RESUMO
Divergence date estimates are central to understand evolutionary processes and depend, in the case of molecular phylogenies, on tests of molecular clocks. Here we propose two non-parametric tests of strict and relaxed molecular clocks built upon a framework that uses the empirical cumulative distribution (ECD) of branch lengths obtained from an ensemble of Bayesian trees and well known non-parametric (one-sample and two-sample) Kolmogorov-Smirnov (KS) goodness-of-fit test. In the strict clock case, the method consists in using the one-sample Kolmogorov-Smirnov (KS) test to directly test if the phylogeny is clock-like, in other words, if it follows a Poisson law. The ECD is computed from the discretized branch lengths and the parameter λ of the expected Poisson distribution is calculated as the average branch length over the ensemble of trees. To compensate for the auto-correlation in the ensemble of trees and pseudo-replication we take advantage of thinning and effective sample size, two features provided by Bayesian inference MCMC samplers. Finally, it is observed that tree topologies with very long or very short branches lead to Poisson mixtures and in this case we propose the use of the two-sample KS test with samples from two continuous branch length distributions, one obtained from an ensemble of clock-constrained trees and the other from an ensemble of unconstrained trees. Moreover, in this second form the test can also be applied to test for relaxed clock models. The use of a statistically equivalent ensemble of phylogenies to obtain the branch lengths ECD, instead of one consensus tree, yields considerable reduction of the effects of small sample size and provides a gain of power.
Assuntos
Evolução Molecular , Modelos Genéticos , Filogenia , Animais , Ascomicetos/classificação , Ascomicetos/genética , Teorema de Bayes , Simulação por Computador , Ciclo-Oxigenase 1/genética , DNA/genética , Bases de Dados Genéticas , Produtos do Gene env/genética , Humanos , Lentivirus/classificação , Lentivirus/genética , Distribuição de Poisson , Primatas/classificação , Primatas/genética , Proteínas/genética , Estatísticas não Paramétricas , Fatores de TempoRESUMO
Small ruminant lentiviruses (SRLV) cause a multisystemic chronic disease affecting animal production and welfare. SRLV infections are spread across the world with the exception of Iceland. Success in controlling SRLV spread depends largely on the use of appropriate diagnostic tools, but the existence of a high genetic/antigenic variability among these viruses, the fluctuant levels of antibody against them and the low viral loads found in infected individuals hamper the diagnostic efficacy. SRLV have a marked in vivo tropism towards the monocyte/macrophage lineage and attempts have been made to identify the genome regions involved in tropism, with two main candidates, the LTR and env gene, since LTR contains primer binding sites for viral replication and the env-encoded protein (SU ENV), which mediates the binding of the virus to the host's cell and has hypervariable regions to escape the humoral immune response. Once inside the host cell, innate immunity may interfere with SRLV replication, but the virus develops counteraction mechanisms to escape, multiply and survive, creating a quasi-species and undergoing compartmentalization events. So far, the mechanisms of organ tropism involved in the development of different disease forms (neurological, arthritic, pulmonary and mammary) are unknown, but different alternatives are proposed. This is an overview of the current state of knowledge on SRLV genetic variability and its implications in tropism as well as in the development of alternative diagnostic assays.
Assuntos
Lentivirus/fisiologia , Ruminantes/virologia , Animais , Variação Genética , Lentivirus/classificação , Infecções por Lentivirus/diagnóstico , Filogenia , Tropismo ViralRESUMO
The first lentivirus isolated from sheep in Brazil was analysed phylogenetically. Evolutionary trees of the proviral 597 nucleotide gag and 432 nucleotide pol sequences obtained by the maximum likelihood method demonstrated that the sheep isolate clustered with prototype Maedi Visna virus whereas three lentiviruses isolated from goats in the same geographic region were close to caprine arthritis encephalitis prototypes. A subsequent comparison of sequence data of these viruses with those contained in the EMBL sequence database revealed that, in contrast to caprine prototypic viruses, all prototypic Maedi Visna viruses contain a deletion of six nucleotides in the gag gene resulting in the deletion of two residues in the central region of capsid protein. This deletion may be a useful marker in the analysis of small ruminant lentiviruses, especially when considering possible transmission of lentiviruses between sheep and goats.
Assuntos
Produtos do Gene gag/genética , Produtos do Gene pol/genética , Cabras/virologia , Lentivirus/genética , Ovinos/virologia , Sequência de Aminoácidos , Animais , Sequência de Bases , Brasil , DNA Viral , Lentivirus/classificação , Lentivirus/isolamento & purificação , Dados de Sequência Molecular , Filogenia , Homologia de Sequência de AminoácidosRESUMO
La familia de los Retrovirus se encuentra en el hombre y en los animales y son una causa considerable de mortalidad. Aunque se sabe que existen hace casi 100 años, su rol como agentes patógenos humano se recononoció hace aproximadamente 15 años. Su Genoma está compuesto por ARN. Los cuadro Retrovirus humanos: HIV-1, HIV-2, HTLV-1 y HTLV-II comparten cararterísticas comunes aunque se trata de entidades diferentes. Los ensayos que se utilizan para cada uno de estos virus son similares tanto en los principios como en las técnicas. En este primer apartado (I) del ensayo "Los Retrovirus" de detallará: etipatología, configuración antigénetica, respuesta inmune específica del huésped, clasificación de los métodos de diagnósticos sérico de HIV-1 y HIV-2 luego se completará el dictum mediante una lista parcial de los equipos comerciales de diagnóstico en el Anexo 1
Assuntos
Humanos , Algoritmos , Ensaio de Imunoadsorção Enzimática , Anticorpos Anti-HIV , HIV/imunologia , Sorodiagnóstico da AIDS/métodos , Síndrome da Imunodeficiência Adquirida/diagnóstico , Western Blotting , Árvores de Decisões , Ensaio de Imunoadsorção Enzimática/classificação , HIV/ultraestrutura , Imunoensaio , Lentivirus/classificação , Ensaio de Radioimunoprecipitação , Sorodiagnóstico da AIDS/classificação , Sorodiagnóstico da AIDS/normas , Imunofluorescência/normasRESUMO
La familia de los Retrovirus se encuentra en el hombre y en los animales y son una causa considerable de mortalidad. Aunque se sabe que existen hace casi 100 años, su rol como agentes patógenos humano se recononoció hace aproximadamente 15 años. Su Genoma está compuesto por ARN. Los cuadro Retrovirus humanos: HIV-1, HIV-2, HTLV-1 y HTLV-II comparten cararterísticas comunes aunque se trata de entidades diferentes. Los ensayos que se utilizan para cada uno de estos virus son similares tanto en los principios como en las técnicas. En este primer apartado (I) del ensayo "Los Retrovirus" de detallará: etipatología, configuración antigénetica, respuesta inmune específica del huésped, clasificación de los métodos de diagnósticos sérico de HIV-1 y HIV-2 luego se completará el dictum mediante una lista parcial de los equipos comerciales de diagnóstico en el Anexo 1 (AU)