An interactive biplot implementation in R for modeling genotype-by-environment interaction

Classical and GGE biplot methods are graphical procedures that allow multivariate data to be analyzed. In particular, the GGE biplot displays the genotype main effect (G) and the genotype by environment interaction (GE) in two-way data. The GGE biplot originates from data graphical analysis of multi-environment trials (MET). Thus, agronomists, crop scientists and geneticists are potential users of this method. However, it can also be used to visualize and analyze other types of data. In this paper, we propose a new interactive computational implementation in R language to perform the main functions of the classical and GGE biplot methods, so it is also useful for MET data visual analysis. This implementation is organized in an R package named GGEBiplotGUI . This package is the only interactive, noncommercial and open source software that currently exists, offering a free alternative to available commercial software. In addition, it can be used without to practically have knowledge of the R programming language. Here, we present and discuss the capabilities and features of the GGEBiplotGUI package and illustrate them by using real data. The GGEBiplotGUI package graphically addresses the questions that a researcher likely asks. This R package is not only a tool for visual data analysis of multi-environment trials, useful for plant breeders and geneticists, in order to study yields from genotypes and interactions between genotype and environment, but also data from other areas can be analyzed by the GGEBiplotGUI package.     

A new approach to define surface/sub-surface transition in gravel beds

The vertical structure of river beds varies temporally and spatially in response to hydraulic regime, sediment mobility, grain size distribution and faunal interaction. Implicit are changes to the active layer depth and bed porosity, both critical in describing processes such as armour layer development, surface-subsurface exchange processes and siltation/ sealing. Whilst measurements of the bed surface are increasingly informed by quantitative and spatial measurement techniques (e.g., laser displacement scanning), material opacity has precluded the full 3D bed structure analysis required to accurately define the surface-subsurface transition. To overcome this problem, this paper provides magnetic resonance imaging (MRI) data of vertical bed porosity profiles. Uniform and bimodal (?? _g = 2.1) sand-gravel beds are considered following restructuring under sub-threshold flow durations of 60 and 960 minutes. MRI data are compared to traditional 2.5D laser displacement scans and six robust definitions of the surface-subsurface transition are provided; these form the focus of discussion.     

The Zoning of Semi-Enclosed Bodies of Water According to the Sediment Pollution: The Bay of Algeciras as a Case Example

This paper reports a study of the occurrence and levels of polycyclic aromatic hydrocarbons (PAHs) in a bay characterised by a chronic persistent impact. A total of 55 sediment samples were taken at different depths up to 111 m in two sampling campaigns. Chemical analyses were carried out by gas chromatography-mass spectroscopy. The results indicate that: (1) significant spatial variations exist, (2) levels of PAHs are related more strongly to the spatial distribution of sediments than to mineralogy/granulometry, (3) the sediments are slightly-to-moderately contaminated by PAHs, and (4) these PAHs derive from pyrolytic and petrogenic sources. Through use of an innovative data classification system (proposed according to depth and spatial location of sampling points), and using factorial and cluster techniques, five zones have been differentiated depending on the contamination level and source.     

Microbial dynamics in cyclonic and anticyclonic mode-water eddies in the northwestern Sargasso Sea

