Nonsynonymous substitution in abalone sperm fertilization genes exceeds substitution in introns and mitochondrial DNA

Strong positive Darwinian selection acts on two sperm fertilization proteins, lysin and 18-kDa protein, from abalone (Haliotis). To understand the phylogenetic context for this dramatic molecular evolution, we obtained sequences of mitochondrial cytochrome c oxidase subunit I (mtCOI), and genomic sequences of lysin, 18-kDa, and a G protein subunit. Based on mtDNA differentiation, four north Pacific abalone species diverged within the past 2 million years (Myr), and remaining north Pacific species diverged over a period of 4–20 Myr. Between-species nonsynonymous differences in lysin and 18-kDa exons exceed nucleotide differences in introns by 3.5- to 24-fold. Remarkably, in some comparisons nonsynonymous substitutions in lysin and 18-kDa genes exceed synonymous substitutions in mtCOI. Lysin and 18-kDa intron/exon segments were sequenced from multiple red abalone individuals collected over a 1,200-km range. Only two nucleotide changes and two sites of slippage variation were detected in a total of >29,000 nucleotides surveyed. However, polymorphism in mtCOI and a G protein intron was found in this species. This finding suggests that positive selection swept one lysin allele and one 18-kDa allele to fixation. Similarities between mtCOI and lysin gene trees indicate that rapid adaptive evolution of lysin has occurred consistently through the history of the group. Comparisons with mtCOI molecular clock calibrations suggest that nonsynonymous substitutions accumulate 2–50 times faster in lysin and 18-kDa genes than in rapidly evolving mammalian genes.

Aptian to Cenomanian dinoflagellate cysts from the Mazagan Plateau

Eighty-eight samples of Aptian to lower Cenomanian sediments of Sites 545 and 547, DSDP Leg 79, from the Mazagan Plateau area (offshore Northwest Africa) were analyzed for palynomorphs. The very rich dinoflagellate cyst assemblages make it possible to narrow shipboard age determinations and to correlate Sites 545 and 547. The distribution of 174 dinoflagellate cyst taxa is tabulated in this study and the biostratigraphic value of selected dinoflagellate cysts is discussed. Additional taxonomic remarks are made about some species. The new dinoflagellate cyst species Aptea almohadensis, Occisucysta hinzü, O. mazaganensis, and the subspecies Maghrebinia perforata (Clarke and Verdier, 1967) Below, 1981 ssp. mirabilis are described.

Dinoflagellate cyst abundances at DSDP Site 94-607 from the North Atlantic (Appendix B)

The climatic deterioration related to the onset of Northern Hemisphere glaciations (circa 2.52 Ma BP) must have lead to reorganization and relocation of species associations and may have enhanced species turnover. The present study investigates how this deterioration affects the dinoflagellate cyst and acritarch assemblages from two locations, DSDP Site 607 (North Atlantic) and the Singa section (southern Italy). The records from these locations cover the interval from 2.8 to 2.2 Ma with at least a 5 ka resolution and they have been correlated to the Milankovitch periodicities on a cycle to cycle basis by means of integrated high resolution stable isotope, calcium carbonate, foraminiferal, palynological and magnetostratigraphical datasets. In the present study this high resolution stratigraphic framework is used for a detailed correlation of events occurring in each of the depositional sequences. It also enables further assessment of the palaeoenvironmental preferences of some dinoflagellate cyst forms. Comparison of the two palynological records reveals a close correspondence in the timing of major assemblage changes and extinction events, confirming their Milankovitch cycle based correlation. A close link between periods of Northern Hemisphere cooling (at oxygen isotope stages 110, 104 and 100-96) and increased dinoflagellate cyst turnover appears to be present for both DSDP Site 607 and the Singa section. The turnover events can also be recognized in the records of planktic foraminifera and calcamous nannoplankton. Comparison of the Singa section with Site 607 and with other time equivalent marine palynological data sets, shows that some oceanic taxa respond similarly over a large area. The biostratigraphical implications are discussed. Notably the last occurrence of Invertocystu lucrymosa appears to be a valuable marker for isotope stage 110 in the Mediterranean and North Atlantic.

