Combining environmental factors and agriculturalists' observations of environmental changes in the traditional terrace system of the Amalfi coast (southern Italy).
ABSTRACT: Terraces are traditional engineered ecosystems that affect the hydro-geological equilibrium, slope stability, and local communities. The aims of this paper are (i) identifying environmental factors that affect terrace stability in the Amalfi Coast, (ii) defining agriculturalists' observations on environmental changes within that system and (iii) exploring potentiality of these observations to better define conservation strategies. All available data on physical and ecological factors recognized to affect the terrace system were collected and analyzed. Interviews were conducted with agriculturalists to obtain long-term observations on environmental factors that interact with this system. Landslides are more frequent where rainfall is high and during winter. Fires have an uneven annual distribution, with higher frequency during summers. Agriculturalists detailed complex interactions among environmental factors, economic elements, and terraces. These observations represent a valuable resource for defining causes and effects of abandonment and for better addressing conservation strategies.
Project description:Motivation:The presence of terraces in phylogenetic tree space, i.e. a potentially large number of distinct tree topologies that have exactly the same analytical likelihood score, was first described by Sanderson et al. However, popular software tools for maximum likelihood and Bayesian phylogenetic inference do not yet routinely report, if inferred phylogenies reside on a terrace, or not. We believe, this is due to the lack of an efficient library to (i) determine if a tree resides on a terrace, (ii) calculate how many trees reside on a terrace and (iii) enumerate all trees on a terrace. Results:In our bioinformatics practical that is set up as a programming contest we developed two efficient and independent C++ implementations of the SUPERB algorithm by Constantinescu and Sankoff (1995) for counting and enumerating trees on a terrace. Both implementations yield exactly the same results, are more than one order of magnitude faster, and require one order of magnitude less memory than a previous thirrd party python implementation. Availability and implementation:The source codes are available under GNU GPL at https://github.com/terraphast. Supplementary information:Supplementary data are available at Bioinformatics online.
Project description:In phylogenomics the analysis of concatenated gene alignments, the so-called supermatrix, is commonly accompanied by the assumption of partition models. Under such models each gene, or more generally partition, is allowed to evolve under its own evolutionary model. Although partition models provide a more comprehensive analysis of supermatrices, missing data may hamper the tree search algorithms due to the existence of phylogenetic (partial) terraces. Here, we introduce the phylogenetic terrace aware (PTA) data structure for the efficient analysis under partition models. In the presence of missing data PTA exploits (partial) terraces and induced partition trees to save computation time. We show that an implementation of PTA in IQ-TREE leads to a substantial speedup of up to 4.5 and 8 times compared with the standard IQ-TREE and RAxML implementations, respectively. PTA is generally applicable to all types of partition models and common topological rearrangements thus can be employed by all phylogenomic inference software.
Project description:Nanotwinned copper (nt-Cu) shows a broad application prospects as interconnection materials in integrated circuit industry, since it combines the excellent mechanical and electrical properties. However, the formation and growth behavior of twin lamellae in pulse electrodeposited copper films are not fully understood. In this work, a series of electroplated copper films are prepared by verifying the electroplating parameters and the microstructures are analyzed using scanning electron microscope (SEM) and transmission electron microscope (TEM). The surface morphology indicates strong evidence of stacked twin terraces and layers, suggesting that nanotwins grow up layer by layer. Combined with in situ characterization by SEM and molecular dynamics (MD) simulation, it is proved that the terraces originate from the triple junction of grain boundaries and grow up by extending along the lateral (111) crystal plane. A twin terrace-growing model for nt-Cu is then deduced, which distinguishes from deformation twins or annealed twins. This growth model would be prospective to help obtain high quality of nt-Cu in industry.
