| 1. |
- Zhang, Guojie, et al.
(författare)
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Comparative genomics reveals insights into avian genome evolution and adaptation
- 2014
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Ingår i: Science. - : American Association for the Advancement of Science (AAAS). - 0036-8075 .- 1095-9203. ; 346:6215, s. 1311-1320
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Tidskriftsartikel (refereegranskat)abstract
- Birds are the most species-rich class of tetrapod vertebrates and have wide relevance across many research fields. We explored bird macroevolution using full genomes from 48 avian species representing all major extant clades. The avian genome is principally characterized by its constrained size, which predominantly arose because of lineage-specific erosion of repetitive elements, large segmental deletions, and gene loss. Avian genomes furthermore show a remarkably high degree of evolutionary stasis at the levels of nucleotide sequence, gene synteny, and chromosomal structure. Despite this pattern of conservation, we detected many non-neutral evolutionary changes in protein-coding genes and noncoding regions. These analyses reveal that pan-avian genomic diversity covaries with adaptations to different lifestyles and convergent evolution of traits.
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| 2. |
- Feng, Shaohong, et al.
(författare)
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Dense sampling of bird diversity increases power of comparative genomics
- 2020
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Ingår i: Nature. - : Springer Science and Business Media LLC. - 0028-0836 .- 1476-4687. ; 587:7833
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Tidskriftsartikel (refereegranskat)abstract
- Whole-genome sequencing projects are increasingly populating the tree of life and characterizing biodiversity(1-4). Sparse taxon sampling has previously been proposed to confound phylogenetic inference(5), and captures only a fraction of the genomic diversity. Here we report a substantial step towards the dense representation of avian phylogenetic and molecular diversity, by analysing 363 genomes from 92.4% of bird families-including 267 newly sequenced genomes produced for phase II of the Bird 10,000 Genomes (B10K) Project. We use this comparative genome dataset in combination with a pipeline that leverages a reference-free whole-genome alignment to identify orthologous regions in greater numbers than has previously been possible and to recognize genomic novelties in particular bird lineages. The densely sampled alignment provides a single-base-pair map of selection, has more than doubled the fraction of bases that are confidently predicted to be under conservation and reveals extensive patterns of weak selection in predominantly non-coding DNA. Our results demonstrate that increasing the diversity of genomes used in comparative studies can reveal more shared and lineage-specific variation, and improve the investigation of genomic characteristics. We anticipate that this genomic resource will offer new perspectives on evolutionary processes in cross-species comparative analyses and assist in efforts to conserve species. A dataset of the genomes of 363 species from the Bird 10,000 Genomes Project shows increased power to detect shared and lineage-specific variation, demonstrating the importance of phylogenetically diverse taxon sampling in whole-genome sequencing.
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| 3. |
- Chen, Sijie, et al.
(författare)
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Inverse Estimation of Soil Hydraulic Parameters in a Landslide Deposit Based on a DE-MC Approach
- 2022
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Ingår i: Water. - : MDPI AG. - 2073-4441. ; 14:22
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Tidskriftsartikel (refereegranskat)abstract
- Extreme rainfall is a common triggering factor of landslide disasters, for infiltration and pore water pressure propagation can reduce suction stress and shear strength at the slip surface. The subsurface hydrological model is an essential component in the early-warning system of rainfall-triggered landslides, whereas soil moisture and pore water pressure simulated by the Darcy–Richards equation could be significantly affected by uncertainties in soil hydraulic parameters. This study conducted an inverse analysis of in situ measured soil moisture in an earthquake-induced landslide deposit, and the soil hydraulic parameters were optimized with the Differential Evolution Markov chain Monte Carlo method (DE-MC). The DE-MC approach was initially validated with a synthetic numerical experiment to demonstrate its effectiveness in finding the true soil hydraulic parameters. Besides, the soil water characteristic curve (SWCC) and hydraulic conductivity function (HCF) described with optimized soil hydraulic parameter sets had similar shapes despite the fact that soil hydraulic parameters may be different. Such equifinality phenomenon in inversely estimated soil hydraulic parameters, however, did not affect the performance of simulated soil moisture dynamics in the synthetic numerical experiment. The application of DE-MC to a real case study of a landslide deposit also indicated satisfying model performance in terms of accurate match between the in situ measured soil moisture content and ensemble of simulations. In conclusion, based on the satisfying performance of simulated soil moisture and the posterior probability density function (PDF) of parameter sets, the DE-MC approach can significantly reduce uncertainties in specified prior soil hydraulic parameters. This study suggested the integration of the DE-MC approach with the Darcy–Richards equation for an accurate quantification of unsaturated soil hydrology, which can be an essential modeling strategy to support the early-warning of rainfall-triggered landslides.
