Subgenomic Stability of Progenitor Genomes During Repeated Allotetraploid Origins of the Same Grass Brachypodium hybridum

Both homeologous exchanges and homeologous expression bias are generally found in most allopolyploid species. Whether homeologous exchanges and homeologous expression bias differ between repeated allopolyploid speciation events from the same progenitor species remains unknown. Here, we detected a third independent and recent allotetraploid origin for the model grass Brachypodium hybridum. Our homeologous exchange with replacement analyses indicated the absence of significant homeologous exchanges in any of the three types of wild allotetraploids, supporting the integrity of their progenitor subgenomes and the immediate creation of the amphidiploids. Further homeologous expression bias tests did not uncover significant subgenomic dominance in different tissues and conditions of the allotetraploids. This suggests a balanced expression of homeologs under similar or dissimilar ecological conditions in their natural habitats. We observed that the density of transposons around genes was not associated with the initial establishment of subgenome dominance; rather, this feature is inherited from the progenitor genome. We found that drought response genes were highly induced in the two subgenomes, likely contributing to the local adaptation of this species to arid habitats in the third allotetraploid event. These findings provide evidence for the consistency of subgenomic stability of parental genomes across multiple allopolyploidization events that led to the same species at different periods. Our study emphasizes the importance of selecting closely related progenitor species genomes to accurately assess homeologous exchange with replacement in allopolyploids, thereby avoiding the detection of false homeologous exchanges when using less related progenitor species genomes

Scattered differentiation of unlinked loci across the genome underlines ecological divergence of the selfing grass Brachypodium stacei

Ecological divergence without geographic isolation, as an early speciation process that may lead finally to reproductive isolation through natural selection, remains a captivating topic in evolutionary biology. However, the pattern of genetic divergence underlying this process across the genome may vary between species and mating systems. Here, we present evidence that Brachypodium stacei, an annual and highly selfing grass model species, has undergone sympatric ecological divergence without geographic isolation. Genomic, transcriptomic, and metabolomic analyses together with lab experiments mimicking the two opposite environmental conditions suggest that diploid B. stacei populations have diverged sympatrically in two slopes characterized by distinct biomes at Evolution Canyon I (ECI), Mount Carmel, Israel. Despite ongoing gene flow, primarily facilitated by seed dispersal, the level of gene flow has progressively decreased over time. This local adaptation involves the scattered divergence of many unlinked loci across the total genome that include both coding genes and noncoding regions. Additionally, we have identified significant differential expressions of genes related to the ABA signaling pathway and contrasting metabolome composition between the arid- vs. forest-adapted B. stacei populations in ECI. These results suggest that multiple small loci involved in environmental responses act additively to account for ecological adaptations by this selfing species in contrasting environments

Radiocarbon Dating of Charcoal and Bone Collagen Associated with Early Pottery at Yuchanyan Cave, Hunan Province, China

Yuchanyan Cave in Daoxian County, Hunan Province (People's Republic of China), yielded fragmentary remains of 2 or more ceramic vessels, in addition to large amounts of ash, a rich animal bone assemblage, cobble and flake artifacts, bone tools, and shell tools. The artifacts indicate that the cave was a Late Paleolithic foragers' camp. Here we report on the radiocarbon ages of the sediments based on analyses of charcoal and bone collagen. The best-preserved charcoal and bone samples were identified by prescreening in the field and laboratory. The dates range from around 21,000 to 13,800 cal BP. We show that the age of the ancient pottery ranges between 18,300 and 15,430 cal BP. Charcoal and bone collagen samples located above and below one of the fragments produced dates of around 18,000. These ceramic potsherds therefore provide some of the earliest evidence for pottery making in China.Anthropolog

Microbial assemblies associated with temperature sensitivity of soil respiration along an altitudinal gradient