The EDdy Dynamics, mixing, Export, and Species composition (EDDIES) project provided a unique opportunity to evaluate the response of the microbial community and further understand the biological and biogeochemical consequences of mesoscale perturbation events in an oligotrophic system. In order to characterize microbial dynamics, we performed measurements of bacterial biomass (BB) and production (BP) and phytoplankton pigment analyses in two upwelling eddies in the Sargasso Sea sampled in 2004 and 2005. We also observed a 3-fold increase in BP at the Bermuda Atlantic Time-series Study (BATS) site during the passage of a cyclonic eddy in 2003. Although the integrated BB and BP over 140 m in 2004 and 2005 eddies remained within the climatological range measured at the BATS site, there was systematic variability in bacterioplankton dynamics across both eddies. Cyclonic eddy C1 demonstrated decreased BP at the feature's center relative to its periphery, and BP was not correlated with total chlorophyll a (TChl a) variability. However, BP correlated with prymnesiophyte pigments throughout the feature. In contrast, mode-water eddy A4 showed an enhancement in BP at the eddy center (EC) relative to its edges and was coincident with elevated TChl a, high primary production measurements, and a high concentration of diatoms. In eddy A4, the tight relationship between enhanced BP, TChl a and specific phytoplankton taxa implies that the phytoplankton community structure was an important factor influencing BP variability. While the heterotrophic bacterial response in C1 and A4 was not enhanced relative to BATS summer climatology, these data and the presence of similar nutrient fields across both eddies suggest that BP and BB were influenced by the eddy perturbations and responded to changes in the phytoplankton community.     

Diagnostics,deterioration and provenance of stone materials from the Jefferson Page tomb (Non-Catholic Cemetery of Rome,Italy)

The monumental tomb of Jefferson Page, an officer in the American Navy, was built in 1899 and is located in the Non-Catholic Cemetery of Rome (Italy). This study presents complementary diagnostic studies characterizing the stone of the tomb and the weathering and decay phenomena it has undergone. The monument is made of a single type of whitish marble, variously veined and often covered with black patinas. Petrographic, isotopic and LA-ICP-MS analyses attribute the marble to the Carrara district. SEM/EDS and microbiological analyses indicate that the black patinas are due to cyanobacterial autotrophic and fungin heterotrophic colonization. Fourier-transform infrared spectroscopy revealed the presence of organic material on some portions of the tomb, due to undocumented restoration carried out with a mixture of marble powder and a polyester resin.     

Modeling of Landslide‐Generated Tsunamis with GRASS

The following research aims to enhance and spread the capacity of assessing risk due to landslide‐generated tsunamis by fostering the use of a GIS (Geographic Information System), and in this particular instance, an Open Source GIS (where “Open Source” can be loosely defined as freely available source code). For this purpose, we tested a procedure to be spatially implemented in the Open Source GRASS GIS through developing a module named r.impact.tsunami that simulates landslide‐generated tsunami. In this article we present its application in a case study performed on Como Lake (Lago di Como) in northern Italy. The review of the results identified sources of uncertainties while the model sensitivity outlined the influence of the parameters governing the model. Moreover, in order to verify the model validity, we implemented a new module (r.swe), that simulates the tsunami propagation and run‐up with the shallow water equations, and compared the results. Notwithstanding non‐negligible differences, the two models produced results of the same magnitude; this confirmed the validity of both models, although a rigorous validation of the models could not be performed due to the lack of observed data.     

Changes in eruptive style during the A.D. 1538 Monte Nuovo eruption (Phlegrean Fields, Italy): the role of syn-eruptive crystallization