Does terrestrial epidemiology apply to marine systems?

Most of epidemiological theory has been developed for terrestrial systems, but the significance of disease in the ocean is now being recognized. However, the extent to which terrestrial epidemiology can be directly transferred to marine systems is uncertain. Many broad types of disease-causing organism occur both on land and in the sea, and it is clear that some emergent disease problems in marine environments are caused by pathogens moving from terrestrial to marine systems. However, marine systems are qualitatively different from terrestrial environments, and these differences affect the application of modelling and management approaches that have been developed for terrestrial systems. Phyla and body plans are more diverse in marine environments and marine organisms have different life histories and probably different disease transmission modes than many of their terrestrial counterparts. Marine populations are typically more open than terrestrial ones, with the potential for long-distance dispersal of larvae. Potentially, this might enable unusually rapid propagation of epidemics in marine systems, and there are several examples of this. Taken together, these differences will require the development of new approaches to modelling and control of infectious disease in the ocean.

Stochastic models for mainland-island metapopulations in static and dynamic landscapes

This paper has three primary aims: to establish an effective means for modelling mainland-island metapopulations inhabiting a dynamic landscape: to investigate the effect of immigration and dynamic changes in habitat on metapopulation patch occupancy dynamics; and to illustrate the implications of our results for decision-making and population management. We first extend the mainland-island metapopulation model of Alonso and McKane [Bull. Math. Biol. 64:913-958,2002] to incorporate a dynamic landscape. It is shown, for both the static and the dynamic landscape models, that a suitably scaled version of the process converges to a unique deterministic model as the size of the system becomes large. We also establish that. under quite general conditions, the density of occupied patches, and the densities of suitable and occupied patches, for the respective models, have approximate normal distributions. Our results not only provide us with estimates for the means and variances that are valid at all stages in the evolution of the population, but also provide a tool for fitting the models to real metapopulations. We discuss the effect of immigration and habitat dynamics on metapopulations, showing that mainland-like patches heavily influence metapopulation persistence, and we argue for adopting measures to increase connectivity between this large patch and the other island-like patches. We illustrate our results with specific reference to examples of populations of butterfly and the grasshopper Bryodema tuberculata.

The effect of larval age on morphology and gene expression during ascidian metamorphosis

Metamorphosis is both an ecological and a developmental genetic transition that an organism undergoes as a normal part of ontogeny. Many organisms have the ability to delay metamorphosis when conditions are unsuitable. This strategy carries obvious benefits, but may also result in severe consequences for older larvae that run low on energy. In the marine environment, some lecithotrophic larvae that have prolonged periods in the plankton may begin forming postlarval and juvenile structures that normally do not appear until after settlement and the initiation of metamorphosis. This precocious activation of the postlarval developmental program may reflect an adaptation to increase the survival of older, energy-depleted larvae by allowing them to metamorphose more quickly. In the present study, we investigate morphological and genetic consequences of delay of metamorphosis in larvae of Herdmania momus (a solitary stolidobranch ascidian). We observe significant morphological and genetic changes during prolonged larval life, with older larvae displaying significant changes in RNA levels, precocious migration of mesenchyme cells, and changes in larval shape including shortening of the tail. While these observations suggest that the older H. momus larvae are functionally different from younger larvae and possibly becoming more predisposed to undergo metamorphosis, we did not find any significant differences in gene expression levels between postlarvae arising from larvae that metamorphosed as soon as they were competent and postlarvae developing from larvae that postponed metamorphosis. This recalibration, or convergence, of transcript levels in the early postlarva suggests that changes that occur during prolonged larval life of H. momus are not necessarily associated with early activation of adult organ differentiation. Instead, it suggests that an autonomous developmental program is activated in H. momus upon the induction of metamorphosis regardless of the history of the larva.

