Chromosomal rearrangements(CRs)often cause phenotypic variations.Although several major rearrangements have been identified in Triticeae,a comprehensive study of the order,timing,and breakpoints of CRs has not been co...Chromosomal rearrangements(CRs)often cause phenotypic variations.Although several major rearrangements have been identified in Triticeae,a comprehensive study of the order,timing,and breakpoints of CRs has not been conducted.Here,we reconstruct high-quality ancestral genomes for the most recent common ancestor(MRCA)of the Triticeae,and the MRCA of the wheat lineage(Triticum and Aegilops).The protogenes of MRCA of the Triticeae and the wheat lineage are 22,894 and 29,060,respectively,which were arranged in their ancestral order.By partitioning modern Triticeae chromosomes into sets of syntenic regions and linking each to the corresponding protochromosomes,we revisit the rye chromosome structural evolution and propose alternative evolutionary routes.The previously identified 4L/5L reciprocal translocation in rye and Triticum urartu is found to have occurred independently and is unlikely to be the result of chromosomal introgression following distant hybridization.We also clarify that the 4AL/7BS translocation in tetraploid wheat was a bidirectional rather than unidirectional translocation event.Lastly,we identify several breakpoints in protochromosomes that independently reoccur following Triticeae evolution,representing potential CR hotspots.This study demonstrates that these reconstructed ancestral genomes can serve as special comparative references and facilitate a better understanding of the evolution of structural rearrangements in Triticeae.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
Traditional ancestral halls play an important role in the inheritance of the clan system.They carry strong clan ritual culture and are the hall of the clan spirit.In China’s traditional society,the clan concept was v...Traditional ancestral halls play an important role in the inheritance of the clan system.They carry strong clan ritual culture and are the hall of the clan spirit.In China’s traditional society,the clan concept was very deep,and a village was often formed by a single clan.An ancestral hall is a place where people sacrifice their ancestors and thus is given the most important significance,which is related to the rise and fall of the clan.Based on the instinct of biological benefit and avoidance,the site selection of ancestral halls must be the most favorable.In this paper,the site selection of Yu Ancestral Hall in Wangkou Village,Wuyuan County,Jiangxi Province was surveyed and analyzed,and the layout modes and artistic characteristics of site selection of traditional ancestral halls in Jiangxi were studied to provide reference for the protection and sustainable development of traditional ancestral halls.展开更多
Although the effects of the coalescent process on sequence divergence and genealogies are well understood, the vir- tual majority of studies that use molecular sequences to estimate times of divergence among species h...Although the effects of the coalescent process on sequence divergence and genealogies are well understood, the vir- tual majority of studies that use molecular sequences to estimate times of divergence among species have failed to account for the coalescent process. Here we study the impact of ancestral population size and incomplete lineage sorting on Bayesian estimates of species divergence times under the molecular clock when the inference model ignores the coalescent process. Using a combination of mathematical analysis, computer simulations and analysis of real data, we find that the errors on estimates of times and the molecular rate can be substantial when ancestral populations are large and when there is substantial incomplete lineage sorting. For example, in a simple three-species case, we find that if the most precise fossil calibration is placed on the root of the phylogeny, the age of the internal node is overestimated, while if the most precise calibration is placed on the internal node, then the age of the root is underestimated. In both cases, the molecular rate is overestimated. Using simulations on a phylogeny of nine species, we show that substantial errors in time and rate estimates can be obtained even when dating ancient divergence events. We analyse the hominoid phylogeny and show that estimates of the neutral mutation rate obtained while ignoring the coalescent are too high. Using a coalescent-based technique to obtain geological times of divergence, we obtain estimates of the mutation rate that are within experimental estimates and we also obtain substantially older divergence times within the phylogeny [Current Zoology 61 （5）： 874-885, 2015].展开更多
