for the cox1, cox2, 16S, 28S genes, the regions between the cox2 and atp8 genes, and between the nad3 and nad5 genes. Relative rate tests indicated generally that the parasitic lifestyle was not associated with an increased rate of genetic divergence in the Diptera but reaffirmed that it was in the Hymenoptera. Similarly, a departure from compositional stationarity was not associated with parasitic Diptera but was in parasitic Hymenoptera. Finally, mitochondrial (mt) gene rearrangements were not observed in any of the dipteran species examined. The results indicate that these genetic phenomena are not accelerated in parasitic Diptera compared with nonparasitic Diptera. A possible explanation for the differences in the rate of mt molecular evolution in parasitic Diptera and Hymenoptera is the extraordinary level of radiation that has occurred within the parasitic Hymenoptera but not in any of the dipteran parasitic lineages. If speciation events in the parasitic Hymenoptera are associated with founder events...

Sociality and the rate of molecular evolution

Bromham, Lindell; Leijs, Remko
Fonte: Oxford University Press Publicador: Oxford University Press
Tipo: Artigo de Revista Científica
Publicado em //2005 EN
Relevância na Pesquisa
55.91%
The molecular clock does not tick at a uniform rate in all taxa but may be influenced by species characteristics. Eusocial species (those with reproductive division of labor) have been predicted to have faster rates of molecular evolution than their nonsocial relatives because of greatly reduced effective population size; if most individuals in a population are nonreproductive and only one or few queens produce all the offspring, then eusocial animals could have much lower effective population sizes than their solitary relatives, which should increase the rate of substitution of "nearly neutral" mutations. An earlier study reported faster rates in eusocial honeybees and vespid wasps but failed to correct for phylogenetic nonindependence or to distinguish between potential causes of rate variation. Because sociality has evolved independently in many different lineages, it is possible to conduct a more wide-ranging study to test the generality of the relationship. We have conducted a comparative analysis of 25 phylogenetically independent pairs of social lineages and their nonsocial relatives, including bees, wasps, ants, termites, shrimps, and mole rats, using a range of available DNA sequences (mitochondrial and nuclear DNA coding for proteins and RNAs...

Molecular Evolution of Hepatitis B Virus over 25 Years

Osiowy, Carla; Giles, Elizabeth; Tanaka, Yasuhito; Mizokami, Masashi; Minuk, Gerald Y.
Fonte: American Society for Microbiology Publicador: American Society for Microbiology
Tipo: Artigo de Revista Científica
Publicado em /11/2006 EN
Relevância na Pesquisa
55.81%
Determining the longitudinal molecular evolution of hepatitis B virus (HBV) is difficult due to HBV's genomic complexity and the need to study paired samples collected over long periods of time. In this study, serial samples were collected from eight hepatitis B virus e antigen-negative asymptomatic carriers of HBV genotype B in 1979 and 2004, thus providing a 25-year period to document the long-term molecular evolution of HBV. The rate, nature, and distribution of mutations that emerged over 25 years were determined by phylogenetic and linear regression analysis of full-length HBV genome sequences. Nucleotide hypervariability was observed within the polymerase and pre-S/S overlap region and within the core gene. The calculated mean number of nucleotide substitutions/site/year (7.9 × 10−5) was slightly higher than published estimates (1.5 × 10−5 to 5 × 10−5). Nucleotide changes in the quasispecies population did not significantly alter the molecular evolutionary rate, based on linear regression analysis of evolutionary distances among serial clone pre-S region sequences. Therefore, the directly amplified or dominant sequence was sufficient to estimate the putative molecular evolutionary rate for these long-term serial samples. On average...