10 páginas.. 4 figuras.- referencias.- Supplementary data to this article can be found online at https://doi. org/10.1016/j.scitotenv.2022.153257Identifying the drivers of the response of soil microbial respiration to warming is integral to accurately forecasting the carbon-climate feedbacks in terrestrial ecosystems. Microorganisms are the fundamental drivers of soil microbial respiration and its response to warming; however, the specific microbial communities and properties involved in the process remain largely undetermined. Here, we identified the associations between microbial community and temperature sensitivity (Q10) of soil microbial respiration in alpine forests along an altitudinal gradient (from 2974 to 3558 m) from the climate-sensitive Tibetan Plateau. Our results showed that changes in microbial community composition accounted for more variations of Q10 values than a wide range of other factors, including soil pH, moisture, substrate quantity and quality, microbial biomass, diversity and enzyme activities. Specifically, co-occurring microbial assemblies (i.e., ecological clusters or modules) targeting labile carbon consumption were negatively correlated with Q10 of soil microbial respiration, whereas microbial assemblies associated with recalcitrant carbon decomposition were positively correlated with Q10 of soil microbial respiration. Furthermore, there were progressive shifts of microbial assemblies from labile to recalcitrant carbon consumption along the altitudinal gradient, supporting relatively high Q10 values in high-altitude regions. Our results provide new insights into the link between changes in major microbial assemblies with different trophic strategies and Q10 of soil microbial respiration along an altitudinal gradient, highlighting that warming could have stronger effects on microbially-mediated soil organic matter decomposition in high-altitude regions than previously thought.This research was supported by the National Natural Science Foundation of China (32071595 and 41830756). We also thank the Fundamental Research Funds for the Central Universities (Program no. 2662019PY010 and 2662019QD055), Natural Science Fund of Hubei Province (2019CFA094), and the Strategic Priority Research Program (A) of the Chinese Academy of Sciences (Grant No. XDA20040502). We thank Hailong Li for his assistance in field sampling, and Jinhuang Lin for mapping sample locations. M.D-B. is supported by a Ramón y Cajal grant from the Spanish Government (agreement no. RYC2018-025483-I). ReferencesPeer reviewe

Evolutionary origin of genomic structural variations in domestic yaks

Yak has been subject to natural selection, human domestication and interspecific introgression during its evolution. However, genetic variants favored by each of these processes have not been distinguished previously. We constructed a graph-genome for 47 genomes of 7 cross-fertile bovine species. This allowed detection of 57,432 high-resolution structural variants (SVs) within and across the species, which were genotyped in 386 individuals. We distinguished the evolutionary origins of diverse SVs in domestic yaks by phylogenetic analyses. We further identified 334 genes overlapping with SVs in domestic yaks that bore potential signals of selection from wild yaks, plus an additional 686 genes introgressed from cattle. Nearly 90% of the domestic yaks were introgressed by cattle. Introgression of an SV spanning the KIT gene triggered the breeding of white domestic yaks. We validated a significant association of the selected stratified SVs with gene expression, which contributes to phenotypic variations. Our results highlight that SVs of different origins contribute to the phenotypic diversity of domestic yaks

SoccerNet 2023 Challenges Results

peer reviewedThe SoccerNet 2023 challenges were the third annual video understanding challenges organized by the SoccerNet team. For this third edition, the challenges were composed of seven vision-based tasks split into three main themes. The first theme, broadcast video understanding, is composed of three high-level tasks related to describing events occurring in the video broadcasts: (1) action spotting, focusing on retrieving all timestamps related to global actions in soccer, (2) ball action spotting, focusing on retrieving all timestamps related to the soccer ball change of state, and (3) dense video captioning, focusing on describing the broadcast with natural language and anchored timestamps. The second theme, field understanding, relates to the single task of (4) camera calibration, focusing on retrieving the intrinsic and extrinsic camera parameters from images. The third and last theme, player understanding, is composed of three low-level tasks related to extracting information about the players: (5) re-identification, focusing on retrieving the same players across multiple views, (6) multiple object tracking, focusing on tracking players and the ball through unedited video streams, and (7) jersey number recognition, focusing on recognizing the jersey number of players from tracklets. Compared to the previous editions of the SoccerNet challenges, tasks (2-3-7) are novel, including new annotations and data, task (4) was enhanced with more data and annotations, and task (6) now focuses on end-to-end approaches. More information on the tasks, challenges, and leaderboards are available on https://www.soccer-net.org. Baselines and development kits can be found on https://github.com/SoccerNet

