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| 1 | Distant hybridization leads to different ploidy fishes显示文摘Distant hybridization makes it possible to transfer the genome of one species to another, which results in changes in phenotypes and genotypes of the progenies. This study shows that distant hybridization or the combination of this method with gynogenesis or androgenesis lead to different ploidy fishes with genetic variation, including fertile tetraploid hybrids, sterile triploid hybrids, fertile diploid hybrids, fertile diploid gynogenetic fish, and their derived progenies. The formations of the different ploidy fishes depend on the genetic relationship between the parents. In this study, several types of distant hybridization, including red crucian carp (Carassius auratus red var.) (2n=100, abbreviated as RCC) (♀)×common carp (Cyprinus carpio L.) (2n=100, abbreviated as CC) (♂), and RCC (2n=100) (♀)×blunt snout bream (Megalobrama amblycephala) (2n=48, abbreviated as BSB) (♂) are described. In the distant hybridization of RCC (♀)×CC (♂), bisexual fertile F3–F18 allotetraploid hybrids (4n=200, abbreviated as 4nAT) were formed. The diploid hybrid eggs and diploid sperm generated by the females and males of 4nAT developed into diploid gynogenetic hybrids and diploid androgenetic hybrids, respectively, by gynogenesis and androgenesis, without treatment for doubling the chromosome. Improved tetraploid hybrids and improved diploid fishes with genetic variation were derived from the gynogenetic hybrid line. The improved diploid fishes included the high-body RCC and high-body goldfish. The formation of the tetraploid hybrids was related to the occurrence of unreduced gametes generated from the diploid hybrids, which involved in premeiotic endoreduplication, endomitosis, or fusion of germ cells. The sterile triploid hybrids (3n=150) were produced on a large scale by crossing the males of tetraploid hybrids with females of diploid fish (2n=100). In another distant hybridization of RCC (♀)×BSB (♂), different ploidy fishes were obtained, including diploid bisexual fertile natural gynogenetic fish (2n=100), sterile triploid hybrids (3n=124), and bisexual fertile tetraploid hybrids (4n=148). Furthermore, two kinds of pentaploid hybrids (5n=172 and 5n=198) were formed. The biological characteristics and the mechanisms of formation of the different ploidy fish were compared and discussed at the cellular and molecular level. The results indicated distant hybridization or the combination of this method with gynogenesis or androgenesis affects the formation of different ploidy fish with genetic variation. | LIU ShaoJun Key Laboratory of Protein Chemistry and Fish Developmental Biology of Education Ministry of China, College of Life Sciences, Hunan Normal University, Changsha 410081, China | 2010 | Science China(Life Sciences)2010，53，4： | 39 |
| 2 | A New Evolutionary Algorithm for Function Optimization显示文摘A new algorithm based on genetic algorithm(GA) is developed for solving function optimization problems with inequality constraints. This algorithm has been used to a series of standard test problems and exhibited good performance. The computation results show that its generality, precision, robustness, simplicity and performance are all satisfactory. | GUO Tao, KANG Li shan State Key Laboratory of Software Engineering, Wuhan University,Wuhan 430072, China | 1999 | Wuhan University Journal of Natural Sciences1999，4，4： | 37 |
| 3 | 一种基于正态分布交叉的ε-MOEA显示文摘实数编码的多目标进化算法常使用模拟二进制交叉(simulated binary crossover,称SBX)算子.通过对SBX以及进化策略中变异算子进行对比分析,并引入进化策略中的离散重组算子,提出了一种正态分布交叉(normal distribution crossover,称NDX)算子.首先在一维搜索空间实例中对NDX与SBX算子进行比较和分析,然后将NDX算子应用于Deb等人提出的稳态多目标进化算法ε-MOEA(ε-dominance based multiobjective evolutionary algorithm)中.采用NDX算子的ε-MOEA(记为ε-MOEA/NDX)算法在多目标优化标准测试集ZDT和DTLZ的10个函数上进行了实验比较.实验结果和分析表明,采用NDX的ε-MOEA所求得的Pareto最优解集质量明显优于经典算法ε-MOEA/SBX和NSGA-Ⅱ. | 张敏 罗文坚 王煦法 | 2009 | 软件学报2009，20，2： | 33 |
