一个基于遗传算法的TSP问题解决方案

介绍了遗传算法的基本思想、TSP问题及其应用.基于经典的遗传算法思想,在一个解决TSP问题方案的基础上提出了改进方案.从问题的解决中可以看到,利用遗传算法解决实际问题,主要依赖于问题的编码以及遗传操作算子.     

Escape from adaptive conflict after duplication in an anthocyanin pathway gene

Gene duplications have been recognized as an important source of evolutionary innovation and adaptation since at least Haldane, and their varying fates may partly explain the vast disparity in observed genome sizes. The expected fates of most gene duplications involve primarily non-adaptive substitutions leading to either non-functionalization of one duplicate copy or subfunctionalization, neither of which yields novel function. A significant evolutionary problem is thus elucidating the mechanisms of adaptive evolutionary change leading to evolutionary novelty. Currently, the most widely recognized adaptive process involving gene duplication is neo-functionalization (NEO-F), in which one copy undergoes directional selection to perform a novel function after duplication. An alternative, but understudied, adaptive fate that has been proposed is escape from adaptive conflict (EAC), in which a single-copy gene is selected to perform a novel function while maintaining its ancestral function. This gene is constrained from improving either novel or ancestral function because of detrimental pleiotropic effects on the other function. After duplication, one copy is free to improve novel function, whereas the other is selected to improve ancestral function. Here we first present two criteria that can be used to distinguish NEO-F from EAC. Using both tests for positive selection and assays of enzyme function, we then demonstrate that adaptive evolutionary change in a duplicated gene of the anthocyanin biosynthetic pathway in morning glories (Ipomoea) is best interpreted as EAC. Finally, we argue that this phenomenon likely occurs more often than has been previously believed and may thus represent an important mechanism in generating evolutionary novelty.     

Evolution driven by differential dispersal within a wild bird population

Evolutionary theory predicts that local population divergence will depend on the balance between the diversifying effect of selection and the homogenizing effect of gene flow. However, spatial variation in the expression of genetic variation will also generate differential evolutionary responses. Furthermore, if dispersal is non-random it may actually reinforce, rather than counteract, evolutionary differentiation. Here we document the evolution of differences in body mass within a population of great tits, Parus major, inhabiting a single continuous woodland, over a 36-year period. We show that genetic variance for nestling body mass is spatially variable, that this generates different potential responses to selection, and that this diversifying effect is reinforced by non-random dispersal. Matching the patterns of variation, selection and evolution with population ecological data, we argue that the small-scale differentiation is driven by density-related differences in habitat quality affecting settlement decisions. Our data show that when gene flow is not homogeneous, evolutionary differentiation can be rapid and can occur over surprisingly small spatial scales. Our findings have important implications for questions of the scale of adaptation and speciation, and challenge the usual treatment of dispersal as a force opposing evolutionary differentiation.     

Speciation along environmental gradients

Traditional discussions of speciation are based on geographical patterns of species ranges. In allopatric speciation, long-term geographical isolation generates reproductively isolated and spatially segregated descendant species. In the absence of geographical barriers, diversification is hindered by gene flow. Yet a growing body of phylogenetic and experimental data suggests that closely related species often occur in sympatry or have adjacent ranges in regions over which environmental changes are gradual and do not prevent gene flow. Theory has identified a variety of evolutionary processes that can result in speciation under sympatric conditions, with some recent advances concentrating on the phenomenon of evolutionary branching. Here we establish a link between geographical patterns and ecological processes of speciation by studying evolutionary branching in spatially structured populations. We show that along an environmental gradient, evolutionary branching can occur much more easily than in non-spatial models. This facilitation is most pronounced for gradients of intermediate slope. Moreover, spatial evolutionary branching readily generates patterns of spatial segregation and abutment between the emerging species. Our results highlight the importance of local processes of adaptive divergence for geographical patterns of speciation, and caution against pitfalls of inferring past speciation processes from present biogeographical patterns.     

