Going nuclear: gene family evolution and vertebrate phylogeny reconciled

Gene duplications have been common throughout vertebrate evolution, introducing paralogy and so complicating phylogenctic inference from nuclear genes. Reconciled trees are one method capable of dealing with paralogy, using the relationship between a gene phylogeny and the phylogeny of the organisms containing those genes to identify gene duplication events. This allows us to infer phylogenies from gene families containing both orthologous and paralogous copies. Vertebrate phylogeny is well understood from morphological and palaeontological data, but studies using mitochondrial sequence data have failed to reproduce this classical view. Reconciled tree analysis of a database of 118 vertebrate gene families supports a largely classical vertebrate phylogeny

Arturo Campión ntre la historia y la cultura

Reseña bibliográfica de la obra "Arturo Campién entre la historia y la cultura", de José Javier López Antón, en la que presenta un estudio del investigador Arturo Campión. Divide su obra en dos partes mediante las que estudia por una parte la evolución personal y político-ideológica de Campión , y aborda su labor de historiador y su proyección literaia por otra

Moluscos

El éxito evolutivo de los moluscos queda patente en la gran cantidad de especies vivas existentes (son el segundo filo de metazoos más diverso), así como en su abundancia y en su capacidad de colonizar casi cualquier hábitat. Los moluscos representan una parte importantísima de la biomasa marina, pero también se han adaptado de manera exitosa al medio terrestre y al dulceacuícola. Se caracterizan por la presencia de 1) rádula, un órgano especializado para la alimentación; 2) manto, un epitelio especializado situado en la zona dorsal del cuerpo que cubre la masa visceral, capaz de segregar espículas o conchas; y 3) un pie ciliado ventralmente. Actualmente se reconocen ocho grandes grupos de moluscos: Neomeniomorpha, Chaetodermomorpha, Polyplacophora, Monoplacophora, Bivalvia, Scaphopoda, Cephalopoda y Gastropoda. A pesar de que la monofilia de cada uno de estos linajes está apoyada por datos morfológicos y moleculares, sus relaciones evolutivas son un tema de debate y un reto para la era de la genómica, que apenas comienza en los moluscos. Las hipótesis morfológicas sitúan a Neomeniomorpha, Chaetodermomorpha y poliplacóforos como los linajes de moluscos más basales, y dejan al resto en una posición más derivada, agrupados bajo el nombre de Conchifera, un grupo caracterizado por la presencia de una concha en una única pieza. Recientemente se han inferido las relaciones filogenéticas entre estos grupos basándose en datos moleculares. Los resultados iniciales en base a pocos genes fueron poco concluyentes pero dos trabajos recientes en base a datos procedentes de transcriptomas apoyan la hipótesis Conchifera, la relación cercana de poliplacóforos, neomeniomorfos y chaetodermomorfos (hipótesis Aculifera) y que neomeniomorfos y chaetodermomorfos son grupos hermanos (hipótesis Aplacophora). Dentro de Conchifera, los cefalópodos y los monoplacóforos serían el grupo hermano de gasterópodos, bivalvos y escafópodos.N

Relative role of life-history traits and historical factors in shaping genetic population structure of sardines (Sardina pilchardus)

<p>Abstract</p> <p>Background</p> <p>Marine pelagic fishes exhibit rather complex patterns of genetic differentiation, which are the result of both historical processes and present day gene flow. Comparative multi-locus analyses based on both nuclear and mitochondrial genetic markers are probably the most efficient and informative approach to discerning the relative role of historical events and life-history traits in shaping genetic heterogeneity. The European sardine (<it>Sardina pilchardus</it>) is a small pelagic fish with a relatively high migratory capability that is expected to show low levels of genetic differentiation among populations. Previous genetic studies based on meristic and mitochondrial control region haplotype frequency data supported the existence of two sardine subspecies (<it>S. p. pilchardus </it>and <it>S. p. sardina</it>).</p> <p>Results</p> <p>We investigated genetic structure of sardine among nine locations in the Atlantic Ocean and Mediterranean Sea using allelic size variation of eight specific microsatellite loci. Bayesian clustering and assignment tests, maximum likelihood estimates of migration rates, as well as classical genetic-variance-based methods (hierarchical AMOVA test and <it>R</it>_{<it>ST </it>}pairwise comparisons) supported a single evolutionary unit for sardines. These analyses only detected weak but significant genetic differentiation, which followed an isolation-by-distance pattern according to Mantel test.</p> <p>Conclusion</p> <p>We suggest that the discordant genetic structuring patterns inferred based on mitochondrial and microsatellite data might indicate that the two different classes of molecular markers may be reflecting different and complementary aspects of the evolutionary history of sardine. Mitochondrial data might be reflecting past isolation of sardine populations into two distinct groupings during Pleistocene whereas microsatellite data reveal the existence of present day gene flow among populations, and a pattern of isolation by distance.</p

