We present a simulation for the reconstruction of the rotational quantum state of linear molecules to retrieve the density matrix. An optimal approach in the sense of minimal error limit is proposed, in which a variab...We present a simulation for the reconstruction of the rotational quantum state of linear molecules to retrieve the density matrix. An optimal approach in the sense of minimal error limit is proposed, in which a variable set of angular frequency is properly chosen and the least square inversion is then applied. This approach of reconstruction from time-dependent molecular-axis angular distribution is proved adaptable for various object states, which has a good numerical stability independent of the selected rotational space.展开更多
We establish a reconstruction approach for the rotational quantum state of linear molecules possessing a magnetic manifold. Our approximate method contains an iteration with generalized matrix inverses, processing the...We establish a reconstruction approach for the rotational quantum state of linear molecules possessing a magnetic manifold. Our approximate method contains an iteration with generalized matrix inverses, processing the tomographic integral of the time-dependent molecular-axis distribution in a polar angle. As shown in a simulated example for an alignment state, the density matrix is determined in a high fidelity. An analytic tomographic formula is also derived for the symmetric top rotation. The state coherent in the quantum space of both the angular momentum and its magnetic projection can be approximately retrieved from the observable time-resolved solid-angle distribution of the molecular axis.展开更多
Our current understanding of how species have evolved is mainly based on comparative phylogenetic methods,which use phylogenies to infer the evolution of traits.The development of ancestral state reconstruction(ASR)me...Our current understanding of how species have evolved is mainly based on comparative phylogenetic methods,which use phylogenies to infer the evolution of traits.The development of ancestral state reconstruction(ASR)methods has provided the tools to reconstruct trait evolution,which are widely used in fields like evolutionary biology,macroecology and paleontology.As there are different elements involved in those analyses,with different levels of uncertainty(i.e.relating to branch length estimation,trait coding,statistical framework,taxon sampling or software),the various combinations of these elements likely have a strong impact on the reconstruction of the evolution of traits,potentially leading to opposite conclusions.To assess the impact of these different elements in ASR,we performed a set of analyses,including all possible combinations of such elements and using the evolution of migratory behavior in Sylvia warblers as a case study,which was coded as a continuous or as a discrete character.Our results show that taxon sampling,character coding,tree shape,statistical framework and software all significantly affect ASR,both individually and in combination.Not all reconstructed tree nodes show discrepancies,but in the critical ones most pairwise comparisons between analyses lead to conflicting and unexpectedly antagonistic results(zero migration vs fully migratory),thus challenging interpretations of trait evolution.We propose some possible solutions to partly inform decisions,involving the method selection and the incorporation of biological or fossil evidence regarding how traits evolve,but our results demand serious rethinking about how the research community currently uses ASR.展开更多
Certain deterministic nonlinear systems may show chaotic behavior. We consider the motion of qualitative information and the practicalities of extracting a part from chaotic experimental data. Our approach based on a ...Certain deterministic nonlinear systems may show chaotic behavior. We consider the motion of qualitative information and the practicalities of extracting a part from chaotic experimental data. Our approach based on a theorem of Takens draws on the ideas from the generalized theory of information known as singular system analysis. We illustrate this technique by numerical data from the chaotic region of the chaotic experimental data. The method of the singular-value decomposition is used to calculate the eigenvalues of embedding space matrix. The corresponding concrete algorithm to calculate eigenvectors and to obtain the basis of embedding vector space is proposed in this paper. The projection on the orthogonal basis generated by eigenvectors of timeseries data and concrete paradigm are also provided here. Meanwhile the state space reconstruction technology of different kinds of chaotic data obtained from dynamical system has also been discussed in detail.展开更多
The state space, reconstruction is the major important quantitative index for describing non-linear chaotic time series. Based on the work of many scholars, such as: AT. H. Packard, F. Takens, M. Casdagli, J. F. Gibso...The state space, reconstruction is the major important quantitative index for describing non-linear chaotic time series. Based on the work of many scholars, such as: AT. H. Packard, F. Takens, M. Casdagli, J. F. Gibson, CHEN Yu-shu et al, the state space was reconstructed using the method of Legendre coordinate. Several different scaling regimes for lag time tau were identified. The influence for state space reconstruction of lag time tau was discussed. The result tells us that is a good practical method for state space reconstruction.展开更多