A rapidly evolving secretome builds and patterns a sea shell

Background: Instructions to fabricate mineralized structures with distinct nanoscale architectures, such as seashells and coral and vertebrate skeletons, are encoded in the genomes of a wide variety of animals. In mollusks, the mantle is responsible for the extracellular production of the shell, directing the ordered biomineralization of CaCO3 and the deposition of architectural and color patterns. The evolutionary origins of the ability to synthesize calcified structures across various metazoan taxa remain obscure, with only a small number of protein families identified from molluskan shells. The recent sequencing of a wide range of metazoan genomes coupled with the analysis of gene expression in non-model animals has allowed us to investigate the evolution and process of biomineralization in gastropod mollusks. Results: Here we show that over 25% of the genes expressed in the mantle of the vetigastropod Haliotis asinina encode secreted proteins, indicating that hundreds of proteins are likely to be contributing to shell fabrication and patterning. Almost 85% of the secretome encodes novel proteins; remarkably, only 19% of these have identifiable homologues in the full genome of the patellogastropod Lottia scutum. The spatial expression profiles of mantle genes that belong to the secretome is restricted to discrete mantle zones, with each zone responsible for the fabrication of one of the structural layers of the shell. Patterned expression of a subset of genes along the length of the mantle is indicative of roles in shell ornamentation. For example, Has-sometsuke maps precisely to pigmentation patterns in the shell, providing the first case of a gene product to be involved in molluskan shell pigmentation. We also describe the expression of two novel genes involved in nacre (mother of pearl) deposition. Conclusion: The unexpected complexity and evolvability of this secretome and the modular design of the molluskan mantle enables diversification of shell strength and design, and as such must contribute to the variety of adaptive architectures and colors found in mollusk shells. The composition of this novel mantle-specific secretome suggests that there are significant molecular differences in the ways in which gastropods synthesize their shells.

Data compilation on the biological response to ocean acidification: environmental and experimental context of data sets and related literature

The exponential growth of studies on the biological response to ocean acidification over the last few decades has generated a large amount of data. To facilitate data comparison, a data compilation hosted at the data publisher PANGAEA was initiated in 2008 and is updated on a regular basis (doi:10.1594/PANGAEA.149999). By January 2015, a total of 581 data sets (over 4 000 000 data points) from 539 papers had been archived. Here we present the developments of this data compilation five years since its first description by Nisumaa et al. (2010). Most of study sites from which data archived are still in the Northern Hemisphere and the number of archived data from studies from the Southern Hemisphere and polar oceans are still relatively low. Data from 60 studies that investigated the response of a mix of organisms or natural communities were all added after 2010, indicating a welcomed shift from the study of individual organisms to communities and ecosystems. The initial imbalance of considerably more data archived on calcification and primary production than on other processes has improved. There is also a clear tendency towards more data archived from multifactorial studies after 2010. For easier and more effective access to ocean acidification data, the ocean acidification community is strongly encouraged to contribute to the data archiving effort, and help develop standard vocabularies describing the variables and define best practices for archiving ocean acidification data.

Conservação genética da orquídea Cattleya granulosa Lindley

Cattleya granulosa Lind is a large and endemic orchid in Atlantic Forest fragments in Northeast Brazil. The facility of collecting, uniqueness of their flowers, which have varying colors between green and reddish brown, and distribution in coastal areas of economic interest make their populations a constant target of predation, which also suffer from environmental degradation. Due to the impact on their populations, the species is threatened. In this study, we evaluate the levels of spatial aggregation in a preserved population, analyze the phylogenetic relationships of C. granulosa Lindl. with four other Laeliinae species (Brassavola tuberculata, C. bicolor, C. labiata and C. schofieldiana) and also to evaluate the genetic diversity of 12 remaining populations of C. granulosa Lindl. through ISSR. There was specificity of epiphytic C. granula Lindl. with a single host tree, species of Eugenia sp. C. granulosa Lindl. own spatial pattern, with the highest density of neighbors within up to 5 m. Regarding the phylogenetic relationships and genetic patterns with other species of the genus, C. bicolor exhibited the greatest genetic diversity (HE = 0.219), while C. labiata exhibited the lowest level (HE = 0.132). The percentage of genetic variation among species (AMOVA) was 23.26%. The principal component analysis (PCA) of ISSR data showed that unifoliate and bifoliolate species are genetically divergent. PCA indicated a close relationship between C. granulosa Lindl. and C. schofieldiana, a species considered to be a variety of C. granulosa Lindl. by many researchers. Population genetic analysis using ISSR showed all polymorphic loci. The high genetic differentiation between populations (ФST = 0.391, P < 0.0001) determined the structure into nine groups according to log-likelihood of Bayesian analysis, with a similar pattern in the dendrogram (UPGMA) and PCA. A positive and significant correlation between geographic and genetic distances between populations was identified (r = 0.794, P = 0.017), indicating isolation by distance. Patterns of allelic diversity suggest the occurrence of population bottlenecks in most populations of C. granulosa Lindl. (n = 8). Genetic data indicate that enable the maintenance of genetic diversity of the species is complex and is directly related to the conservation of different units or groups that are spatially distant.