Rapid evolution drives ecological dynamics in a predator-prey system

Ecological and evolutionary dynamics can occur on similar timescales. However, theoretical predictions of how rapid evolution can affect ecological dynamics are inconclusive and often depend on untested model assumptions. Here we report that rapid prey evolution in response to oscillating predator density affects predator-prey (rotifer-algal) cycles in laboratory microcosms. Our experiments tested explicit predictions from a model for our system that allows prey evolution. We verified the predicted existence of an evolutionary tradeoff between algal competitive ability and defence against consumption, and examined its effects on cycle dynamics by manipulating the evolutionary potential of the prey population. Single-clone algal cultures (lacking genetic variability) produced short cycle periods and typical quarter-period phase lags between prey and predator densities, whereas multi-clonal (genetically variable) algal cultures produced long cycles with prey and predator densities nearly out of phase, exactly as predicted. These results confirm that prey evolution can substantially alter predator-prey dynamics, and therefore that attempts to understand population oscillations in nature cannot neglect potential effects from ongoing rapid evolution.     

二氧化碳排放演变驱动力的理论与实证研究

通过IPAT方程理论和实证分析表明,在技术进步驱动下,二氧化碳排放随着时间的演变依次遵循三个"倒U型"曲线规律,即碳排放强度倒U型曲线、人均碳排放量倒U型曲线和碳排放总量倒U型曲线。依据该规律,可以将碳排放演化过程划分为碳排放强度高峰前阶段、碳排放强度高峰到人均碳排放量高峰阶段、人均碳排放量高峰到碳排放总量高峰阶段以及碳排放总量稳定下降阶段等四个阶段。在不同演化阶段下,碳排放的主导驱动力存在明显差异。在碳排放强度高峰之前阶段,碳排放增长主要由碳密集型技术进步驱动,在碳排放强度高峰到人均碳排放量高峰阶段,则主要由经济增长驱动,在人均碳排放量高峰到碳排放总量高峰阶段,则主要由碳减排技术进步来驱动,进入碳排放总量的稳定下降阶段后,碳减排技术进步将占据绝对主导地位。提出了相应的对策和建议。     

通过进化模块审视拟南芥尿苷二磷酸葡糖基转移酶功能多样性

属于糖基转移酶(GTs)家族1的尿苷二磷酸(UDP)-糖基转移酶(UGT)在转移拟南芥中的糖基的转移和糖基化次级代谢物中起重要作用.重建的系统发育树对这个多基因家族的进化关系和功能提供了新的见解和研究.通过综合分析系统发育谱和重建的系统发育树,我们系统地分析了112个拟南芥UGTs.在我们的工作中,我们检测到五个不同的进化保守模块,大多数UGTs分为同一模块,表明拟南芥UGTs在进化过程中是相当保守的.接下来收集拟南芥UGT的底物,并将它们映射到直向同源组,揭示UGT在结合特异性底物中的进化关系.通过扫描271不同物种,还预测一些未报告的蛋白质与拟南芥UGTs密切相关.     

Predator-induced behaviour shifts and natural selection in field-experimental lizard populations

The role of behaviour in evolutionary change has long been debated. On the one hand, behavioural changes may expose individuals to new selective pressures by altering the way that organisms interact with the environment, thus driving evolutionary divergence. Alternatively, behaviour can act to retard evolutionary change: by altering behavioural patterns in the face of new environmental conditions, organisms can minimize exposure to new selective pressures. This constraining influence of behaviour has been put forward as an explanation for evolutionary stasis within lineages and niche conservatism within clades. Nonetheless, the hypothesis that behavioural change prevents natural selection from operating in new environments has never been experimentally tested. We conducted a controlled and replicated experimental study of selection in entirely natural populations; we demonstrate that lizards alter their habitat use in the presence of an introduced predator, but that these behavioural shifts do not prevent patterns of natural selection from changing in experimental populations.     