A class of latent ancestral graph for modelling the dependence structure of structural vector autoregressive(VAR)model affected by latent variables is proposed.The graphs are mixed graphs with possibly two kind of edg...A class of latent ancestral graph for modelling the dependence structure of structural vector autoregressive(VAR)model affected by latent variables is proposed.The graphs are mixed graphs with possibly two kind of edges,namely directed and bidirected edges.The vertex set denotes random variables at dif-ferent times.In Gaussian case,the latent ancestral graph leads to a simple parameterization model.A modified iterative conditional fitting algorithm is presented to obtain maximum likelihood esti-mation of the parameters.Furthermore,a log-likelihood criterion is used to select the most appropriate models.Simulations are performed using illustrative examples and results are provided to demonstrate the validity of the methods.展开更多
As the most important sacrificial architecture in rural China, ancestral halls are material expressions of the traditional social, cultural and artistic spirit, which contain rich historical and cultural value. Taking...As the most important sacrificial architecture in rural China, ancestral halls are material expressions of the traditional social, cultural and artistic spirit, which contain rich historical and cultural value. Taking the Wan Clan Ancestral Hall of Sanjiang Town, Nanchang County, Nanchang City, Jiangxi Province for example, this study analyzed its spatial sequence, the planar shape and the facade form, and explained the connotation of "respecting law and discipline rites and advocating moral integrity" contained in the spirit of ancestral halls.展开更多
To explore the correlation between ancestor temple sacrifice culture and clan etiquettes in traditional settlements of Jiangxi Province, this paper analyzed origination and development of ancestor temple, focused on t...To explore the correlation between ancestor temple sacrifice culture and clan etiquettes in traditional settlements of Jiangxi Province, this paper analyzed origination and development of ancestor temple, focused on the patriarchal thought that respects ancestors and unifies the clan, the relationship between clan power and political power, sacrifice and patriarchy. The research found that the plain clan etiquettes were significant for unifying the clansmen, inheriting historical context, and stabilizing primarylevel organizations in rural areas.展开更多
In this article, three Guangdong’s ancestral temples are taken as case studies to explore strategies for cultural heritage conservation. Heritage conservation is very important not only for our missing of past, but i...In this article, three Guangdong’s ancestral temples are taken as case studies to explore strategies for cultural heritage conservation. Heritage conservation is very important not only for our missing of past, but in order that our own cultural identity can be formed today. In China, different stakeholders hold various views on heritage protection and conflicts often take place. Particularly, many folk religion’s cultural heritages face a dangerous scenario and could even be damaged or destroyed for a variety of “reason”. This article tries to re-examine fundamental values and assessment criteria for cultural heritage conservation. The authenticity is a core concept involved with those of issues. Based on the views of culture place, the author puts forward the concept of “emic culture authenticity” as a hinge to explore authentic culture ecology of heritage and its model, to facilitate the cultural heritage conservation and reuse by the strategies of classification and adaptation.展开更多
Ancestral temple culture is the core part of village culture,which infl uences the spatial pattern of villages from various aspects,occupying an important position in traditional villages.Facing the loss of village cu...Ancestral temple culture is the core part of village culture,which infl uences the spatial pattern of villages from various aspects,occupying an important position in traditional villages.Facing the loss of village culture and the dissipation of cohesion,it is particularly important to study village culture.The impacts of ancestral temple on village layout,building orientation and street pattern are analyzed,which will guide the construction of modern beautiful countryside by using rational planning methods.展开更多
Local cattle breeds continue to decline in numbers partly due to the use of high performing breeds in advanced production systems where genetic material of elite animals is widely spread. The objective of this study w...Local cattle breeds continue to decline in numbers partly due to the use of high performing breeds in advanced production systems where genetic material of elite animals is widely spread. The objective of this study was to assess the within and across breed genetic diversity of the Angler and Red-and-White dual-purpose (DP) cattle breeds applying different inbreeding concepts. Classical and ancestral inbreeding coefficients were computed from pedigree data using the gene dropping method. Effective population size was calculated based on the increase of classical inbreeding, and based on ancestral inbreeding to obtain what was termed as ancestral effective population size. Furthermore, the effective number of founders and ancestors were computed