| 4 | A Review on Swarm Intelligence and Evolutionary Algorithms for Solving Flexible Job Shop Scheduling Problems显示文摘Flexible job shop scheduling problems(FJSP)have received much attention from academia and industry for many years.Due to their exponential complexity,swarm intelligence(SI)and evolutionary algorithms(EA)are developed,employed and improved for solving them.More than 60%of the publications are related to SI and EA.This paper intents to give a comprehensive literature review of SI and EA for solving FJSP.First,the mathematical model of FJSP is presented and the constraints in applications are summarized.Then,the encoding and decoding strategies for connecting the problem and algorithms are reviewed.The strategies for initializing algorithms?population and local search operators for improving convergence performance are summarized.Next,one classical hybrid genetic algorithm(GA)and one newest imperialist competitive algorithm(ICA)with variables neighborhood search(VNS)for solving FJSP are presented.Finally,we summarize,discus and analyze the status of SI and EA for solving FJSP and give insight into future research directions. | Kaizhou Gao Zhiguang Cao Le Zhang Zhenghua Chen Yuyan Han Quanke Pan | 2019 | IEEE/CAA Journal of Automatica Sinica2019，6，4： | 32 |
| 5 | Diversity,evolutionary contribution and ecological roles of aquatic viruses显示文摘Aquatic viruses include infected viruses in aquatic animals, plants and microorganisms, and free-floating viruses(virioplankton)in water environments. In the last three decades, a huge number of aquatic viruses, especially diverse free-floating viruses,including cyanophages, phycoviruses, archaea viruses, giant viruses, and even virophages, have been identified by virological experiments and metagenomic analyses. Based on a comprehensive introduction of aquatic virus classification and their morphological and genetic diversity, here, we summarize and outline main virus species, their evolutionary contribution to aquatic communities through horizontal gene transfer, and their ecological roles for cyanobacterial bloom termination and global biogeochemical cycling in freshwater and marine ecosystems. Thereby, some novel insights of aquatic viruses and virus-host interactions, especially their evolutionary contribution and ecological rolesin diverse aquatic communities and ecosystems, are highlighted in this review. | Qi-Ya Zhang Jian-Fang Gui | 2018 | Science China(Life Sciences)2018，61，12： | 19 |
| 6 | A Tentative Research on Complexity of Automatic Programming显示文摘In this paper, based on the following theoretical framework: Evolutionary Algorithms + Program Structures = Automatic Programming , some results on complexity of automatic programming for function modeling is given, which show that the complexity of automatic programming is an exponential function of the problem dimension N , the size of operator set |F| and the height of the program parse tree H . Following this results, the difficulties of automatic programming are discussed. Some function models discovered automatically from database by evolutionary modeling method are given, too. | Kang Li\|shan, Li Yan, Chen Yu\|ping Computation Center, State Key Laboratory of Software Engineering,Wuhan University,Wuhan 430072,China | 2001 | Wuhan University Journal of Natural Sciences2001，6，Z1： | 18 |
| 7 | Early-Mid Ordovician brachiopod diversification in South China显示文摘Affected by paleogeographic position, paleoclimatic condition and depositional environments, the increase of the Early-Mid Ordovician brachiopod diversity of South China commenced at the beginning of the Ordovician (early Tremadoc), accelerated from the Tetra- graptus approximatus Biozone (base of Arenig), and reached its first acme in the Didymograptus eobifidus Biozone (mid early Arenig) when the number of brachiopod genera was over 7 times as great as that at the start of the Ordovician. This was the first radiation in the history of brachiopod macroevolution in South China, which occurred nearly 5 graptolitic biozones earlier than the global trend of the great Ordovician biodiversification (in the lower part of the Undulograptus austrodentatus Biozone). It is also characterized by (1) the origination or first occurrences of some major groups, such as the punctate dalmanelloids and the pseudopunctate stro- phomenoids including Plectambonitoidea (cardinal process simple or absent) and Stro- phomenoidea (cardinal process bilobed) in South China; (2) niche expansion, particularly in the first occupation of deeper water benthic regimes by the Euorthisina-Nocturnellia Association developed at Houping, Chengkou, northern Chongqing; and (3) the differentiation of brachiopod faunas under different environmental conditions. The gradual and increasing separation from Gondwana may have been one of the factors responsible for the radiation in South China. | ZHAN Renbin, RONG Jiayu, CHENG Jinhui & CHEN Pengfei Nanjing Institute of Geology and Palaeontology, Chinese Academy of Sciences State Key Laboratory of Palaeobiology and Stratigraphy, Nanjing 210008, China | 2005 | Science China Earth Sciences2005，48，5： | 14 |