We propose a method for reconstructing the distributed forward state of polarization(SOP)in single-mode fibers(SMFs)to solve the problem of an unpredictable blind box of SOP evolution in many applications such as fibe...We propose a method for reconstructing the distributed forward state of polarization(SOP)in single-mode fibers(SMFs)to solve the problem of an unpredictable blind box of SOP evolution in many applications such as fiber-optic parametric amplification systems.Using polarization-sensitive optical frequency domain reflectometry(POFDR)and a quaternion-based model to describe polarization changes,our approach achieves high spatial resolution and precision.By an improved iterative fitting algorithm,the mean square error(MSE)of forward SOP reconstruction for approximately 100 consecutive measurement points was reduced to below 0.1%.This method enables visualization of SOP dynamics along the fiber,offering critical insights for polarization-dependent systems.展开更多
Rhododendron is famous for its high ornamental value.However,the genus is taxonomically difficult and the relationships within Rhododendron remain unresolved.In addition,the origin of key morphological characters with...Rhododendron is famous for its high ornamental value.However,the genus is taxonomically difficult and the relationships within Rhododendron remain unresolved.In addition,the origin of key morphological characters with high horticulture value need to be explored.Both problems largely hinder utilization of germplasm resources.Most studies attempted to disentangle the phylogeny of Rhododendron,but only used a few genomic markers and lacked large-scale sampling,resulting in low clade support and contradictory phylogenetic signals.Here,we used restriction-site associated DNA sequencing(RAD-seq)data and morphological traits for 144 species of Rhododendron,representing all subgenera and most sections and subsections of this species-rich genus,to decipher its intricate evolutionary history and reconstruct ancestral state.Our results revealed high resolutions at subgenera and section levels of Rhododendron based on RAD-seq data.Both optimal phylogenetic tree and split tree recovered five lineages among Rhododendron.Subg.Therorhodion(cladeⅠ)formed the basal lineage.Subg.Tsutsusi and Azaleastrum formed cladeⅡand had sister relationships.CladeⅢincluded all scaly rhododendron species.Subg.Pentanthera(cladeⅣ)formed a sister group to Subg.Hymenanthes(cladeⅤ).The results of ancestral state reconstruction showed that Rhododendron ancestor was a deciduous woody plant with terminal inflorescence,ten stamens,leaf blade without scales and broadly funnelform corolla with pink or purple color.This study shows significant distinguishability to resolve the evolutionary history of Rhododendron based on high clade support of phylogenetic tree constructed by RAD-seq data.It also provides an example to resolve discordant signals in phylogenetic trees and demonstrates the application feasibility of RAD-seq with large amounts of missing data in deciphering intricate evolutionary relationships.Additionally,the reconstructed ancestral state of six important characters provides insights into the innovation of key characters in Rhododendron.展开更多
Recent years have witnessed a proliferation of quantitative methods for biogeographic inference. In particular, novel parametric approaches represent exciting new opportunities for the study of range evolution. Here, ...Recent years have witnessed a proliferation of quantitative methods for biogeographic inference. In particular, novel parametric approaches represent exciting new opportunities for the study of range evolution. Here, we review a selection of current methods for biogeographic analysis and discuss their respective properties. These methods include generalized parsimony approaches, weighted ancestral area analysis, dispersal-vicariance analysis, the dispersal--extinction--cladogenesis model and other maximum likelihood approaches, and Bayesian stochastic mapping of ancestral ranges, including a novel approach to inferring range evolution in the context of island biogeography. Some of these methods were developed specifically for problems of ancestral range reconstruction, whereas others were designed for more general problems of character state reconstruction and subsequently applied to the study of ancestral ranges. Methods for reconstructing ancestral history on a phylogenetic tree differ not only in the types of ancestral range states that are allowed, but also in the various historical events that may change the ancestral ranges. We explore how the form of allowed ancestral ranges and allowed transitions can both affect the outcome of ancestral range estimation. Finally, we mention some promising avenues for future work in the development of model-based approaches to biogeographic analysis.展开更多
Two varieties of Bouteloua aristidoides have been recognized,the widespread var.aristidoides and the more narrowly distributed var.arizonica.The two varieties differ in inflorescence form even more than that seen betw...Two varieties of Bouteloua aristidoides have been recognized,the widespread var.aristidoides and the more narrowly distributed var.arizonica.The two varieties differ in inflorescence form even more than that seen between many other closely related species of Bouteloua.We therefore asked whether these taxa might be better regarded as distinct species.A total of 93 vouchers were studied by using morphometry(principal components analysis and statistical tests),leaf micromorphology,ancestral state reconstruction,and/or molecular(ITS,trnC-rpoB and trnT-L-F)phylogenetic analyses.Except from the ITS tree,all results supported elevation of B.aristidoides var.arizonica to the rank of species,thus the new combination Bouteloua arizonica(M.E.Jones)L.F.Cuellar&Columbus