Explore the vast range of titles available.

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 data structure for the efficient analysis under partition models. In the presence of missing data exploits (partial) terraces and induced partition trees to save computation time. We show that an implementation of 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.

The Honghe Hani Rice Terraces (China) is an ancient world heritage agricultural landscape that has been evolved in centuries as a result of farmers’ indigenous practices and knowledge. The area, however, is prone to landslides that can burden the conservation of these landscapes including their social, cultural, economic and aesthetic value. In June 2018, a landslide threatened the villages of Duosha and Mengpin affecting 138 inhabitants and the terraces structure. This event marked the need to understand how farmers coexist with these natural hazards and which are the behaviours people adopt to conserve their environment and safeguard their livelihood. Results from 125 in-person interviews showed that farmers feel threaten by landslide events derived by their personal experience, but their poor perceived preparedness and the inefficient disaster information make them more vulnerable to those events. Nevertheless, they demonstrated a desire to increase their knowledge on terraces restoration and conservation practices. This is an important signal for public authorities and practitioners that need to underpin training activities and create momentum for discussion. The demonstrated high trust in authorities’ decisions is a crucial element to pursue the objective and sustain the conservation of the terraces and the tourism economy.

This paper presents version 1.0 of the World Atlas of Last Interglacial Shorelines (WALIS), a global database of sea-level proxies and samples dated to marine isotope stage 5 (∼ 80 to 130 ka). The database includes a series of datasets compiled in the framework of a special issue published in this journal (https://essd.copernicus.org/articles/special_issue1055.html, last access: 15 December 2022). This paper collates the individual contributions (archived in a Zenodo community at https://zenodo.org/communities/walis_database/, last access: 15 December 2022) into an open-access, standalone database (Rovere et al., 2022, https://doi.org/10.5281/zenodo.7348242). The release of WALIS 1.0 includes complete documentation and scripts to download, analyze, and visualize the data (https://alerovere.github.io/WALIS/, last access: 15 December 2022). The database contains 4545 sea-level proxies (e.g., marine terraces or fossil beach deposits), 4110 dated samples (e.g., corals dated with U-series), and 280 other time constraints (e.g., biostratigraphic constraints or tephra layers) interconnected with several tables containing accessory data and metadata. By creating a centralized database of sea-level proxy data for the Last Interglacial, the WALIS database will be a valuable resource to the broader paleoclimate community to facilitate data–model integration and intercomparisons, assessments of sea-level reconstructions between different studies and different regions, as well as comparisons between past sea-level history and other paleoclimate proxy data.

Marine terraces have long been a subject of paleoseismology, revealing the rupture history of megathrust earthquakes. However, the crustal deformation mechanisms responsible for their formation remain inadequately explained by conventional kinematic models. A major challenge lies in the tendency of seismically uplifted shorelines to subside back to sea level during interseismic periods. This study focuses on the residual, permanent vertical deformation produced by repeated megathrust earthquakes. We investigate the effects of irregularities in the plate interface, particularly subducted seamounts. To address this, we introduce a mechanical subducting plate model (MSPM) that incorporates more realistic boundary conditions and three-dimensional geometry of the plate interface and subducting slab, using stress-boundary conditions. As a result, subducted seamounts significantly affect surface deformation, resulting in concentrated permanent uplift directly above them. We apply the MSPM to the geometry of the Sagami Trough, central Japan, and compare the simulation outcomes with the observations of marine terraces. The modeled earthquake sequences demonstrate that coseismic uplift can persist over time and contribute to terrace formation. These findings suggest that geological observations of both coseismic and long-term deformations can be explained by the influence of a subducted seamount, previously identified in seismic surveys. Graphical Abstract

Terraces, farmlands built along hillside contours, are common anthropogenically designed landscapes. Terraces control soil and water loss and improve land productivity; therefore, obtaining their spatial distribution is necessary for soil and water conservation and agricultural production. Spatial information of large-scale terraces can be obtained using satellite images and through deep learning. However, when extracting terraces, accurately segmenting the boundaries of terraces and identifying small terraces in diverse scenarios continues to be challenging. To solve this problem, we combined two deep learning modules, ANB-LN and DFB, to produce a new deep learning framework (NLDF-Net) for terrace extraction using remote sensing images. The model first extracted the features of the terraces through the coding area to obtain abstract semantic features, and then gradually recovered the original size through the decoding area using feature fusion. In addition, we constructed a terrace dataset (the HRT-set) for Guangdong Province and conducted a series of comparative experiments on this dataset using the new framework. The experimental results show that our framework had the best extraction effect compared to those of other deep learning methods. This framework provides a method and reference for extracting ground objects using remote sensing images.

