Browsing by Author "Zhang P"

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    Comparison of Genotype Imputation for SNP Array and Low-Coverage Whole-Genome Sequencing Data
    (Frontiers Media S A, 2022-01-03) Deng T; Zhang P; Garrick D; Gao H; Wang L; Zhao F; Lingzhao F
    Genotype imputation is the term used to describe the process of inferring unobserved genotypes in a sample of individuals. It is a key step prior to a genome-wide association study (GWAS) or genomic prediction. The imputation accuracy will directly influence the results from subsequent analyses. In this simulation-based study, we investigate the accuracy of genotype imputation in relation to some factors characterizing SNP chip or low-coverage whole-genome sequencing (LCWGS) data. The factors included the imputation reference population size, the proportion of target markers /SNP density, the genetic relationship (distance) between the target population and the reference population, and the imputation method. Simulations of genotypes were based on coalescence theory accounting for the demographic history of pigs. A population of simulated founders diverged to produce four separate but related populations of descendants. The genomic data of 20,000 individuals were simulated for a 10-Mb chromosome fragment. Our results showed that the proportion of target markers or SNP density was the most critical factor affecting imputation accuracy under all imputation situations. Compared with Minimac4, Beagle5.1 reproduced higher-accuracy imputed data in most cases, more notably when imputing from the LCWGS data. Compared with SNP chip data, LCWGS provided more accurate genotype imputation. Our findings provided a relatively comprehensive insight into the accuracy of genotype imputation in a realistic population of domestic animals.
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    Developing a Framework for Sustainable Management of Archaeological Site Parks: Cross-Case Analysis Based on Public Perception
    (MDPI, Basel, Switzerland, 2025-04) Xi Y; Liu T; Wang Y; Ying FJ; Han Y; Luo S; Zhang P
    As official terms included in the International Council on Monuments and Sites (ICOMOS) documents, archaeological site parks have gradually emphasized the establishment of sustainable management frameworks for archaeological sites open to the public and enhancing public experiences. The management frameworks should be closely related to the goals of the United Nations and other international conventions on sustainable development. However, they lack implementation strategies to promote archaeological site protection and provide responsible tourism. This research adopts a multi-case study approach to analyze the management of representative archaeological site parks in the United States, Japan, and China to develop a framework for the sustainable management of archaeological site parks. Various values, heritage tourism activities, and public perceptions of each park are examined based on cross-case analysis, which identifies principal elements and strategies for the sustainable management of archaeological parks. The principal elements reflect the archaeological parks’ intrinsic value, utility value, and other values. The strategies are closely related to the design of heritage tourism activities and are in alignment with the UN’s sustainable development goals. The theoretical and practical contributions of this research include the reflection and explanation of the sustainable management practices of archaeological site parks in different national and cultural contexts, considering public perceptions. The proposed framework and strategy integrate management guidelines, theoretical knowledge, and practical experience of public archaeological site parks. The outcomes of this research provide a reference for the study of archaeological parks and the management of heritage landscapes.
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    Obligate mutualism within a host drives the extreme specialization of a fig wasp genome
    (BioMed Central Ltd, 20/12/2013) Xiao J-H; Yue Z; Jia L-Y; Yang X-H; Niu L-H; Wang Z; Zhang P; Sun B-F; He S-M; Li Z; Xiong T-L; Xin W; Gu H-F; Wang B; Werren JH; Murphy RW; Wheeler D; Niu L-M; Ma G-C; Tang T; Bian S-N; Wang N-X; Yang C-Y; Wang N; Fu Y-G; Li W-Z; Yi SV; Yang X-Y; Zhou Q; Lu C-X; Xu C-Y; He L-J; Yu L-L; Chen M; Zheng Y; Wang S-W; Zhao S; Li Y-H; Yu Y-Y; Qian X-J; Cai Y; Bian L-L; Zhang S; Wang J-Y; Yin Y; Xiao H; Wang G-H; Yu H; Wu W-S; Cook JM; Wang J; Huang D-W
    Background: Fig pollinating wasps form obligate symbioses with their fig hosts. This mutualism arose approximately 75 million years ago. Unlike many other intimate symbioses, which involve vertical transmission of symbionts to host offspring, female fig wasps fly great distances to transfer horizontally between hosts. In contrast, male wasps are wingless and cannot disperse. Symbionts that keep intimate contact with their hosts often show genome reduction, but it is not clear if the wide dispersal of female fig wasps will counteract this general tendency. We sequenced the genome of the fig wasp Ceratosolen solmsi to address this question. Results: The genome size of the fig wasp C. solmsi is typical of insects, but has undergone dramatic reductions of gene families involved in environmental sensing and detoxification. The streamlined chemosensory ability reflects the overwhelming importance of females finding trees of their only host species, Ficus hispida, during their fleeting adult lives. Despite long-distance dispersal, little need exists for detoxification or environmental protection because fig wasps spend nearly all of their lives inside a largely benign host. Analyses of transcriptomes in females and males at four key life stages reveal that the extreme anatomical sexual dimorphism of fig wasps may result from a strong bias in sex-differential gene expression. Conclusions: Our comparison of the C. solmsi genome with other insects provides new insights into the evolution of obligate mutualism. The draft genome of the fig wasp, and transcriptomic comparisons between both sexes at four different life stages, provide insights into the molecular basis for the extreme anatomical sexual dimorphism of this species. © 2013 Xiao et al.; licensee BioMed Central Ltd.