| 8 | A hybrid evolutionary algorithm for distribution feeder reconfiguration显示文摘This paper presents a new method to reduce the distribution system loss by feeder reconfiguration.This new method combines self-adaptive particle swarm optimization(SAPSO) with shuffled frog-leaping algorithm(SFLA) in an attempt to find the global optimal solutions for the distribution feeder reconfiguration(DFR).In PSO algorithm,appropriate adjustment of the parameters is cumbersome and usually requires a lot of time and effort.Thus,a self-adaptive framework is proposed to improve the robustness of PSO.In SAPSO the learning factors of PSO coevolve with the particles.SFLA is combined with the SAPSO algorithm to improve its performance.The proposed algorithm is tested on two distribution test networks.The results of simulation show that the proposed algorithm is very powerful and guarantees to obtain the global optimization in minimum time. | Taher NIKNAM Ehsan AZAD FARSANI | 2010 | Science China(Technological Sciences)2010，53，4： | 10 |
| 9 | Biodiversity-based development and evolution:the emerging research systems in model and non-model organisms显示文摘Evolutionary developmental biology,or Evo-Devo for short,has become an established field that,broadly speaking,seeks to understand how changes in development drive major transitions and innovation in organismal evolution.It does so via integrating the principles and methods of many subdisciplines of biology.Although we have gained unprecedented knowledge from the studies on model organisms in the past decades,many fundamental and crucially essential processes remain a mystery.Considering the tremendous biodiversity of our planet,the current model organisms seem insufficient for us to understand the evolutionary and physiological processes of life and its adaptation to exterior environments.The currently increasing genomic data and the recently available gene-editing tools make it possible to extend our studies to non-model organisms.In this review,we review the recent work on the regulatory signaling of developmental and regeneration processes,environmental adaptation,and evolutionary mechanisms using both the existing model animals such as zebrafish and Drosophila,and the emerging nonstandard model organisms including amphioxus,ascidian,ciliates,single-celled phytoplankton,and marine nematode.In addition,the challenging questions and new directions in these systems are outlined as well. | Long Zhao Feng Gao Shan Gao Yujun Liang Hongan Long Zhiyi Lv Ying Su Naihao Ye Liusuo Zhang Chengtian Zhao Xiaoyu Wang Weibo Song Shicui Zhang Bo Dong | 2021 | Science China(Life Sciences)2021，64，8： | 9 |
| 10 | Population Genomic Analysis and De Novo Assembly Reveal the Origin of Weedy Rice as an Evolutionary Game显示文摘Crop weediness,especially that of weedy rice(Oryza sativa f.spontanea),remains mysterious.Weedy rice possesses robust ecological adaptability;however,how this strain originated and gradually formed proprietary genetic features remains unclear?Here,we demonstrate that weedy rice at Asian high latitudes(WRAH)is phylogenetically well defined and possesses unselected genomic characteristics in many divergence regions between weedy and cultivated rice.We also identified novel quantitative trait loci underlying weedy-specific traits,and revealed that a genome block on the end of chromosome 1 is associated with rice weediness.To identify the genomic modifications underlying weedy rice evolution,we generated the first de novo assembly of a high-quality weedy rice genome(WR04-6),and conducted a comparative genomics study between WR04-6 with other rice reference genomes.Multiple lines of evidence,including the results of demographic scenario comparisons,suggest that differentiation between weedy rice and cultivated rice was initiated by genetic improvement of cultivated rice and that the essence of weediness arose through semi-domestication.A plant height model further implied that the origin of WRAH can be modeled as an evolutionary game and indicated that strategy-based selection driven by fitness shaped its genomic diversity. | Jian Sun Dianrong Ma Liang Tang Minghui Zhao Guangchen Zhangh Wenjia Wang Jiayu Song Xiang Li Zimeng Liu Wenxing Zhang Quan Xu Yuncheng Zhou Jianzhong Wu Toshio Yamamoto Fei Dai Yan Lei Song Li Gang Zhou Hongkun Zheng Zhengjin Xu Wenfu Chen | 2019 | Molecular Plant2019，12，5： | 9 |