Distribution of microorganisms in recent sediments of Kiel Bay

Die angewandte Mikropaläontologie bestimmt heute im wesentlichen das Alter eines Gesteins mit Hilfe von Faunenvergesellschaftungen. Aus der Zusammensetzung der Fauna, aus dem Einsatz oder Fehlen bestimmter Gattungen und Arten, aus den Mineralien, die das Gestein aufbauen, aus dem ganzen Bild, das eine aus einem Gestein herausgeschlämmte Fauna dem Bearbeiter gibt, läßt sich das Alter dieses Gesteins festlegen. Will man aber verschiedene Bohrungen, vor allem auch räumlich weit voneinander getrennter Gebiete, miteinander parallelisieren, so liegt das Kernproblem der Mikropaläontologie in der Frage, ob es sich bei verschiedenen Faunen tatsächlich um Alters- oder nur um Faziesunterschiede handelt. Da die Grundlagen der mikropaläontologischen Arbeitsweise zum weitaus größten Teil auf den Ergebnissen von Untersuchungen fossiler Faunen beruhen, müssen zu ihrer Unterbauung Untersuchungen an recentem Material folgen. Besonders spielt das Ineinandergreifen mariner und brackischer Sedimente in der angewandten Mikropaläontologie eine große Rolle. Auf Grund der Tatsache, daß ein großer Teil von Gattungen und Arten der Foraminiferen an der Wende Kreide/Tertiär ausstirbt und neue an ihre Stelle treten, stellt Glässner (1948) die Behauptung auf, daß die aktualistisch gewonnenen Ergebnisse für vortertiäre Faunen nur eine geringe Bedeutung besitzen. Auch seien vortertiäre, brackische Foraminiferen nicht bekannt (Glässner 1948, S. 191). Hiltermann (1948) konnte aber bereits im nordwestdeutschen Malm brackische, d. h. in Brackwasser eindringende Foraminiferen nachweisen. Auf jeden Fall behalten aktualistische Unterlagen ihren Wert für das Tertiär und Quartär. Die Faunen, die in recenten, brackischen Sedimenten nebeneinander auftreten, sind in einem Bohrprofil in einem Gestein übereinander zu erwarten. Gelingt es, die Beziehungen einer recenten Fauna zu ihrer Umwelt zu klären, dann können umgekehrt aus fossilen, ihnen gleichen oder ähnlichen Faunen Rückschlüsse auf die Entstehungsbedingungen von Gesteinen gezogen werden. Unter Umständen können der Verlauf einer Transgression, Küstennähe, die Höhe des Salzgehaltes des Meerwassers, die vorherrschenden Temperaturen u. a., aus ihnen abgelesen werden. Die Ostsee ist ein klassisches Brackwassergebiet der Erde. Ihr westlicher Teil, die Kieler Bucht, wurde erst in jüngster geologischer Zeit vom Meer überflutet. Nach Tapfer (1940) begann hier die flandrische Transgression erst etwa um 7500 v. d. Zw. mit dem Erreichen des heutigen Meeresniveaus. Seit dieser Zeit erst entstehen neue Küstenformen, wird der Meeresboden umgelagert und bilden sich marine und brackische Absätze in diesem Gebiet.