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Structural variations (SVs) constitute a significant source of genetic variability in virus genomes. Yet knowledge about SV variability and contribution to the evolutionary process in large double-stranded (ds)DNA viruses is limited. Cyprinid herpesvirus 3 (CyHV-3), also commonly known as koi herpesvirus (KHV), has the largest dsDNA genome within herpesviruses. This virus has become one of the biggest threats to common carp and koi farming, resulting in high morbidity and mortalities of fishes, serious environmental damage, and severe economic losses. A previous study analyzing CyHV-3 virulence evolution during serial passages onto carp cell cultures suggested that CyHV-3 evolves, at least in vitro, through an assembly of haplotypes that alternatively become dominant or under-represented. The present study investigates the SV diversity and dynamics in CyHV-3 genome during 99 serial passages in cell culture using, for the first time, ultra-deep whole-genome and amplicon-based sequencing. The results indicate that KHV polymorphism mostly involves SVs. These SVs display a wide distribution along the genome and exhibit high turnover dynamics with a clear bias towards inversion and deletion events. Analysis of the pathogenesis-associated ORF150 region in ten intermediate cell passages highlighted mainly deletion, inversion and insertion variations that deeply altered the structure of ORF150. Our findings indicate that SV turnovers and defective genomes represent key drivers in the viral population dynamics and in vitro evolution of KHV. Thus, the present study can contribute to the basic research needed to design safe live-attenuated vaccines, classically obtained by viral attenuation after serial passages in cell culture. International audience

International audience; The major climatic oscillations during the Quaternary Period significantly influenced the evolution and distribution of ancient and modern coastal systems. Here we investigate the morphology and sedimentary infilling of submerged Late Quaternary incised valleys along the northern coast of Java Island (Indonesia) using high-resolution geophysical, sedimentological and geochronological data. Our results indicate that the spatial development and morphology of the incised valleys are predominantly controlled by Quaternary glacial–interglacial eustatic fluctuations, within a marked subsiding setting. The valleys were incised during prominent Quaternary lowstands and most of the valley fill was emplaced during the last postglacial sea level rise. The valley fill forms a transgressive succession, consisting mainly of fluvial deposits at the base (possibly amalgamated from older sequences) overlain by shallow marine sediments and capped by hemipelagic deposits. The valley-fill architecture is strongly dependent on the valley morphology (depth of incision, width of the valleys, and extent of the intertidal zone). The shallow marine deposits contained within the narrow and linear valleys are mostly aggrading muds. The vertical incision and valley formation was chiefly controlled by the extent of glacial sea-level fluctuations. The studied sections represent the continental-offshore extension of a paleodeltaic system. The implication of our work is that even in predominantly enclosed shallow marine systems that are located distal to the shelf break, the response of the sedimentary system and ensuing stratigraphic configuration can be effectively impacted by the rapid and abrupt Quaternary global climatic transition and eustatic sea-level fluctuations.

SummaryTrade restrictions for many endangered elasmobranch species exist to disincentivise their exploitation and curb their declines. However, the variety of products and the complexity of import/export routes make trade monitoring challenging. We investigate the use of a portable, universal, DNA-based tool which would greatly facilitatein-situmonitoring. We collected shark and ray samples across the Island of Java, Indonesia, and selected 28 species (including 22 CITES-listed species) commonly encountered in landing sites and export hubs to test a recently developed real-time PCR single-assay originally developed for screening bony fish. We employed a deep learning algorithm to recognize species based on DNA melt-curve signatures. By combining visual and machine learning assignment methods, we distinguished 25 out of 28 species, 20 of which were CITES-listed. With further refinement, this method can provide a practical tool for monitoring elasmobranch trade worldwide, without the need for a lab or the bespoke design of species-specific assays.HighlightsWe applied a portable, universal, closed-tube DNA barcoding approach originally developed for bony fishes to distinguish between shark and ray species traded in Indonesia.We built a deep machine learning model to automatically assign species from the qPCR fluorescence spectra produced by two barcodesThe model achieved 79.41% accuracy for classifying 28 elasmobranch species, despite the barcode regions being designed for teleost speciesThis tool can serve as a potent single-assayin-situdiagnostic tool to regulate trade operations and it will be significantly enhanced by further optimisation of the barcode regions to fit elasmobranch DNA sequence variation

