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Abstract Background The Marburg virus (MARV) has a negative-sense single-stranded RNA genome, belongs to the family Filoviridae, and is responsible for several outbreaks of highly fatal hemorrhagic fever. Codon usage patterns of viruses reflect a series of evolutionary changes that enable viruses to shape their survival rates and fitness toward the external environment and, most importantly, their hosts. To understand the evolution of MARV at the codon level, we report a comprehensive analysis of synonymous codon usage patterns in MARV genomes. Multiple codon analysis approaches and statistical methods were performed to determine overall codon usage patterns, biases in codon usage, and influence of various factors, including mutation pressure, natural selection, and its two hosts, Homo sapiens and Rousettus aegyptiacus. Results Nucleotide composition and relative synonymous codon usage (RSCU) analysis revealed that MARV shows mutation bias and prefers U- and A-ended codons to code amino acids. Effective number of codons analysis indicated that overall codon usage among MARV genomes is slightly biased. The Parity Rule 2 plot analysis showed that GC and AU nucleotides were not used proportionally which accounts for the presence of natural selection. Codon usage patterns of MARV were also found to be influenced by its hosts. This indicates that MARV have evolved codon usage patterns that are specific to both of its hosts. Moreover, selection pressure from R. aegyptiacus on the MARV RSCU patterns was found to be dominant compared with that from H. sapiens. Overall, mutation pressure was found to be the most important and dominant force that shapes codon usage patterns in MARV. Conclusions To our knowledge, this is the first detailed codon usage analysis of MARV and extends our understanding of the mechanisms that contribute to codon usage and evolution of MARV.

SummaryProtists play a fundamental role in all ecosystems, but we are still far from estimating the total diversity of many lineages, in particular in highly diverse environments, such as freshwater. Here, we survey the protist diversity of the Paraná River using metabarcoding, and we applied an approach that includes sequence similarity and phylogeny to evaluate the degree of genetic novelty of the protists' communities against the sequences described in the reference database PR2. We observed that ~28% of the amplicon sequence variants were classified as novel according to their similarity with sequences from the reference database; most of them were related to heterotrophic groups traditionally overlooked in freshwater systems. This lack of knowledge extended to those groups within the green algae (Archaeplastida) that are well documented such as Mamiellophyceae, and also to the less studied Pedinophyceae, for which we found sequences representing novel deep‐branching clusters. Among the groups with potential novel protists, Bicosoecida (Stramenopiles) were the best represented, followed by Codosiga (Opisthokonta), and the Perkinsea (Alveolata). This illustrates the lack of knowledge on freshwater planktonic protists and also the need for isolation and/or cultivation of new organisms to better understand their role in ecosystem functioning.

Marine microbial communities provide much of the energy upon which all higher trophic levels depend, particularly in open-ocean and oligotrophic systems, and play a pivotal role in biogeochemical cycling. How and why species are distributed in the global oceans, and whether net ecosystem function can be accurately predicted from community composition are fundamental questions for marine scientists. Many of the most abundant clades of marine bacteria, including the Prochlorococcus, Synechococcus, SAR11, SAR86 and Roseobacter, have a very broad, if not a cosmopolitan distribution. However this is not reflected in an underlying genetic identity. Rather, widespread distribution in these organisms is achieved by the existence of closely related but discrete ecotypes that display niche adaptations. Closely related ecotypes display specific nutritional or energy generating mechanisms and are adapted to different physical parameters including temperature, salinity, and hydrostatic pressure. Furthermore, biotic phenomena such as selective grazing and viral loss contribute to the success or failure of ecotypes allowing some to compete effectively in particular marine provinces but not in others. An additional layer of complexity is added by ocean currents and hydrodynamic specificity of water body masses that bound microbial dispersal and immigration. These vary in space and time with respect to intensity and direction, making the definition of large biogeographic provinces problematic. A deterministic theory aimed at understanding how all these factors shape microbial life in the oceans can only proceed through analysis of microbial traits, rather than pure phylogenetic assessments. Trait based approaches seek mechanistic explanations for the observed temporal and spatial patterns. This review will present successful recent advances in phylogenetic and trait based biogeographic analyses in some of the most abundant marine taxa.