comb.nov.et stat.nov.,is proposed.Chloroplast and combined chloroplast-nuclear molecular trees depicted var.arizonica as monophyletic(even in sympatric populations with var.aristidoides)and reveals phylogenetic structure within var.aristidoides for which the presence of new undescribed varieties of B.aristidoides(different from B.arizonica)is addressed.B.arizonica differs from B.aristidoides in having fewer branches per inflorescence,a bigger branch with more spikelets,and a shorter branch extension.Scanning electron microscopy revealed the presence of papillae on leaves of B.arizonica as a clear synapomorphy.Growing mature plants of B.arizonica from seeds in a greenhouse revealed a strong cleistogamous nature for this species for which gene flow in sympatric populations with B.aristidoides seems unlikely.A taxonomic treatment and distribution map for identification of B.arizonica is provided.展开更多
Background: This paper describes the chick plumage of spurfowl(Pternistis) and francolin(Francolinus, Dendroperdix Peliperdix and Scleroptila) chicks, tests its significance for phylogenetic relationships and also exp...Background: This paper describes the chick plumage of spurfowl(Pternistis) and francolin(Francolinus, Dendroperdix Peliperdix and Scleroptila) chicks, tests its significance for phylogenetic relationships and also explores the patterns of character evolution in the francolin and spurfowl lineages.Previously regarded as monophyletic, the two evolutionar?ily distant clades are now divided into five genera.Questions considered were whether chick plumage supports the dichotomy between spurfowls and francolins and what role habitat matching plays.Methods: The study was based mainly on photographs of chick skins from the American Museum of Natural History and the Natural History Museum at Tring.Eight plumage characters were selected for comparative scoring, summa?rised in a matrix.These characters were subsequently analysed phylogenetically and their evolution was traced on the existing molecular phylogeny using a parsimony approach.Results: Based on chick plumage the phylogeny of species groups among francolins and spurfowls, was largely unresolved possibly ascribed to a high degree of symplesiomorphy inherent among the Phasianids.This possibly could have resulted in a high degree of polytomy particularly among the spurfowls and francolins.Furthermore, the ancestral state reconstructions revealed high prevalence of symplesiomorphic states and reversals which do not help in the classification of groups.Although the differences are described that separate some African francolins from spurfowls, other francolins(in Asia and Africa) share remarkably similar characteristics with spurfowls.Plain dark dorsal plumage is probably advantageous for avoiding detection by predators in forests, while facial stripes optimise the breaking of body shapes in dense grass cover(as in Scleroptila spp.) and semi?striped faces are advantageous for stationary camouflage under tree and bush cover(as in Pternistis spp.).Conclusions: Although symplesiomorphy is a hereditary explanation for downy colours and patterns, the traits rel?evant for habitat matching are combined in a manner which is determined(adaptation) by natural selection.展开更多
Based on the Bayesian information criterion, this paper proposes the improved local linear prediction method to predict chaotic time series. This method uses spatial correlation and temporal correlation simultaneously...Based on the Bayesian information criterion, this paper proposes the improved local linear prediction method to predict chaotic time series. This method uses spatial correlation and temporal correlation simultaneously. Simulation results show that the improved local linear prediction method can effectively make multi-step and one-step prediction of chaotic time series and the multi-step prediction performance and one-step prediction accuracy of the improved local linear prediction method are superior to those of the traditional local linear prediction method.展开更多
Despite increasing knowledge of barnyardgrass(Echinochloa crus-galli) interference with rice, relatively little is known how endophytes improve the ability of rice against barnyardgrass stress. Here, we provided a det...Despite increasing knowledge of barnyardgrass(Echinochloa crus-galli) interference with rice, relatively little is known how endophytes improve the ability of rice against barnyardgrass stress. Here, we provided a detailed temporal characterization of rice root-associated microbiomes during co-cultivation with barnyardgrass and a comparison with the microbiomes of weed-free rice plants. Alpha diversity analysis indicated that barnyardgrass had the opposite effects on endophytic bacteria and fungi in rice roots, in terms of the community diversity, richness and coverage at the rice seedling stage. Principal coordinate analysis showed that barnyardgrass had only a minor effect on the community composition of endophytes in rice roots at the rice seedling stage, but showed a significant and maximum interference at the heading stage. Rice recruited many endophytes to resist biotic stress from barnyardgrass, especially for fungi. PICRUSt(phylogenetic investigation of communities by reconstruction of unobserved states) predictive analysis indicated that 23 metabolic pathways of bacteria were overrepresented in rice. In addition, the main trophic mode of fungi was pathotroph according to FUNGuild analysis. A positive correlation between bacteria and fungi in rice roots was found via network analysis. Anaeromyxobacter, Azospira and Pseudolabrys were the vital bacteria, Phaeosphaeria and Funneliformis were the dominant fungi in maintaining the stability of the ecological network. These results provided data and a theoretical basis for the in-depth understanding of what role endophytes play in rice resistance to barnyardgrass stress and will have implications on improving the resistance of rice against biotic stress using root microbiota.展开更多