to assess the disequilibrium of founder contribution in the reference populations. The analyses were performed separately for each breed and for a combined dataset. The Angler pedigree was more complete (88%) in the first parental generation but completeness declined with increasing pedigree depth. Average classical inbreeding coefficients of inbred individuals were 2.19%, 1.94% and 2.07%, while average Ballou’s ancestral inbreeding coefficients were 3.69%, 1.39% and 2.21% for the Angler, Red-and-White DP and the combined breed pedigree analyses, respectively. Ancestral history coefficient is a novel coefficient and its estimates were similar and strongly correlated to Ballou’s coefficients (r = 0.99, p < 0.001). The effective population size estimates ranged from 156 to 170 for the classical inbreeding based method, and as low as from 50 to 54 for the ancestral history coefficient based method. The effective number of founders and ancestors ranged from 310 to 532, and 90 to 189, respectively. Our results show that the Red Holstein breed is a key progenitor of the breed populations under study. This highlights cross breeding schemes introduced to improve the milk trait performance of the Angler and Red-and-White DP breeds some decades ago.展开更多
This paper studies the clan temples in four periods,namely,the development period(early Ming Dynasty and before),the shaping period(mid-Ming Dynasty to early Qing Dynasty),the maturity period(mid-Qing Dynasty),and the...This paper studies the clan temples in four periods,namely,the development period(early Ming Dynasty and before),the shaping period(mid-Ming Dynasty to early Qing Dynasty),the maturity period(mid-Qing Dynasty),and the programmed period(late Qing Dynasty),analyzes and summarizes their prototypical planform features and attempts to summarize and construct a genealogy of the architectural characteristics of the plane shape of clan temples.During the Ming and Qing dynasties,Guangfu ancestral halls in general showed a journey of development from a centripetal-single-linear-multi-linear-grid pattern,forming the unique Guangsanlu classic pattern in the Guangfu area.展开更多
This paper discusses ancestral hall architecture within the context of the Cantonese folk lineage in the Pearl River Delta.Using a typological research approach and chronological analysis,various factors that have inf...This paper discusses ancestral hall architecture within the context of the Cantonese folk lineage in the Pearl River Delta.Using a typological research approach and chronological analysis,various factors that have influenced the evolution of ancestral hall architecture are analyzed.The study specifically investigates the features of ancestral halls during the Ming and Qing dynasties.Three periods of ancient China are analyzed:The transition from Ming to Qing,the mid-Qing dynasty,and the late Qing dynasty.The variables of each period and how they influence the evolution of architectural typological features are identified.Based on our analysis,architectural features are related to economic and social factors,materials available,and craftsmanship of the construction workers.展开更多
All extant cellular organisms derive from a common ancestor,which can be illustrated by the universality of many pivotal metabolic traits,including the utilization of ATP as an energy currency and multiple mechanisms ...All extant cellular organisms derive from a common ancestor,which can be illustrated by the universality of many pivotal metabolic traits,including the utilization of ATP as an energy currency and multiple mechanisms processing the genetic information flow as demonstrated by the Central Dogma of biology(Theobald,2010;Hug et al.,2016).展开更多
Evidence of whole-genome duplications(WGDs)and subsequent karyotype changes has been detected in most major lineages of living organisms on Earth.To clarify the complex resulting multi-layered patterns of gene colline...Evidence of whole-genome duplications(WGDs)and subsequent karyotype changes has been detected in most major lineages of living organisms on Earth.To clarify the complex resulting multi-layered patterns of gene collinearity in genome analyses,there is a need for convenient and accurate toolkits.To meet this need,we developed WGDI(Whole-Genome Duplication Integrated analysis),a Python-based command-line tool that facilitates comprehensive analysis of recursive polyploidization events and cross-species genome alignments.WGDI supports three main workflows(polyploid inference,hierarchical inference of genomic homology,and ancestral chromosome karyotyping)that can improve the detection of WGD and characterization of WGD-related events based on high-quality chromosome-level genomes.Significantly,it can extract complete synteny blocks and facilitate reconstruction of detailed karyotype evolution.This toolkit is freely available at GitHub(https://github.com/SunPengChuan/wgdi).As an example of its application,WGDI convincingly clarified karyotype evolution in Aquilegia coerulea and Vitis vinifera following WGDs and rejected the hypothesis that Aquilegia contributed as a parental lineage to the allopolyploid origin of core dicots.展开更多