The Emerging Regulatory Role of Circular RNAs in Periodontal Tissues and Cells

Periodontitis is a chronic complex inflammatory disease associated with a destructive host immune response to microbial dysbiosis, leading to irreversible loss of tooth-supporting tissues. Regeneration of functional periodontal soft (periodontal ligament and gingiva) and hard tissue components (cementum and alveolar bone) to replace lost tissues is the ultimate goal of periodontal treatment, but clinically predictable treatments are lacking. Similarly, the identification of biomarkers that can be used to accurately diagnose periodontitis activity is lacking. A relatively novel category of molecules found in oral tissue, circular RNAs (circRNAs) are single-stranded endogenous, long, non-coding RNA molecules, with covalently circular-closed structures without a 5’ cap and a 3’ tail via non-classic backsplicing. Emerging research indicates that circRNAs are tissue and disease-specific expressed and have crucial regulatory functions in various diseases. CircRNAs can function as microRNA or RNA binding sites or can regulate mRNA. In this review, we explore the biogenesis and function of circRNAs in the context of the emerging role of circRNAs in periodontitis pathogenesis and the differentiation of periodontal cells. CircMAP3K11, circCDK8, circCDR1as, circ_0062491, and circ_0095812 are associated with pathological periodontitis tissues. Furthermore, circRNAs are expressed in periodontal cells in a cell-specific manner. They can function as microRNA sponges and can form circRNA–miRNA–mRNA networks during osteogenic differentiation for periodontal-tissue (or dental pulp)-derived progenitor cells

The influence of basicity and TiO2 on the crystallization behavior of high Ti-bearing slags

China has abundant vanadium-titanium magnetite resources. It is important to extract the Fe, Ti and V elements from vanadium-titanium magnetite by recycling. The HIsmelt smelting reduction process is an effective method to smelt vanadium-titanium magnetite. In the present study, the phase composition of the high-titanium slag produced under different temperature and composition conditions under the HIsmelt smelting reduction process was first analyzed via thermodynamic calculations. An experimental scheme was further designed to study the influence of different factors on the crystallization behavior of the high-titanium slag. The thermodynamic calculation results showed that perovskite and pseudobrookite are the main enrichment phases of the high-titanium slag during the slag cooling phase. With the increase in the TiO content, the main titanium-rich phase changed from perovskite to pseudobrookite. As the basicity decreased, the main titanium-rich phase that precipitated was pseudobrookite. The experimental results were basically consistent with the thermodynamic results. With the decrease in the TiO content, the main titanium-rich phase in the slag evolved from plate-like anosovite to columnar or dendritic perovskite, and the size of the precipitated crystals decreased. When the content of TiO decreased to 23%, the precipitate morphology of some perovskite crystals changed from columnar to dendritic. As the basicity of the slag decreased, the titanium-rich phase in the slag changed from perovskite to anosovite. When the basicity of the slag was 0.8, anosovite became the only titanium-rich phase. Anorthite was also formed and had a thin rod shape. In addition, with the decrease in the MgO/AlO ratio, the composition of anosovite changed from (MgTiO)·(AlTiO) to (MgTiO)·(AlTiO). The research results provide a reference for the further understanding of the crystallization behavior of the high-titanium slag produced by the HIsmelt smelting reduction process and the utilization of the titanium-rich slag as a resource

Review of viscosity prediction models of liquid pure metals and alloys

Viscosity is an important property which could determine the flow liquid metal characteristics and reflect the liquidus structure. Therefore, the existence of an accurate model is necessary to calibrate the experimental measurement value of viscosity. At present, many models have been proposed to estimate the viscosity of pure liquid metal, the temperature dependence of viscosity and the viscosity of multicomponent alloy systems. In this paper, a number of the familiar models are given, and their fundamental modelling theory, model characteristics and applicability are adequately discussed. The general semi-empirical models which have been very successful in predicting the viscosity of pure liquid metal are divided into Andrade and Eyring two branches. The common multivariate melt viscosity prediction models are mostly based on the fundamental molecular theory method, which combines the thermodynamic parameters and achieves good validity. It is expected in the final that the corresponding viscosity prediction model of phase diagram might be more likely to replace the independent general prediction equation in the future