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

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

The mitochondrial genome of Ifremeria nautilei and the phylogenetic position of the enigmatic deep-sea Abyssochrysoidea (Mollusca: Gastropoda)

The complete nucleotide sequence of the mitochondrial (mt) genome of the deep-sea vent snail Ifremeria nautilei (Gastropoda: Abyssochrysoidea) was determined. The double stranded circular molecule is 15,664 pb in length and encodes for the typical 37 metazoan mitochondrial genes. The gene arrangement of the Ifremeria mt genome is most similar to genome organization of caenogastropods and differs only on the relative position of the trnW gene. The deduced amino acid sequences of the mt protein coding genes of Ifremeria mt genome were aligned with orthologous sequences from representatives of the main lineages of gastropods and phylogenetic relationships were inferred. The reconstructed phylogeny supports that Ifremeria belongs to Caenogastropoda and that it is closely related to hypsogastropod superfamilies. Results were compared with a reconstructed nuclear-based phylogeny. Moreover, a relaxed molecular-clock timetree calibrated with fossils dated the divergence of Abyssochrysoidea in the Late Jurassic-Early Cretaceous indicating a relatively modern colonization of deep-sea environments by these snails. © 2014 Elsevier B.V.This work was supported by the Spanish Ministry of Science and Innovation (CGL2007-60954 and CGL2010-18216 to RZ; BES-2008-009562 to DO).Peer Reviewe

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

Beyond Conus: Phylogenetic relationships of Conidae based on complete mitochondrial genomes

Understanding how the extraordinary taxonomic and ecological diversity of cone snails (Caenogastropoda: Conidae) evolved requires a statistically robust phylogenetic framework, which thus far is not available. While recent molecular phylogenies have been able to distinguish several deep lineages within the family Conidae, including the genera Profundiconus, Californiconus, Conasprella, and Conus (and within this one, several subgenera), phylogenetic relationships among these genera remain elusive. Moreover, the possibility that additional deep lineages may exist within the family is open. Here, we reconstructed with probabilistic methods a molecular phylogeny of Conidae using the newly sequenced complete or nearly complete mitochondrial (mt) genomes of the following nine species that represent all main Conidae lineages and potentially new ones: Profundiconus teramachii, Californiconus californicus, Conasprella wakayamaensis, Lilliconus sagei, Pseudolilliconus traillii, Conus (Kalloconus) venulatus, Conus (Lautoconus) ventricosus, Conus (Lautoconus) hybridus, and Conus (Eugeniconus) nobilis. To test the monophyly of the family, we also sequenced the nearly complete mt genomes of the following three species representing closely related conoidean families: Benthomangelia sp. (Mangeliidae), Tomopleura sp. (Borsoniidae), and Glyphostoma sp. (Clathurellidae). All newly sequenced conoidean mt genomes shared a relatively constant gene order with rearrangements limited to tRNA genes. The reconstructed phylogeny recovered with high statistical support the monophyly of Conidae and phylogenetic relationships within the family. The genus Profundiconus was placed as sister to the remaining genera. Within these, a clade including Californiconus and Lilliconus + Pseudolilliconus was the sister group of Conasprella to the exclusion of Conus. The phylogeny included a new lineage whose relative phylogenetic position was unknown (Lilliconus) and uncovered thus far hidden diversity within the family (Pseudolilliconus). Moreover, reconstructed phylogenetic relationships allowed inferring that the peculiar diet of Californiconus based on worms, mollusks, crustaceans and fish is derived, and reinforce the hypothesis that the ancestor of Conidae was a worm hunter. A chronogram was reconstructed under an uncorrelated relaxed molecular clock, which dated the origin of the family shortly after the Cretaceous-Tertiary boundary (about 59 million years ago) and the divergence among main lineages during the Paleocene and the Eocene (56–30 million years ago).This work was supported by the Spanish Ministry of Science and Innovation – Spain (CGL2010-18216 and CGL2013-45211-C2-2-P to RZ; BES-2011-051469 to JEU),Peer Reviewe