A comprehensive examination of uplifted mid-late Pleistocene marine terraces along the eastern coast of Korea offers valuable insights into the temporal and spatial variability of uplift rates spanning ∼200 ka. Focusing on the Gangneung–Samcheok region of the Korean peninsula’s east coast, the study area is delineated into three distinct areas (i.e., Anin, Jeongdongjin–Donghae, and Samcheok) by two NNE-SSW to NE-SE-striking faults. Three flights of marine terraces are developed in each area, with terraces typically observed at elevations of 10 to 20 m and 20 to 35 m across all three areas. Conversely, upper terraces exceeding these elevations are mainly observed at 50 to 60 m or 60 to 80 m, with regional variations noted. Quartz optically stimulated luminescence dating (OSL) was used for dating marine terrace deposits. However, it could not be applied to older deposits beyond the upper limit of quartz OSL. Therefore, IRSL and post IR-IRSL dating using K-rich feldspar, which has a higher upper limit than quartz OSL, were applied in this study. The results indicate that marine terraces at elevations of 10 to 20 m and 20 to 35 m formed during MIS 5a and MIS 5e. Depositional ages of MIS 7 were obtained from terraces ranging from 50 to 60 m or 60 to 80 m, exhibiting elevation differences across regions. Consequently, the estimated temporal variation in uplift rates revealed an average uplift rate of 0.52–0.79 m/ka from MIS 7 to MIS 5e, followed by 0.2–0.3 m/ka after MIS 5e. Spatial variation in uplift rates was observed from MIS 7 to MIS 5e. Specifically, the uplift rate in the Jeongdongjin–Donghae area, located in the middle part of the study area, was 0.79 m/ka (Min. 0.68 m/ka, Max. 0.90 m/ka), whereas the uplift rate in the other study areas was 0.52 m/ka (Min. 0.41 m/ka, Max. 0.62 m/ka). This discrepancy is probably attributed to the influence of the two faults that subdivide the study area.

Abstract For a set of binary unrooted subtrees generating all binary unrooted trees compatible with them, i.e. generating their stand, is one of the classical problems in phylogenetics. Here, we introduce Gentrius—an efficient algorithm to tackle this task. The algorithm has a direct application in practice. Namely, Gentrius generates phylogenetic terraces—topologically distinct, equally scoring trees due to missing data. Despite stand generation being computationally intractable, we showed on simulated and biological datasets that Gentrius generates stands with millions of trees in feasible time. We exemplify that depending on the distribution of missing data across species and loci and the inferred phylogeny, the number of equally optimal terrace trees varies tremendously. The strict consensus tree computed from them displays all the branches unaffected by the pattern of missing data. Thus, by solving the problem of stand generation, in practice Gentrius provides an important systematic assessment of phylogenetic trees inferred from incomplete data. Furthermore, Gentrius can aid theoretical research by fostering understanding of tree space structure imposed by missing data.

Perovskite solar cells (PSCs) with an inverted structure (often referred to as the p–i–n architecture) are attractive for future commercialization owing to their easily scalable fabrication, reliable operation and compatibility with a wide range of perovskite-based tandem device architectures 1 , 2 . However, the power conversion efficiency (PCE) of p–i–n PSCs falls behind that of n–i–p (or normal) structure counterparts 3 – 6 . This large performance gap could undermine efforts to adopt p–i–n architectures, despite their other advantages. Given the remarkable advances in perovskite bulk materials optimization over the past decade, interface engineering has become the most important strategy to push PSC performance to its limit 7 , 8 . Here we report a reactive surface engineering approach based on a simple post-growth treatment of 3-(aminomethyl)pyridine (3-APy) on top of a perovskite thin film. First, the 3-APy molecule selectively reacts with surface formamidinium ions, reducing perovskite surface roughness and surface potential fluctuations associated with surface steps and terraces. Second, the reaction product on the perovskite surface decreases the formation energy of charged iodine vacancies, leading to effective n-type doping with a reduced work function in the surface region. With this reactive surface engineering, the resulting p–i–n PSCs obtained a PCE of over 25 per cent, along with retaining 87 per cent of the initial PCE after over 2,400 hours of 1-sun operation at about 55 degrees Celsius in air. A reactive surface engineering approach is used to produce an inverted perovskite solar cell that reaches a power conversion efficiency of 25% and has good operational stability.

We analyze the processing of cereals and its role at Early Neolithic Göbekli Tepe, southeastern Anatolia (10th / 9th millennium BC), a site that has aroused much debate in archaeological discourse. To date, only zooarchaeological evidence has been discussed in regard to the subsistence of its builders. Göbekli Tepe consists of monumental round to oval buildings, erected in an earlier phase, and smaller rectangular buildings, built around them in a partially contemporaneous and later phase. The monumental buildings are best known as they were in the focus of research. They are around 20 m in diameter and have stone pillars that are up to 5.5 m high and often richly decorated. The rectangular buildings are smaller and-in some cases-have up to 2 m high, mostly undecorated, pillars. Especially striking is the number of tools related to food processing, including grinding slabs/bowls, handstones, pestles, and mortars, which have not been studied before. We analyzed more than 7000 artifacts for the present contribution. The high frequency of artifacts is unusual for contemporary sites in the region. Using an integrated approach of formal, experimental, and macro- / microscopical use-wear analyses we show that Neolithic people at Göbekli Tepe have produced standardized and efficient grinding tools, most of which have been used for the processing of cereals. Additional phytolith analysis confirms the massive presence of cereals at the site, filling the gap left by the weakly preserved charred macro-rests. The organization of work and food supply has always been a central question of research into Göbekli Tepe, as the construction and maintenance of the monumental architecture would have necessitated a considerable work force. Contextual analyses of the distribution of the elements of the grinding kit on site highlight a clear link between plant food preparation and the rectangular buildings and indicate clear delimitations of working areas for food production on the terraces the structures lie on, surrounding the circular buildings. There is evidence for extensive plant food processing and archaeozoological data hint at large-scale hunting of gazelle between midsummer and autumn. As no large storage facilities have been identified, we argue for a production of food for immediate use and interpret these seasonal peaks in activity at the site as evidence for the organization of large work feasts.