Early‐diagenetic cementation of tropical carbonates results from the combination of numerous physico‐chemical and biological processes. In the marine phreatic environment it represents an essential mechanism for the development and stabilization of carbonate platforms. However, diagenetic cements that developed early in the marine phreatic environment are likely to become obliterated during later stages of meteoric or burial diagenesis. When lithified sediment samples are studied, this complicates the recognition of processes involved in early cementation, and their geological implications. In this contribution, a petrographic microfacies analysis of Holocene Halimeda segments collected on a coral island in the Spermonde Archipelago, Indonesia, is presented. Through electron microscopical analyses of polished samples, this study shows that segments are characterized by intragranular cementation of fibrous aragonite, equant High‐Mg calcite (3.9 to 7.2 Mol% Mg), bladed Low‐Mg calcite (0.4 to 1.0 Mol% Mg) and mini‐micritic Low‐Mg calcite (3.2 to 3.3 Mol% Mg). The co‐existence and consecutive development of fibrous aragonite and equant High‐Mg calcite results initially from the flow of oversaturated seawater along the aragonite template of the Halimeda skeleton, followed by an adjustment of cement mineralogy towards High‐Mg calcite as a result of reduced permeability and fluid flow rates in the pores. Growth of bladed Low‐Mg calcite cements on top of etched substrates of equant High‐Mg calcite is explained by shifts in pore water pH and alkalinity through microbial sulphate reduction. Microbial activity appears to be the main trigger for the precipitation of mini‐micritic Low‐Mg calcite as well, based on the presumable detection of an extracellular polymeric matrix during an early stage of mini‐micrite Low‐Mg calcite cement precipitation. Radiocarbon analyses of five Halimeda segments furthermore indicate that virtually complete intragranular cementation in the marine phreatic environment with thermodynamically/kinetically controlled aragonite and High‐Mg calcite takes place in about 100 years. Collectively, this study shows that early‐diagenetic cements are highly diverse and provides new quantitative constraints on the rate of diagenetic cementation in tropical carbonate factories. Deutsche Forschungsgemeinschaft http://dx.doi.org/10.13039/501100001659 https://doi.pangaea.de/10.1594/PANGAEA.923980

Abstract. The Spermonde Archipelago, off the coast of southwest Sulawesi, consists of more than 100 small islands and hundreds of shallow-water reef areas. Most of the islands are bordered by coral reefs that grew in the past in response to paleo relative sea-level changes. Remnants of these reefs are preserved today in the form of fossil microatolls. In this study, we report the elevation, age, and paleo relative sea-level estimates derived from fossil microatolls surveyed in five islands of the Spermonde Archipelago. We describe 24 new sea-level index points, and we compare our dataset with both previously published proxies and with relative sea-level predictions from a set of 54 glacial isostatic adjustment (GIA) models, using different assumptions on both ice melting histories and mantle structure and viscosity. We use our new data and models to discuss Late Holocene (0–6 ka) relative sea-level changes in our study area and their implications in terms of modern relative sea-level estimates in the broader South and Southeast Asia region.

This paper is a semiotic study of Hayao Miyazaki’s anime Ponyo on the Cliff by the Sea. The purpose of thi s study is t o reveal the Japanese views on sea in the anime. This anime was selected because it is considered to represents the modern Japanese narrative related to the sea, and regarding that anime as a popular literary work is generally more acceptable at various age levels of audience than classical literary works. The results of semiotic reading on this anime are five Japanese views on sea, which are 1) sea as a source of life; 2) sea as a source of prosperity; 3) sea as a source of strength or energy; 4) sea as a source of beliefs; and 5) sea as a source of beauty.

We report a study of the magnetic stratigraphy and the anisotropy of isothermal remanent magnetization of Pliocene sediments from International Ocean Discovery Program (IODP) Site U1467 drilled in the Maldives platform (Indian Ocean) during Exp. 359. Magnetic stratigraphy gives a precise record of geomagnetic reversals of the early Pliocene from approximately 5.3 Ma to 3.1 Ma providing a detailed age model in an interval where the biostratigraphic record is scarce. We use the anisotropy of isothermal remanent magnetization (AIRM) to investigate the statistical orientation of fine magnetic particles and provide data on the strength and direction of bottom currents during the early Pliocene. The strength of bottom currents recorded by the AIRM, shows a prominent increase at the top of Chron C3n.1n (about 4.2 Ma), and the current direction (NE - SW) is consistent with that of modern instrumental measurements. Since bottom currents in the Maldives are driven by the monsoon, we speculate that the 4.2 Ma increase of bottom currents could mark the onset of the present-day setting, probably related to the coeval uplift phase of the Himalayan plateau. University of Urbino (DiSPeA) IODP-Italia