Emergence of cooperation and evolutionary stability in finite populations

To explain the evolution of cooperation by natural selection has been a major goal of biologists since Darwin. Cooperators help others at a cost to themselves, while defectors receive the benefits of altruism without providing any help in return. The standard game dynamical formulation is the 'Prisoner's Dilemma', in which two players have a choice between cooperation and defection. In the repeated game, cooperators using direct reciprocity cannot be exploited by defectors, but it is unclear how such cooperators can arise in the first place. In general, defectors are stable against invasion by cooperators. This understanding is based on traditional concepts of evolutionary stability and dynamics in infinite populations. Here we study evolutionary game dynamics in finite populations. We show that a single cooperator using a strategy like 'tit-for-tat' can invade a population of defectors with a probability that corresponds to a net selective advantage. We specify the conditions required for natural selection to favour the emergence of cooperation and define evolutionary stability in finite populations.     

一种有效的基于4D图形表示法的DNA序列相似性比较方法

研究了一种有效地DNA序列相似性比较方法,在将每条DNA序列平均分成两个片段的基础上,采用4D图形表示法构建了每个片段的中心几何点重现模型,以此为基点,建立了DNA序列间的相似性与不相似性的欧氏距离比较法.最后,11个物种球蛋白基因的第一个外显子的DNA序列比较的结果验证表明:欧氏距离越小,其相似性越大,在进化上越趋于同源性;反之,欧氏距离越大,则物种差异性越大.实验结果表明,通过这样的方式可以有效避免信息的丢失,结果更具有统计显著性,并更有效地反映位置信息,可以对DNA序列的研究提供良好的支撑作用.     

Two aspects of evolutionary algorithms

In this paper we discuss the paradigm of evolutionary algorithms (EAs). We argue about the need for new heuristics in real-world problem solving, discussing reasons why some problems are difficult to solve. After introducing the main concepts of evolutionary algorithms, we concentrate on two issues: (1) self-adaptation of the parameters of EA, and (2) handling constraints. Biography: Zbigniew Michalewicz(1952-), male, Professor, research interest: evolutionary computation     

基于演化博弈理论的食品生产企业监管分析与调控

本文分别在有无政府监管的状态下,建立食品市场的演化博弈模型,在模型中分析各个参数对食品市场演化方向的重要影响。从两种模型的分析结果中可以看出,增加政府监管收益、降低政府监管成本、加大违法企业惩处力度、提高诚信合格企业的声誉收益以及减少企业生产和交易成本能够有效地减少我国食品安全问题,分析结果能够为监管部门决策提出建议。     

生态位构建的进化意义及其生态与行为响应

生态位构建是指有机体对局部环境中重要组成成分的建造、修复以及选择的一种能力.重点讨论了生态位构建的进化意义以及由生态位构建引起的生态和行为响应,主要结果包括:(1)生态继承作为与基因继承并行的遗传途径,扩展了对有机体适应性的机理解释;(2)环境变化与有机体对该变化导致的选择压的响应之间存在的时滞能够产生进化惯量与动量;(3)生态位构建与生态系统工程之间存在三个层面的差异;(4)Baldwin效应、自然选择和生态位构建分别体现了有机体对环境变化的中性、被动和主动等三种不同响应;(5)由于生态位构建可取决于学习的过程,因此它可以解释动物行为对策的进化.通过对生态位构建中这些热点问题以及其理论研究不足的讨论,提出了该领域中三个潜在的研究方向.     

Direct estimation of per nucleotide and genomic deleterious mutation rates in Drosophila

Spontaneous mutations are the source of genetic variation required for evolutionary change, and are therefore important for many aspects of evolutionary biology. For example, the divergence between taxa at neutrally evolving sites in the genome is proportional to the per nucleotide mutation rate, u (ref. 1), and this can be used to date speciation events by assuming a molecular clock. The overall rate of occurrence of deleterious mutations in the genome each generation (U) appears in theories of nucleotide divergence and polymorphism, the evolution of sex and recombination, and the evolutionary consequences of inbreeding. However, estimates of U based on changes in allozymes or DNA sequences and fitness traits are discordant. Here we directly estimate u in Drosophila melanogaster by scanning 20 million bases of DNA from three sets of mutation accumulation lines by using denaturing high-performance liquid chromatography. From 37 mutation events that we detected, we obtained a mean estimate for u of 8.4 x 10(-9) per generation. Moreover, we detected significant heterogeneity in u among the three mutation-accumulation-line genotypes. By multiplying u by an estimate of the fraction of mutations that are deleterious in natural populations of Drosophila, we estimate that U is 1.2 per diploid genome. This high rate suggests that selection against deleterious mutations may have a key role in explaining patterns of genetic variation in the genome, and help to maintain recombination and sexual reproduction.     