Durian(Durio zibethinus)is a tropical fruit that has a unique flavor and aroma.It occupies a significant phylogenetic position within the Malvaceae family.Extant core-eudicot plants are reported to share seven ancestr...Durian(Durio zibethinus)is a tropical fruit that has a unique flavor and aroma.It occupies a significant phylogenetic position within the Malvaceae family.Extant core-eudicot plants are reported to share seven ancestral karyotypes that have undergone reshuffling,resulting in an abundant genomic diversity.However,the ancestral karyotypes of the Malvaceae family,as well as the evolution trajectory leading to the28 chromosomes in durian,remain poorly understood.Here,we report the high-quality assembly of the durian genome with comprehensive comparative genomic analyses.By analyzing the collinear blocks between cacao and durian,we inferred 11 Malvaceae ancestral karyotypes.These blocks were present in a single-copy form in cacao and mainly in triplicates in durian,possibly resulting from a recent whole genome triplication(WGT)event that led to hexaploidization of the durian genome around 20(17–24)million years ago.A large proportion of the duplicated genes in durian,such as those involved in the lignin biosynthesis module for phenylpropane biosynthesis,are derived directly from whole genome duplication,which makes it an important force in reshaping its genomic architecture.Transcriptome studies have revealed that genes involved in feruloyl-Co A formations were highly preferentially expressed in fruit peels,indicating that the thorns produced on durian fruit may comprise guaiacyl and syringyl lignins.Among all the analyzed transcription factors(TFs),members of the heat shock factor family(HSF)were the most significantly upregulated under heat stress.All subfamilies of genes encoding heat shock proteins(HSPs)in the durian genome appear to have undergone expansion.The potential interactions between HSF Dzi05.397 and HSPs were examined and experimentally verified.Our study provides a high-quality durian genome and reveals the reshuffling mechanism of ancestral Malvaceae chromosomes to produce the durian genome.We also provide insights into the mechanism underlying lignin biosynthesis and heat stress tolerance.展开更多
Necessary and sufficient conditions for a maximal ancestral graph(MAnG)to be Markov equivalent to another MAnG and to a DAG are provided respectively.Also a polynomial-time algorithm for converting a MAnG into its equ...Necessary and sufficient conditions for a maximal ancestral graph(MAnG)to be Markov equivalent to another MAnG and to a DAG are provided respectively.Also a polynomial-time algorithm for converting a MAnG into its equivalent DAG is given for the first time.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
Identification of population structure can help trace population histories and identify disease genes.Structured association(SA)is a commonly used approach for population structure identification and association mappi...Identification of population structure can help trace population histories and identify disease genes.Structured association(SA)is a commonly used approach for population structure identification and association mapping.A major issue with SA is that its performance greatly depends on the informa-tiveness and the numbers of ancestral informative markers(AIMs).Present major AIM selection meth-ods mostly require prior individual ancestry information,which is usually not available or uncertain in practice.To address this potential weakness,we herein develop a novel approach for AIM selection based on principle component analysis(PCA),which does not require prior ancestry information of study subjects.Our simulation and real genetic data analysis results suggest that,with equivalent AIMs,PCA-based selected AIMs can significantly increase the accuracy of inferred individual ancestries compared with traditionally randomly selected AIMs.Our method can easily be applied to whole genome data to select a set of highly informative AIMs in population structure,which can then be used to identify potential population structure and correct possible statistical biases caused by population stratification.展开更多
SHEXIAN, located in the southern foothills of Huangshan Mountain in Anhui Province, is an ancient county which was once the seat of Huizhou Prefecture. The area is also known as the birthplace of Anhui merchants. With...SHEXIAN, located in the southern foothills of Huangshan Mountain in Anhui Province, is an ancient county which was once the seat of Huizhou Prefecture. The area is also known as the birthplace of Anhui merchants. With a long history, favorable geographic position and a unique culture created mainly by those rich Anhui merchants, Shexian has retained a large number of cultural relics, especially ancient archways,展开更多
The stone archway in the style of the Ming Dynasty also has more than 400 years of history. Located by a busy street, the old and new buildings of the ancient county set each other off radiantly.