| 11 | Phylogenetic community ecology: integrating community ecology and evolutionary biology显示文摘The species composition of a biological community results from the interplay between evolutionary and ecological processes(Ricklefs 1987).It depends on the availability of species in the species pool of the region where the community is located,the dispersal ability of species in the regional species pool that allows them to reach the community and the degree to which the species that have reached the community can tolerate abiotic and biotic conditions in the locality(Willis et al.2010).However,evolutionary and ecological processes assembling species into biological communities have generally been studied in isolation from one another(Johnson and Stinchcombe 2007).In the face of widespread and various anthropogenic threats to biological communities worldwide,it is urgent to understand how evolutionary and ecological processes interplay to generate and maintain biodiversity patterns and species membership in biological communities across the globe. | Hong Qian Lin Jiang | 2014 | Journal of Plant Ecology2014，7，2： | 8 |
| 12 | Ascomycota has a faster evolutionary rate and higher species diversity than Basidiomycota显示文摘Differences in rates of nucleotide or amino acid substitutions among major groups of organisms are repeatedly found and well documented. A growing body of evidence suggests a link between the rate of neutral molecular change within populations and the evolution of species diversity. More than 98% of terrestrial fungi belong to the phyla Ascomycota or Basidiomycota. The former is considerably richer in number of species than the latter. We obtained DNA sequences of 21 protein-coding genes from the lichenized fungus Rhizoplaca chrysoleuca and used them together with sequences from GenBank for subsequent analyses. Three datasets were used to test rate discrepancies between Ascomycota and Basidiomycota and that within Ascomycota: (i) 13 taxa including 105 protein-coding genes, (ii) nine taxa including 21 protein-coding genes, and (iii) nuclear LSU rDNA of 299 fungal species. Based on analyses of the 105 protein-coding genes and nuclear LSU rDNA datasets, we found that the evolutionary rate was higher in Ascomycota than in Basidiomycota. The differences in substitution rates between Ascomycota and Basidiomycota were significant. Within Ascomycota, the species-rich Sordariomycetes has the fastest evolutionary rate, while Leotiomycetes has the slowest. Our results indicate that the main contribution to the higher substitution rates in Ascomycota does not come from mutualism, ecological conditions, sterility, metabolic rate or shorter generation time, but is possibly caused by the founder effect. This is another example of the correlation between species number and evolutionary rates, which is consistent with the hypothesis that the founder effect is responsible for accelerated substitution rates in diverse clades. | Lumbsch H. THORSTEN | 2010 | Science China(Life Sciences)2010，53，10： | 8 |
| 13 | Evolutionary game dynamics of combining the Moran and imitation processes显示文摘One of the assumptions of previous research in evolutionary game dynamics is that individuals use only one rule to update their strategy. In reality, an individual's strategy update rules may change with the environment, and it is possible for an individual to use two or more rules to update their strategy. We consider the case where an individual updates strategies based on the Moran and imitation processes, and establish mixed stochastic evolutionary game dynamics by combining both processes. Our aim is to study how individuals change strategies based on two update rules and how this affects evolutionary game dynamics. We obtain an analytic expression and properties of the fixation probability and fixation times(the unconditional fixation time or conditional average fixation time) associated with our proposed process. We find unexpected results. The fixation probability within the proposed model is independent of the probabilities that the individual adopts the imitation rule update strategy. This implies that the fixation probability within the proposed model is equal to that from the Moran and imitation processes. The one-third rule holds in the proposed mixed model. However, under weak selection, the fixation times are different from those of the Moran and imitation processes because it is connected with the probability