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| 4. |
- Gao, Hongkai, et al.
(författare)
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Stepwise modeling and the importance of internal variables validation to test model realism in a data scarce glacier basin
- 2020
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Ingår i: Journal of Hydrology. - : Elsevier BV. - 0022-1694. ; 591
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Tidskriftsartikel (refereegranskat)abstract
- Model realism is of vital importance in science of hydrology, in terms of realistic representation of hydrological processes and reliability of future prediction. Here, we employed a stepwise modeling approach that leverages flexible model structures and multi-source observations for robust streamflow simulation and internal variables validation with improved model realism. This framework is demonstrated in Yigong Zangbu River (YZR) basin, a data scarce glacier basin in the upper Brahmaputra River. We designed six experiments (Exp1–6) to use modeling as a tool to understand hydrological processes in this remote cold basin with extremely high altitude. In Exp1, we started with a distributed rainfall-runoff model (FLEXD) - representing the case that snow and glacier processes were ignored. Then, we stepwisely added snow and glacier processes into FLEXD, denoted as FLEXD-S (Exp2) and FLEXD-SG (Exp3), respectively, and such improvement of model structure led to significantly improved streamflow estimates. To explore the impact of different precipitation forcing on model performance, FLEXD-SG was driven by Theissen average (Exp3) and three individual stations’ precipitation (Exp4–6). The model realism was tested by observed hydrograph, snow cover area (SCA) and glacier mass balance (GMB). Results showed that a robust and realistic hydrological modeling system was achieved in Exp6. In this modeling study, we learned that: 1) stepwise modeling is effective in investigating catchment behavior, and snow and glacier melting are the dominant hydrological processes in the YZR basin; 2) internal variables validation is beneficial to test model realism in data scarce basin; 3) the FLEXD-SG model calibrated by only one year hydrograph is sufficient to reproduce snow and glacier variations; 4) precipitation of a single station as forcing data could outperform Theissen average; 5) based on the well tested model configuration in Exp6, we analyzed simulated results, and reconstructed the long term hydrography (1961–2013), to support the potential competence for decision making on water resources management in practice. The proposed framework may significantly improve our skills in hydrological modeling over data-poor regions.
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| 5. |
- Lei, Xiaoqin, et al.
(författare)
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A generalized interpolation material point method for modelling coupled thermo-hydro-mechanical problems
- 2021
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Ingår i: Computer Methods in Applied Mechanics and Engineering. - : Elsevier BV. - 0045-7825. ; 386
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Tidskriftsartikel (refereegranskat)abstract
- This paper proposes a Generalized Interpolation Material Point Method (GIMP) for modelling coupled thermo-hydro-mechanical (THM) processes within unsaturated porous media. The governing equations for the coupled thermo-hydro-mechanical problems are derived based on the conservation laws of mass, momentum and energy, and are discretized within the framework of the explicit three-phase single-point GIMP. The proposed THM-coupled GIMP is validated against available analytical solutions and FEM-based numerical solutions, and is used for simulating a climate-driven slope failure process involving both temperature variation and rainfall infiltration. The proposed THM-coupled GIMP is proved to be capable to capture the fully coupled thermo-hydro-mechanical process within unsaturated porous media associated with large deformations.
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| 6. |
- Shao, Wei, et al.