The chaotic nonlinear time series method is applied to analyze the sliver irregularity in textile processing.Because it unifies the system's determinacy and randomness,it seems more adaptive to describe the sliver...The chaotic nonlinear time series method is applied to analyze the sliver irregularity in textile processing.Because it unifies the system's determinacy and randomness,it seems more adaptive to describe the sliver irregularity than conventional methods.Firstly,the chaos character,i.e.fractal dimension,positive Lyapunov exponent,and state space parameters,including time delay and reconstruction dimension,are calculated respectively.As a result,a positive Lyapunov exponent and a fractal dimension are obtained,which demonstrates that the system is chaotic in fact.Secondly,both local linear forecast and global forecast models based on the reconstructed state are adopted to predict a segment part of the sliver irregularity series,which proves the validity of this analysis.Therefore,the sliver irregularity series shows the evidence of chaotic phenomena,and thus laying the theoretical foundation for analyzing and modeling the sliver irregularity series by applying the chaos theory,and providing a new way to understand the complexity of the sliver irregularity much better.展开更多
A linear quadric (LQ) optimal speed control algorithm is proposed for the speed control of a pump controlled motor hydraulic system. The control theme consists of optimal state feedback and disturbing compensation bas...A linear quadric (LQ) optimal speed control algorithm is proposed for the speed control of a pump controlled motor hydraulic system. The control theme consists of optimal state feedback and disturbing compensation based on observation. The optimal state feedback bases on LQ cost function. The disturbing compensation is realized through reconstructing the state of load torque. A series of simulation are performed, and the results show that the control performance is satisfactory and can be maintained under changes of load torque.展开更多
Reconstructing climate states during geological periods is a key focus in studying Earth system evolution. Substantial progress has been achieved in reconstructing paleoclimate and paleoenvironment using both Earth sy...Reconstructing climate states during geological periods is a key focus in studying Earth system evolution. Substantial progress has been achieved in reconstructing paleoclimate and paleoenvironment using both Earth system models and paleoclimate proxies. However, current paleoclimate reconstructions face several challenges: the accuracy of Earth system model simulations relies on model parameter settings. Paleoclimate proxy data exhibit significant variability across different periods and regions, and proxy data are often sparse, hindering the accuracy and global relevance of proxy-based reconstructions.Addressing the pros and cons of these methods, paleoclimate data assimilation can effectively integrate Earth system models and paleoclimate proxy data, enhancing the precision and global relevance of reconstructions. Using approaches such as the ensemble Kalman filter as an example, this paper introduces the principles of paleoclimate data assimilation and reviews recent advancements in reconstructing paleoclimate states using these techniques. Paleoclimate data assimilation offers new insights and advanced techniques for paleoclimate reconstruction, with potential applications extending to the entire Cenozoic, Mesozoic, and even Paleozoic eras. These applications could deepen our understanding of the past climatic backgrounds of extreme climate events such as glacial-interglacial cycles, hyperthermals, and oceanic anoxic events, providing a reference for predicting future climate change.展开更多
An unknown state of a quantum system S is usually determined by repeatedly measuring a set of non-commuting observables. The state can also be obtained from the repeated measurements of a single separable observable w...An unknown state of a quantum system S is usually determined by repeatedly measuring a set of non-commuting observables. The state can also be obtained from the repeated measurements of a single separable observable when the system S interacts with an assistant system A in a known state. In this paper, we study the quantum state tomography of a three-level atom （the system S） interacting with two radiation fields as the assistant system A. We obtain the initial state of S by repeatedly measuring a separable observable O = Sz n1 n2, in which Sz is the atom operator, and hi and h2 are the photon number operators of the two radiation fields. We achieve the one-to-one mapping M between the initial density matrix of the system S and the measured results of the single separable observable. We also give a concrete numerical example.展开更多
文摘We present a simulation for the reconstruction of the rotational quantum state of linear molecules to retrieve the density matrix. An optimal approach in the sense of minimal error limit is proposed, in which a variable set of angular frequency is properly chosen and the least square inversion is then applied. This approach of reconstruction from time-dependent molecular-axis angular distribution is proved adaptable for various object states, which has a good numerical stability independent of the selected rotational space.