A new method of research on molecular evolution of proteinase superfamily

The molecular evolutionary tree, also known as a phylogenetic tree, of the serine proteinase superfamily was constructed by means of structural alignment. Three-dimensional structures of proteins were aligned by the SSAP program of Orengo and Taylor to obtain evolutionary distances. The resulting evolutionary tree provides a topology graph that can reflect the evolution of structure and function of homology proteinase. Moreover, study on evolution of the serine proteinase superfamily can lead to better understanding of the relationship and evolutionary difference among proteins of the superfamily, and is of significance to protein engineering, molecular design and protein structure prediction. Structure alignment is one of the useful methods of research on molecular evolution of protein.     

结合小波变换分析系统在演变非平稳随机激励下的响应

针对非均匀调制演变非平稳随机激励,提出一种分析系统演变非平稳随机响应问题的一般方法.在演变非平稳随机激励模型的基础上,通过小波变换建立起演变非平稳随机激励的演变功率谱,然后进行随机响应分析,得到系统在非均匀调制演变非平稳随机激励下的响应.结合具体算例,通过数值仿真说明所提方法的有效性和正确性.     

基于收益-风险的建筑项目管理模式分析

运用进化博弈理论建立了基于收益-风险的建筑施工项目管理模式进化博弈模型，分析了建筑企业施工项目管理模式演变的动态过程．研究表明，基于风险-收益的施工项目管理模式演化与企业和项目组双方博弈的支付矩阵相关，系统的演化方向由双方在劳务清包模式中的成本、收益和风险等的综合影响决定．提高建筑企业与项目组从劳务清包模式中的获利能力将有助于推广劳务清包模式．     

基于组织进化和信息熵的数据驱动分类算法

提出了一种分类算法---基于组织进化和信息熵的数据驱动分类算法(a data-driven classification algorithm based on organizational evolution and entropy,DDCAOEE),与已有进化算法的运行机制不同,它的进化操作直接作用于数据而不是规则,进化结束后再从各组织中提取规则,这样有利于避免在进化过程中产生无意义的规则。根据分类问题的特点,设计了信息系统的组织,提出了3种进化算子和一种组织选择机制,给出了基于信息熵的属性重要度的进化方式,并基于此定义了组织适应度函数,最后,将算法用于6个试验数据集,并与现有的2个分类方法(Ant-Miner和CN2)进行了比较,实验结果表明,该方法获得了更高的预测准确率,产生了更小的规则集。     

Evolutionary change in the insulin receptors of hystricomorph rodents

INSULIN receptors have been thought to have remained unaltered despite evolutionary changes in the hormone(1). Because insulins from hystricomorph rodents are known to be highly substituted compared with other mammalian insulins, we decided to investigate the insulin receptor of some hystricomorphs to determine whether evolutionary change had occurred within the receptor itself. Here we present the first evidence that hystricomorph rodent insulin receptors have undergone evolutionary change.     

产品实例种群及产品基因研究

提出了一种新的产品基因表达和获取方法.通过对产品实例适当分类,划分不同的产品实例种群,建立实例种群表达模型;抽取种群实例的方案设计知识,规范化成功能、原理和结构基,合成产品基因,建立产品实例的层次分解基因树,用面向对象方法表达基因树及其节点.使用此种方法,有助于设计知识的规范化、累积和重用.结合遗传算法,能够实现自动化方案演化设计,从功能、原理和结构等多方面多层次优化设计方案,提高产品方案设计创新性.