基金CAs Youth Interdisciplinary Team(JCTD-2022-06)the National Nature Science Foundation of China(31870209).
文摘Chromosomal rearrangements(CRs)often cause phenotypic variations.Although several major rearrangements have been identified in Triticeae,a comprehensive study of the order,timing,and breakpoints of CRs has not been conducted.Here,we reconstruct high-quality ancestral genomes for the most recent common ancestor(MRCA)of the Triticeae,and the MRCA of the wheat lineage(Triticum and Aegilops).The protogenes of MRCA of the Triticeae and the wheat lineage are 22,894 and 29,060,respectively,which were arranged in their ancestral order.By partitioning modern Triticeae chromosomes into sets of syntenic regions and linking each to the corresponding protochromosomes,we revisit the rye chromosome structural evolution and propose alternative evolutionary routes.The previously identified 4L/5L reciprocal translocation in rye and Triticum urartu is found to have occurred independently and is unlikely to be the result of chromosomal introgression following distant hybridization.We also clarify that the 4AL/7BS translocation in tetraploid wheat was a bidirectional rather than unidirectional translocation event.Lastly,we identify several breakpoints in protochromosomes that independently reoccur following Triticeae evolution,representing potential CR hotspots.This study demonstrates that these reconstructed ancestral genomes can serve as special comparative references and facilitate a better understanding of the evolution of structural rearrangements in Triticeae.
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Sponsored by Foundation for Humanities and Social Sciences Planning of Ministry of Education of China:Study on the Art of Ancestral Halls in Jiangxi under the Background of Beautiful Countryside(18YJC760149)Project for Humanities and Social Sciences Planning of Colleges and Universities in 2017 in Jiangxi Province(YS17217)+1 种基金Project for Artistic Sciences Planning in 2017 in Jiangxi Province(YG2017164)Project for Artistic Sciences Planning in 2014 in Jiangxi Province(YG2014115)
文摘Traditional ancestral halls play an important role in the inheritance of the clan system.They carry strong clan ritual culture and are the hall of the clan spirit.In China’s traditional society,the clan concept was very deep,and a village was often formed by a single clan.An ancestral hall is a place where people sacrifice their ancestors and thus is given the most important significance,which is related to the rise and fall of the clan.Based on the instinct of biological benefit and avoidance,the site selection of ancestral halls must be the most favorable.In this paper,the site selection of Yu Ancestral Hall in Wangkou Village,Wuyuan County,Jiangxi Province was surveyed and analyzed,and the layout modes and artistic characteristics of site selection of traditional ancestral halls in Jiangxi were studied to provide reference for the protection and sustainable development of traditional ancestral halls.
文摘Although the effects of the coalescent process on sequence divergence and genealogies are well understood, the vir- tual majority of studies that use molecular sequences to estimate times of divergence among species have failed to account for the coalescent process. Here we study the impact of ancestral population size and incomplete lineage sorting on Bayesian estimates of species divergence times under the molecular clock when the inference model ignores the coalescent process. Using a combination of mathematical analysis, computer simulations and analysis of real data, we find that the errors on estimates of times and the molecular rate can be substantial when ancestral populations are large and when there is substantial incomplete lineage sorting. For example, in a simple three-species case, we find that if the most precise fossil calibration is placed on the root of the phylogeny, the age of the internal node is overestimated, while if the most precise calibration is placed on the internal node, then the age of the root is underestimated. In both cases, the molecular rate is overestimated. Using simulations on a phylogeny of nine species, we show that substantial errors in time and rate estimates can be obtained even when dating ancient divergence events. We analyse the hominoid phylogeny and show that estimates of the neutral mutation rate obtained while ignoring the coalescent are too high. Using a coalescent-based technique to obtain geological times of divergence, we obtain estimates of the mutation rate that are within experimental estimates and we also obtain substantially older divergence times within the phylogeny [Current Zoology 61 （5）： 874-885, 2015].