文摘We establish a reconstruction approach for the rotational quantum state of linear molecules possessing a magnetic manifold. Our approximate method contains an iteration with generalized matrix inverses, processing the tomographic integral of the time-dependent molecular-axis distribution in a polar angle. As shown in a simulated example for an alignment state, the density matrix is determined in a high fidelity. An analytic tomographic formula is also derived for the symmetric top rotation. The state coherent in the quantum space of both the angular momentum and its magnetic projection can be approximately retrieved from the observable time-resolved solid-angle distribution of the molecular axis.
基金This work was supported by a grant of the Spanish Ministerio de Economía y Competitividad and FEDER CGL2013-40924-P,CGL2017-89898-R(AEI/FEDER,UE)a BiodivERsA:EC21C ERANet grant to DRV.RP was supported by an FPU predoctoral fellowship from the Spanish Ministerio de Educación.
文摘Our current understanding of how species have evolved is mainly based on comparative phylogenetic methods,which use phylogenies to infer the evolution of traits.The development of ancestral state reconstruction(ASR)methods has provided the tools to reconstruct trait evolution,which are widely used in fields like evolutionary biology,macroecology and paleontology.As there are different elements involved in those analyses,with different levels of uncertainty(i.e.relating to branch length estimation,trait coding,statistical framework,taxon sampling or software),the various combinations of these elements likely have a strong impact on the reconstruction of the evolution of traits,potentially leading to opposite conclusions.To assess the impact of these different elements in ASR,we performed a set of analyses,including all possible combinations of such elements and using the evolution of migratory behavior in Sylvia warblers as a case study,which was coded as a continuous or as a discrete character.Our results show that taxon sampling,character coding,tree shape,statistical framework and software all significantly affect ASR,both individually and in combination.Not all reconstructed tree nodes show discrepancies,but in the critical ones most pairwise comparisons between analyses lead to conflicting and unexpectedly antagonistic results(zero migration vs fully migratory),thus challenging interpretations of trait evolution.We propose some possible solutions to partly inform decisions,involving the method selection and the incorporation of biological or fossil evidence regarding how traits evolve,but our results demand serious rethinking about how the research community currently uses ASR.
基金The project supported by the National Natural Science Foundation of China(19672043)
文摘Certain deterministic nonlinear systems may show chaotic behavior. We consider the motion of qualitative information and the practicalities of extracting a part from chaotic experimental data. Our approach based on a theorem of Takens draws on the ideas from the generalized theory of information known as singular system analysis. We illustrate this technique by numerical data from the chaotic region of the chaotic experimental data. The method of the singular-value decomposition is used to calculate the eigenvalues of embedding space matrix. The corresponding concrete algorithm to calculate eigenvectors and to obtain the basis of embedding vector space is proposed in this paper. The projection on the orthogonal basis generated by eigenvectors of timeseries data and concrete paradigm are also provided here. Meanwhile the state space reconstruction technology of different kinds of chaotic data obtained from dynamical system has also been discussed in detail.
基金the National Natural Science Foundation of China(19990510)
文摘The state space, reconstruction is the major important quantitative index for describing non-linear chaotic time series. Based on the work of many scholars, such as: AT. H. Packard, F. Takens, M. Casdagli, J. F. Gibson, CHEN Yu-shu et al, the state space was reconstructed using the method of Legendre coordinate. Several different scaling regimes for lag time tau were identified. The influence for state space reconstruction of lag time tau was discussed. The result tells us that is a good practical method for state space reconstruction.
