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.
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Dostopno za:
BFBNIB, DOBA, IZUM, KILJ, NMLJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
In order to investigate the impact of environmental conditions on the distribution and migration of 90Sr in the Longji terrace environment, the activity concentrations of 90Sr and 137Cs were ...determined. The activity concentration ranges of 90Sr and 137Cs in surface soil were 0.15–1.04 Bq/kg and 2.16–6.94 Bq/kg, respectively. These results showed that there was a similar trend between the activity concentration of 90Sr and 137Cs in the surface soil along the runoff path and their activity concentration were influenced by the slope of the terraced terrain. On the other hand, the activity ranges of 90Sr and 137Cs in soil cores were 0.01–2.74 Bq/kg and 0.43–7.19 Bq/kg, respectively. These results indicate that the migration mechanism of 90Sr is different from that of 137Cs. As compared with 137Cs, 90Sr is significantly influenced by the moisture content. In addition, high span of 137Cs/90Sr activity ratios were found in this study, which were attributed to the characteristics of cultivated land and frequent artificial disturbances that intensified the migration of 90Sr.
•The first research of 90Sr in the terraces.•Runoff and slope are key factors driving 90Sr and 137Cs levels in terraced soil.•Compared with 137Cs, the migration trend of 90Sr in the core of terraced soil is more affected by moisture.
Located in the arid basalt desert of northeastern Jordan, the settlement of Jawa is by far the largest and best-preserved archaeological site in the region. The Early Bronze Age (EBA) settlement ...phase of Jawa (3500–3000 BCE) is characterized by a highly sophisticated water storage system made of a series of pools, dams, and canals. In addition, recent archaeological and geoarchaeological surveys have uncovered agricultural terrace systems in the nearby vicinity.
In this study, four of these runoff terrace systems were investigated by detailed mapping. Additionally, thirteen sediment profiles from inside and outside the terrace systems were recorded and sampled. The examined samples were analyzed for bulk chemistry, texture, phytoliths, diatoms, and dung spherulites to supply information on the environmental and depositional conditions. The terrace systems were dated using optically stimulated luminescence (OSL).
Ancient terrace agriculture was practiced on slopes, small plateaus, and valleys close to Jawa through the use of surface canals, which collected and diverted floodwater from nearby wadis or runoff from adjacent slopes. The terraced fields were usually arranged in cascades and comprised a system of risers, canals, and spillways. The terrace fills investigated yield OSL ages of around 3300 BCE, indicating that the terraces were constructed in the Early Bronze Age. The terrace fill sequences are composed of mixed unstratified fine sediments of local origin, reflecting low-energy fluvial deposition regimes. The phytolith record is dominated by Pooid grasses that include the most common Near Eastern cereals, such as wheat and barley. Increased phytolith concentrations in terrace fill sediments, as compared to samples from non-terrace deposits nearby, suggest increased plant growth and water availability within the terraces. Whether the terrace systems were used for growing food crops only or whether they were additionally used for grazing cannot be ascertained. Overall, quantitative phytolith analyses in arid environments are well suited to investigate temporal and spatial distributions of plant microfossil concentrations and their relation to human activity or paleoenvironmental conditions.
The northeast-striking Axial and Bootheel faults (AF and BHF) in the central USA are components of the New Madrid seismic zone (NMSZ) fault complex, source of M > 7 earthquakes in 1811–1812. Previous ...work shows Holocene displacement of the AF and BHF to be primarily right-lateral strike-slip movement west and south of the NMSZ restraining bend. In this study, treads of two Late Pleistocene alluvial terraces of the Mississippi River, the 14–16 ka Kennett and the 12 ka Morehouse terraces, were used as structural datums to assess any long-wavelength vertical component of deformation across these two faults. Using 10 m-resolution LiDAR, we constructed a best-fit polynomial trend surface of these terrace treads. Our results reveal a subtle ≤4 m-deep, 40 km-wide, 190 km-long, topographic trough. In the south, it corresponds to the southern segment of the AF and parallels the BHF for 50 km. Farther north it corresponds to a syncline in subsurface Paleozoic strata 10 to 20 km northwest of and parallel to the BHF.
The trough axis crosses obliquely down-valley from the younger Morehouse terrace to the older Kennett terrace and does not correspond to major drainages. Significantly, the Malden-Bernie fluvial scarp separating the two terraces continues into the trough but is down-warped, inconsistent with an erosional origin of the trough. Along the southern segment of the trough, the older Kennett tread is topographically lower than the Morehouse tread, but relict Kennett braided channels were not buried during deposition of younger Morehouse alluvium. This suggests the Kennett terrace tectonically subsided along the trough after Morehouse terrace deposition. We interpret this trough as a subtle syncline along the western margin of the NMSZ restraining bend that developed in response to down-on-the-northwest fault movement after deposition of Morehouse alluvium.
•LiDAR analyses reveal a fault-parallel trough on alluvial terraces in the New Madrid seismic zone.•Polynomial surfaces fit to LiDAR topography show a subtle trough 4 m-deep, 40 km-wide, 190 km-long.•Trough length suggests the trough-parallel Bootheel fault may pose a significant seismic hazard.