基金supported in part by the National Natural Science Foundation of China(60375003)the Aeronautics and Astronautics Basal Science Foundation of China(03I53059)
文摘A class of latent ancestral graph for modelling the dependence structure of structural vector autoregressive(VAR)model affected by latent variables is proposed.The graphs are mixed graphs with possibly two kind of edges,namely directed and bidirected edges.The vertex set denotes random variables at dif-ferent times.In Gaussian case,the latent ancestral graph leads to a simple parameterization model.A modified iterative conditional fitting algorithm is presented to obtain maximum likelihood esti-mation of the parameters.Furthermore,a log-likelihood criterion is used to select the most appropriate models.Simulations are performed using illustrative examples and results are provided to demonstrate the validity of the methods.
基金Sponsored by Youth Fund for Humanities and Social Sciences Research of the Ministry of Education of China(18YJC760149)2017 Humanities and Social Sciences Research Project of Jiangxi Province(YS17217)2017 Cultural and Artistic Science Planning Project of Jiangxi Province(YG2017164)
文摘As the most important sacrificial architecture in rural China, ancestral halls are material expressions of the traditional social, cultural and artistic spirit, which contain rich historical and cultural value. Taking the Wan Clan Ancestral Hall of Sanjiang Town, Nanchang County, Nanchang City, Jiangxi Province for example, this study analyzed its spatial sequence, the planar shape and the facade form, and explained the connotation of "respecting law and discipline rites and advocating moral integrity" contained in the spirit of ancestral halls.
基金Sponsored by Jiangxi Provincial Program of Art and Science 2015(YG2015033)
文摘To explore the correlation between ancestor temple sacrifice culture and clan etiquettes in traditional settlements of Jiangxi Province, this paper analyzed origination and development of ancestor temple, focused on the patriarchal thought that respects ancestors and unifies the clan, the relationship between clan power and political power, sacrifice and patriarchy. The research found that the plain clan etiquettes were significant for unifying the clansmen, inheriting historical context, and stabilizing primarylevel organizations in rural areas.
文摘In this article, three Guangdong’s ancestral temples are taken as case studies to explore strategies for cultural heritage conservation. Heritage conservation is very important not only for our missing of past, but in order that our own cultural identity can be formed today. In China, different stakeholders hold various views on heritage protection and conflicts often take place. Particularly, many folk religion’s cultural heritages face a dangerous scenario and could even be damaged or destroyed for a variety of “reason”. This article tries to re-examine fundamental values and assessment criteria for cultural heritage conservation. The authenticity is a core concept involved with those of issues. Based on the views of culture place, the author puts forward the concept of “emic culture authenticity” as a hinge to explore authentic culture ecology of heritage and its model, to facilitate the cultural heritage conservation and reuse by the strategies of classification and adaptation.
基金Research on Architectural Art of Ancestral Temples in Jiangxi Under the Background of Beautiful Countryside Construction(18YJC760149)Planning for Humanities and Social Sciences of the Ministry of Education+1 种基金Research on Building Skills of Ancestral Temples in Jiangxi Under the Background of Beautiful Countryside Construction(19YS04)Social Science Planning of Jiangxi Province.
文摘Ancestral temple culture is the core part of village culture,which infl uences the spatial pattern of villages from various aspects,occupying an important position in traditional villages.Facing the loss of village culture and the dissipation of cohesion,it is particularly important to study village culture.The impacts of ancestral temple on village layout,building orientation and street pattern are analyzed,which will guide the construction of modern beautiful countryside by using rational planning methods.
基金part of the research activities of the operational group,“Animal Genetic Resources”that operates under the auspices of the Agricultural European Innovation Partnership(EIP-AGRI)projectthe European Commission for providing funds for the project.