Neogastropod phylogenetic relationships based on entire mitochondrial genomes

<p>Abstract</p> <p>Background</p> <p>The Neogastropoda is a highly diversified group of predatory marine snails (Gastropoda: Caenogastropoda). Traditionally, its monophyly has been widely accepted based on several morphological synapomorphies mostly related with the digestive system. However, recent molecular phylogenetic studies challenged the monophyly of Neogastropoda due to the inclusion of representatives of other caenogastropod lineages (e.g. Littorinimorpha) within the group. Neogastropoda has been classified into up to six superfamilies including Buccinoidea, Muricoidea, Olivoidea, Pseudolivoidea, Conoidea, and Cancellarioidea. Phylogenetic relationships among neogastropod superfamilies remain unresolved.</p> <p>Results</p> <p>The complete mitochondrial (mt) genomes of seven Neogastropoda (<it>Bolinus brandaris</it>, <it>Cancellaria cancellata</it>, <it>Conus borgesi</it>, <it>Cymbium olla</it>, <it>Fusiturris similis</it>, <it>Nassarius reticulatus</it>, and <it>Terebra dimidiata</it>) and of the tonnoidean <it>Cymatium parthenopeum </it>(Littorinimorpha), a putative sister group to Neogastropoda, were sequenced. In addition, the partial sequence of the mitochondrial genome of the calyptraeoidean <it>Calyptraea chinensis </it>(Littorinimorpha) was also determined. All sequenced neogastropod mt genomes shared a highly conserved gene order with only two instances of <it>tRNA </it>gene translocation. Phylogenetic relationships of Neogastropoda were inferred based on the 13 mt protein coding genes (both at the amino acid and nucleotide level) of all available caenogastropod mitochondrial genomes. Maximum likelihood (ML) and Bayesian inference (BI) phylogenetic analyses failed to recover the monophyly of Neogastropoda due to the inclusion of the tonnoidean <it>Cymatium parthenopeum </it>within the group. At the superfamily level, all phylogenetic analyses questioned the taxonomic validity of Muricoidea, whereas the monophyly of Conoidea was supported by most phylogenetic analyses, albeit weakly. All analyzed families were recovered as monophyletic except Turridae due to the inclusion of Terebridae. Further phylogenetic analyses based on either a four mt gene data set including two additional Littorinimorpha or combining mt and nuclear sequence data also rejected the monophyly of Neogastropoda but rendered rather unresolved topologies. The phylogenetic performance of each mt gene was evaluated under ML. The total number of resolved internal branches of the reference (whole-mt genome) topology was not recovered in any of the individual gene phylogenetic analysis. The <it>cox2 </it>gene recovered the highest number of congruent internal branches with the reference topology, whereas the combined <it>tRNA </it>genes, <it>cox1</it>, and <it>atp8 </it>showed the lowest phylogenetic performance.</p> <p>Conclusion</p> <p>Phylogenetic analyses based on complete mt genome data resolved a higher number of internal branches of the caenogastropod tree than individual mt genes. All performed phylogenetic analyses agreed in rejecting the monophyly of the Neogastropoda due to the inclusion of Littorinimorpha lineages within the group. This result challenges morphological evidence, and prompts for further re-evaluation of neogastropod morphological synapomorphies. The important increase in number of analyzed positions with respect to previous studies was not enough to achieve conclusive results regarding phylogenetic relationships within Neogastropoda. In this regard, sequencing of complete mtDNAs from all closely related caenogastropod lineages is needed. Nevertheless, the rapid radiation at the origin of Neogastropoda may not allow full resolution of this phylogeny based only on mt data, and in parallel more nuclear sequence data will also need to be incorporated into the phylogenetic analyses.</p

Genetic structuring and migration patterns of Atlantic bigeye tuna, Thunnus obesus (Lowe, 1839)