that individuals adopt an imitation update rule. Numerical examples are presented to illustrate the relationships between fixation times and the probability that an individual adopts the imitation update rule, as well as between fixation times and selection intensity. From the simulated analysis, we find that the fixation time for a mixed process is greater than that of the Moran process, but is less than that of the imitation process. Moreover, the fixation times for a cooperator in the proposed process increase as the probability of adopting an imitation update increases; however, the relationship becomes more complex than a linear relationship. | 王先甲 顾翠伶 吕少杰 全吉 | 2019 | Chinese Physics B2019，28，2： | 7 |
| 14 | Divergent evolutionary patterns of the MAPK cascade genes in Brassica rapa and plant phylogenetics显示文摘Mitogen-activated protein kinase(MAPK)cascade signal transduction modules play crucial roles in regulating many biological processes in plants.These cascades are composed of three classes of hierarchically organized protein kinases,MAPKKKs,MAPKKs and MAPKs.Here,we analyzed gene retention,phylogenetic,evolution and expression patterns of MAPK cascade genes in Brassica rapa.We further found that the MAPK branches,classes III and IV,appeared after the split of bryophytes and green algae after analyzing the MAPK cascade genes in 8 species,and their rapid expansion led to the great size of the families of MAPKs.In contrast,the ancestral class I subfamily of MAPKK gene families have been highly conserved from algae to angiosperms.For the MAPKKK family,the MEKK and Raf subfamily share a common evolutionary origin,and Raf plays a major role in the expansion of the MAPKKK gene family.The cis-elements and interaction network analyses showed the important function of MAPK cascade genes in development and stress responses in B.rapa.This study provides a solid foundation for molecular evolution analyses of MAPK cascade genes. | Peng Wu Wenli Wang Ying Li Xilin Hou | 2017 | Horticulture Research2017，4，1： | 6 |
| 15 | Evolutionary pattern of fusulinacean foraminifer in Maokouan, middle Permian显示文摘A composite standard section (CSS) has been established for the Maokouan (≈Guadalupian) in Guizhou Province, southwestern China, which includes stratigraphical ranges of 179 fusulinacean species from five sections of the Maokou Formation in this area. Based on statistical results of the first and last appearances of fusulinacean species in the CSS, three evolutionary radiations and four pulses of extinction, characterized by high rates of species origination and extinction significantly different from the rates of background evolution, are recognized in the Maokouan fusulinacean fauna. The evolutionary pattern of fusulinacean foraminifer suggests that the Maokouan mass extinction probably started at the middle Maokouan and dramatically intensified in the late Maokouan. | 杨湘宁 周建平 刘家润 施贵军 | 1999 | Science China Earth Sciences1999，42，5： | 6 |
| 16 | A system-wide approach to minimize the operational cost of bench production in open-cast mining operations显示文摘The production cycle of open-cast coal mines generally in eludes drilling, blasting, loading, hauling and coal preparation activities. Individual optimization of these activities does not mean that the whole system is optimized. This paper proposes a cost model considering all activities in mining cycle and system-wide approach to minimize the total mining cost of bench production. Since the fragmentation size and blast-hole diameter are linked to all activities of mining system, they are considered as decision variables in the problem form ul at io n. The operatio n costs are then minimized by using the evolutionary algorithm. Moreover, the impact of the change in the explosive price, and the hourly unit cost of equipment on total mining cost is quantified by sensitivity analysis. A case study is implemented to demonstrate the developed model. | Burak Ozdemir Mustafa Kumral | 2019 | International Journal of Coal Science & Technology2019，6，1： | 5 |