Project description:We demonstrate that localized excitons in luminescent carbon nanotubes can be utilized to study electrostatic fluctuations in the nanotube environment with sensitivity down to the elementary charge. By monitoring the temporal evolution of the cryogenic photoluminescence from individual carbon nanotubes grown on silicon oxide and hexagonal boron nitride, we characterize the dynamics of charge trap defects for both dielectric supports. We find a one order of magnitude reduction in the photoluminescence spectral wandering for nanotubes on extended atomically flat terraces of hexagonal boron nitride. For nanotubes on hexagonal boron nitride with pronounced spectral fluctuations, our analysis suggests proximity to terrace ridges where charge fluctuators agglomerate to exhibit areal densities exceeding those of silicon oxide. Our results establish carbon nanotubes as sensitive probes of environmental charge fluctuations and highlight their potential for applications in electrometric nanodevices with all-optical readout.
Project description:We present the first remotely operated vehicle investigation of megabenthic communities (1004-1695?m water depth) on the Hebrides Terrace Seamount (Northeast Atlantic). Conductivity-temperature-depth casts showed rapid light attenuation below the summit and an oceanographic regime on the flanks consistent with an internal tide, and high short-term variability in water temperature, salinity, light attenuation, aragonite and oxygen down to 1500?m deep. Minor changes in species composition (3-14%) were explained by changes in depth, substratum and oceanographic stability, whereas environmental variability explained substantially more variation in species richness (40-56%). Two peaks in species richness occurred, the first at 1300-1400?m where cooler Wyville Thomson Overflow Water (WTOW) mixes with subtropical gyre waters and the second at 1500-1600?m where WTOW mixes with subpolar mode waters. Our results suggest that internal tides, substrate heterogeneity and oceanographic interfaces may enhance biological diversity on this and adjacent seamounts in the Rockall Trough.
Project description:In phylogenomic analysis the collection of trees with identical score (maximum likelihood or parsimony score) may hamper tree search algorithms. Such collections are coined phylogenetic terraces. For sparse supermatrices with a lot of missing data, the number of terraces and the number of trees on the terraces can be very large. If terraces are not taken into account, a lot of computation time might be unnecessarily spent to evaluate many trees that in fact have identical score. To save computation time during the tree search, it is worthwhile to quickly identify such cases. The score of a species tree is the sum of scores for all the so-called induced partition trees. Therefore, if the topological rearrangement applied to a species tree does not change the induced partition trees, the score of these partition trees is unchanged. Here, we provide the conditions under which the three most widely used topological rearrangements (nearest neighbor interchange, subtree pruning and regrafting, and tree bisection and reconnection) change the topologies of induced partition trees. During the tree search, these conditions allow us to quickly identify whether we can save computation time on the evaluation of newly encountered trees. We also introduce the concept of partial terraces and demonstrate that they occur more frequently than the original "full" terrace. Hence, partial terrace is the more important factor of timesaving compared to full terrace. Therefore, taking into account the above conditions and the partial terrace concept will help to speed up the tree search in phylogenomic inference.
Project description:The Honghe-Hani landscape in China is a UNESCO World Natural Heritage site due to the beauty of its thousands of rice terraces, but these structures are in danger from the invasive crayfish Procambarus clarkii. Crayfish dig nest holes, which collapse terrace walls and destroy rice production. Under the current control strategy, farmers self-report crayfish and are issued pesticide, but this strategy is not expected to eradicate the crayfish nor to prevent their spread since farmers are not able to detect small numbers of crayfish. Thus, we tested whether environmental DNA (eDNA) from paddy-water samples could provide a sensitive detection method. In an aquarium experiment, Real-time Quantitative polymerase chain reaction (qPCR) successfully detected crayfish, even at a simulated density of one crayfish per average-sized paddy (with one false negative). In a field test, we tested eDNA and bottle traps against direct counts of crayfish. eDNA successfully detected crayfish in all 25 paddies where crayfish were observed and in none of the 7 paddies where crayfish were absent. Bottle-trapping was successful in only 68% of the crayfish-present paddies. eDNA concentrations also correlated positively with crayfish counts. In sum, these results suggest that single samples of eDNA are able to detect small crayfish populations, but not perfectly. Thus, we conclude that a program of repeated eDNA sampling is now feasible and likely reliable for measuring crayfish geographic range and for detecting new invasion fronts in the Honghe Hani landscape, which would inform regional control efforts and help to prevent the further spread of this invasive crayfish.