The Monte Nuovo eruption is the most recent event that occurred at Phlegrean Fields (Italy) and lasted from 29 September to 6 October 1538. It was characterized by 2 days of quasi-sustained phreatomagmatic activity generating pumice-bearing pyroclastic density currents and forming a 130-m-high tuff cone (Lower Member deposits). The activity resumed after a pause of 2 days with two discrete Vulcanian explosions that emplaced radially distributed, scoria-bearing pyroclastic flows (Upper Member deposits). The juvenile products of Lower and Upper Members are, respectively, phenocryst-poor, light-coloured pumice and dark scoria fragments with K-phonolitic bulk compositions, identical in terms of both major and trace elements. Groundmass is formed by variable proportions of K-feldspar and glass, along with minor sodalite and Fe-Ti oxide present in the most crystallized samples. Investigations of groundmass compositions and textures were performed to assess the mechanisms of magma ascent, degassing and fragmentation along the conduit and implications for the eruptive dynamics. In pumice of the Lower Member groundmass crystal content increases from 13 to 28 vol% from the base to the top of the sequence. Products of the Upper Member consist of clasts with a groundmass crystal content between 30 and 40 vol% and of totally crystallized fragments. Crystal size distributions of groundmass feldspars shift from a single population at the base of the Lower Member to a double population in the remaining part of the sequence. The average size of both populations regularly increases from the Lower to the Upper Member. Crystal number density increases by two orders of magnitude from the Lower to the Upper Member, suggesting that nucleation dominated during the second phase of the eruption. The overall morphological, compositional and textural data suggest that the juvenile components of the Monte Nuovo eruption are likely to record variations of the magma properties within the conduit. The different textures of pumice clasts from the Lower Member possibly reflect horizontal gradients of the physical properties (P, T) of the ascending magma column, while scoriae from the second phase are thought to result from the disruption of a slowly rising plug crystallizing in response to degassing. In particular, crystal size distribution data point to syn-eruptive degassing-induced crystallization as responsible for the transition in eruptive style from the first to the second phase of the eruption. This mechanism not only has been proved to profoundly affect the dynamics of dome-forming calc-alkaline eruptions, but may also have a strong influence in driving the eruption dynamics of alkaline magmas of intermediate to evolved compositions.Editorial responsibility: J. Donnelly-Nolan     

Intense drought and flooding events in the Rio Negro and relation with the tropical Pacific and Atlantic variability modes

The relationship of the hydrological variability of the Rio Negro in Manaus and the dominant large-scale climate variability patterns for the 1902–2007 period is investigated using the quantile method and composite analyses. Variations of the Rio Negro Level (RNL) during its 3-month high (May to July—MJJ) and low (October to December—OND) phases are examined separately. The El Niño (La Niña) related maximum warming (cooling) in the central tropical Pacific during its mature and decaying stages modulates the atmospheric circulation in the tropics and displaces the Walker circulation cell eastward (westward), so that its sinking (rising) branch occurs over western Amazon and causes negative (positive) precipitation anomalies in this region. These anomalous climate conditions occur before the Rio Negro high phase (MJJ) and contribute to reduce (increase) the RNL and lead to a very low (very high) event in the river. On the other hand, the SST variability modes in the tropical Atlantic mainly during the transition from wet to dry season modulate the precipitation variations over western Amazon in OND. The very high events are more frequent after the 1960’s decade and the very low events, before the 1930’s decade. Therefore, the occurrence of these events contains a multidecadal scale variability. The results also indicate that the variations in the rainfall in western Amazon occur up to 9 months in advance and modulate the RNL in Manaus. The results presented here might be useful for monitoring purposes of the RNL.

     

Influence of microclimate and geomorphological factors on alpine vegetation in the Western Swiss Alps

Among the numerous environmental factors affecting plant communities in alpine ecosystems, the influence of geomorphic processes and landforms has been minimally investigated. Subjected to persistent climate warming, it is vital to understand how these factors affect vegetation properties. Here, we studied 72 vegetation plots across three sites located in the Western Swiss Alps, characterized by high geomorphological variability and plant diversity. For each plot, vascular plant species were inventoried and ground surface temperature, soil moisture, topographic variables, earth surface processes (ESPs) and landform morphodynamics were assessed. The relationships between plant communities and environmental variables were analysed using non-metric multi-dimensional scaling (NMDS) and multivariate regression techniques (generalized linear model, GLM, and generalized additive model, GAM). Landform morphodynamics, growing degree days (sum of degree days above 5°C) and mean ground surface temperature were the most important explanatory variables of plant community composition. Furthermore, the regression models for species cover and species richness were significantly improved by adding a morphodynamics variable. This study provides complementary support that landform morphodynamics is a key factor, combined with growing degree days, to explain alpine plant distribution and community composition. © 2019 John Wiley & Sons, Ltd. © 2019 John Wiley & Sons, Ltd.