(författare)
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Reduce uncertainty in soil hydrological modeling : A comparison of soil hydraulic parameters generated by random sampling and pedotransfer function
- 2023
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Ingår i: Journal of Hydrology. - 0022-1694 .- 1879-2707. ; 623
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Tidskriftsartikel (refereegranskat)abstract
- Numerical simulation of unsaturated soil hydrology relies on calibrated soil hydraulic parameters, which are subject to uncertainty due to imperfect information during the inverse modelling. This study investigates the effectiveness of reducing parameter uncertainty using the recently developed Rosetta 3 pedotransfer function. The GLUE method was employed for numerical modeling using the Darcy-Richards equation under two strategies for sampling Mualem-van Genuchten (MvG) parameters: the first uses conventional random generation of MvG parameters (GLUE-random), while the second adopts Rosetta 3 to transfer soil particle composition to MvG parameter (GLUE-Rosetta). Both approaches were used for inverse modeling of 9 typical soils, each with a recommended parameter set defined as true values and associated soil moisture dynamics as observations. The posterior parameters selected with both GLUE-random and GLUE-Rosetta show an equifinality phenomenon. GLUE-random fails to provide well-constrained posterior parameters to recover the pre-defined true values, and its posterior results of soil water characteristic curve (SWCC) and soil hydraulic conductivity function (HCF) are poorly constrained. In contrast, GLUE-Rosetta significantly improves the accuracy of the inversely-estimated soil hydraulic parameters, and the ensemble of posterior SWCC and HCF also encompasses the predefined true curves. The results demonstrate the effectiveness of using Rosetta 3 to reduce the dimensionality of the optimization problem, which results in reliable estimation of soil hydraulic parameters and soil particle compositions. Moreover, GLUE-Rosetta outperforms GLUE-random in predicting soil moisture dynamics under different rainfall intensities. Overall, it is recommended to integrate Rosetta 3 with existing optimization tools to reduce the uncertainty of soil parameters and support more reliable modeling of unsaturated soil hydrology.
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| 7. |
- Shao, Wei, et al.
(författare)
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Reducing uncertainties in hydromechanical modeling with a recently developed Rosetta 3 podeotransfer function
- 2023
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Ingår i: Engineering Geology. - 0013-7952 .- 1872-6917. ; 324
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Tidskriftsartikel (refereegranskat)abstract
- Stability analysis of unsaturated landslide deposits requires reliable estimates of soil moisture and pore water pressure. However, modeled soil moisture and pore water pressure contain substantial uncertainties due to imperfect information on soil hydraulic properties. Due to the relatively high dimensionality, commonly used parameter optimization strategies can be significantly affected by equifinality problems. This study investigates the effectiveness of reducing parameter estimation dimensionality using soil pedo-transfer functions. Specifically, we first estimated soil hydraulic parameters using the traditional Generalized Likelihood Uncertainty Estimation (GLUE) method, with parameters randomly drawn from the entire space (refer to as GLUE-random). In a second strategy, we use the Rosetta 3 pedotransfer function to constrain soil hydraulic parameters (refer to as GLUE-Rosetta). The two methods were tested in a typical landslide deposit with in-situ measured soil moisture dynamics for inverse modeling. The GLUE-random estimated soil hydraulic parameters contained substantial uncertainties –resulting in poorly constrained soil water retention curves (SWCC) and hydraulic conductivity functions (HCF). As a result, the uncertainty bands of pore water pressure and slope stability can cross values with several orders of magnitudes. In contrast, GLUE-Rosetta provided well-constrained SWCC and HCF, which significantly reduce the uncertainties in pore water pressure and slope stability estimates. These results suggest that the Rosetta 3 pedotransfer function can significantly improve the reliability of soil hydraulic parameters by reducing the dimensionality of the optimization problem and high-quality prior information of soil hydraulic properties. In conclusion, Rosetta 3 can enhance the reliability of soil parameters estimates and the reliability of subsurface hydrology, which may benefit the development of landslide early-warning systems.
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