文摘Local cattle breeds continue to decline in numbers partly due to the use of high performing breeds in advanced production systems where genetic material of elite animals is widely spread. The objective of this study was to assess the within and across breed genetic diversity of the Angler and Red-and-White dual-purpose (DP) cattle breeds applying different inbreeding concepts. Classical and ancestral inbreeding coefficients were computed from pedigree data using the gene dropping method. Effective population size was calculated based on the increase of classical inbreeding, and based on ancestral inbreeding to obtain what was termed as ancestral effective population size. Furthermore, the effective number of founders and ancestors were computed to assess the disequilibrium of founder contribution in the reference populations. The analyses were performed separately for each breed and for a combined dataset. The Angler pedigree was more complete (88%) in the first parental generation but completeness declined with increasing pedigree depth. Average classical inbreeding coefficients of inbred individuals were 2.19%, 1.94% and 2.07%, while average Ballou’s ancestral inbreeding coefficients were 3.69%, 1.39% and 2.21% for the Angler, Red-and-White DP and the combined breed pedigree analyses, respectively. Ancestral history coefficient is a novel coefficient and its estimates were similar and strongly correlated to Ballou’s coefficients (r = 0.99, p < 0.001). The effective population size estimates ranged from 156 to 170 for the classical inbreeding based method, and as low as from 50 to 54 for the ancestral history coefficient based method. The effective number of founders and ancestors ranged from 310 to 532, and 90 to 189, respectively. Our results show that the Red Holstein breed is a key progenitor of the breed populations under study. This highlights cross breeding schemes introduced to improve the milk trait performance of the Angler and Red-and-White DP breeds some decades ago.
文摘This paper studies the clan temples in four periods,namely,the development period(early Ming Dynasty and before),the shaping period(mid-Ming Dynasty to early Qing Dynasty),the maturity period(mid-Qing Dynasty),and the programmed period(late Qing Dynasty),analyzes and summarizes their prototypical planform features and attempts to summarize and construct a genealogy of the architectural characteristics of the plane shape of clan temples.During the Ming and Qing dynasties,Guangfu ancestral halls in general showed a journey of development from a centripetal-single-linear-multi-linear-grid pattern,forming the unique Guangsanlu classic pattern in the Guangfu area.
文摘This paper discusses ancestral hall architecture within the context of the Cantonese folk lineage in the Pearl River Delta.Using a typological research approach and chronological analysis,various factors that have influenced the evolution of ancestral hall architecture are analyzed.The study specifically investigates the features of ancestral halls during the Ming and Qing dynasties.Three periods of ancient China are analyzed:The transition from Ming to Qing,the mid-Qing dynasty,and the late Qing dynasty.The variables of each period and how they influence the evolution of architectural typological features are identified.Based on our analysis,architectural features are related to economic and social factors,materials available,and craftsmanship of the construction workers.
基金supported by the National Natural Science Foundation of China(Grant Nos.92351301,32393974)the Science and Technology Innovation Committee of Shenzhen Municipality(Grant No.20200925173954005)。
文摘All extant cellular organisms derive from a common ancestor,which can be illustrated by the universality of many pivotal metabolic traits,including the utilization of ATP as an energy currency and multiple mechanisms processing the genetic information flow as demonstrated by the Central Dogma of biology(Theobald,2010;Hug et al.,2016).
基金This work was supported equally by the Strategic Priority Research Program of the Chinese Academy of Sciences(XDB31000000)the National Natural Science Foundation of China(grant numbers 31590821 and 91731301 to J.L.and 32070669to X.W.)+1 种基金the National Key Research and Development Program of China(2017YFC0505203 to Z.X.)also by the Fundamental Research Funds for the Central Universities(SCU2019D013 and 2020SCUNL207)and theNational High-Level Talents Special Support Plan(10 Thousand People Plan)。
文摘Evidence of whole-genome duplications(WGDs)and subsequent karyotype changes has been detected in most major lineages of living organisms on Earth.To clarify the complex resulting multi-layered patterns of gene collinearity in genome analyses,there is a need for convenient and accurate toolkits.To meet this need,we developed WGDI(Whole-Genome Duplication Integrated analysis),a Python-based command-line tool that facilitates comprehensive analysis of recursive polyploidization events and cross-species genome alignments.WGDI supports three main workflows(polyploid inference,hierarchical inference of genomic homology,and ancestral chromosome karyotyping)that can improve the detection of WGD and characterization of WGD-related events based on high-quality chromosome-level genomes.Significantly,it can extract complete synteny blocks and facilitate reconstruction of detailed karyotype evolution.This toolkit is freely available at GitHub(https://github.com/SunPengChuan/wgdi).As an example of its application,WGDI convincingly clarified karyotype evolution in Aquilegia coerulea and Vitis vinifera following WGDs and rejected the hypothesis that Aquilegia contributed as a parental lineage to the allopolyploid origin of core dicots.
