Genetic and developmental basis of evolutionary pelvic reduction in threespine sticklebacks

Hindlimb loss has evolved repeatedly in many different animals by means of molecular mechanisms that are still unknown. To determine the number and type of genetic changes underlying pelvic reduction in natural populations, we carried out genetic crosses between threespine stickleback fish with complete or missing pelvic structures. Genome-wide linkage mapping shows that pelvic reduction is controlled by one major and four minor chromosome regions. Pitx1 maps to the major chromosome region controlling most of the variation in pelvic size. Pelvic-reduced fish show the same left-right asymmetry seen in Pitx1 knockout mice, but do not show changes in Pitx1 protein sequence. Instead, pelvic-reduced sticklebacks show site-specific regulatory changes in Pitx1 expression, with reduced or absent expression in pelvic and caudal fin precursors. Regulatory mutations in major developmental control genes may provide a mechanism for generating rapid skeletal changes in natural populations, while preserving the essential roles of these genes in other processes.     

TIT FOR TAT in sticklebacks and the evolution of cooperation

The problems of achieving mutual cooperation can be formalized in a game called the Prisoner's Dilemma in which selfish defection is always more rewarding than cooperation. If the two protagonists have a certain minimum probability of meeting again a strategy called TIT FOR TAT is very successful. In TIT FOR TAT the player cooperates on the first move and thereafter does whatever the opponent did on the previous move. I have studied the behaviour of fish when confronting a potential predator, because conflicts can arise within pairs of fish in these circumstances which I argue resemble a series of games of Prisoner's Dilemma. Using a system of mirrors, single three-spined sticklebacks (Gasterosteus aculeatus) approaching a live predator were provided with either a simulated cooperating companion or a simulated defecting one. In both cases the test fish behaved according to TIT FOR TAT supporting the hypothesis that cooperation can evolve among egoists.     

Natural selection and adaptive evolution of leptin

Leptin is an adiposity-secreted hormone that is pivotal in regulating feeding behavior,energy metabolism and body mass.The study of leptin has been of crucial importance for public health and pharmaceutical intervention given its role in obesity.Generally,leptin is highly conserved due to its functional importance.However,episodes of rapid sequence evolution and positive selection have been observed in some mammalian species,indicating that the leptin functions in these animals may have undergone adaptive modification to their environments.In this article,we review the adaptive evolution of leptin and its potential functional consequences.This review is expected to guide future research of molecular evolution and functional assays of this gene,and also to provide a theoretical foundation for the use of leptin in therapeutic applications.     

Statistical analysis on adaptive evolution of SQUA genes in angiosperms

SQUAMOSA (SQUA) subfamily includes important perianth identity genes of MADS-box gene family. SQUA genes of Dendrocalamus latiflorus were sequenced, and phylogenetic form on SQUA genes in angiosperms was analyzed. Relative rate and adaptive evolution after SQUA gene duplication in recent common ancestor of monocots and eudicots were analyzed using the methods of relative rate test, statistic on synonymous and non-synonymous coden substitution sites and likelihood rate test. The results show that both of relative rate and synonymous and non-synonymous coden substitution in eudicot clade are significantly higher than those in monocot clade, and the value of dN/ds uncovered possible positive selective pressure in eudicot clade.     

The genetic architecture of divergence between threespine stickleback species.

The genetic and molecular basis of morphological evolution is poorly understood, particularly in vertebrates. Genetic studies of the differences between naturally occurring vertebrate species have been limited by the expense and difficulty of raising large numbers of animals and the absence of molecular linkage maps for all but a handful of laboratory and domesticated animals. We have developed a genome-wide linkage map for the three-spined stickleback (Gasterosteus aculeatus), an extensively studied teleost fish that has undergone rapid divergence and speciation since the melting of glaciers 15,000 years ago. Here we use this map to analyse the genetic basis of recently evolved changes in skeletal armour and feeding morphologies seen in the benthic and limnetic stickleback species from Priest Lake, British Columbia. Substantial alterations in spine length, armour plate number, and gill raker number are controlled by genetic factors that map to independent chromosome regions. Further study of these regions will help to define the number and type of genetic changes that underlie morphological diversification during vertebrate evolution.     

