Coevolutionary Framework for Generalized Multimodal Multi-Objective Optimization

Most multimodal multi-objective evolutionary algorithms(MMEAs)aim to find all global Pareto optimal sets(PSs)for a multimodal multi-objective optimization problem(MMOP).However,in real-world problems,decision makers(DMs)may be also interested in local PSs.Also,searching for both global and local PSs is more general in view of dealing with MMOPs,which can be seen as generalized MMOPs.Moreover,most state-of-theart MMEAs exhibit poor convergence on high-dimension MMOPs and are unable to deal with constrained MMOPs.To address the above issues,we present a novel multimodal multiobjective coevolutionary algorithm(Co MMEA)to better produce both global and local PSs,and simultaneously,to improve the convergence performance in dealing with high-dimension MMOPs.Specifically,the Co MMEA introduces two archives to the search process,and coevolves them simultaneously through effective knowledge transfer.The convergence archive assists the Co MMEA to quickly approach the Pareto optimal front.The knowledge of the converged solutions is then transferred to the diversity archive which utilizes the local convergence indicator and the-dominance-based method to obtain global and local PSs effectively.Experimental results show that Co MMEA is competitive compared to seven state-of-the-art MMEAs on fifty-four complex MMOPs.

Coevolution of Brachiopod Paleobiogeography and Tectonopaleogeography during the Early–Middle Permian

A comprehensive compilation and systematic analysis of known early and middle Permian brachiopod faunas shows that the early Permian brachiopod faunas comprise three realms, six regions, and eleven provinces, while those of the middle Permian comprise three realms, four regions, and eight provinces. A comparison and analysis of brachiopod faunal patterns reveal a coevolution between global brachiopod paleobiogeography and tectonopaleogeography during the early-middle Permian. Although temperature/latitude is the main factor controlling the formation of three realms, tectonopaleogeographic factors determine the temperature/latitude in which the continents were located. The ＇continental barrier＇ of Pangea, as a ＇central axis＇ continent, divided the three realms into six regions, which indicates that the formation of biogeographic regions was controlled mainly by the tectonopaleogeographic factors. The evolution of tectonopaleogeography was sometimes a long-term process, so that the biogeographic regions（or provinces） controlled by tectonopaleogeography displayed relative stability. Shifts in the nature of biogeographic provinces（e.g., from cool water to warm water, and vice versa）, extensions or narrowing of geographical ranges, and recombinations of some provinces were all related to regional tectonic evolution. The study of the coevolution between brachiopod paleobiogeography and tectonopaleogeography not only accounts for the formation mechanisms of brachiopod paleobiogeographic patterns during the early-middle Permian, but also provides evidences for the locations and configurations of oceans and plates（blocks） during this period.

Development of Species-Specific PCR Primers and Sensitive Detection of the Tylenchulus semipenetrans in China

Tylenchulus semipenetrans is the most economically important and widespread nematode pest of citrus in China.rDNA-ITS of 14 populations of T.semipenetrans which were collected from different citrus groves or Chinese fir（Cunninghamia lanceolata） plantations in China were amplified and sequenced.The species-specific primers were designed for the first time to diagnosis T.semipenetrans based on the sequences of rDNA-ITS regions of geographic population above.The primers were sensitive to amplify the expected band size（297 bp） from DNA template of a single second-stage juvenile（J2） or different life stages of T.semipenetrans.No specific band was amplified from 15 non-target nematode species which were commonly found in citrus groves.Specificity and reliability of the primers were validated by further PCR amplification of 16 extra populations of T.semipenetrans collected from 4 provinces of China.The primers successfully detected a single J2 of T.semipenetrans within a whole nematode community comprising a large numbers of non-target nematode.The developed diagnostic technique can be used for accurate identification of T.semipenetrans and also as a decision tool for nematode management for citrus or Chinese fir in China.

