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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.

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.

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

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.

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.

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.

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.

Alluvial rivers aggrade, incise, and adjust their sediment‐transport rates in response to changing sediment and water supply. Fluvial landforms, such as river terraces, and downstream stratigraphic archives may therefore record information about past environmental change. Using a physically based model describing sediment transport and long‐profile evolution of alluvial rivers, we explore how their responses to environmental change depend on distance downstream, forcing timescales, and whether sediment or water supply is varied. We show that amplitudes of aggradation and incision, and therefore the likelihood of terrace formation, are greater upstream and in shorter and/or wetter catchments. Aggradation and incision, and therefore terrace ages, may also lag behind environmental change. How sediment‐transport rates evolve depends strongly on whether water or sediment supply is varied. Diverse responses to environmental change could arise in natural alluvial valleys, controlled by their geometry and hydrology, with important implications for paleo‐environmental interpretations of fluvial archives. Plain Language Summary Rivers carry sediment from upland regions, where it is produced by weathering and erosion, to low‐lying areas where it is deposited and stored. This process is sensitive to climate: for example, wetter conditions enhance rivers' capacity to transport sediment, causing rivers to cut into their beds, which in turn remobilizes sediment that is transported downstream. Changing climate may also lead to enhanced sediment production and supply to rivers, causing them to accumulate sediment in their beds. Climate cycles can therefore produce alternating periods of sediment accumulation and removal, resulting in ancient floodplains being abandoned and preserved alongside modern rivers (“terraces”), and in variations in the amounts of sediment delivered downstream. Terraces and patterns of sediment accumulation downstream could therefore provide valuable records of past climatic change. We develop a mathematical model that describes the effects of climatic change on river‐bed height and sediment‐transport rates. We show how the amount and timing of river in‐filling and down‐cutting, and the timescales over which they occur, depend on the rate of climatic change, on river length and associated drainage‐basin area, and on the amount of water it carries. These predictions will facilitate more detailed interpretations of terrace records along rivers and of the sedimentary deposits that they leave behind. Key Points Alluvial rivers respond in diverse ways to cyclical climatic change depending on their geometry and hydrology and on the forcing frequency Terrace formation is favored upstream and in shorter and wetter catchments and may lag appreciably behind environmental change Variation in sediment output lags variation in sediment supply but can lead and be amplified with respect to variation in water supply

Uplifted Pleistocene marine terrace sequences are used to quantify uplift rates along active margins by knowing terrace age and elevation, and sea level (SL) position at the time of terrace formation. When terraces are undated, ages are assigned by correlating terraces at progressively higher elevations with progressively older highstands. Uplift at convergent margins can be constant over time or occur coseismically during upper plate earthquakes. We explore the formation of terrace sequences under conditions of constant and earthquake‐driven uplift by using a forward numerical model. The modeling reveals that terraces are generally abandoned at SL highstands but they are carved during all stands, depending on the time spent within the sea erosional‐depth‐range. Therefore sea reoccupation of a same platform after formation is a common occurrence that decreases with increasing uplift rates, suggesting that most platforms in nature may be in fact polygenetic. Furthermore, the model run time influences the terrace sequences: terraces formed at the beginning of longer runs constitute an ‘inherited morphology’ affecting subsequent sequences. When coseismic uplift is applied, the formation and preservation of terraces for a given average uplift rate depend stochastically on the coseismic displacement ‐ recurrence interval combination in relation to the SL position at the time of the earthquake. These factors significantly contribute to a higher likelihood of non‐preserved terraces along a terrace sequence, which may affect age correlation and, consequently, the resulting uplift rates. Further research is needed to explore the effect of the full seismic cycle in shaping a terrace sequence. Plain Language Summary The topography of the upper plate in a subduction zone is subject to uplift over time. The action of the sea on the coast creates marine terraces, horizontal erosional platforms that, if uplifted, form a staircase morphology. Terrace staircase sequences are used to calculate the average uplift rate of the coast if the terrace age is known. In absence of datable material, the terrace age is inferred by assuming that terraces are preserved in chronological order of formation along the sequence. We use numerical models to explore the generation of subsequent marine terraces forming a staircase sequence on coastal margins subject to constant uplift over time or to instantaneous uplift caused by earthquakes occurring at a certain frequency (recurrence interval). We observe that: terraces are carved as long as they lie within the sea erosional depth; sea reoccupation of previously formed terraces occurs frequently, increasing with decreasing uplift rates; running the model for longer or shorter periods of time has changes morphology of the sequence; varying the earthquake recurrence interval results in different staircase morphologies even if the average uplift rate remains unchanged. The potential absence of terraces increases the chance of assigning, through cross correlation, wrong terrace ages, resulting in inexact uplift rates. Key Points Terraces form during all sea‐level stands, and sea reoccupation is common at uplift rates ≤0.5 mm/yr; most natural terraces may be polygenetic Earthquake‐driven uplift may cause non‐preservation of individual terraces, depending on the recurrence interval ‐ coseismic uplift values By keeping parameters constant and varying the model run time, terrace sequences with different morphology are created