基金supported by the National Key R&D Program of China(No.2023YFB2804900)the National Natural Science Foundation of China(Nos.62275151 and 62405178)。
文摘We propose a method for reconstructing the distributed forward state of polarization(SOP)in single-mode fibers(SMFs)to solve the problem of an unpredictable blind box of SOP evolution in many applications such as fiber-optic parametric amplification systems.Using polarization-sensitive optical frequency domain reflectometry(POFDR)and a quaternion-based model to describe polarization changes,our approach achieves high spatial resolution and precision.By an improved iterative fitting algorithm,the mean square error(MSE)of forward SOP reconstruction for approximately 100 consecutive measurement points was reduced to below 0.1%.This method enables visualization of SOP dynamics along the fiber,offering critical insights for polarization-dependent systems.
基金supported by Ten Thousand Talent Program of Yunnan Province(Grant No.YNWR-QNBJ-2018-174)the Key Basic Research Program of Yunnan Province,China(Grant No.202101BC070003)+3 种基金National Natural Science Foundation of China(Grant No.31901237)Conservation Program for Plant Species with Extremely Small Populations in Yunnan Province(Grant No.2022SJ07X-03)Key Technologies Research for the Germplasmof Important Woody Flowers in Yunnan Province(Grant No.202302AE090018)Natural Science Foundation of Guizhou Province(Grant No.Qiankehejichu-ZK2021yiban 089&Qiankehejichu-ZK2023yiban 035)。
文摘Rhododendron is famous for its high ornamental value.However,the genus is taxonomically difficult and the relationships within Rhododendron remain unresolved.In addition,the origin of key morphological characters with high horticulture value need to be explored.Both problems largely hinder utilization of germplasm resources.Most studies attempted to disentangle the phylogeny of Rhododendron,but only used a few genomic markers and lacked large-scale sampling,resulting in low clade support and contradictory phylogenetic signals.Here,we used restriction-site associated DNA sequencing(RAD-seq)data and morphological traits for 144 species of Rhododendron,representing all subgenera and most sections and subsections of this species-rich genus,to decipher its intricate evolutionary history and reconstruct ancestral state.Our results revealed high resolutions at subgenera and section levels of Rhododendron based on RAD-seq data.Both optimal phylogenetic tree and split tree recovered five lineages among Rhododendron.Subg.Therorhodion(cladeⅠ)formed the basal lineage.Subg.Tsutsusi and Azaleastrum formed cladeⅡand had sister relationships.CladeⅢincluded all scaly rhododendron species.Subg.Pentanthera(cladeⅣ)formed a sister group to Subg.Hymenanthes(cladeⅤ).The results of ancestral state reconstruction showed that Rhododendron ancestor was a deciduous woody plant with terminal inflorescence,ten stamens,leaf blade without scales and broadly funnelform corolla with pink or purple color.This study shows significant distinguishability to resolve the evolutionary history of Rhododendron based on high clade support of phylogenetic tree constructed by RAD-seq data.It also provides an example to resolve discordant signals in phylogenetic trees and demonstrates the application feasibility of RAD-seq with large amounts of missing data in deciphering intricate evolutionary relationships.Additionally,the reconstructed ancestral state of six important characters provides insights into the innovation of key characters in Rhododendron.
基金support from the National Institute of Environmental Health Sciences (USA) training grant to the NCSU Bioinformatics Research Centersupported by National Institutes of Health (USA) grant no.GM070806
文摘Recent years have witnessed a proliferation of quantitative methods for biogeographic inference. In particular, novel parametric approaches represent exciting new opportunities for the study of range evolution. Here, we review a selection of current methods for biogeographic analysis and discuss their respective properties. These methods include generalized parsimony approaches, weighted ancestral area analysis, dispersal-vicariance analysis, the dispersal--extinction--cladogenesis model and other maximum likelihood approaches, and Bayesian stochastic mapping of ancestral ranges, including a novel approach to inferring range evolution in the context of island biogeography. Some of these methods were developed specifically for problems of ancestral range reconstruction, whereas others were designed for more general problems of character state reconstruction and subsequently applied to the study of ancestral ranges. Methods for reconstructing ancestral history on a phylogenetic tree differ not only in the types of ancestral range states that are allowed, but also in the various historical events that may change the ancestral ranges. We explore how the form of allowed ancestral ranges and allowed transitions can both affect the outcome of ancestral range estimation. Finally, we mention some promising avenues for future work in the development of model-based approaches to biogeographic analysis.