Coevolution of Male and Female Response Preferences to Sexual Signals in Music Frogs

Male signaling influences both female choice and male-male competition. Although male signaling characteristics and female preferences have been shown to coevolve in many species, few studies have examined whether male signal characteristics and male receiver responses related to male-male competition also coevolve. The present study tested the hypothesis that male and female signal receiver preferences may coevolve in parallel for flogs in the genus Babina by comparing the acoustic structure of male advertisement calls of four closely related and geographically isolated Babina species. Then we assessed the behavioral responses of both male and female B. daunchina （Emei music frog） to male call playbacks from each of the four species. The results support the hypothesis that male and female signal receiver preferences have coevolved in this species. Specifically, both male and female B. daunchina respond strongly to the heterospecific calls of B. hainanensis, suggesting that preexisting biases exist in both females and males. Both male and female individuals showed a slight response to the calls of B. adenopleura while no response was evoked by the calls ofB. lini. The manifestation of similar response profiles in male and female B. daunchina to the calls of the four species support the idea that male and female signal receiver preferences evolved in parallel and that the origin of these receiver biases reflects adaptations dependent on the same neural and cognitive systems in both sexes.

Species-specific COI primers for rapid identification of a globally significant invasive pest, the cassava mealybug Phenacoccus manihoti Matile-Ferrero

The globally invasive cassava mealybug Phenacoccus manihoti Matile-Ferrero is a pernicious pest of cassava,and its recent introduction into Asia has raised considerable alarm.To slow or prevent further invasion,an accurate,simple,and developmental-stage-independent detection method for P.manihoti is required.In the present study,a PCR method based on a species-specific mitochondrial DNA cytochrome oxidase I(SS-COI)marker was developed for rapid identification of P.manihoti.One pair of SS-COI primers(PMSSZW-1F and PMSSZW-1R)was designed based on sequence variations in the COI gene among P.manihoti and related mealybug species.Specificity of the primer pair was validated on 21 closely related species.Sensitivity tests were performed on four immature developmental stages and female adults.Efficacy tests demonstrated that at the relatively low concentration of(135.2±14.7)pgresuspended DNA,the specific fragment was detected in all replicates.Furthermore,the SS-COI primer pair was assayed on three populations of P.manihoti from major exporting countries of cassava.The PCR assay was proved to be a rapid,simple,and reliable molecular measure for the identification of P.manihoti.This tool will be useful for quarantine,monitoring,and management of this invasive pest.

Use of species-specific PCR for the identification of 10 sea cucumber species

We developed a species-specific PCR method to identify species among dehydrated products of 10 sea cucumber species.Ten reverse species-specific primers designed from the 16 S rRNA gene,in combination with one forward universal primer,generated PCR fragments of ca.270 bp length for each species.The specificity of the PCR assay was tested with DNA of samples of 21 sea cucumber species.Amplification was observed in specific species only.The species-specific PCR method we developed was successfully applied to authenticate species of commercial products of dehydrated sea cucumber,and was proven to be a useful,rapid,and low-cost technique to identify the origin of the sea cucumber product.

Species-specific PCR-based assays for identification and detection of Botryosphaeriaceae species causing stem blight on blueberry in China

Botryosphaeriaceae species are important causal agents of blueberry stem blight worldwide. Blueberry stem blight has become an important disease, potentially affecting the quality and production of blueberries in China. It is difficult and time-consuming to identify at the species level using morphological methods. The aim of this study was to develop polymerase chain reaction（PCR） assays for the diagnosis and early detection of latent infections of blueberry stems by Botryosphaeria spp. Species-specific primers, based on the ribosomal DNA internal transcribed spacer region and β-tubulin gene, were designed and selected for use in PCR assays. Three primer pairs, Lt347-F/R for Lasiodiplodia theobromae, Np304-F/R for Neofusicoccum parvum and FaF/Bt2b for Botryosphaeria dothidea, successfully amplified specific PCR fragments of different sizes on pure cultures or from blueberry stems inoculated and naturally infected blueberry plants with three pathogens, respectively. These primers did not amplify any PCR fragments from other blueberry stem disease-associated pathogens, such as Phomopsis spp. and Pestalotiopsis spp. This PCR protocol could detect as low as 1 00 pg to 1 ng of purified fungal DNA. This PCR-based protocol could be used for the diagnosis and detection of these pathogens from pure cultures or from infected blueberry plants.

