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

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

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

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

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

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

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