Divergent sexual selection enhances reproductive isolation in sticklebacks

Sexual selection may facilitate speciation because it can cause rapid evolutionary diversification of male mating signals and female preferences. Divergence in these traits can then contribute to reproductive isolation. The sensory drive hypothesis predicts that three mechanisms underlie divergence in sexually selected traits: (1) habitat-specific transmission of male signals; (2) adaptation of female perceptual sensitivity to local ecological conditions; and (3) matching of male signals to female perceptual sensitivity. I test these mechanisms in threespine sticklebacks (Gasterosteus spp.) that live in different light environments. Here I show that female perceptual sensitivity to red light varies with the extent of redshift in the light environment, and contributes to divergent preferences. Male nuptial colour varies with environment and is tuned to female perceptual sensitivity. The extent of divergence among populations in both male signal colour and female preference for red is correlated with the extent of reproductive isolation in these recently diverged species. These results demonstrate that divergent sexual selection generated by sensory drive contributes to speciation.     

基于个体强度的自适应差分多目标免疫算法

考虑到支配解可能携带有利于算法搜索到最优解的信息, 在克隆阶段选择一部分非支配解和支配解克隆以提高种群多样性和避免算法早熟收敛。在进化阶段, 先采用自适应差分进化算子交叉变异, 然后用多项式变异算子进行扰动以有效地平衡算法的全局搜索和局部搜索。基于个体强度建立外部文档储存一定数量的较好解, 并让这些较好解在每次迭代中参与进化且被更新。对10个标准测试函数进行仿真实验, 并与其他5种算法进行比较, 结果表明所提算法在收敛性和解的分布性方面均表现出明显优势。     

基于自适应HereBoy算法的电路进化设计实验研究

针对电路进化设计演化后期种群收敛速度放慢等问题,采用自适应Here Boy算法,融入遗传算法的群体概念,研究自适应因子在进化算法中对演化收敛速度的影响。运用类神经网络的电路模型和矩阵编码方法对组合电路进行编码,建立了电路编码到电路功能的映射关系,采用外部进化方式进行电路适应度值评估,引入自适应遗传算子提高算法收敛速度和种群多样性。二位二进制乘法器电路的进化结果表明,该方法较传统Here Boy算法在电路进化设计进程中电路平均演化代数及演化时间明显减小,在进化后期,随着种群演化代数增加适应度值平均涨幅提高。     

Testing the neutral theory of molecular evolution with genomic data from Drosophila

Although positive selection has been detected in many genes, its overall contribution to protein evolution is debatable. If the bulk of molecular evolution is neutral, then the ratio of amino-acid (A) to synonymous (S) polymorphism should, on average, equal that of divergence. A comparison of the A/S ratio of polymorphism in Drosophila melanogaster with that of divergence from Drosophila simulans shows that the A/S ratio of divergence is twice as high---a difference that is often attributed to positive selection. But an increase in selective constraint owing to an increase in effective population size could also explain this observation, and, if so, all genes should be affected similarly. Here we show that the difference between polymorphism and divergence is limited to only a fraction of the genes, which are also evolving more rapidly, and this implies that positive selection is responsible. A higher A/S ratio of divergence than of polymorphism is also observed in other species, which suggests a rate of adaptive evolution that is far higher than permitted by the neutral theory of molecular evolution.     

Prediction of sites under adaptive evolution in flavin-containing monooxygenases: Selection pattern revisited

Flavin-containing monooxygenase (FMO), like cytochrome P450 (CYP), is a monooxygenase that uses the reducing equivalents of NADPH to reduce one atom of molecular oxygen to water, while the other atom is used to oxidize the substrate. Recently, it was shown that some CYP isoforms have been subject to positive selection. However, it is unknown whether the highly conserved phase I detoxification enzyme, FMO, has undergone similar positive Darwinian selection. We used maximum-likelihood models of codon substitution, evolutionary fingerprinting, and cross species comparison to investigate the occurrence of adaptive evolution in FMO sequences. We used recent genomic data from a range of species, including vertebrates and invertebrates. We present the evidence for the occurrence of adaptive evolution in mammalian FMO 3, 4, 5, and fugu FMOs but not in mammalian FMO 1, FMO 2, frog FMOs, other fish FMOs and invertebrate FMOs. The sites under adaptive evolution were significantly associated with the insertion domain in mammalian FMO 5. We identified specific amino acid sites in FMOs 3–5 that are likely targets for selection based on the patterns of parallel amino acid change. The most likely role of adaptive evolution is the repair of mutations that permitted optimal NADP+ binding and improved catalytic efficiency. The occurrence of positive selection during the evolution of phase I detoxification enzymes such as FMOs 3–5 and fugu FMO suggests the occurrence of both high selection pressure acting on species within their unique habitats and significant changes in intensity and direction (forms of xenobiotics and drugs) resulting from changes in microhabitat and food.     