<p>Abstract</p> <p>Background</p> <p>Large pelagic fishes are generally thought to have little population genetic structuring based on their cosmopolitan distribution, large population sizes and high dispersal capacities. However, gene flow can be influenced by ecological (e.g. homing behaviour) and physical (e.g. present-day ocean currents, past changes in sea temperature and levels) factors. In this regard, Atlantic bigeye tuna shows an interesting genetic structuring pattern with two highly divergent mitochondrial clades (Clades I and II), which are assumed to have been originated during the last Pleistocene glacial maxima. We assess genetic structure patterns of Atlantic bigeye tuna at the nuclear level, and compare them with mitochondrial evidence.</p> <p>Results</p> <p>We examined allele size variation of nine microsatellite loci in 380 individuals from the Gulf of Guinea, Canary, Azores, Canada, Indian Ocean, and Pacific Ocean. To investigate temporal stability of genetic structure, three Atlantic Ocean sites were re-sampled a second year. Hierarchical AMOVA tests, <it>R</it>_{<it>ST </it>}pairwise comparisons, isolation by distance (Mantel) tests, Bayesian clustering analyses, and coalescence-based migration rate inferences supported unrestricted gene flow within the Atlantic Ocean at the nuclear level, and therefore interbreeding between individuals belonging to both mitochondrial clades. Moreover, departures from HWE in several loci were inferred for the samples of Guinea, and attributed to a Wahlund effect supporting the role of this region as a spawning and nursery area. Our microsatellite data supported a single worldwide panmictic unit for bigeye tunas. Despite the strong Agulhas Current, immigration rates seem to be higher from the Atlantic Ocean into the Indo-Pacific Ocean, but the actual number of individuals moving per generation is relatively low compared to the large population sizes inhabiting each ocean basin.</p> <p>Conclusion</p> <p>Lack of congruence between mt and nuclear evidences, which is also found in other species, most likely reflects past events of isolation and secondary contact. Given the inferred relatively low number of immigrants per generation around the Cape of Good Hope, the proportions of the mitochondrial clades in the different oceans may keep stable, and it seems plausible that the presence of individuals belonging to the mt Clade I in the Atlantic Ocean may be due to extensive migrations that predated the last glaciation.</p

Conotoxin Diversity in the Venom Gland Transcriptome of the Magician’s Cone, Pionoconus magus

The transcriptomes of the venom glands of two individuals of the magician’s cone, Pionoconus magus, from Okinawa (Japan) were sequenced, assembled, and annotated. In addition, RNA-seq raw reads available at the SRA database from one additional specimen of P. magus from the Philippines were also assembled and annotated. The total numbers of identified conotoxin precursors and hormones per specimen were 118, 112, and 93. The three individuals shared only five identical sequences whereas the two specimens from Okinawa had 30 sequences in common. The total number of distinct conotoxin precursors and hormones for P. magus was 275, and were assigned to 53 conotoxin precursor and hormone superfamilies, two of which were new based on their divergent signal region. The superfamilies that had the highest number of precursors were M (42), O1 (34), T (27), A (18), O2 (17), and F (13), accounting for 55% of the total diversity. The D superfamily, previously thought to be exclusive of vermivorous cones was found in P. magus and contained a highly divergent mature region. Similarly, the A superfamily alpha 4/3 was found in P. magus despite the fact that it was previously postulated to be almost exclusive of the genus Rhombiconus. Di erential expression analyses of P. magus compared to Chelyconus ermineus, the only fish-hunting cone from the Atlantic Ocean revealed that M and A2 superfamilies appear

A new species of sand racer, Psammodromus (Squamata: Lacertidae), from the Western Iberian Peninsula

[EN] A new species of lacertid lizard of the genus Psammodromus is described from the Iberian Peninsula. Genetic and recently published phenotypic data support the differentiation of Psammodromus hispanicus into three, and not as previously sug-gested two, distinct lineages. Age estimates, lineage allopatry, the lack of mitochondrial and nuclear haplotype sharing between lineages, ecological niche divergence, and the current biogeographic distribution, indicated that the three lineages correspond to three independent species. Here, we describe a new species, Psammodromus occidentalis sp. n., which is genetically different from the other sand racers and differentiated by the number of femoral pores, number of throat scales, snout shape, head ratio, green nuptial coloration, and number of supralabial scales below the subocular scale. We also pro-pose to upgrade the two previously recognized subspecies, Psammodromus hispanicus hispanicus Fitzinger, 1826 from central Spain and Psammodromus hispanicus edwardsianus (Dugès, 1829) from eastern Spain, to the species level: Psam-modromus hispanicus stat. nov. and Psammodromus edwardsianus stat. nov. Given that the holotype of Psammodromus hispanicus was lost, we designate a neotype. We also analysed museum specimens of P. blanci, P. microdactylus and P. algirus to describe differentiation of the Psammodromus hispanicus lineages/species from their closest relatives. Copyright © 2011 Magnolia Press.Peer Reviewe

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