Population size and molecular evolution on islands

Woolfit, Megan; Bromham, Lindell
Fonte: Royal Society of London Publicador: Royal Society of London
Tipo: Artigo de Revista Científica
Relevância na Pesquisa
65.83%
The nearly neutral theory predicts that the rate and pattern of molecular evolution will be influenced by effective population size (Ne), because in small populations more slightly deleterious mutations are expected to drift to fixation. This important pr

The Modern Molecular Clock

Bromham, Lindell; Penny, David
Fonte: Nature Publishing Group Publicador: Nature Publishing Group
Tipo: Artigo de Revista Científica
Relevância na Pesquisa
55.83%
The discovery of the molecular clock - a relatively constant rate of molecular evolution-provided an insight into the mechanisms of molecular evolution, and created one of the most useful new tools in biology. The unexpected constancy of rate was explaine

Metabolic rate does not calibrate the molecular clock

Lanfear, Robert; Thomas, Jessica; Welch, John J.; Brey, Thomas; Bromham, Lindell
Fonte: National Academy of Sciences (USA) Publicador: National Academy of Sciences (USA)
Tipo: Artigo de Revista Científica
Relevância na Pesquisa
55.83%
Rates of molecular evolution vary widely among lineages, but the causes of this variation remain poorly understood. It has been suggested that mass-specific metabolic rate may be one of the key factors determining the rate of molecular evolution, and that

Sociality and the Rate of Molecular Evolution

Bromham, Lindell; Leys, Remko
Fonte: Society for Molecular Biology Evolution Publicador: Society for Molecular Biology Evolution
Tipo: Artigo de Revista Científica
Relevância na Pesquisa
75.83%
The molecular clock does not tick at a uniform rate in all taxa but may be influenced by species characteristics. Eusocial species (those with reproductive division of labor) have been predicted to have faster rates of molecular evolution than their nonso

Contribution of recombination and selection to molecular evolution of Citrus tristeza virus

Martín, Susana; Sambade, Adrián; Rubio, Luis; Vives, María C.; Moya, Patricia; Guerri, José; Elena, Santiago F.; Moreno, Pedro
Fonte: Society for General Microbiology Publicador: Society for General Microbiology
Tipo: Artículo Formato: 472319 bytes; application/pdf
ENG
Relevância na Pesquisa
65.83%
30 páginas, 3 figuras, 2 tablas.; The genetic variation of Citrus tristeza virus (CTV) was analyzed comparing the predominant sequence variants in seven genomic regions (p33, p65, p61, p18, p13, p20, and p23) of 18 pathogenically distinct isolates from seven different countries. Analyses of the selective constraints acting on each codon suggest that most regions were under purifying selection. Phylogenetic analysis show diverse patterns of molecular evolution for different genomic regions. A first clade composed by isolates genetically close to the reference mild isolates T385 or T30 was inferred from all genomic regions. A second clade, mostly comprising virulent isolates, was defined from regions p33, p65, p13, p20, and p23. For regions p65, p61, p18, p13, and p23 a third clade that mostly included South American isolates could not be related with any reference genotype. Phylogenetic relationships among isolates did not reflect their geographical origin, suggesting significant gene flow between geographically distant areas. Incongruent phylogenetic trees for different genomic regions suggested recombination events, an extreme that was supported by several recombination-detecting methods. A phylogenetic network incorporating the effect of recombination showed an explosive radiation pattern for the evolution of some isolates and grouped isolates by virulence. Taken together...

Modeling the Impact of DNA Methylation on the Evolution of BRCA1 in Mammals

Huttley, Gavin Austin
Fonte: Society for Molecular Biology Evolution Publicador: Society for Molecular Biology Evolution
Tipo: Artigo de Revista Científica
Relevância na Pesquisa
65.83%
The modified base 5-methylcytosine (mC) plays an important functional role in the biology of mammals as an epigenetic modification and appears to exert a striking impact on the molecular evolution of mammal genomes. The collective epigenetic functions of

Molecular evolution of VH9 germline genes isolated from DBA, BALB, 129 and C57BL mouse strains and sublines