Weak K-amplitudes in the chiral and 1/Nc-expansions

It is shown that there exist symmetry constraints for non-leptonic weak amplitudes which emerge when the 1/N-c-expansion restricted to the leading and next-to-leading approximations only is systematically combined with chi PT limited to the lowest non-trivial order. We discuss these constraints for the couplings g(8) and g(27) of Delta S = 1 transitions and the B-K-parameter of K-0-K-0 mixing

GenDecoder: genetic code prediction for metazoan mitochondria

Although the majority of the organisms use the same genetic code to translate DNA, several variants have been described in a wide range of organisms, both in nuclear and organellar systems, many of them corresponding to metazoan mitochondria. These variants are usually found by comparative sequence analyses, either conducted manually or with the computer. Basically, when a particular codon in a query-species is linked to positions for which a specific amino acid is consistently found in other species, then that particular codon is expected to translate as that specific amino acid. Importantly, and despite the simplicity of this approach, there are no available tools to help predicting the genetic code of an organism. We present here GenDecoder, a web server for the characterization and prediction of mitochondrial genetic codes in animals. The analysis of automatic predictions for 681 metazoans aimed us to study some properties of the comparative method, in particular, the relationship among sequence conservation, taxonomic sampling and reliability of assignments. Overall, the method is highly precise (99%), although highly divergent organisms such as platyhelminths are more problematic. The GenDecoder web server is freely available from

Evolution of gastropod mitochondrial genome arrangements

<p>Abstract</p> <p>Background</p> <p>Gastropod mitochondrial genomes exhibit an unusually great variety of gene orders compared to other metazoan mitochondrial genome such as e.g those of vertebrates. Hence, gastropod mitochondrial genomes constitute a good model system to study patterns, rates, and mechanisms of mitochondrial genome rearrangement. However, this kind of evolutionary comparative analysis requires a robust phylogenetic framework of the group under study, which has been elusive so far for gastropods in spite of the efforts carried out during the last two decades. Here, we report the complete nucleotide sequence of five mitochondrial genomes of gastropods (<it>Pyramidella dolabrata</it>, <it>Ascobulla fragilis</it>, <it>Siphonaria pectinata</it>, <it>Onchidella celtica</it>, and <it>Myosotella myosotis</it>), and we analyze them together with another ten complete mitochondrial genomes of gastropods currently available in molecular databases in order to reconstruct the phylogenetic relationships among the main lineages of gastropods.</p> <p>Results</p> <p>Comparative analyses with other mollusk mitochondrial genomes allowed us to describe molecular features and general trends in the evolution of mitochondrial genome organization in gastropods. Phylogenetic reconstruction with commonly used methods of phylogenetic inference (ME, MP, ML, BI) arrived at a single topology, which was used to reconstruct the evolution of mitochondrial gene rearrangements in the group.</p> <p>Conclusion</p> <p>Four main lineages were identified within gastropods: Caenogastropoda, Vetigastropoda, Patellogastropoda, and Heterobranchia. Caenogastropoda and Vetigastropoda are sister taxa, as well as, Patellogastropoda and Heterobranchia. This result rejects the validity of the derived clade Apogastropoda (Caenogastropoda + Heterobranchia). The position of Patellogastropoda remains unclear likely due to long-branch attraction biases. Within Heterobranchia, the most heterogeneous group of gastropods, neither Euthyneura (because of the inclusion of <it>P. dolabrata</it>) nor Pulmonata (polyphyletic) nor Opisthobranchia (because of the inclusion <it>S. pectinata</it>) were recovered as monophyletic groups. The gene order of the Vetigastropoda might represent the ancestral mitochondrial gene order for Gastropoda and we propose that at least three major rearrangements have taken place in the evolution of gastropods: one in the ancestor of Caenogastropoda, another in the ancestor of Patellogastropoda, and one more in the ancestor of Heterobranchia.</p