基金The authors acknowledge to the Consejo Nacional de Ciencia y Tecnologia(Mexico)for its support to Luis Fernando Cuellar-Garrido with the master's degree scholarship 615539。
文摘Two varieties of Bouteloua aristidoides have been recognized,the widespread var.aristidoides and the more narrowly distributed var.arizonica.The two varieties differ in inflorescence form even more than that seen between many other closely related species of Bouteloua.We therefore asked whether these taxa might be better regarded as distinct species.A total of 93 vouchers were studied by using morphometry(principal components analysis and statistical tests),leaf micromorphology,ancestral state reconstruction,and/or molecular(ITS,trnC-rpoB and trnT-L-F)phylogenetic analyses.Except from the ITS tree,all results supported elevation of B.aristidoides var.arizonica to the rank of species,thus the new combination Bouteloua arizonica(M.E.Jones)L.F.Cuellar&Columbus comb.nov.et stat.nov.,is proposed.Chloroplast and combined chloroplast-nuclear molecular trees depicted var.arizonica as monophyletic(even in sympatric populations with var.aristidoides)and reveals phylogenetic structure within var.aristidoides for which the presence of new undescribed varieties of B.aristidoides(different from B.arizonica)is addressed.B.arizonica differs from B.aristidoides in having fewer branches per inflorescence,a bigger branch with more spikelets,and a shorter branch extension.Scanning electron microscopy revealed the presence of papillae on leaves of B.arizonica as a clear synapomorphy.Growing mature plants of B.arizonica from seeds in a greenhouse revealed a strong cleistogamous nature for this species for which gene flow in sympatric populations with B.aristidoides seems unlikely.A taxonomic treatment and distribution map for identification of B.arizonica is provided.
文摘Background: This paper describes the chick plumage of spurfowl(Pternistis) and francolin(Francolinus, Dendroperdix Peliperdix and Scleroptila) chicks, tests its significance for phylogenetic relationships and also explores the patterns of character evolution in the francolin and spurfowl lineages.Previously regarded as monophyletic, the two evolutionar?ily distant clades are now divided into five genera.Questions considered were whether chick plumage supports the dichotomy between spurfowls and francolins and what role habitat matching plays.Methods: The study was based mainly on photographs of chick skins from the American Museum of Natural History and the Natural History Museum at Tring.Eight plumage characters were selected for comparative scoring, summa?rised in a matrix.These characters were subsequently analysed phylogenetically and their evolution was traced on the existing molecular phylogeny using a parsimony approach.Results: Based on chick plumage the phylogeny of species groups among francolins and spurfowls, was largely unresolved possibly ascribed to a high degree of symplesiomorphy inherent among the Phasianids.This possibly could have resulted in a high degree of polytomy particularly among the spurfowls and francolins.Furthermore, the ancestral state reconstructions revealed high prevalence of symplesiomorphic states and reversals which do not help in the classification of groups.Although the differences are described that separate some African francolins from spurfowls, other francolins(in Asia and Africa) share remarkably similar characteristics with spurfowls.Plain dark dorsal plumage is probably advantageous for avoiding detection by predators in forests, while facial stripes optimise the breaking of body shapes in dense grass cover(as in Scleroptila spp.) and semi?striped faces are advantageous for stationary camouflage under tree and bush cover(as in Pternistis spp.).Conclusions: Although symplesiomorphy is a hereditary explanation for downy colours and patterns, the traits rel?evant for habitat matching are combined in a manner which is determined(adaptation) by natural selection.
文摘Based on the Bayesian information criterion, this paper proposes the improved local linear prediction method to predict chaotic time series. This method uses spatial correlation and temporal correlation simultaneously. Simulation results show that the improved local linear prediction method can effectively make multi-step and one-step prediction of chaotic time series and the multi-step prediction performance and one-step prediction accuracy of the improved local linear prediction method are superior to those of the traditional local linear prediction method.