Abstract. Soft-sediment deformation structures can provide valuable information about the conditions of parent flows, the sediment state and the surrounding environment. Here, examples of soft-sediment deformation in deposits of dilute pyroclastic density currents are documented and possible syn-eruptive triggers suggested. Outcrops from six different volcanoes have been compiled in order to provide a broad perspective on the variety of structures: Soufrière Hills (Montserrat), Tungurahua (Ecuador), Ubehebe craters (USA), Laacher See (Germany), and Tower Hill and Purrumbete lakes (both Australia). The variety of features can be classified in four groups: (1) tubular features such as pipes; (2) isolated, laterally oriented deformation such as overturned or oversteepened laminations and vortex-shaped laminae; (3) folds-and-faults structures involving thick (>30 cm) units; (4) dominantly vertical inter-penetration of two layers such as potatoids, dishes, or diapiric flame-like structures. The occurrence of degassing pipes together with basal intrusions suggest fluidization during flow stages, and can facilitate the development of other soft-sediment deformation structures. Variations from injection dikes to suction-driven, local uplifts at the base of outcrops indicate the role of dynamic pore pressure. Isolated, centimeter-scale, overturned beds with vortex forms have been interpreted to be the signature of shear instabilities occurring at the boundary of two granular media. They may represent the frozen record of granular, pseudo Kelvin–Helmholtz instabilities. Their recognition can be a diagnostic for flows with a granular basal boundary layer. Vertical inter-penetration and those folds-and-faults features related to slumps are driven by their excess weight and occur after deposition but penecontemporaneous to the eruption. The passage of shock waves emanating from the vent may also produce trains of isolated, fine-grained overturned beds that disturb the surface bedding without occurrence of a sedimentation phase in the vicinity of explosion centers. Finally, ballistic impacts can trigger unconventional sags producing local displacement or liquefaction. Based on the deformation depth, these can yield precise insights into depositional unit boundaries. Such impact structures may also be at the origin of some of the steep truncation planes visible at the base of the so-called "chute and pool" structures. Dilute pyroclastic density currents occur contemporaneously with seismogenic volcanic explosions. They can experience extremely high sedimentation rates and may flow at the border between traction, granular and fluid-escape boundary zones. They are often deposited on steep slopes and can incorporate large amounts of water and gas in the sediment. These are just some of the many possible triggers acting in a single environment, and they reveal the potential for insights into the eruptive and flow mechanisms of dilute pyroclastic density currents.

Abstract The cone penetration test (CPT) is a method widely used for site characterization as measurements are continuous, fast and economical compared to laboratory testing. However unlike laboratory testing that quantifies soil properties directly, readings obtained from CPT are indirect and needs to be interpreted. Hence many correlations have been proposed to infer a wide range of soil properties from CPT readings. Existing correlations have discovered separate relationships between normalized cone tip resistance (Qt) and effective friction angles (ϕ’), as well as Qt and overconsolidation ratio (OCR). This study employs the press-replace method (PRM), a novel simplified numerical technique, to perform systematic and extensive undrained investigations of CPT in a modified Cam-clay (MCC) soil model. It is the first comprehensive numerical study with an advanced soil model that considers rough cone-soil interactions. The PRM numerical approach overcomes the need to assume the CPT process as analogous to spherical or cylindrical cavity expansions, therefore produces results that are more authentic to real CPT. From the large database of numerical results, an equation is formulated that provides a framework on how Qt is related to both ϕ’ and OCR, rather than separately to ϕ’ or OCR as described in previous correlations. The proposed equation is then simplified so that ϕ’ and OCR can be easily estimated from Qt. Numerical results and predictions from the new equations are then compared to soil behaviour charts, other correlations and field data from different sites.