Phylogenetic origins and adaptive evolution of avian and mammalian haemoglobin genes

Recent years have seen rapid growth in amino acid sequence data on globins and nucleotide sequence data on haemoglobin genes and pseudogenes, and cladistic analysis of these data continues to reveal new facets of globin evolution. Our present findings demonstrate: (1) avian and mammalian embryonic alpha genes (pi and xi, respectively) had a monophyletic origin involving an alpha locus duplication about 400 Myr ago soon after the duplication which separated alpha and beta genes; (2) much later in phylogeny, independent beta-gene duplications produced the embryonic rho locus of birds and embryonic epsilon and fetal gamma loci of mammals. This parallels the earlier finding that myoglobins evolved more than once from generalized globin ancestors. Here we support the view that such globin evolution resulted from natural selection acting on mutations in duplicated genes. Thus, our evidence contradicts the neutralist view in which almost all amino acid substitutions in descent to extant globins evaded positive selection.     

Escherichia coli K-12 undergoes adaptive evolution to achieve in silico predicted optimal growth

Annotated genome sequences can be used to reconstruct whole-cell metabolic networks. These metabolic networks can be modelled and analysed (computed) to study complex biological functions. In particular, constraints-based in silico models have been used to calculate optimal growth rates on common carbon substrates, and the results were found to be consistent with experimental data under many but not all conditions. Optimal biological functions are acquired through an evolutionary process. Thus, incorrect predictions of in silico models based on optimal performance criteria may be due to incomplete adaptive evolution under the conditions examined. Escherichia coli K-12 MG1655 grows sub-optimally on glycerol as the sole carbon source. Here we show that when placed under growth selection pressure, the growth rate of E. coli on glycerol reproducibly evolved over 40 days, or about 700 generations, from a sub-optimal value to the optimal growth rate predicted from a whole-cell in silico model. These results open the possibility of using adaptive evolution of entire metabolic networks to realize metabolic states that have been determined a priori based on in silico analysis.     

基于RBF神经网络的电力系统自适应励磁控制器的设计

采用后推设计算法设计了SISO严格反馈系统的RBF神经网络自适应控制器。权值的调整算法基于所选择的积分型的Lyapunov函数 ,能保证整个闭环系统是最终一致有界的。把所设计的控制方案用于电力系统的励磁控制中。仿真结果表明 ,所设计的控制器具有良好的跟踪性能和鲁棒性     

基于RBF神经网络的电力系统自适应励磁控制器的设计

采用后推设计算法设计了SISO严格反馈系统的：RBF、神经网络自适应控制器。权值的调整算法基于所选择的积分型的Lyapunov函数,能保证整个闭环系统是最终一致有界的。把所设计的控制方案用于电力系统的励磁控制中。仿真结果表明,所设计的控制器具有良好的跟踪性能和鲁棒性。     

一种求解冗余机械臂逆运动学的自适应动态差分进化算法

针对冗余机械臂逆运动学难以直接求解且具有多解的问题,提出一种基于改进差分进化算法的逆运动学求解方法.以KUKA LBR iiwa七自由度机械臂为研究对象,验证该方法的有效性.针对基本差分进化算法易陷入局部搜索问题,引入自适应变异操作和随机变化交叉操作,使算法可根据迭代进程调整搜索强度.基于Denavit-Hartenb...     

Using maximum likelihood method to detect adaptive evolution of HCV envelope protein-coding genes

The basic process of adaptive evolution by natural selection is the replacement of one allele gene by an- other with a higher fitness in a population. Detecting the adaptive evolution would be helpful for better un- derstanding of bio-evolutionary mechani…