| 17 | Evolutionary trace analysis of eukaryotic DNA topoisomerase I superfamily: Identification of novel antitumor drug binding site显示文摘The studies of novel inhibitors of DNA topoisomerase I (Topo I) have already be-come very promising in cancer chemotherapy. Identifying the new drug-binding residues is playing an important role in the design and optimization of Topo I inhibitors. The designed com-pounds may have novel scaffolds, thus will be helpful to overcome the toxicities of current camptothecin (CPT) drugs and may provide a solution to cross resistance with these drugs. Mul-tiple sequence alignments were performed on eukaryotic DNA topoisomerase I superfamily and thus the evolutionary tree was constructed. The Evolutionary Trace method was applied to iden-tify functionally important residues of human Topo I. It has been demonstrated that class-specific hydrophobic residues Ala351, Met428, Pro431 are located around the 7,9-position of CPT, indi-cating suitable substitution of hydrophobic group on CPT will increase antitumor activity. The conservative residue Lys436 in the superfamily is of particular interest and new CPT derivatives designed based on this residue may greatly increase water solubility of such drugs. It has also been demonstrated that the residues Asn352 and Arg364 were conservative in the superfamily, whose mutation will render CPT resistance. As our molecular docking studies demonstrated they did not make any direct interaction with CPT, they are important drug-binding site residues for future design of novel non-camptothecin lead compounds. This work provided a strong basis for the design and synthesis of novel highly potent CPT derivatives and virtual screening for novel lead compounds. | SONG Yunlong QI Yunpeng ZHANG Wannian SHENG Chunquan ZHANG Min YAO Jianzhong YU Jianxin MIAO Zhenyuan ZHOU Youjun ZHU Ju L(U) Jiaguo | 2005 | Science China(Life Sciences)2005，48，4： | 5 |
| 18 | The Early Evolution of the Acanthomorphic Acritarchs in China and Their Biostratigraphical Implication显示文摘On the basis of a study of the acanthomorphic acritarchs discovered in the Late Proterozoicto Early Cambrian Meishucunian Stage in different regions of China, especially in southernShaanxi and the Yangtze Platform, coupled with a study of the assemblages, morphological cor-relation, microstructure, and evolutional relations of the acanthorphic acritarchs, as well as awide correlation with those found in different regions of the world, the authors discuss the earlyevolutionary stages of the acanthomorphs, features of their assemblages in various stages, theirbiostratigraphical significance, and their evolutionary trend in China. | Yin Chongyu and Gao Linzhi Institute of Geology, Chinese Academy of Geological Sciences, Beijing | 1996 | Acta Geologica Sinica(English Edition)1996，70，2： | 5 |
| 19 | Bio-inspired geomagnetic navigation method for autonomous underwater vehicle显示文摘This paper presents a bio-inspired geomagnetic navigation method for autonomous underwater vehicle(AUV) without using any a priori geomagnetic information. Firstly, the multi-objective search problem is raised. Secondly, the geomagnetic navigation model is established by constructing a cost function. Then, by taking into consideration the biological magneto-taxis movement behavior for the geomagnetic environment stimulus, the multiobjective evolutionary search algorithm is derived to describe the search process. Finally, compared to the state-of-the-art, the proposed method presents better robustness. The simulation results demonstrate the reliability and feasibility of the proposed method. | Hong Li Mingyong Liu Kun Liu | 2017 | Journal of Systems Engineering and Electronics2017，28，6： | 5 |
| 20 | Integrating Evolutionary Testing with Reinforcement Learning for Automated Test Generation of Object-Oriented Software显示文摘Recent advances in evolutionary test generation greatly facilitate the testing of Object-oriented(OO) software. Existing test generation approaches are still limited when the Software under test(SUT) includes Inherited class hierarchies(ICH) and Non-public methods(NPM). This paper presents an approach to generate test cases for OO software via integrating evolutionary testing with reinforcement learning. For OO software with ICH and NPM, two kinds of particular isomorphous substitution actions are presented and a Q-value matrix is maintained to assist the evolutionary test generation. A prototype called Evo Q is developed based on this approach and is applied to generate test cases for actual Java programs.Empirical results show that Evo Q can efficiently generate test cases for SUT with ICH and NPM and achieves higher branch coverage than two state-of-the-art test generation approaches within the same time budget. | HE Wei ZHAO Ruilian ZHU Qunxiong | 2015 | Chinese Journal of Electronics2015，24，1： | 5 |
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