基金supported by Shaanxi Normal University Academician Expert Workstation Foundation(1110010375)the National Key Laboratory of Protein and Plant Gene Research Open Project(ZD2021058)。
文摘Durian(Durio zibethinus)is a tropical fruit that has a unique flavor and aroma.It occupies a significant phylogenetic position within the Malvaceae family.Extant core-eudicot plants are reported to share seven ancestral karyotypes that have undergone reshuffling,resulting in an abundant genomic diversity.However,the ancestral karyotypes of the Malvaceae family,as well as the evolution trajectory leading to the28 chromosomes in durian,remain poorly understood.Here,we report the high-quality assembly of the durian genome with comprehensive comparative genomic analyses.By analyzing the collinear blocks between cacao and durian,we inferred 11 Malvaceae ancestral karyotypes.These blocks were present in a single-copy form in cacao and mainly in triplicates in durian,possibly resulting from a recent whole genome triplication(WGT)event that led to hexaploidization of the durian genome around 20(17–24)million years ago.A large proportion of the duplicated genes in durian,such as those involved in the lignin biosynthesis module for phenylpropane biosynthesis,are derived directly from whole genome duplication,which makes it an important force in reshaping its genomic architecture.Transcriptome studies have revealed that genes involved in feruloyl-Co A formations were highly preferentially expressed in fruit peels,indicating that the thorns produced on durian fruit may comprise guaiacyl and syringyl lignins.Among all the analyzed transcription factors(TFs),members of the heat shock factor family(HSF)were the most significantly upregulated under heat stress.All subfamilies of genes encoding heat shock proteins(HSPs)in the durian genome appear to have undergone expansion.The potential interactions between HSF Dzi05.397 and HSPs were examined and experimentally verified.Our study provides a high-quality durian genome and reveals the reshuffling mechanism of ancestral Malvaceae chromosomes to produce the durian genome.We also provide insights into the mechanism underlying lignin biosynthesis and heat stress tolerance.
基金This research was partly supported by the National Natural Science Foundation of China(Grant Nos.39930160&19871003).
文摘Necessary and sufficient conditions for a maximal ancestral graph(MAnG)to be Markov equivalent to another MAnG and to a DAG are provided respectively.Also a polynomial-time algorithm for converting a MAnG into its equivalent DAG is given for the first time.
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Supported by Xi’an Jiaotong University,NIH(Grant Nos.R01 AR050496,R21 AG 027110,R01 AG026564 and P50 AR055081)Fok Ying Tung Education Foundation and Framingham Heart Study and the Framingham SHARe Project
文摘Identification of population structure can help trace population histories and identify disease genes.Structured association(SA)is a commonly used approach for population structure identification and association mapping.A major issue with SA is that its performance greatly depends on the informa-tiveness and the numbers of ancestral informative markers(AIMs).Present major AIM selection meth-ods mostly require prior individual ancestry information,which is usually not available or uncertain in practice.To address this potential weakness,we herein develop a novel approach for AIM selection based on principle component analysis(PCA),which does not require prior ancestry information of study subjects.Our simulation and real genetic data analysis results suggest that,with equivalent AIMs,PCA-based selected AIMs can significantly increase the accuracy of inferred individual ancestries compared with traditionally randomly selected AIMs.Our method can easily be applied to whole genome data to select a set of highly informative AIMs in population structure,which can then be used to identify potential population structure and correct possible statistical biases caused by population stratification.
文摘SHEXIAN, located in the southern foothills of Huangshan Mountain in Anhui Province, is an ancient county which was once the seat of Huizhou Prefecture. The area is also known as the birthplace of Anhui merchants. With a long history, favorable geographic position and a unique culture created mainly by those rich Anhui merchants, Shexian has retained a large number of cultural relics, especially ancient archways,
文摘The stone archway in the style of the Ming Dynasty also has more than 400 years of history. Located by a busy street, the old and new buildings of the ancient county set each other off radiantly.
