Análisis de la variabilidad a nivel nucleotídico de la región rp49 en Drosophila subobscura

[spa] Se ha analizado la variabilidad existente en una región de 1.6 KB. que incluye al locus RP49 (Ribosome Protein 49) en distintas ordenaciones cromosómicas de Drosophila subobscura. El estudio se ha efectuado mediante comparación de mapas de restricción según la técnica "Four-Cutter Analysis". Se han estudiado las siguientes poblaciones naturales: Barcelona (49 líneas), Ter Apel -Holanda- (58 líneas), Tenerife (54 líneas) y Santiago de Chile (54 líneas). Tras el análisis de los mapas de restricción se han detectado un total de 19 polimorfismos por substitución nucleotídica y 8 por inserción/deleción y un total de 96 haplotipos. La heterozigosidad por nucleótido fue de 0.0045 en las poblaciones europeas, de 0.0028 en la población de Tenerife y de 0.0056 en la población de Santiago de Chile. Las principales conclusiones del trabajo han sido: 1) No existencia de heterogeneidad entre las dos poblaciones europeas para ninguna de las 3 ordenaciones cromosómicas que se consideraron (OST' 03+4 Y 03+4+8). 2) Existencia de un importante intercambio genético entre distintas ordenaciones cromosómicas. 3) Mayor antigüedad de la ordenación cromosómica 03+4 respecto a la de la ordenación OST. 4) Gran diferenciación genética de la población de Tenerife respecto a las poblaciones europeas. 5) Gran reducción del número de haplotipos en la población de Santiago de Chile. 6) Evidencia de que los haplotipos de la región RP49 que se hallan en la actualidad en Santiago de Chile son descendientes por réplica de únicamente 6 a 8 cromosomas

Bioinformática y evolución molecular

Aunque la bioinformática y la evolución molecular pueden parecer disciplinas científicas muy heterogéneas, comparten gran parte de sus intereses y fundamentos, concretamente, el mismo interés por el estudio y análisis de secuencias de DNA y proteínas; no sólo eso: estos estudios son el núcleo central de ambas disciplina

BadiRate Software

Podeu consultar l'article relacionat a: http://hdl.handle.net/2445/53350Podeu consultar la pàgina de desenvolupament del programari: http://www.ub.edu/softevol/badirate/BadiRate is a software package to estimate, within a phylogenetic context and by likelihood-based methods (or parsimony): (1) the gain, birth, death and innovation family turnover rates (2) most likely number of family members in internal nodes (3) families with turnover rates higher or lower than that estimated for the whole dat

Comment on 'The Molecular Evolutionary Patterns of the Insulin/FOXO Signaling Pathway'

Letter to the Editor on Wang M, Wang Q, Wang Z, Zhang X, Pan Y. The molecular evolutionary patterns of the insulin/FOXO signaling pathwa

Comparative genomics reveals thousands of novel chemosensory genes and massive changes in chemoreceptor repertories across chelicerates

Chemoreception is a widespread biological function that is essential for the survival, reproduction, and social communication of animals. Though the molecular mechanisms underlying chemoreception are relatively well known in insects, they are poorly studied in the other major arthropod lineages. Current availability of a number of chelicerate genomes constitutes a great opportunity to better characterize gene families involved in this important function in a lineage that emerged and colonized land independently of insects. At the same time, that offers new opportunities and challenges for the study of this interesting animal branch in many translational research areas. Here, we have performed a comprehensive comparative genomics study that explicitly considers the high fragmentation of available draft genomes and that for the first time included complete genome data that cover most of the chelicerate diversity. Our exhaustive searches exposed thousands of previously uncharacterized chemosensory sequences, most of them encoding members of the gustatory and ionotropic receptor families. The phylogenetic and gene turnover analyses of these sequences indicated that the whole-genome duplication events proposed for this subphylum would not explain the differences in the number of chemoreceptors observed across species. A constant and prolonged gene birth and death process, altered by episodic bursts of gene duplication yielding lineage-specific expansions, has contributed significantly to the extant chemosensory diversity in this group of animals. This study also provides valuable insights into the origin and functional diversification of other relevant chemosensory gene families different from receptors, such as odorant-binding proteins and other related molecules

VariScan Software

Linux / Mac OS X : The package includes executables for linux (variscan) and Mac OS X (variscan). For other Unix-based platforms you will have to compile it from the source files included in the VariScan package. Windows: The package includes (src directory), the source code, the project (variscan.dev) and makefile (variscan.win) files to be used, for instance, for the Dev-C++ (a free Integrated Development Environment for the C/C++ programming language)Podeu consultar l'article relacionat a: http://hdl.handle.net/2445/7384Podeu consultar la pàgina de desenvolupament del programari: http://www.ub.edu/softevol/VariScan is a software package for the analysis of DNA sequence polymorphisms at the whole genome scale. Among other features, the software: (1) can conduct many population genetic analyses; (2) incorporates a multiresolution wavelet transform-based method that allows capturing relevant information from DNA polymorphism data; and (3) it facilitates the visualization of the results in the most commonly used genome browsers

Filogenómica y genómica de la adaptación

La posibilidad técnica actual de secuenciar genomas y transcriptomas completos de cualquier especie abre la puerta a cumplir la predicción de Darwin de poder reconstruir de forma rigurosa el árbol de la vida (las relaciones filogenéticas de todos los seres vivos actuales) mediante la filogenómica

Filogenómica y genómica de la adaptación

La posibilidad técnica actual de secuenciar genomas y transcriptomas completos de cualquier especie abre la puerta a cumplir la predicción de Darwin de poder reconstruir de forma rigurosa el árbol de la vida (las relaciones filogenéticas de todos los seres vivos actuales) mediante la filogenómica

Mycobacterial Phylogenomics: An Enhanced Method for Gene Turnover Analysis Reveals Uneven Levels of Gene Gain and Loss among Species and Gene Families

Species of the genus Mycobacterium differ in several features, from geographic ranges, and degree of pathogenicity, to ecological and host preferences. The recent availability of several fully sequenced genomes for a number of these species enabled the comparative study of the genetic determinants of this wide lifestyle diversity. Here, we applied two complementary phylogenetic-based approaches using information from 19 Mycobacterium genomes to obtain a more comprehensive view of the evolution of this genus. First, we inferred the phylogenetic relationships using two new approaches, one based on a Mycobacterium-specific amino acid substitution matrix and the other on a gene content dissimilarity matrix. Then, we utilized our recently developed gain-and-death stochastic models to study gene turnover dynamics in this genus in a maximum-likelihood framework. We uncovered a scenario that differs markedly from traditional 16S rRNA data and improves upon recent phylogenomic approaches. We also found that the rates of gene gain and death are high and unevenly distributed both across species and across gene families, further supporting the utility of the new models of rate heterogeneity applied in a phylogenetic context. Finally, the functional annotation of the most expanded or contracted gene families revealed that the transposable elements and the fatty acid metabolism-related gene families are the most important drivers of gene content evolution in Mycobacterium