A coevolutionary framework based on temporal and spatial ecology of host-parasite interactions:A missing link in studies of brood parasitism

A central tenet of coevolutionary theory,including theory of the coevolutionary relationship between brood parasites and their hosts,is that temporal and spatial patterns may reveal important information about ecological and evolutionary dynamics.For instance,level of genetic structure of populations provides important information about the role of genetics and gene ow in determining local patterns of selection on hosts due to parasitism(i.e.,egg rejection) and on parasites due to selection by hosts(i.e.,egg mimicry).Furthermore,abiotic(i.e.,climatic conditions) and biotic(phenotypic characteristics of animals) factors that also vary spatially may directly or indirectly a ect populations of hosts and brood parasites and,therefore,their interaction.By reviewing the literature,we found considerable evidence for an e ect of the spatially and temporally structured abiotic environment on the phenotype of both parasite and host eggs and the degree of mimicry.Moreover,we found examples suggesting that speci c life history characteristics of hosts that vary geographically and/or temporally may a ect the probability of initial colonization of a new host species and the direction and the speed of coevolution.We provide an exhaustive review of studies investigating temporal and spatial patterns of the interaction between brood parasites and their hosts.Such temporal and spatial trends in parasite and host traits are,together with genetic information on rejection and signi cant e ects of gene ow,consistent with coevolutionary dynamics.However,gene ow and changes in the temporal and spatial patterns of abundance of both parasites and hosts may result in frequent cases of counter-intuitive relationships between the phenotype of the parasite and that of the host(i.e.,poor or no mimicry),which may suggest limits to the degree of adaptation.We provide a list of scienti c questions in need of further investigation,concluding that studies of brood parasites and their hosts may play a central role in testing the geographic theory of coevolution and several alternative hypotheses.

A coevolutionary framework of business-IT alignment via the lens of enterprise architecture

Due to the turbulent external business environment, the complexity of internal relations of the organization and the emergence of subversive IT roles, the business-IT alignment(BITA)has become increasingly difficult. The unsuccessful realization of BITA will lead to the waste of organizational resources, the reduction of return on investment and eventually the loss of competitive advantage. In recent years, coevolution has received widespread attention due to its ability to describe the dynamic relationship between IT and business. Multiple principles such as quickening learning action loops and adopt suitable organizing principles for achieving business and IT coevolution(BITC) are obtained. However, the continuous BITC is still hard to be achieved because of the lack of complete BITC management. This paper focuses on the management process of the BITC and how to perform it gradually. A coevolution framework combines the enterprise architecture(EA) approach with the coevolution analysis is proposed, which contains the design of EA, the sensing and governance of the misalignment and the procedure of the EA misalignment prevention.The steps for the governance and prevention of misalignment are discussed in particular. Through comparison with the principles,characteristics and methods of coevolution in the literature, the proposed framework is evaluated. The results show that the proposed framework is effective for BITC implementation.

Coevolution of acoustical communication between obligate avian brood parasites and their hosts

The mutually antagonistic processes producing adaptations and counter-adaptations in avian brood parasites and their hosts provide a model system for the study of coevolution;this topic has long been an area of focus in ornithology and evolutionary biology.Although there is an extensive body of literature dealing with avian brood parasitism,few empirical studies have considered the effects of the coevolutionary processes associated with brood parasitism on the acoustic characteristics of parent–offspring communication.Under the strong selection pressures associated with brood parasitism,parasitic birds may,for instance,produce deceptive songs.The host may in turn evolve the ability to recognize these sounds as deceptive.At present,the mechanisms underlying the different competitive strategies employed by hosts and parasitic birds remain unclear.Here,we reviewed previous studies that investigated acoustic traits in scenarios of brood parasitism,highlighting possible adaptive functions.Using a meta-analysis,we identified no heterogeneity among studies of begging call adaptations in parasitic nestlings.However,our results may have been affected by the small number of applicable papers available for analysis.Our meta-analysis also suggested that studies of acoustic communication and transmission in adult hosts were highly heterogenous,suggesting that research methods were inconsistent among studies.Finally,we identified knowledge gaps and proposed several lines of future research.