Acid mine drainage (AMD) is harmful to the environment and human health. Microorganisms-mineral interactions are responsible for AMD generation but can also remediate AMD contamination. Understanding ...the microbial response to AMD irrigation will reveal microbial survival strategies and provide approaches for AMD remediation. A terrace with sharp geochemical gradients caused by AMD flooding were selected to study the microbial response to changes in environmental parameters related to AMD contamination. AMD intrusion reduced soil microbial community diversity and further changed phylogenetic clustering patterns along the terrace gradient. We observed several genera seldom reported in AMD-related environments (i.e., Corynebacterium, Ochrobactrum, Natronomonas), suggesting flexible survival strategies such as nitrogen fixation, despite the poor nutritional environment. A co-occurrence network of heavily-contaminated fields was densely connected. The phyla Proteobacteria, Acidobacteria, Chloroflexi, and Euryarchaeota were all highly interconnected members, which may affect the formation of AMD. Detailed microbial response to different soil characterizations were highlighted by random forest model. Results revealed the top three parameters influencing the microbial diversity and interactions were pH, Fe(III), and sulfate. Various acidophilic Fe- and S-metabolizing bacteria were enriched in the lower fields, which were heavily contaminated by AMD, and more neutrophiles prevailed in the less-contaminated upper fields. Many indicator species in the lower fields were identified, including Desulfosporosinus, Thermogymnomonas, Corynebacterium, Shewanella, Acidiphilium, Ochrobactrum, Leptospirillum, and Allobaculum, representing acid-tolerant bacteria community in relevant environment. The detection of one known sulfate-reducing bacteria (i.e., Desulfosporosinus) suggested that biotic sulfate reduction may occur in acidic samples, which offers multiple advantages to AMD contamination treatment. Collectively, results suggested that the geochemical gradients substantially altered the soil microbiota and enriched the relevant microorganisms adapted to the different conditions. These findings provide mechanistic insights into the effects of contamination on the soil microbiota and establish a basis for in situ AMD bioremediation strategies.
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•A terrace with sharp geochemical gradients caused by AMD flooding were selected.•AMD intrusion reduced soil microbial community diversity and phylogenetic interactions.•Microbe showed flexible survival strategies in the poor nutritional environment.•pH, Fe(III), and sulfate were main factors influencing the soil microbial community.•Many acid-tolerant microorganisms were identified in the heavily contaminated fields.
This work revealed the soil microbial community diversity and phylogenetic interactions in response to the terrace gradient irrigated by AMD irrigation.
Ancient terraced lands are considered badlands without profitable utilization except for urbanization. Nevertheless, this attitude prevents further agricultural utilization in addition to the loss of ...archaeological data. The study hypothesizes that the main influencing part in these systems is the retaining walls (RW). An analysis of their current influence on soil fertility, stability, and hydrology will indicate their adequate reclamation strategy. The objectives are to gather the influences and correlate them to the RW constructional state. In the Yeroham Hills, three parallel located terraced systems (one on the Wadi Shualim channel and the other, which is located on its banks) were studied. Their ancient agricultural utilization was dated, after in‐site excavations, to the Roman until early Islamic eras. Ten representative RWs were chosen, five from each terraced system. Their influences on the soil fertility, hydrology, and physical properties of the adjacent soil and 2 m ahead (the terrace) were studied. The finding indicates that the RW serves as a physical ecosystem engineer with positive influences on soil organic matter (0.5% higher content compared to the terrace) and land stability properties (maturated soil biocrust and higher aggregate stability). Comparison of the finding from both terraced irrigation systems, which differ in their conservation state, enables to determine the agricultural utilization and land stabilization after an adequate reclamation strategy, which is based on the RWs constructional parameters analyzed in‐site, and adaption to the current floodwater paths. The study's principles and analysis scheme enable the study and conservation of similar areas worldwide for increased utilization and profitability.
Runoff response to multiple land‐use changes and climate perturbations is distinct, and the main influencing factors vary significantly in different regions. However, few have simultaneously ...considered the effects of multiple land use changes (vegetation cover changes, terraces and check‐dams construction, and urban expansion) and climatic perturbations (precipitation, potential evapotranspiration, and temperature) on runoff and constructed separate expressions for distinct study areas. This article attempted to determine the main influencing factors of runoff according to the fitting function in the eight subregions of the middle Yellow River (MYR), construct the expressions between the controlling parameter in the Budyko framework and the main factors, and quantify the contribution of climate factors and land use changes to runoff by combining the elasticity coefficient in each subregion. The results indicated that climate factors and land use changes could significantly impact controlling parameters, and there were differences between regions. Climate change promoted an increase in runoff, while land use change promoted its reduction, and the reduction value outweighed its increase. In terms of land use changes, increasing vegetation coverage could suppress runoff reduction, while constructing terraces and check‐dams could promote its reduction. The urban expansion benefited runoff collection and, therefore, could suppress runoff reduction. Its absolute contribution rate exceeded 200% in apparent urban expansion areas. In addition, the contribution rates of land use to runoff changes in the northern arid and semi‐arid regions were significantly higher than those in the southern, and they were more sensitive to land use changes. The research results can provide a reference for analysing the runoff response to different land‐use changes and can further advance people's understanding of the water cycle.
Climate change promotes an increase in runoff, while land use change promotes its reduction, and the reduction value outweighs its increase. Increasing vegetation coverage and urban expansion can suppress runoff reduction, while constructing terraces and check‐dams can promote reduction. The runoff changes in the arid and semi‐arid regions in the northern are more sensitive to land use changes.
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