Project description:Across North America, human activities have been shown to cause river incision into unconsolidated alluvium. Human-caused erosion through bedrock, however, has only been observed in local and isolated outcrops. Here, we test whether splash-dam logging, which decreased in-stream alluvial cover by removing much of the alluvium-trapping wood, caused basin-wide bedrock river incision in a forested mountain catchment in Washington State. We date incision of the youngest of four strath terraces, using dendrochronology and radiocarbon, to between 1893 CE and 1937 CE in the Middle Fork Teanaway River and 1900 CE and 1970 CE in the West Fork Teanaway River, coincident with timber harvesting and splash damming in the basins. Other potential drivers of river incision lack a recognized mechanism to cause T1 incision or are not synchronous with T1 incision. Hence, the close temporal correspondence suggests that reduced sediment retention triggered by splash damming led to the observed 1.1 mm?y<sup>-1</sup> to 23 mm?y<sup>-1</sup> of bedrock river incision and reduction of the active floodplain to 20% and 53% of its preincision extent on the Middle and West Forks, respectively. The development of such anthropogenic bedrock terraces may be an emerging, globally widespread physiographic signature of the Anthropocene.
Project description:The Dinarides fold-thrust belt on the Balkan Peninsula resulted from convergence between the Adriatic and Eurasian plates since Mid-Jurassic times. Under the Dinarides, S-wave receiver functions, P-wave tomographic models, and shear-wave splitting data show anomalously thin lithosphere overlying a short down-flexed slab geometry. This geometry suggests a delamination of Adriatic lithosphere. Here, we link the evolution of this continental convergence system to hitherto unreported sets of extensively uplifted Oligocene-Miocene (28-17 Ma) marine terraces preserved at elevations of up to 600 m along the Dinaric coastal range. River incision on either side of the Mediterranean-Black Sea drainage divide is comparable to the amounts of terrace uplift. The preservation of the uplifted terraces implies that the most External Dinarides did not experience substantial deformation other than surface uplift in the Neogene. These observations and the contemporaneous emplacement of igneous rocks (33-22 Ma) in the internal Dinarides suggest that the Oligo-Miocene orogen-wide uplift was driven by post-break-off delamination of the Adriatic lithospheric mantle, this was followed by isostatic readjustment of the remaining crust. Our study details how lithospheric delamination exerts an important control on crustal deformation and that its crustal signature and geomorphic imprint can be preserved for millions of years.
Project description:Luminescence signals of quartz and feldspar minerals are widely used to determine the burial age of Quaternary sediments. Although luminescence signals bleach rapidly with sunlight exposure, incomplete bleaching may affect luminescence ages, in particular in fluvial settings where an unbleached remnant signal is commonly encountered in modern alluvium. Here, we use feldspar single-grain post-infrared IR stimulation (pIRIR) dating to show that recent (<11 ka) fluvial terraces of the Rangitikei River (New Zealand) were formed in a context of non-linear incision rate. We relate this pattern to the rapid reinstatement of steady-state incision following the formation of a major, climate-driven, aggradation terrace, causing a phase of accelerated incision. In addition, we show systematic variations in the proportion of unbleached grains in the fluvial sediments over time, mirroring incision rate at the time of deposition. Deposits formed during rapid incision contain fewer bleached grains, which we attribute to large input of unbleached material and limited bleaching opportunities during fluvial transport. This finding demonstrates that the luminescence signals recorded in fluvial terraces not only yield age information, but also inform us on past fluvial transport and ultimately, landscape dynamics.