Zylstra, Paula; Franklin, Andrew; Hassan, Karl; Powell, Kim; Steele, Edward J; Blanden, Robert
Fonte: Springer Publicador: Springer
Tipo: Artigo de Revista Científica
Relevância na Pesquisa
65.8%
We have used the polymerase chain reaction (PCR) in an attempt to clone and sequence the exons and hitherto unavailable contiguous flanks of all members of the small VH9 germline gene family from inbred mouse strains and sublines that have had a common ancestry within the last century, and to analyze the molecular evolution of these sequences. Fifteen genuine germline genes were isolated (designated VH9.1 through VH9.15) from strains and sublines of DBA, BALB, 129 and C57BL inbred mice. Of the 15 genuine isolates, nine are novel: seven sequences from DBA strains and sublines (VH9.3 to VH9.9) and two sequences from C57BL strains (VH9.13 and VH9.14). We have identified sequencing errors and PCR recombinant artefacts in previously published sequences. We detected no sequence divergence of individual genes shared by the strains and sublines studied. However, we isolated two genes from DBA strains and sublines, VH9.1 and VH9.3, that differ only by five nucleotides encoding three amino acid changes that are concentrated within a 33 nucleotide (11 codon) region. Of these 11 codons, eight encode a putative antigen binding site. There were no differences in the remaining 733 nucleotides sequenced (including both 5′ and 3′ flanking regions). Potential explanations for the generation of VH9.1 and VH9.3 are discussed.

Quantum Genetics and Quantum Automata Models of Quantum-Molecular Evolution Involved in the Evolution of Organisms and Species

I. C. Baianu
Fonte: Nature Preceedings Publicador: Nature Preceedings
Tipo: Manuscript
Relevância na Pesquisa
55.94%
Previous theoretical or general approaches to the problems of Quantum Genetics and Molecular Evolution are considered in this article from the point of view of Quantum Automata Theory first published by the author in 1971 and further developed in several recent articles. The representation of genomes and Interactome networks in categories of many-valued logic LMn –algebras that are naturally transformed during biological evolution, or evolve through interactions with the environment provide a new insight into the mechanisms of molecular evolution, as well as organismal evolution, in terms of sequences of quantum automata. Phenotypic changes are expressed only when certain environmentally-induced quantum-molecular changes are coupled with an internal re-structuring of major submodules of the genome and Interactome networks related to cell cycling and cell growth. Contrary to the commonly held view of `standard’ Darwinist models of evolution, the evolution of organisms and species occurs through coupled multi-molecular transformations induced not only by the environment but actually realized through internal re-organizations of genome and interactome networks. The biological, evolutionary processes involve certain epigenetic transformations that are responsible for phenotypic expression of the genome and Interactome transformations initiated at the quantum-molecular level. It can thus be said that only quantum genetics can provide correct explanations of evolutionary processes that are initiated at the quantum--multi-molecular levels and propagate to the higher levels of organismal and species evolution. Biological evolution should be therefore regarded as a multi-scale process which is initiated by underlying quantum (coupled) multi-molecular transformations of the genomic and interactomic networks...

Quantum Genetics and Quantum Automata Models of Quantum-Molecular Evolution Involved in the Evolution of Organisms and Species

I. C. Baianu
Fonte: Nature Preceedings Publicador: Nature Preceedings
Tipo: Manuscript
Relevância na Pesquisa
55.94%
Previous theoretical or general approaches to the problems of Quantum Genetics and Molecular Evolution are considered in this article from the point of view of Quantum Automata Theory first published by the author in 1971 and further developed in several recent articles. The representation of genomes and Interactome networks in categories of many-valued logic LMn –algebras that are naturally transformed during biological evolution, or evolve through interactions with the environment provide a new insight into the mechanisms of molecular evolution, as well as organismal evolution, in terms of sequences of quantum automata. Phenotypic changes are expressed only when certain environmentally-induced quantum-molecular changes are coupled with an internal re-structuring of major submodules of the genome and Interactome networks related to cell cycling and cell growth. Contrary to the commonly held view of 'standard’ Darwinist models of evolution, the evolution of organisms and species occurs through coupled multi-molecular transformations induced not only by the environment but actually realized through internal re-organizations of genome and interactome networks. The biological, evolutionary processes involve certain epigenetic transformations that are responsible for phenotypic expression of the genome and Interactome transformations initiated at the quantum-molecular level. It can thus be said that only quantum genetics can provide correct explanations of evolutionary processes that are initiated at the quantum--multi-molecular levels and propagate to the higher levels of organismal and species evolution. Biological evolution should be therefore regarded as a multi-scale process which is initiated by underlying quantum (coupled) multi-molecular transformations of the genomic and interactomic networks...