Using the theory of coevolution to predict protein-protein interactions in non-small cell lung cancer

Systems biology has become an effective approach for understanding the molecular mechanisms underlying the development of lung cancer.In this study,sequences of 100 non-small cell lung cancer (NSCLC)-related proteins were downloaded from the National Center for Biotechnology Information (NCBI) databases.The Theory of Coevolution was then used to build a protein-protein interaction (PPI) network of NSCLC.Adopting the reverse thinking approach,we analyzed the NSCLC proteins one at a time.Fifteen key proteins were identified and categorized into a special protein family F(K),which included Cyclin D1 (CCND1),E-cadherin (CDH1),Cyclin-dependent kinase inhibitor 2A (CDKN2A),chemokine (C-X-C motif) ligand 12 (CXCL12),epidermal growth factor (EGF),epidermal growth factor receptor (EGFR),TNF receptor superfamily,member 6(FAS),FK506 binding protein 12-rapamycin associated protein 1 (FRAP1),O-6-methylguanine-DNA methyltransferase (MGMT),parkinson protein 2,E3 ubiquitin protein ligase (PARK2),phosphatase and tensin homolog (PTEN),calcium channel voltage-dependent alpha 2/delta subunit 2 (CACNA2D2),tubulin beta class I (TUBB),SWI/SNF-related,matrix-associated,actin-dependent regulator of chromatin,subfamily a,member 2 (SMARCA2),and wingless-type MMTV integration site family,member 7A (WNT7A).Seven key nodes of the sub-network were identified,which included PARK2,WNT7A,SMARCA2,FRAP1,CDKN2A,CCND1,and EGFR.The PPI predictions of EGFR-EGF,PARK2-FAS,PTEN-FAS,and CACNA2D2-CDH1 were confirmed experimentally by retrieving the Biological General Repository for Interaction Datasets (BioGRID) and PubMed databases.We proposed that the 7 proteins could serve as potential diagnostic molecular markers for NSCLC.In accordance with the developmental mode of lung cancer established by Sekine et al.,we assumed that the occurrence and development of lung cancer were linked not only to gene loss in the 3p region (WNT7A,3p25) and genetic mutations in the 9p region but also to similar events in the regions of 1p36.2 (FRAP1),6q25.2-q27 (PARK2),and 11q13 (CCND1).Lastly,the invasion or metastasis of lung cancer happened.

Cuckoo parasitism on two closely-related Acrocephalus warblers in distant areas:a case of parallel coevolution?

Common Cuckoos(Cuculus canorus) parasitize nests of small passerines.e Cuckoo chicks cause the death of their nest-mates when evicting eggs or nestlings from the nests;consequently,hosts su er from a high loss of reproduction.Host adaptations against parasitism,e.g.,by egg discrimination behavior,and cuckoo counter-adaptations to hosts,e.g.,by mimetic eggs,are often regarded as a result of the arms race between the two interacting species.In Hungary Great Reed Warblers(Acrocephalus arundinaceus) are the main hosts of cuckoos,su ering from heavy parasitism(ca.40-65%).e Oriental Reed Warbler(A.orientalis),formerly a subspecies of the Great Reed Warbler(A.a.orientalis),is also a highly parasitized host in Japan(25-40%).We compared main characteristics of Cuckoo parasitism in these two distant areas from the Western and Eastern Palearctic by comparing cuckoo egg mimicry.We measured color characteristics of host and parasitic eggs by spectrophotometer.Visual modeling revealed lower chromatic distances between Cuckoo and host eggs in Hungary than in Japan,but high variation both in host and Cuckoo eggs may cause matching problems in Hungary.Achromatic(brightness) di erence between host and Cuckoo eggs were lower in Japan than in Hungary,and it proved to be the most important factor a ecting egg rejection.Hosts rejected Cuckoo eggs at similar frequencies(37% and 35% in Hungary and Japan,respectively).Host adaptation,i.e.,egg rejection behavior,seems to be preceding Cuckoo counter-adaptations to hosts in Japan.We suggest that the Cuckoo-Great/Oriental Reed Warbler relationships developed in alternative ways in Japan and Hungary,and they represent di erent stages of their arms race.