基金supported by the National Natural Science Foundation of China(Grant No.31701803)Changsha Natural Science Foundation,China(Grant No.kq2202336)the Special Project of Hunan Innovative Province Construction,China(Grant No.S2021ZCKPZT0004)。
文摘Despite increasing knowledge of barnyardgrass(Echinochloa crus-galli) interference with rice, relatively little is known how endophytes improve the ability of rice against barnyardgrass stress. Here, we provided a detailed temporal characterization of rice root-associated microbiomes during co-cultivation with barnyardgrass and a comparison with the microbiomes of weed-free rice plants. Alpha diversity analysis indicated that barnyardgrass had the opposite effects on endophytic bacteria and fungi in rice roots, in terms of the community diversity, richness and coverage at the rice seedling stage. Principal coordinate analysis showed that barnyardgrass had only a minor effect on the community composition of endophytes in rice roots at the rice seedling stage, but showed a significant and maximum interference at the heading stage. Rice recruited many endophytes to resist biotic stress from barnyardgrass, especially for fungi. PICRUSt(phylogenetic investigation of communities by reconstruction of unobserved states) predictive analysis indicated that 23 metabolic pathways of bacteria were overrepresented in rice. In addition, the main trophic mode of fungi was pathotroph according to FUNGuild analysis. A positive correlation between bacteria and fungi in rice roots was found via network analysis. Anaeromyxobacter, Azospira and Pseudolabrys were the vital bacteria, Phaeosphaeria and Funneliformis were the dominant fungi in maintaining the stability of the ecological network. These results provided data and a theoretical basis for the in-depth understanding of what role endophytes play in rice resistance to barnyardgrass stress and will have implications on improving the resistance of rice against biotic stress using root microbiota.
文摘The chaotic nonlinear time series method is applied to analyze the sliver irregularity in textile processing.Because it unifies the system's determinacy and randomness,it seems more adaptive to describe the sliver irregularity than conventional methods.Firstly,the chaos character,i.e.fractal dimension,positive Lyapunov exponent,and state space parameters,including time delay and reconstruction dimension,are calculated respectively.As a result,a positive Lyapunov exponent and a fractal dimension are obtained,which demonstrates that the system is chaotic in fact.Secondly,both local linear forecast and global forecast models based on the reconstructed state are adopted to predict a segment part of the sliver irregularity series,which proves the validity of this analysis.Therefore,the sliver irregularity series shows the evidence of chaotic phenomena,and thus laying the theoretical foundation for analyzing and modeling the sliver irregularity series by applying the chaos theory,and providing a new way to understand the complexity of the sliver irregularity much better.
文摘A linear quadric (LQ) optimal speed control algorithm is proposed for the speed control of a pump controlled motor hydraulic system. The control theme consists of optimal state feedback and disturbing compensation based on observation. The optimal state feedback bases on LQ cost function. The disturbing compensation is realized through reconstructing the state of load torque. A series of simulation are performed, and the results show that the control performance is satisfactory and can be maintained under changes of load torque.
基金supported by the National Key Research and Development Program of China (Grant Nos. 2022YFF0802900 & 2021YFA0718200)the High-performance Computing Platform of Peking University。
文摘Reconstructing climate states during geological periods is a key focus in studying Earth system evolution. Substantial progress has been achieved in reconstructing paleoclimate and paleoenvironment using both Earth system models and paleoclimate proxies. However, current paleoclimate reconstructions face several challenges: the accuracy of Earth system model simulations relies on model parameter settings. Paleoclimate proxy data exhibit significant variability across different periods and regions, and proxy data are often sparse, hindering the accuracy and global relevance of proxy-based reconstructions.Addressing the pros and cons of these methods, paleoclimate data assimilation can effectively integrate Earth system models and paleoclimate proxy data, enhancing the precision and global relevance of reconstructions. Using approaches such as the ensemble Kalman filter as an example, this paper introduces the principles of paleoclimate data assimilation and reviews recent advancements in reconstructing paleoclimate states using these techniques. Paleoclimate data assimilation offers new insights and advanced techniques for paleoclimate reconstruction, with potential applications extending to the entire Cenozoic, Mesozoic, and even Paleozoic eras. These applications could deepen our understanding of the past climatic backgrounds of extreme climate events such as glacial-interglacial cycles, hyperthermals, and oceanic anoxic events, providing a reference for predicting future climate change.
基金the National Natural Science Foundation of China (Grant Nos. 60978009 and 91121023)the National Basic Research Program of China (Grant No. 2011CBA00200)
文摘An unknown state of a quantum system S is usually determined by repeatedly measuring a set of non-commuting observables. The state can also be obtained from the repeated measurements of a single separable observable when the system S interacts with an assistant system A in a known state. In this paper, we study the quantum state tomography of a three-level atom （the system S） interacting with two radiation fields as the assistant system A. We obtain the initial state of S by repeatedly measuring a separable observable O = Sz n1 n2, in which Sz is the atom operator, and hi and h2 are the photon number operators of the two radiation fields. We achieve the one-to-one mapping M between the initial density matrix of the system S and the measured results of the single separable observable. We also give a concrete numerical example.