The timing of the diversification of placental mammals relative to the Cretaceous-Paleogene (KPg) boundary mass extinction remains highly controversial. In particular, there have been seemingly irreconcilable differences in the dating of the early placental radiation not only between fossil-based and molecular datasets but also among molecular datasets. To help resolve this discrepancy, we performed genome-scale analyses using 4,388 loci from 90 taxa, including representatives of all extant placental orders and transcriptome data from flying lemurs (Dermoptera) and pangolins (Pholidota). Depending on the gene partitioning scheme, molecular clock model, and genic deviation from molecular clock assumptions, extensive sensitivity analyses recovered widely varying diversification scenarios for placental mammals from a given gene set, ranging from a deep Cretaceous origin and diversification to a scenario spanning the KPg boundary, suggesting that the use of suboptimal molecular clock markers and methodologies is a major cause of controversies regarding placental diversification timing. We demonstrate that reconciliation between molecular and paleontological estimates of placental divergence times can be achieved using the appropriate clock model and gene partitioning scheme while accounting for the degree to which individual genes violate molecular clock assumptions. A birth-death-shift analysis suggests that placental mammals underwent a continuous radiation across the KPg boundary without apparent interruption by the mass extinction, paralleling a genus-level radiation of multituberculates and ecomorphological diversification of both multituberculates and therians. These findings suggest that the KPg catastrophe evidently played a limited role in placental diversification, which, instead, was likely a delayed response to the slightly earlier radiation of angiosperms.

The Wharton Basin in the Indian Ocean is one of the most extensively deforming ocean basins, as confirmed by the occurrence of several very large earthquakes starting from January 12, 2012 with Mw 7.2 followed by the great earthquakes of April 11, 2012 with Mw 8.6 and Mw 8.2. Although the Mw 7.2 and Mw 8.2 earthquakes seem to have ruptured the re-activated N–S striking fracture zones, the largest event (Mw 8.6) required the rupturing of several faults, oblique to each other, in a very complex manner. In order to understand the nature of deformation in these earthquakes rupture zones, we recently acquired 90 000 km2 of bathymetry, 11 400 km of sub-bottom profiling, gravity and magnetic data covering the rupture areas of the 2012 earthquakes east of the Ninety-East Ridge, in the northwestern Wharton Basin. These new data reveal six N8°E striking re-activated fracture zones (F5b, F6a, f6b, F7a, F7b and F8), where the fracture zone F6a can be followed for over 400 km and seems to be most active. The epicenters of the Mw 8.6 and Mw 8.2 earthquakes lie on the fracture zones F6a and F7b, respectively. The newly observed fracture F5b in the east is short, and has an extensional basin at its southern tip. The fracture zone F8 defines the eastern boundary of the Ninety-East Ridge. The presence of en echelon faults and pull-apart basins indicate left-lateral motion along these fracture zones. In between these fracture zones, we observe pervasive 290° striking right-lateral shear zones at 4–8 km intervals; one of which has cut through a seamount that might have ruptured during the Mw 8.6 earthquake. We also observe another N20°E striking left-lateral shear zones in the vicinity of F7b and F8, which is coincident with the strike of one of the nodal planes of the Mw 8.6 focal mechanism. These N20°E striking shear zones are interpreted as R Riedel shears and the N290°E striking shear zones as R′ Riedel shears. These shear zones are formed by a series of N335°E striking en echelon normal faults. Our data also show the presence of N65°E striking thrust faults east of the Ninety-East Ridge, orthogonal to the regional principal direction of compression. Furthermore, extensive bending-related faulting is also observed close to the Sumatra trench with normal faults also striking at N335°E, similar to the normal faults that form the shear zones. Normal faults with a similar orientation are also present at the southern tip of F5b. We explain all these observations with a single coherent model of deformation in the Wharton Basin, where a dominant part of the regional NW–SE compressional stress is accommodated along the N8°E re-activated fracture zones, and the rest is distributed along shear zones, thrust and normal faults between these fracture zones. The thrust and normal faults are orthogonal to each other and define the direction of principal compressive and extensive stresses in the region whereas the two shear zone systems form a conjugate pair. NRF (Natl Research Foundation, S’pore) MOE (Min. of Education, S’pore) Published version