Coevolutionary insights between promoters and transcription factors in the plant and animal kingdoms

The divergence and continuous evolution of plants and animals contribute to ecological diversity.Promoters and transcription factors(TFs) are key determinants of gene regulation and transcription throughoutlife.However,theevolutionary trajectories and relationships of promoters and TFs are still poorly understood. Here, we conducted extensive analysis of large-scale multi-omics sequences in 420 animal species and 223 plant species spanning nearly a billion years of evolutionary history. Results showed that promoter GC-contentandTFisoelectricpoints,as features/signatures that accompany long biological evolution, exhibited increasing growth in animal cells but a decreasing trend in plant cells. Furthermore, the evolutionary trajectories of promoter and TF signatures in the animal kingdom provided further evidence that Mammalia as well as Aves evolved directly from the ancestor Reptilia. The strong correlation between promoter and TF signatures indicates that promoters and TFs formed antagonistic coevolution in the animal kingdom, but mutualistic coevolution in the plant kingdom. The distinct coevolutionary patterns potentially drive the plant-animal divergence, divergent evolution and ecological diversity.

A Rapid Identification Method of Bactrocera cilifera (Hendel) with Species-Specific Primers(SS-COI)

[Objective]The paper was to establish a rapid identification method of Bactrocera cilifera(Hendel)with species-specific primers(SS-COI).[Method]Using B.cilifera(Hendel)as the positive control,and 19 species of fruit flies such as B.diaphora(Coquillett)and B.dorsalis(Hendel)as the negative controls,a pair of species-specific primers,YF290 and YR511,were designed and screened for accurate identification of B.cilifera,based on mitochondrial DNA COI sequence.[Result]The PCR products were amplified and detected by electrophoresis.Only a clear and single band was observed at about 222 bp in the positive control,while no bands were found in the other negative controls.[Conclusion]The established rapid identification method with species-specific primers(SS-COI)is of great practical significance for rapid identification of fruit flies intercepted from import and export fruits and vegetables at ports,and for rapid clearance and early warning of import fruits and vegetables at ports.

Identification of various Biomphalaria alexandrina strains collected from five Egyptian governorates using RAPD and species-specific PCR techniques

The first generation of Biomphalaria snails collected from five Egyptian governorates (Giza, Fayoum, Kafr El-Sheikh, Ismailia and Damietta) were sub-jected to species-specific PCR assays and the results showed that snails collected from the field were B. alexandrina, and there was no evidence for the pres-ence of B. glabrata. The snails were subjected also to RAPD- PCR technique. The results showed that dif-ferent fingerprints with each B. alexandrina strain were produced with varying numbers of bands rang-ing in size from 123.6 to 796.6 bp depending on the snail strain and the primer used. Many specific bands were obtained with the four primers in each strain. Primer OPA-1 amplified the highest number of spe-cific bands (26 bands) and gave the highest poly-morphism among the primers used (100% polymor-phism). The estimated similarity coefficients among B. alexandrina strains based on the RAPD-PCR pro-files ranged from 0.56 to 0.72. The highest similarity coefficient (0.72) was recorded between the strains of Ismailia and Kafr El-Sheikh, while the lowest coeffi-cient (0.56) was reported between the strains of SPSC and Ismailia.

Construction of Agropyrum intermedium 2Ai-2 Chromosome DNA Library and Cloning of Species-Specific DNA Sequences

The univalent from the meiosis-metaphase spreads of F1 (Z2× wheat variety Wan7107) wasidentified to be Agropyrum intermedium 2Ai-2 chromosome by GISH. The 2Ai-2 chromosomes weremicroisolated and collected. After two rounds of PCR amplification, the PCR products wereranged from 150-3 000 bp,with predominant fragments at about 200-2 000 bp. Using Ag.intermedium genomic DNA as a probe, Southern blotting analysis confirmed the products originatedfrom Ag. intermedium genome. The products were purified, ligated to pUC18 and then transformedinto competence E.coli DH5αto produce a 2Ai-2 chromosome DNA library. The microcloningexperiments produced approximately 5 ×105 clones, the size range of the cloned inserts was 200-1 500 bp, with an average of 580 bp. Using Ag.intermedium genomic DNA as a probe, dot blottingresults showed that 56% clones are unique/low copy sequences, 44% are repetitive sequences inthe library. Four Ag. intermedium clones were screened from the library by RFLP, and threeclones(Mag065, Mag088, Mag139)belong to low/single sequences, one clone(Mag104)was repetitivesequence, and GISH results indicated that Mag104 was Ag.intermedium species-specific repetitiveDNA sequence.

Cowbirds, conservation, and coevolution: potential misconceptions and directions for future research

Avian brood parasitism is a model system for studies of coevolution and ecological interactions between parasites and their hosts. However, recent work may have led to misconceptions concerning the Brown-headed Cowbird (Molothrus ater), the most widely studied brood parasitic bird in the world, and its effects on host species. Potential misconceptions about this species that could affect management issues are as follows: cowbird populations are increasing; cowbirds are relatively new to North America; recently exposed hosts are defenseless against parasitism; cowbirds have caused widespread declines of songbirds; and cowbird control is always effective in increasing the size of endangered host populations. Potential coevolutionary misconceptions are that cowbirds are typically 'host tolerant'; cowbirds evict host nestmates; and the mafia effect is widespread. It is important to clarify these issues because such misconceptions could hinder our understanding of parasite-host interactions, and thus obscure the direction of basic research and of management efforts taken to limit cowbird impacts on endangered species. We discuss these issues and suggest future research directions to enhance our understanding of this fascinating species.

土壤厚度演化模型理论方法研究进展

全球平均土壤厚度仅约为1 m,但土壤厚度的空间分布信息在地貌、生态及水文科学等领域的研究和实践中具有重要价值。由于其具有显著的空间异质性,基于现有土壤制图产品、地球物理勘测及经验统计模型难以获取流域尺度土壤厚度分布信息,亟待发展土壤厚度预测的过程机理模型。本文回顾了土壤厚度演化模型理论方法的研究进展,评价了不同土壤生成及输移模型的适用性。研究指出土壤化学风化成土等机理仍不清晰是制约模型发展的理论瓶颈。此外,模型的方法体系仍需完善,亟待进一步发展描述土壤生成和输移的函数形式及其参数的估计方法等,指出物理与随机结合的模拟方法以及基于数学物理途径的参数确定方法等有望解决模型应用中遇到的难题。最后,在土壤厚度演化模型基础上,提出发展基于流域协同演化理论的土壤发生学模型是定量预测土壤理化全要素发生所亟需突破的难点之一。

LeCMPSO算法求解异构无人机协同多任务重分配问题

无人机系统在军事领域有着广泛应用,由于战场环境复杂多变,无人机遭遇突发状况后需进行任务重分配.异构无人机是指多种类型的无人机,可完成单一无人机无法完成的多类型复杂任务,异构无人机协同多任务重分配问题约束条件复杂且包含混合变量,现有多目标优化算法不能有效处理此类问题.为高效求解上述问题,本文构建多约束异构无人机协同多任务重分配问题模型,提出一种学习引导的协同多目标粒子群优化算法(LeCMPSO),该算法引入基于先验知识的初始化策略和基于历史信息学习的粒子更新策略,能有效避免不可行解的产生并提升算法的搜索效率.通过在4组实例上的仿真实验表明,与其他典型的协同进化多目标优化算法相比,所提算法在解集的多样性、收敛性及搜索时间方面均具有较好的性能.

精英协同进化的蜉蝣算法

蜉蝣算法的种群多样性低、寻优性能差,为此提出基于精英协同进化的蜉蝣算法(ECMA).将雄性蜉蝣种群根据自身种群适应度分为精英种群和普通种群,精英个体进行自我学习以保持种群的多样性,实现高水平的全局搜索;普通个体飞向统一目标进行局部开发,以提高ECMA的收敛速度.根据婚姻市场理论改进雌性蜉蝣的位置更新,提高ECMA的寻优性能;引入新的自适应重力系数平衡全局搜索和局部开发能力,提高ECMA的收敛精度;引入莱维飞行的跳出策略,避免ECMA陷入局部最优.基于20个基准测试函数和CEC2019测试函数进行算法的仿真优化分析,与蜉蝣算法以及其他优秀的群智能算法相比,ECMA在寻优精度、收敛速度和稳定性方面均有较大提升.